--- /dev/null
+---
+layout: lesson
+root: ../..
+title: Introducing the Shell
+---
+<div class="objectives" markdown="1">
+
+#### Objectives
+* Explain how the shell relates to the keyboard, the screen, the operating system, and users' programs.
+* Explain when and why command-line interfaces should be used instead of graphical interfaces.
+
+</div>
+
+Nelle Nemo, a marine biologist,
+has just returned from a six-month survey of the
+[North Pacific Gyre](http://en.wikipedia.org/wiki/North_Pacific_Gyre),
+where she has been sampling gelatinous marine life in the
+[Great Pacific Garbage Patch](http://en.wikipedia.org/wiki/Great_Pacific_Garbage_Patch).
+She has 1520 samples in all, and now needs to:
+
+1. Run each sample through an assay machine
+ that will measure the relative abundance of 300 different proteins.
+ The machine's output for a single sample is
+ a file with one line for each protein.
+2. Calculate statistics for each of the proteins separately
+ using a program her supervisor wrote called `goostat`.
+3. Compare the statistics for each protein
+ with corresponding statistics for each other protein
+ using a program one of the other graduate students wrote called `goodiff`.
+4. Write up.
+ Her supervisor would really like her to do this by the end of the month
+ so that her paper can appear in an upcoming special issue of *Aquatic Goo Letters*.
+
+It takes about half an hour for the assay machine to process each sample.
+The good news is,
+it only takes two minutes to set each one up.
+Since her lab has eight assay machines that she can use in parallel,
+this step will "only" take about two weeks.
+
+The bad news is that if she has to run `goostat` and `goodiff` by hand,
+she'll have to enter filenames and click "OK" 45,150 times
+(300 runs of `goostat`, plus 300×299/2 runs of `goodiff`).
+At 30 seconds each,
+that will take more than two weeks.
+Not only would she miss her paper deadline,
+the chances of her typing all of those commands right are practically zero.
+
+The next few lessons will explore what she should do instead.
+More specifically,
+they explain how she can use a command shell
+to automate the repetitive steps in her processing pipeline
+so that her computer can work 24 hours a day while she writes her paper.
+As a bonus,
+once she has put a processing pipeline together,
+she will be able to use it again whenever she collects more data.
+
+#### What and Why
+
+At a high level, computers do four things:
+
+- run programs;
+- store data;
+- communicate with each other; and
+- interact with us.
+
+They can do the last of these in many different ways,
+including direct brain-computer links and speech interfaces.
+Since these are still in their infancy,
+most of us use windows, icons, mice, and pointers.
+These technologies didn't become widespread until the 1980s,
+but their roots go back to Doug Engelbart's work in the 1960s,
+which you can see in what has been called
+"[The Mother of All Demos](http://www.youtube.com/watch?v=a11JDLBXtPQ)".
+
+Going back even further,
+the only way to interact with early computers was to rewire them.
+But in between,
+from the 1950s to the 1980s,
+most people used line printers.
+These devices only allowed input and output of the letters, numbers, and punctuation found on a standard keyboard,
+so programming languages and interfaces had to be designed around that constraint.
+
+This kind of interface is called a
+[command-line interface](../../gloss.html#cli), or CLI,
+to distinguish it from the
+[graphical user interface](../../gloss.html#gui), or GUI,
+that most people now use.
+The heart of a CLI is a [read-evaluate-print loop](../../gloss.html#repl), or REPL:
+when the user types a command and then presses the enter (or return) key,
+the computer reads it,
+executes it,
+and prints its output.
+The user then types another command,
+and so on until the user logs off.
+
+This description makes it sound as though the user sends commands directly to the computer,
+and the computer sends output directly to the user.
+In fact,
+there is usually a program in between called a
+[command shell](../../gloss.html#shell).
+What the user types goes into the shell;
+it figures out what commands to run and orders the computer to execute them.
+
+A shell is a program like any other.
+What's special about it is that its job is to run other programs
+rather than to do calculations itself.
+The most popular Unix shell is Bash,
+the Bourne Again SHell
+(so-called because it's derived from a shell written by Stephen Bourne—this
+is what passes for wit among programmers).
+Bash is the default shell on most modern implementations of Unix,
+and in most packages that provide Unix-like tools for Windows.
+
+Using Bash or any other shell
+sometimes feels more like programming than like using a mouse.
+Commands are terse (often only a couple of characters long),
+their names are frequently cryptic,
+and their output is lines of text rather than something visual like a graph.
+On the other hand,
+the shell allows us to combine existing tools in powerful ways with only a few keystrokes
+and to set up pipelines to handle large volumes of data automatically.
+In addition,
+the command line is often the easiest way to interact with remote machines.
+As clusters and cloud computing become more popular for scientific data crunching,
+being able to drive them is becoming a necessary skill.
+
+<div class="keypoints" markdown="1">
+
+#### Key Points
+* A shell is a program whose primary purpose is to read commands and run other programs.
+* The shell's main advantages are its high action-to-keystroke ratio,
+ its support for automating repetitive tasks,
+ and that it can be used to access networked machines.
+* The shell's main disadvantages are its primarily textual nature
+ and how cryptic its commands and operation can be.
+
+</div>
--- /dev/null
+---
+layout: lesson
+root: ../..
+title: Files and Directories
+---
+<div class="objectives" markdown="1">
+
+#### Objectives
+* Explain the similarities and differences between a file and a directory.
+* Translate an absolute path into a relative path and vice versa.
+* Construct absolute and relative paths that identify specific files and directories.
+* Explain the steps in the shell's read-run-print cycle.
+* Identify the actual command, flags, and filenames in a command-line call.
+* Demonstrate the use of tab completion, and explain its advantages.
+
+</div>
+
+The part of the operating system responsible for managing files and directories
+is called the [file system](../../gloss.html#filesystem).
+It organizes our data into files,
+which hold information,
+and directories (also called "folders"),
+which hold files or other directories.
+
+Several commands are frequently used to create, inspect, rename, and delete files and directories.
+To start exploring them,
+let's open a shell window:
+
+<div class="in" markdown="1">
+~~~
+$
+~~~
+</div>
+
+The dollar sign is a [prompt](../../gloss.html#prompt),
+which shows us that the shell is waiting for input;
+your shell may show something more elaborate.
+
+Type the command `whoami`,
+then press the Enter key (sometimes marked Return) to send the command to the shell.
+The command's output is the ID of the current user,
+i.e.,
+it shows us who the shell thinks we are:
+
+<div class="in" markdown="1">
+~~~
+$ whoami
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+vlad
+~~~
+</div>
+
+More specifically, when we type `whoami` the shell:
+
+1. finds a program called `whoami`,
+2. runs that program,
+3. displays that program's output, then
+4. displays a new prompt to tell us that it's ready for more commands.
+
+Next,
+let's find out where we are by running a command called `pwd`
+(which stands for "print working directory").
+At any moment,
+our [current working directory](../../gloss.html#current-working-directory)
+is our current default directory,
+i.e.,
+the directory that the computer assumes we want to run commands in
+unless we explicitly specify something else.
+Here,
+the computer's response is `/users/vlad`,
+which is Vlad's [home directory](../../gloss.html#home-directory):
+
+<div class="in" markdown="1">
+~~~
+$ pwd
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+/users/vlad
+~~~
+</div>
+
+> #### Alphabet Soup
+>
+> If the command to find out who we are is `whoami`, the command to find
+> out where we are ought to be called `whereami`, so why is it `pwd`
+> instead? The usual answer is that in the early 1970s, when Unix was
+> first being developed, every keystroke counted: the devices of the day
+> were slow, and backspacing on a teletype was so painful that cutting the
+> number of keystrokes in order to cut the number of typing mistakes was
+> actually a win for usability. The reality is that commands were added to
+> Unix one by one, without any master plan, by people who were immersed in
+> its jargon. The result is as inconsistent as the roolz uv Inglish
+> speling, but we're stuck with it now.
+
+To understand what a "home directory" is,
+let's have a look at how the file system as a whole is organized.
+At the top is the [root directory](../../gloss.html#root-directory)
+that holds everything else.
+We refer to it using a slash character `/` on its own;
+this is the leading slash in `/users/vlad`.
+
+Inside that directory are several other directories:
+`bin` (which is where some built-in programs are stored),
+`data` (for miscellaneous data files),
+`users` (where users' personal directories are located),
+`tmp` (for temporary files that don't need to be stored long-term),
+and so on:
+
+<img src="img/filesystem.svg" alt="The Filesystem" />
+
+We know that our current working directory `/users/vlad` is stored inside `/users`
+because `/users` is the first part of its name.
+Similarly,
+we know that `/users` is stored inside the root directory `/`
+because its name begins with `/`.
+
+Underneath `/users`,
+we find one directory for each user with an account on this machine.
+The Mummy's files are stored in `/users/imhotep`,
+Wolfman's in `/users/larry`,
+and ours in `/users/vlad`,
+which is why `vlad` is the last part of the directory's name.
+
+<img src="img/home-directories.svg" alt="Home Directories" />
+
+> Notice that there are two meanings for the `/` character.
+> When it appears at the front of a file or directory name,
+> it refers to the root directory. When it appears *inside* a name,
+> it's just a separator.
+
+Let's see what's in Vlad's home directory by running `ls`,
+which stands for "listing":
+
+<div class="in" markdown="1">
+~~~
+$ ls
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+bin data mail music
+notes.txt papers pizza.cfg solar
+solar.pdf swc
+~~~
+</div>
+
+<img src="img/vlad-homedir.svg" alt="Vlad's Home Directory" />
+
+`ls` prints the names of the files and directories in the current directory in alphabetical order,
+arranged neatly into columns.
+We can make its output more comprehensible by using the [flag](../../gloss.html#command-line-flag) `-F`,
+which tells `ls` to add a trailing `/` to the names of directories:
+
+<div class="in" markdown="1">
+~~~
+$ ls -F
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+bin/ data/ mail/ music/
+notes.txt papers/ pizza.cfg solar/
+solar.pdf swc/
+~~~
+</div>
+
+Here,
+we can see that `/users/vlad` contains seven [sub-directories](../../gloss.html#sub-directory).
+The names that don't have trailing slashes,
+like `notes.txt`, `pizza.cfg`, and `solar.pdf`,
+are plain old files.
+And note that there is a space between `ls` and `-F`:
+without it,
+the shell thinks we're trying to run a command called `ls-F`,
+which doesn't exist.
+
+> #### What's In A Name?
+>
+> You may have noticed that all of Vlad's files' names are "something dot
+> something". This is just a convention: we can call a file `mythesis` or
+> almost anything else we want. However, most people use two-part names
+> most of the time to help them (and their programs) tell different kinds
+> of files apart. The second part of such a name is called the
+> [filename extension](../../gloss.html#filename-extension), and indicates
+> what type of data the file holds: `.txt` signals a plain text file, `.pdf`
+> indicates a PDF document, `.cfg` is a configuration file full of parameters
+> for some program or other, and so on.
+>
+> This is just a convention, albeit an important one. Files contain
+> bytes: it's up to us and our programs to interpret those bytes
+> according to the rules for PDF documents, images, and so on.
+>
+> Naming a PNG image of a whale as `whale.mp3` doesn't somehow
+> magically turn it into a recording of whalesong, though it *might*
+> cause the operating system to try to open it with a music player
+> when someone double-clicks it.
+
+Now let's take a look at what's in Vlad's `data` directory by running `ls -F data`,
+i.e.,
+the command `ls` with the parameters `-F` and `data`.
+The second parameter—the one *without* a leading dash—tells `ls` that
+we want a listing of something other than our current working directory:
+
+<div class="in" markdown="1">
+~~~
+$ ls -F data
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+amino-acids.txt elements/ morse.txt
+pdb/ planets.txt sunspot.txt
+~~~
+</div>
+
+The output shows us that there are four text files and two sub-sub-directories.
+Organizing things hierarchically in this way helps us keep track of our work:
+it's possible to put hundreds of files in our home directory,
+just as it's possible to pile hundreds of printed papers on our desk,
+but it's a self-defeating strategy.
+
+Notice, by the way that we spelled the directory name `data`.
+It doesn't have a trailing slash:
+that's added to directory names by `ls` when we use the `-F` flag to help us tell things apart.
+And it doesn't begin with a slash because it's a [relative path](../../gloss.html#relative-path),
+i.e., it tells `ls` how to find something from where we are,
+rather than from the root of the file system.
+
+If we run `ls -F /data` (*with* a leading slash) we get a different answer,
+because `/data` is an [absolute path](../../gloss.html#absolute-path):
+
+<div class="in" markdown="1">
+~~~
+$ ls -F /data
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+access.log backup/ hardware.cfg
+network.cfg
+~~~
+</div>
+
+The leading `/` tells the computer to follow the path from the root of the filesystem,
+so it always refers to exactly one directory,
+no matter where we are when we run the command.
+
+What if we want to change our current working directory?
+Before we do this,
+`pwd` shows us that we're in `/users/vlad`,
+and `ls` without any parameters shows us that directory's contents:
+
+<div class="in" markdown="1">
+~~~
+$ pwd
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+/users/vlad
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ ls
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+bin/ data/ mail/ music/
+notes.txt papers/ pizza.cfg solar/
+solar.pdf swc/
+~~~
+</div>
+
+We can use `cd` followed by a directory name to change our working directory.
+`cd` stands for "change directory",
+which is a bit misleading:
+the command doesn't change the directory,
+it changes the shell's idea of what directory we are in.
+
+<div class="in" markdown="1">
+~~~
+$ cd data
+~~~
+</div>
+
+`cd` doesn't print anything,
+but if we run `pwd` after it, we can see that we are now in `/users/vlad/data`.
+If we run `ls` without parameters now,
+it lists the contents of `/users/vlad/data`,
+because that's where we now are:
+
+<div class="in" markdown="1">
+~~~
+$ pwd
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+/users/vlad/data
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ ls
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+amino-acids.txt elements/ morse.txt
+pdb/ planets.txt sunspot.txt
+~~~
+</div>
+
+We now know how to go down the directory tree:
+how do we go up?
+We could use an absolute path:
+
+<div class="in" markdown="1">
+~~~
+$ cd /users/vlad
+~~~
+</div>
+
+but it's almost always simpler to use `cd ..` to go up one level:
+
+<div class="in" markdown="1">
+~~~
+$ pwd
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+/users/vlad/data
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ cd ..
+~~~
+</div>
+
+`..` is a special directory name meaning
+"the directory containing this one",
+or more succinctly,
+the [parent](../../gloss.html#parent-directory) of the current directory.
+Sure enough,
+if we run `pwd` after running `cd ..`, we're back in `/users/vlad`:
+
+<div class="in" markdown="1">
+~~~
+$ pwd
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+/users/vlad
+~~~
+</div>
+
+The special directory `..` doesn't usually show up when we run `ls`.
+If we want to display it, we can give `ls` the `-a` flag:
+
+<div class="in" markdown="1">
+~~~
+$ ls -F -a
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./ ../ bin/ data/
+mail/ music/ notes.txt papers/
+pizza.cfg solar/ solar.pdf swc/
+~~~
+</div>
+
+`-a` stands for "show all";
+it forces `ls` to show us file and directory names that begin with `.`,
+such as `..` (which, if we're in `/users/vlad`, refers to the `/users` directory).
+As you can see,
+it also displays another special directory that's just called `.`,
+which means "the current working directory".
+It may seem redundant to have a name for it,
+but we'll see some uses for it soon.
+
+> #### Orthogonality
+>
+> The special names `.` and `..` don't belong to `ls`;
+> they are interpreted the same way by every program.
+> For example,
+> if we are in `/users/vlad/data`,
+> the command `ls ..` will give us a listing of `/users/vlad`.
+> When the meanings of the parts are the same no matter how they're combined,
+> programmers say they are [orthogonal](../../gloss.html#orthogonal):
+> Orthogonal systems tend to be easier for people to learn
+> because there are fewer special cases and exceptions to keep track of.
+
+#### Nelle's Pipeline: Organizing Files
+
+Knowing just this much about files and directories,
+Nelle is ready to organize the files that the protein assay machine will create.
+First,
+she creates a directory called `north-pacific-gyre`
+(to remind herself where the data came from).
+Inside that,
+she creates a directory called `2012-07-03`,
+which is the date she started processing the samples.
+She used to use names like `conference-paper` and `revised-results`,
+but she found them hard to understand after a couple of years.
+(The final straw was when she found herself creating
+a directory called `revised-revised-results-3`.)
+
+> Nelle names her directories "year-month-day",
+> with leading zeroes for months and days,
+> because the shell displays file and directory names in alphabetical order.
+> If she used month names,
+> December would come before July;
+> if she didn't use leading zeroes,
+> November ('11') would come before July ('7').
+
+Each of her physical samples is labelled according to her lab's convention
+with a unique ten-character ID,
+such as "NENE01729A".
+This is what she used in her collection log
+to record the location, time, depth, and other characteristics of the sample,
+so she decides to use it as part of each data file's name.
+Since the assay machine's output is plain text,
+she will call her files `NENE01729A.txt`, `NENE01812A.txt`, and so on.
+All 1520 files will go into the same directory.
+
+If she is in her home directory,
+Nelle can see what files she has using the command:
+
+<div class="in" markdown="1">
+~~~
+$ ls north-pacific-gyre/2012-07-03/
+~~~
+</div>
+
+This is a lot to type,
+but she can let the shell do most of the work.
+If she types:
+
+<div class="in" markdown="1">
+~~~
+$ ls no
+~~~
+</div>
+
+and then presses tab,
+the shell automatically completes the directory name for her:
+
+<div class="in" markdown="1">
+~~~
+$ ls north-pacific-gyre/
+~~~
+</div>
+
+If she presses tab again,
+Bash will add `2012-07-03/` to the command,
+since it's the only possible completion.
+Pressing tab again does nothing,
+since there are 1520 possibilities;
+pressing tab twice brings up a list of all the files,
+and so on.
+This is called [tab completion](../../gloss.html#tab-completion),
+and we will see it in many other tools as we go on.
+
+<div class="keypoints" markdown="1">
+
+#### Key Points
+* The file system is responsible for managing information on the disk.
+* Information is stored in files, which are stored in directories (folders).
+* Directories can also store other directories, which forms a directory tree.
+* `/` on its own is the root directory of the whole filesystem.
+* A relative path specifies a location starting from the current location.
+* An absolute path specifies a location from the root of the filesystem.
+* Directory names in a path are separated with '/' on Unix, but '\\' on Windows.
+* '..' means "the directory above the current one";
+ '.' on its own means "the current directory".
+* Most files' names are `something.extension`.
+ The extension isn't required,
+ and doesn't guarantee anything,
+ but is normally used to indicate the type of data in the file.
+* Most commands take options (flags) which begin with a '-'.
+
+</div>
+
+<div class="challenges" markdown="1">
+
+#### Challenges
+
+<img src="img/filesystem-challenge.svg" alt="Filesystem for Challenge Questions" />
+
+1. If `pwd` displays `/users/thing`, what will `ls ../backup` display?
+ 1. `../backup: No such file or directory`
+ 2. `2012-12-01 2013-01-08 2013-01-27`
+ 3. `2012-12-01/ 2013-01-08/ 2013-01-27/`
+ 4. `original pnas_final pnas_sub`
+
+2. If `pwd` displays `/users/backup`,
+ and `-r` tells `ls` to display things in reverse order,
+ what command will display:
+
+ ~~~
+ pnas-sub/ pnas-final/ original/
+ ~~~
+
+ 1. `ls pwd`
+ 2. `ls -r -F`
+ 3. `ls -r -F /users/backup`
+ 4. Either \#2 or \#3 above, but not \#1.
+
+3. What does the command `cd` without a directory name do?
+ 1. It has no effect.
+ 2. It changes the working directory to `/`.
+ 3. It changes the working directory to the user's home directory.
+ 4. It produces an error message.
+
+</div>
--- /dev/null
+---
+layout: lesson
+root: ../..
+title: Creating Things
+---
+<div class="objectives" markdown="1">
+
+#### Objectives
+* Create a directory hierarchy that matches a given diagram.
+* Create files in that hierarchy using an editor or by copying and renaming existing files.
+* Display the contents of a directory using the command line.
+* Delete specified files and/or directories.
+
+</div>
+
+We now know how to explore files and directories,
+but how do we create them in the first place?
+Let's go back to Vlad's home directory,
+`/users/vlad`,
+and use `ls -F` to see what it contains:
+
+<div class="in" markdown="1">
+~~~
+$ pwd
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+/users/vlad
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ ls -F
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+bin/ data/ mail/ music/
+notes.txt papers/ pizza.cfg solar/
+solar.pdf swc/
+~~~
+</div>
+
+Let's create a new directory called `thesis` using the command `mkdir thesis`
+(which has no output):
+
+<div class="in" markdown="1">
+~~~
+$ mkdir thesis
+~~~
+</div>
+
+As you might (or might not) guess from its name,
+`mkdir` means "make directory".
+Since `thesis` is a relative path
+(i.e., doesn't have a leading slash),
+the new directory is made below the current working directory:
+
+<div class="in" markdown="1">
+~~~
+$ ls -F
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+bin/ data/ mail/ music/
+notes.txt papers/ pizza.cfg solar/
+solar.pdf swc/ thesis/
+~~~
+</div>
+
+However, there's nothing in it yet:
+
+<div class="in" markdown="1">
+~~~
+$ ls -F thesis
+~~~
+</div>
+
+Let's change our working directory to `thesis` using `cd`,
+then run a text editor called Nano to create a file called `draft.txt`:
+
+<div class="in" markdown="1">
+~~~
+$ cd thesis
+$ nano draft.txt
+~~~
+</div>
+
+> #### Which Editor?
+>
+> When we say, "`nano` is a text editor," we really do mean "text": it can
+> only work with plain character data, not tables, images, or any other
+> human-friendly media. We use it in examples because almost anyone can
+> drive it anywhere without training, but please use something more
+> powerful for real work. On Unix systems (such as Linux and Mac OS X),
+> many programmers use [Emacs](http://www.gnu.org/software/emacs/) or
+> [Vim](http://www.vim.org/) (both of which are completely unintuitive,
+> even by Unix standards), or a graphical editor such as
+> [Gedit](http://projects.gnome.org/gedit/). On Windows, you may wish to
+> use [Notepad++](http://notepad-plus-plus.org/).
+>
+> No matter what editor you use, you will need to know where it searches
+> for and saves files. If you start it from the shell, it will (probably)
+> use your current working directory as its default location. If you use
+> your computer's start menu, it may want to save files in your desktop or
+> documents directory instead. You can change this by navigating to
+> another directory the first time you "Save As..."
+
+Let's type in a few lines of text,
+then use Control-O to write our data to disk:
+
+<img src="img/nano-screenshot.png" alt="Nano in Action" />
+
+Once our file is saved,
+we can use Control-X to quit the editor and return to the shell.
+(Unix documentation often uses the shorthand `^A` to mean "control-A".)
+`nano` doesn't leave any output on the screen after it exits,
+but `ls` now shows that we have created a file called `draft.txt`:
+
+<div class="in" markdown="1">
+~~~
+$ ls
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+draft.txt
+~~~
+</div>
+
+We can run `ls` with the `-s` flag (for "size")
+to show us how large `draft.txt` is:
+
+<div class="in" markdown="1">
+~~~
+$ ls -s
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 1 draft.txt
+~~~
+</div>
+
+Unfortunately,
+Unix reports sizes in [disk blocks](../../gloss.html#disk-block) by default,
+which might be the least helpful default possible.
+If we add the `-h` flag,
+`ls` switches to more human-friendly units:
+
+<div class="in" markdown="1">
+~~~
+$ ls -s -h
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 512 draft.txt
+~~~
+</div>
+
+Here, 512 is the number of bytes in the file.
+This is more than we actually typed in because the smallest unit of storage on the disk
+is typically a block of 512 bytes.
+
+Let's tidy up by running `rm draft.txt`:
+
+<div class="in" markdown="1">
+~~~
+$ rm draft.txt
+~~~
+</div>
+
+This command removes files ("rm" is short for "remove").
+If we run `ls` again,
+its output is empty once more,
+which tells us that our file is gone:
+
+<div class="in" markdown="1">
+~~~
+$ ls
+~~~
+</div>
+
+> #### Deleting Is Forever
+>
+> Unix doesn't have a trash bin: when we delete files, they are unhooked
+> from the file system so that their storage space on disk can be
+> recycled. Tools for finding and recovering deleted files do exist, but
+> there's no guarantee they'll work in any particular situation, since the
+> computer may recycle the file's disk space right away.
+
+Let's re-create that file
+and then move up one directory to `/users/vlad` using `cd ..`:
+
+<div class="in" markdown="1">
+~~~
+$ pwd
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+/users/vlad/thesis
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ nano draft.txt
+$ ls
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+draft.txt
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ cd ..
+~~~
+</div>
+
+If we try to remove the entire `thesis` directory using `rm thesis`,
+we get an error message:
+
+<div class="in" markdown="1">
+~~~
+$ rm thesis
+~~~
+</div>
+<div class="err" markdown="1">
+~~~
+rm: cannot remove `thesis': Is a directory
+~~~
+</div>
+
+This happens because `rm` only works on files, not directories.
+The right command is `rmdir`,
+which is short for "remove directory".
+It doesn't work yet either, though,
+because the directory we're trying to remove isn't empty:
+
+<div class="in" markdown="1">
+~~~
+$ rmdir thesis
+~~~
+</div>
+<div class="err" markdown="1">
+~~~
+rmdir: failed to remove `thesis': Directory not empty
+~~~
+</div>
+
+This little safety feature can save you a lot of grief,
+particularly if you are a bad typist.
+To really get rid of `thesis` we must first delete the file `draft.txt`:
+
+<div class="in" markdown="1">
+~~~
+$ rm thesis/draft.txt
+~~~
+</div>
+
+The directory is now empty, so `rmdir` can delete it:
+
+<div class="in" markdown="1">
+~~~
+$ rmdir thesis
+~~~
+</div>
+
+> #### With Great Power Comes Great Responsibility
+>
+> Removing the files in a directory just so that we can remove the
+> directory quickly becomes tedious. Instead, we can use `rm` with the
+> `-r` flag (which stands for "recursive"):
+>
+> ~~~
+> $ rm -r thesis
+> ~~~
+>
+> This removes everything in the directory, then the directory itself. If
+> the directory contains sub-directories, `rm -r` does the same thing to
+> them, and so on. It's very handy, but can do a lot of damage if used
+> without care.
+
+Let's create that directory and file one more time.
+(Note that this time we're running `nano` with the path `thesis/draft.txt`,
+rather than going into the `thesis` directory and running `nano` on `draft.txt` there.)
+
+<div class="in" markdown="1">
+~~~
+$ pwd
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+/users/vlad
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ mkdir thesis
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ nano thesis/draft.txt
+$ ls thesis
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+draft.txt
+~~~
+</div>
+
+`draft.txt` isn't a particularly informative name,
+so let's change the file's name using `mv`,
+which is short for "move":
+
+<div class="in" markdown="1">
+~~~
+$ mv thesis/draft.txt thesis/quotes.txt
+~~~
+</div>
+
+The first parameter tells `mv` what we're "moving",
+while the second is where it's to go.
+In this case,
+we're moving `thesis/draft.txt` to `thesis/quotes.txt`,
+which has the same effect as renaming the file.
+Sure enough,
+`ls` shows us that `thesis` now contains one file called `quotes.txt`:
+
+<div class="in" markdown="1">
+~~~
+$ ls thesis
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+quotes.txt
+~~~
+</div>
+
+Just for the sake of inconsistency,
+`mv` also works on directories—there is no separate `mvdir` command.
+
+Let's move `quotes.txt` into the current working directory.
+We use `mv` once again,
+but this time we'll just use the name of a directory as the second parameter
+to tell `mv` that we want to keep the filename,
+but put the file somewhere new.
+(This is why the command is called "move".)
+In this case,
+the directory name we use is the special directory name `.` that we mentioned earlier.
+
+<div class="in" markdown="1">
+~~~
+$ mv thesis/quotes.txt .
+~~~
+</div>
+
+The effect is to move the file from the directory it was in to the current working directory.
+`ls` now shows us that `thesis` is empty:
+
+<div class="in" markdown="1">
+~~~
+$ ls thesis
+~~~
+</div>
+
+Further,
+`ls` with a filename or directory name as a parameter only lists that file or directory.
+We can use this to see that `quotes.txt` is still in our current directory:
+
+<div class="in" markdown="1">
+~~~
+$ ls quotes.txt
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+quotes.txt
+~~~
+</div>
+
+The `cp` command works very much like `mv`,
+except it copies a file instead of moving it.
+We can check that it did the right thing using `ls`
+with two paths as parameters—like most Unix commands,
+`ls` can be given thousands of paths at once:
+
+<div class="in" markdown="1">
+~~~
+$ cp quotes.txt thesis/quotations.txt
+$ ls quotes.txt thesis/quotations.txt
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+quotes.txt thesis/quotations.txt
+~~~
+</div>
+
+To prove that we made a copy,
+let's delete the `quotes.txt` file in the current directory
+and then run that same `ls` again.
+This time it tells us that it can't find `quotes.txt` in the current directory,
+but it does find the copy in `thesis` that we didn't delete:
+
+<div class="in" markdown="1">
+~~~
+$ ls quotes.txt thesis/quotations.txt
+~~~
+</div>
+<div class="err" markdown="1">
+~~~
+ls: cannot access quotes.txt: No such file or directory
+thesis/quotations.txt
+~~~
+</div>
+
+> #### Another Useful Abbreviation
+>
+> The shell interprets the character `~` (tilde) at the start of a path to
+> mean "the current user's home directory". For example, if Vlad's home
+> directory is `/home/vlad`, then `~/data` is equivalent to
+> `/home/vlad/data`. This only works if it is the first character in the
+> path: `here/there/~/elsewhere` is *not* `/home/vlad/elsewhere`.
+
+<div class="keypoints" markdown="1">
+
+#### Key Points
+* Unix documentation uses '^A' to mean "control-A".
+* The shell does not have a trash bin: once something is deleted, it's really gone.
+* Nano is a very simple text editor—please use something else for real work.
+
+</div>
+
+<div class="challenges" markdown="1">
+
+#### Challenges
+
+1. What is the output of the closing `ls` command in the sequence shown below?
+
+ ~~~
+ $ pwd
+ /home/thing/data
+ $ ls
+ proteins.dat
+ $ mkdir recombine
+ $ mv proteins.dat recombine
+ $ cp recombine/proteins.dat ../proteins-saved.dat
+ $ ls
+ ~~~
+
+2. Suppose that:
+
+ ~~~
+ $ ls -F
+ analyzed/ fructose.dat raw/ sucrose.dat
+ ~~~
+
+ What command(s) could you run so that the commands below will produce the output shown?
+
+ ~~~
+ $ ls
+ analyzed raw
+ $ ls analyzed
+ fructose.dat sucrose.dat
+ ~~~
+
+3. What does `cp` do when given several filenames and a directory name, as in:
+
+ ~~~
+ $ mkdir backup
+ $ cp thesis/citations.txt thesis/quotations.txt backup
+ ~~~
+
+ What does `cp` do when given three or more filenames, as in:
+
+ ~~~
+ $ ls -F
+ intro.txt methods.txt survey.txt
+ $ cp intro.txt methods.txt survey.txt
+ ~~~
+
+ Why do you think `cp`'s behavior is different from `mv`'s?
+
+4. The command `ls -R` lists the contents of directories recursively,
+ i.e., lists their sub-directories, sub-sub-directories, and so on
+ in alphabetical order at each level.
+ The command `ls -t` lists things by time of last change,
+ with most recently changed files or directories first.
+ In what order does `ls -R -t` display things?
+
+</div>
--- /dev/null
+---
+layout: lesson
+root: ../..
+title: Pipes and Filters
+---
+<div class="objectives" markdown="1">
+
+#### Objectives
+* Redirect a command's output to a file.
+* Process a file instead of keyboard input using redirection.
+* Construct command pipelines with two or more stages.
+* Explain what usually happens if a program or pipeline isn't given any input to process.
+* Explain Unix's "small pieces, loosely joined" philosophy.
+
+</div>
+
+Now that we know a few basic commands,
+we can finally look at the shell's most powerful feature:
+the ease with which it lets us combine existing programs in new ways.
+We'll start with a directory called `molecules`
+that contains six files describing some simple organic molecules.
+The `.pdb` extension indicates that these files are in Protein Data Bank format,
+a simple text format that specifies the type and position of each atom in the molecule.
+
+<div class="in" markdown="1">
+~~~
+$ ls molecules
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+cubane.pdb ethane.pdb methane.pdb
+octane.pdb pentane.pdb propane.pdb
+~~~
+</div>
+
+Let's go into that directory with `cd` and run the command `wc *.pdb`.
+`wc` is the "word count" command:
+it counts the number of lines, words, and characters in files.
+The `*` in `*.pdb` matches zero or more characters,
+so the shell turns `*.pdb` into a complete list of `.pdb` files:
+
+<div class="in" markdown="1">
+~~~
+$ cd molecules
+$ wc *.pdb
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 20 156 1158 cubane.pdb
+ 12 84 622 ethane.pdb
+ 9 57 422 methane.pdb
+ 30 246 1828 octane.pdb
+ 21 165 1226 pentane.pdb
+ 15 111 825 propane.pdb
+ 107 819 6081 total
+~~~
+</div>
+
+> #### Wildcards
+>
+> `*` is a [wildcard](../../gloss.html#wildcard). It matches zero or more
+> characters, so `*.pdb` matches `ethane.pdb`, `propane.pdb`, and so on.
+> On the other hand, `p*.pdb` only matches `pentane.pdb` and
+> `propane.pdb`, because the 'p' at the front only matches itself.
+>
+> `?` is also a wildcard, but it only matches a single character. This
+> means that `p?.pdb` matches `pi.pdb` or `p5.pdb`, but not `propane.pdb`.
+> We can use any number of wildcards at a time: for example, `p*.p?*`
+> matches anything that starts with a 'p' and ends with '.', 'p', and at
+> least one more character (since the '?' has to match one character, and
+> the final '\*' can match any number of characters). Thus, `p*.p?*` would
+> match `preferred.practice`, and even `p.pi` (since the first '\*' can
+> match no characters at all), but not `quality.practice` (doesn't start
+> with 'p') or `preferred.p` (there isn't at least one character after the
+> '.p').
+>
+> When the shell sees a wildcard, it expands the wildcard to create a
+> list of matching filenames *before* running the command that was
+> asked for. This means that commands like `wc` and `ls` never see
+> the wildcard characters, just what those wildcards matched. This is
+> another example of orthogonal design.
+
+If we run `wc -l` instead of just `wc`,
+the output shows only the number of lines per file:
+
+<div class="in" markdown="1">
+~~~
+$ wc -l *.pdb
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 20 cubane.pdb
+ 12 ethane.pdb
+ 9 methane.pdb
+ 30 octane.pdb
+ 21 pentane.pdb
+ 15 propane.pdb
+ 107 total
+~~~
+</div>
+
+We can also use `-w` to get only the number of words,
+or `-c` to get only the number of characters.
+
+Which of these files is shortest?
+It's an easy question to answer when there are only six files,
+but what if there were 6000?
+Our first step toward a solution is to run the command:
+
+<div class="in" markdown="1">
+~~~
+$ wc -l *.pdb > lengths
+~~~
+</div>
+
+The `>` tells the shell to [redirect](../../gloss.html#redirect) the command's output
+to a file instead of printing it to the screen.
+The shell will create the file if it doesn't exist,
+or overwrite the contents of that file if it does.
+(This is why there is no screen output:
+everything that `wc` would have printed has gone into the file `lengths` instead.)
+`ls lengths` confirms that the file exists:
+
+<div class="in" markdown="1">
+~~~
+$ ls lengths
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+lengths
+~~~
+</div>
+
+We can now send the content of `lengths` to the screen using `cat lengths`.
+`cat` stands for "concatenate":
+it prints the contents of files one after another.
+There's only one file in this case,
+so `cat` just shows us what it contains:
+
+<div class="in" markdown="1">
+~~~
+$ cat lengths
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 20 cubane.pdb
+ 12 ethane.pdb
+ 9 methane.pdb
+ 30 octane.pdb
+ 21 pentane.pdb
+ 15 propane.pdb
+ 107 total
+~~~
+</div>
+
+Now let's use the `sort` command to sort its contents.
+This does *not* change the file;
+instead, it sends the sorted result to the screen:
+
+<div class="in" markdown="1">
+~~~
+$ sort lengths
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 9 methane.pdb
+ 12 ethane.pdb
+ 15 propane.pdb
+ 20 cubane.pdb
+ 21 pentane.pdb
+ 30 octane.pdb
+107 total
+~~~
+</div>
+
+We can put the sorted list of lines in another temporary file called `sorted-lengths`
+by putting `> sorted-lengths` after the command,
+just as we used `> lengths` to put the output of `wc` into `lengths`.
+Once we've done that,
+we can run another command called `head` to get the first few lines in `sorted-lengths`:
+
+<div class="in" markdown="1">
+~~~
+$ sort lengths > sorted-lengths
+$ head -1 sorted-lengths
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 9 methane.pdb
+~~~
+</div>
+
+Using the parameter `-1` with `head` tells it that
+we only want the first line of the file;
+`-20` would get the first 20,
+and so on.
+Since `sorted-lengths` contains the lengths of our files ordered from least to greatest,
+the output of `head` must be the file with the fewest lines.
+
+If you think this is confusing,
+you're in good company:
+even once you understand what `wc`, `sort`, and `head` do,
+all those intermediate files make it hard to follow what's going on.
+We can make it easier to understand by running `sort` and `head` together:
+
+<div class="in" markdown="1">
+~~~
+$ sort lengths | head -1
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 9 methane.pdb
+~~~
+</div>
+
+The vertical bar between the two commands is called a [pipe](../../gloss.html#pipe).
+It tells the shell that we want to use
+the output of the command on the left
+as the input to the command on the right.
+The computer might create a temporary file if it needs to,
+or copy data from one program to the other in memory,
+or something else entirely;
+we don't have to know or care.
+
+We can use another pipe to send the output of `wc` directly to `sort`,
+which then sends its output to `head`:
+
+<div class="in" markdown="1">
+~~~
+$ wc -l *.pdb | sort | head -1
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 9 methane.pdb
+~~~
+</div>
+
+This is exactly like a mathematician nesting functions like *sin(πx)<sup>2</sup>*
+and saying "the square of the sine of *x* times π".
+In our case,
+the calculation is "head of sort of word count of `*.pdb`".
+
+Here's what actually happens behind the scenes when we create a pipe.
+When a computer runs a program—any program—it creates a [process](../../gloss.html#process)
+in memory to hold the program's software and its current state.
+Every process has an input channel called [standard input](../../gloss.html#standard-input).
+(By this point, you may be surprised that the name is so memorable, but don't worry:
+most Unix programmers call it "stdin".
+Every process also has a default output channel called [standard output](../../gloss.html#standard-output)
+(or "stdout").
+
+The shell is actually just another program.
+Under normal circumstances,
+whatever we type on the keyboard is sent to the shell on its standard input,
+and whatever it produces on standard output is displayed on our screen.
+When we tell the shell to run a program,
+it creates a new process
+and temporarily sends whatever we type on our keyboard to that process's standard input,
+and whatever the process sends to standard output to the screen.
+
+Here's what happens when we run `wc -l *.pdb > lengths`.
+The shell starts by telling the computer to create a new process to run the `wc` program.
+Since we've provided some filenames as parameters,
+`wc` reads from them instead of from standard input.
+And since we've used `>` to redirect output to a file,
+the shell connects the process's standard output to that file.
+
+If we run `wc -l *.pdb | sort` instead,
+the shell creates two processes
+(one for each process in the pipe)
+so that `wc` and `sort` run simultaneously.
+The standard output of `wc` is fed directly to the standard input of `sort`;
+since there's no redirection with `>`,
+`sort`'s output goes to the screen.
+And if we run `wc -l *.pdb | sort | head -1`,
+we get three processes with data flowing from the files,
+through `wc` to `sort`,
+and from `sort` through `head` to the screen.
+
+This simple idea is why Unix has been so successful.
+Instead of creating enormous programs that try to do many different things,
+Unix programmers focus on creating lots of simple tools that each do one job well,
+and that work well with each other.
+This programming model is called [pipes and filters](../../gloss.html#pipe-and-filter).
+We've already seen pipes;
+a [filter](../../gloss.html#filter) is a program like `wc` or `sort`
+that transforms a stream of input into a stream of output.
+Almost all of the standard Unix tools can work this way:
+unless told to do otherwise,
+they read from standard input,
+do something with what they've read,
+and write to standard output.
+
+The key is that any program that reads lines of text from standard input
+and writes lines of text to standard output
+can be combined with every other program that behaves this way as well.
+You can *and should* write your programs this way
+so that you and other people can put those programs into pipes to multiply their power.
+
+> #### Redirecting Input
+>
+> As well as using `>` to redirect a program's output, we can use `<` to
+> redirect its input, i.e., to read from a file instead of from standard
+> input. For example, instead of writing `wc ammonia.pdb`, we could write
+> `wc < ammonia.pdb`. In the first case, `wc` gets a command line
+> parameter telling it what file to open. In the second, `wc` doesn't have
+> any command line parameters, so it reads from standard input, but we
+> have told the shell to send the contents of `ammonia.pdb` to `wc`'s
+> standard input.
+
+#### Nelle's Pipeline: Checking Files
+
+Nelle has run her samples through the assay machines
+and created 1520 files in the `north-pacific-gyre/2012-07-03` directory described earlier.
+As a quick sanity check, she types:
+
+<div class="in" markdown="1">
+~~~
+$ cd north-pacific-gyre/2012-07-03
+$ wc -l *.txt
+~~~
+</div>
+
+The output is 1520 lines that look like this:
+
+<div class="out" markdown="1">
+~~~
+300 NENE01729A.txt
+300 NENE01729B.txt
+300 NENE01736A.txt
+300 NENE01751A.txt
+300 NENE01751B.txt
+300 NENE01812A.txt
+... ...
+~~~
+</div>
+
+Now she types this:
+
+<div class="in" markdown="1">
+~~~
+$ wc -l *.txt | sort | head -5
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 240 NENE02018B.txt
+ 300 NENE01729A.txt
+ 300 NENE01729B.txt
+ 300 NENE01736A.txt
+ 300 NENE01751A.txt
+~~~
+</div>
+
+Whoops: one of the files is 60 lines shorter than the others.
+When she goes back and checks it,
+she sees that she did that assay at 8:00 on a Monday morning—someone
+was probably in using the machine on the weekend,
+and she forgot to reset it.
+Before re-running that sample,
+she checks to see if any files have too much data:
+
+<div class="in" markdown="1">
+~~~
+$ wc -l *.txt | sort | tail -5
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 300 NENE02040A.txt
+ 300 NENE02040B.txt
+ 300 NENE02040Z.txt
+ 300 NENE02043A.txt
+ 300 NENE02043B.txt
+~~~
+</div>
+
+Those numbers look good—but what's that 'Z' doing there in the third-to-last line?
+All of her samples should be marked 'A' or 'B';
+by convention,
+her lab uses 'Z' to indicate samples with missing information.
+To find others like it, she does this:
+
+<div class="in" markdown="1">
+~~~
+$ ls *Z.txt
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+NENE01971Z.txt NENE02040Z.txt
+~~~
+</div>
+
+Sure enough,
+when she checks the log on her laptop,
+there's no depth recorded for either of those samples.
+Since it's too late to get the information any other way,
+she must exclude those two files from her analysis.
+She could just delete them using `rm`,
+but there are actually some analyses she might do later where depth doesn't matter,
+so instead, she'll just be careful later on to select files using the wildcard expression `*[AB].txt`.
+As always,
+the '\*' matches any number of characters;
+the expression `[AB]` matches either an 'A' or a 'B',
+so this matches all the valid data files she has.
+
+<div class="keypoints" markdown="1">
+
+#### Key Points
+* `command > file` redirects a command's output to a file.
+* `first | second` is a pipeline: the output of the first command is used as the input to the second.
+* The best way to use the shell is to use pipes to combine simple single-purpose programs (filters).
+
+</div>
+
+<div class="challenges" markdown="1">
+
+#### Challenges
+
+1. If we run `sort` on this file:
+
+ ~~~
+ 10
+ 2
+ 19
+ 22
+ 6
+ ~~~
+
+ the output is:
+
+ ~~~
+ 10
+ 19
+ 2
+ 22
+ 6
+ ~~~
+
+ If we run `sort -n` on the same input, we get this instead:
+
+ ~~~
+ 2
+ 6
+ 10
+ 19
+ 22
+ ~~~
+
+ Explain why `-n` has this effect.
+
+2. What is the difference between:
+
+ ~~~
+ wc -l < mydata.dat
+ ~~~
+
+ and:
+
+ ~~~
+ wc -l mydata.dat
+ ~~~
+
+3. The command `uniq` removes adjacent duplicated lines from its input.
+ For example, if a file `salmon.txt` contains:
+
+ ~~~
+ coho
+ coho
+ steelhead
+ coho
+ steelhead
+ steelhead
+ ~~~
+
+ then `uniq salmon.txt` produces:
+
+ ~~~
+ coho
+ steelhead
+ coho
+ steelhead
+ ~~~
+
+ Why do you think `uniq` only removes *adjacent* duplicated lines?
+ (Hint: think about very large data sets.) What other command could
+ you combine with it in a pipe to remove all duplicated lines?
+
+4. A file called `animals.txt` contains the following data:
+
+ ~~~
+ 2012-11-05,deer
+ 2012-11-05,rabbit
+ 2012-11-05,raccoon
+ 2012-11-06,rabbit
+ 2012-11-06,deer
+ 2012-11-06,fox
+ 2012-11-07,rabbit
+ 2012-11-07,bear
+ ~~~
+
+ What text passes through each of the pipes and the final redirect in the pipeline below?
+
+ ~~~
+ cat animals.txt | head -5 | tail -3 | sort -r > final.txt
+ ~~~
+
+5. The command:
+
+ ~~~
+ $ cut -d , -f 2 animals.txt
+ ~~~
+
+ produces the following output:
+
+ ~~~
+ deer
+ rabbit
+ raccoon
+ rabbit
+ deer
+ fox
+ rabbit
+ bear
+ ~~~
+
+ What other command(s) could be added to this in a pipeline to find
+ out what animals the file contains (without any duplicates in their
+ names)?
+
+</div>
--- /dev/null
+---
+layout: lesson
+root: ../..
+title: Loops
+---
+<div class="objectives" markdown="1">
+
+#### Objectives
+* Write a loop that applies one or more commands separately to each file in a set of files.
+* Trace the values taken on by a loop variable during execution of the loop.
+* Explain the difference between a variable's name and its value.
+* Explain why spaces and some punctuation characters shouldn't be used in files' names.
+* Demonstrate how to see what commands have recently been executed.
+* Re-run recently executed commands without retyping them.
+
+</div>
+
+Wildcards and tab completion are two ways to reduce typing (and typing mistakes).
+Another is to tell the shell to do something over and over again.
+Suppose we have several hundred genome data files named `basilisk.dat`, `unicorn.dat`, and so on.
+When new files arrive,
+we'd like to rename the existing ones to `original-basilisk.dat` and `original-unicorn.dat`.
+We can't use:
+
+<div class="in" markdown="1">
+~~~
+$ mv *.dat original-*.dat
+~~~
+</div>
+
+because that would expand (in the two-file case) to:
+
+<div class="in" markdown="1">
+~~~
+$ mv basilisk.dat unicorn.dat
+~~~
+</div>
+
+This wouldn't back up our files:
+it would replace the content of `unicorn.dat` with whatever's in `basilisk.dat`.
+
+Instead, we can use a [loop](../../gloss.html#for-loop)
+to do some operation once for each thing in a list.
+Here's a simple example that displays the first three lines of each file in turn:
+
+<div class="in" markdown="1">
+~~~
+$ for filename in basilisk.dat unicorn.dat
+> do
+> head -3 $filename
+> done
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+COMMON NAME: basilisk
+CLASSIFICATION: basiliscus vulgaris
+UPDATED: 1745-05-02
+COMMON NAME: unicorn
+CLASSIFICATION: equus monoceros
+UPDATED: 1738-11-24
+~~~
+</div>
+
+When the shell sees the keyword `for`,
+it knows it is supposed to repeat a command (or group of commands) once for each thing in a list.
+In this case, the list is the two filenames.
+Each time through the loop,
+the name of the thing currently being operated on is assigned to
+the [variable](../../gloss.html#variable) called `filename`.
+Inside the loop,
+we get the variable's value by putting `$` in front of it:
+`$filename` is `basilisk.dat` the first time through the loop,
+`unicorn.dat` the second,
+and so on.
+Finally,
+the command that's actually being run is our old friend `head`,
+so this loop prints out the first three lines of each data file in turn.
+
+> #### Follow the Prompt
+>
+> The shell prompt changes from `$` to `>` and back again as we were
+> typing in our loop. The second prompt, `>`, is different to remind
+> us that we haven't finished typing a complete command yet.
+
+We have called the variable in this loop `filename`
+in order to make its purpose clearer to human readers.
+The shell itself doesn't care what the variable is called;
+if we wrote this loop as:
+
+<div class="in" markdown="1">
+~~~
+for x in basilisk.dat unicorn.dat
+do
+ head -3 $x
+done
+~~~
+</div>
+
+or:
+
+<div class="in" markdown="1">
+~~~
+for temperature in basilisk.dat unicorn.dat
+do
+ head -3 $temperature
+done
+~~~
+</div>
+
+it would work exactly the same way.
+*Don't do this.*
+Programs are only useful if people can understand them,
+so meaningless names (like `x`) or misleading names (like `temperature`)
+increase the odds that the program won't do what its readers think it does.
+
+Here's a slightly more complicated loop:
+
+<div class="in" markdown="1">
+~~~
+for filename in *.dat
+do
+ echo $filename
+ head -100 $filename | tail -20
+done
+~~~
+</div>
+
+The shell starts by expanding `*.dat` to create the list of files it will process.
+The [loop body](../../gloss.html#loop-body)
+then executes two commands for each of those files.
+The first, `echo`, just prints its command-line parameters to standard output.
+For example:
+
+<div class="in" markdown="1">
+~~~
+$ echo hello there
+~~~
+</div>
+
+prints:
+
+<div class="out" markdown="1">
+~~~
+hello there
+~~~
+</div>
+
+In this case,
+since the shell expands `$filename` to be the name of a file,
+`echo $filename` just prints the name of the file.
+Note that we can't write this as:
+
+<div class="in" markdown="1">
+~~~
+for filename in *.dat
+do
+ $filename
+ head -100 $filename | tail -20
+done
+~~~
+</div>
+
+because then the first time through the loop,
+when `$filename` expanded to `basilisk.dat`, the shell would try to run `basilisk.dat` as a program.
+Finally,
+the `head` and `tail` combination selects lines 81-100 from whatever file is being processed.
+
+> #### Spaces in Names
+>
+> Filename expansion in loops is another reason you should not use spaces in filenames.
+> Suppose our data files are named:
+>
+> ~~~
+> basilisk.dat
+> red dragon.dat
+> unicorn.dat
+> ~~~
+>
+> If we try to process them using:
+>
+> ~~~
+> for filename in *.dat
+> do
+> head -100 $filename | tail -20
+> done
+> ~~~
+>
+> then the shell will expand `*.dat` to create:
+>
+> ~~~
+> basilisk.dat red dragon.dat unicorn.dat
+> ~~~
+>
+> With older versions of Bash,
+> or most other shells,
+> `filename` will then be assigned the following values in turn:
+>
+> ~~~
+> basilisk.dat
+> red
+> dragon.dat
+> unicorn.dat
+> ~~~
+>
+> That's a problem: `head` can't read files called `red` and `dragon.dat`
+> because they don't exist,
+> and won't be asked to read the file `red dragon.dat`.
+>
+> We can make our script a little bit more robust
+> by [quoting](../../gloss.html#shell-quoting) our use of the variable:
+>
+> ~~~
+> for filename in *.dat
+> do
+> head -100 "$filename" | tail -20
+> done
+> ~~~
+>
+> but it's simpler just to avoid using spaces (or other special characters) in filenames.
+
+Going back to our original file renaming problem,
+we can solve it using this loop:
+
+<div class="in" markdown="1">
+~~~
+for filename in *.dat
+do
+ mv $filename original-$filename
+done
+~~~
+</div>
+
+This loop runs the `mv` command once for each filename.
+The first time,
+when `$filename` expands to `basilisk.dat`,
+the shell executes:
+
+<div class="in" markdown="1">
+~~~
+mv basilisk.dat original-basilisk.dat
+~~~
+</div>
+
+The second time, the command is:
+
+<div class="in" markdown="1">
+~~~
+mv unicorn.dat original-unicorn.dat
+~~~
+</div>
+
+> #### Measure Twice, Run Once
+>
+> A loop is a way to do many things at once—or to make many mistakes at
+> once if it does the wrong thing. One way to check what a loop *would* do
+> is to echo the commands it would run instead of actually running them.
+> For example, we could write our file renaming loop like this:
+>
+> ~~~
+> for filename in *.dat
+> do
+> echo mv $filename original-$filename
+> done
+> ~~~
+>
+> Instead of running `mv`, this loop runs `echo`, which prints out:
+>
+> ~~~
+> mv basilisk.dat original-basilisk.dat
+> mv unicorn.dat original-unicorn.dat
+> ~~~
+>
+> *without* actually running those commands. We can then use up-arrow to
+> redisplay the loop, back-arrow to get to the word `echo`, delete it, and
+> then press "enter" to run the loop with the actual `mv` commands. This
+> isn't foolproof, but it's a handy way to see what's going to happen when
+> you're still learning how loops work.
+
+#### Nelle's Pipeline: Processing Files
+
+Nelle is now ready to process her data files.
+Since she's still learning how to use the shell,
+she decides to build up the required commands in stages.
+Her first step is to make sure that she can select the right files—remember,
+these are ones whose names end in 'A' or 'B', rather than 'Z':
+
+<div class="in" markdown="1">
+~~~
+$ cd north-pacific-gyre/2012-07-03
+$ for datafile in *[AB].txt
+> do
+> echo $datafile
+> done
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+NENE01729A.txt
+NENE01729B.txt
+NENE01736A.txt
+...
+NENE02043A.txt
+NENE02043B.txt
+~~~
+</div>
+
+Her next step is to decide
+what to call the files that the `goostats` analysis program will create.
+Prefixing each input file's name with "stats" seems simple,
+so she modifies her loop to do that:
+
+<div class="in" markdown="1">
+~~~
+$ for datafile in *[AB].txt
+> do
+> echo $datafile stats-$datafile
+> done
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+NENE01729A.txt stats-NENE01729A.txt
+NENE01729B.txt stats-NENE01729B.txt
+NENE01736A.txt stats-NENE01736A.txt
+...
+NENE02043A.txt stats-NENE02043A.txt
+NENE02043B.txt stats-NENE02043B.txt
+~~~
+</div>
+
+She hasn't actually run `goostats` yet,
+but now she's sure she can select the right files and generate the right output filenames.
+
+Typing in commands over and over again is becoming tedious,
+though,
+and Nelle is worried about making mistakes,
+so instead of re-entering her loop,
+she presses the up arrow.
+In response,
+the shell redisplays the whole loop on one line
+(using semi-colons to separate the pieces):
+
+<div class="in" markdown="1">
+~~~
+$ for datafile in *[AB].txt; do echo $datafile stats-$datafile; done
+~~~
+</div>
+
+Using the left arrow key,
+Nelle backs up and changes the command `echo` to `goostats`:
+
+<div class="in" markdown="1">
+~~~
+$ for datafile in *[AB].txt; do bash goostats $datafile stats-$datafile; done
+~~~
+</div>
+
+When she presses enter,
+the shell runs the modified command.
+However, nothing appears to happen—there is no output.
+After a moment, Nelle realizes that since her script doesn't print anything to the screen any longer,
+she has no idea whether it is running, much less how quickly.
+She kills the job by typing Control-C,
+uses up-arrow to repeat the command,
+and edits it to read:
+
+<div class="in" markdown="1">
+~~~
+$ for datafile in *[AB].txt; do echo $datafile; bash goostats $datafile stats-$datafile; done
+~~~
+</div>
+
+> #### Beginning and End
+>
+> We can move to the beginning of a line in the shell by typing `^A`
+> (which means Control-A)
+> and to the end using `^E`.
+
+When she runs her program now,
+it produces one line of output every five seconds or so:
+
+<div class="out" markdown="1">
+~~~
+NENE01729A.txt
+NENE01729B.txt
+NENE01736A.txt
+...
+~~~
+</div>
+
+1518 times 5 seconds,
+divided by 60,
+tells her that her script will take about two hours to run.
+As a final check,
+she opens another terminal window,
+goes into `north-pacific-gyre/2012-07-03`,
+and uses `cat stats-NENE01729B.txt`
+to examine one of the output files.
+It looks good,
+so she decides to get some coffee and catch up on her reading.
+
+> #### Those Who Know History Can Choose to Repeat It
+>
+> Another way to repeat previous work is to use the `history` command to
+> get a list of the last few hundred commands that have been executed, and
+> then to use `!123` (where "123" is replaced by the command number) to
+> repeat one of those commands. For example, if Nelle types this:
+>
+> ~~~
+> $ history | tail -5
+> 456 ls -l NENE0*.txt
+> 457 rm stats-NENE01729B.txt.txt
+> 458 bash goostats NENE01729B.txt stats-NENE01729B.txt
+> 459 ls -l NENE0*.txt
+> 460 history
+> ~~~
+>
+> then she can re-run `goostats` on `NENE01729B.txt` simply by typing
+> `!458`.
+
+<div class="keypoints" markdown="1">
+
+#### Key Points
+* A `for` loop repeats commands once for every thing in a list.
+* Every `for` loop needs a variable to refer to the current "thing".
+* Use `$name` to expand a variable (i.e., get its value).
+* Do not use spaces, quotes, or wildcard characters such as '*' or '?' in filenames, as it complicates variable expansion.
+* Give files consistent names that are easy to match with wildcard patterns to make it easy to select them for looping.
+* Use the up-arrow key to scroll up through previous commands to edit and repeat them.
+* Use `history` to display recent commands, and `!number` to repeat a command by number.
+
+</div>
+
+<div class="challenges" markdown="1">
+
+#### Challenges
+
+1. Suppose that `ls` initially displays:
+
+ ~~~
+ fructose.dat glucose.dat sucrose.dat
+ ~~~
+
+ What is the output of:
+
+ ~~~
+ for datafile in *.dat
+ do
+ ls *.dat
+ done
+ ~~~
+
+2. In the same directory, what is the effect of this loop?
+
+ ~~~
+ for sugar in *.dat
+ do
+ echo $sugar
+ cat $sugar > xylose.dat
+ done
+ ~~~
+
+ 1. Prints `fructose.dat`, `glucose.dat`, and `sucrose.dat`, and
+ copies `sucrose.dat` to create `xylose.dat`.
+ 2. Prints `fructose.dat`, `glucose.dat`, and `sucrose.dat`, and
+ concatenates all three files to create `xylose.dat`.
+ 3. Prints `fructose.dat`, `glucose.dat`, `sucrose.dat`, and
+ `xylose.dat`, and copies `sucrose.dat` to create `xylose.dat`.
+ 4. None of the above.
+
+3. The `expr` does simple arithmetic using command-line parameters:
+
+ ~~~
+ $ expr 3 + 5
+ 8
+ $ expr 30 / 5 - 2
+ 4
+ ~~~
+
+ Given this, what is the output of:
+
+ ~~~
+ for left in 2 3
+ do
+ for right in $left
+ do
+ expr $left + $right
+ done
+ done
+ ~~~
+
+4. Describe in words what the following loop does.
+
+ ~~~
+ for how in frog11 prcb redig
+ do
+ $how -limit 0.01 NENE01729B.txt
+ done
+ ~~~
+
+</div>
--- /dev/null
+---
+layout: lesson
+root: ../..
+title: Shell Scripts
+---
+<div class="objectives" markdown="1">
+
+#### Objectives
+* Write a shell script that runs a command or series of commands for a fixed set of files.
+* Run a shell script from the command line.
+* Write a shell script that operates on a set of files defined by the user on the command line.
+* Create pipelines that include user-written shell scripts.
+
+</div>
+
+We are finally ready to see what makes the shell such a powerful programming environment.
+We are going to take the commands we repeat frequently and save them in files
+so that we can re-run all those operations again later by typing a single command.
+For historical reasons,
+a bunch of commands saved in a file is usually called a [shell script](../../gloss.html#shell-script),
+but make no mistake:
+these are actually small programs.
+
+Let's start by putting the following line in the file `middle.sh`:
+
+<div class="file" markdown="1">
+~~~
+head -20 cholesterol.pdb | tail -5
+~~~
+</div>
+
+This is a variation on the pipe we constructed earlier:
+it selects lines 16-20 of the file `cholesterol.pdb`.
+Remember, we are *not* running it as a command just yet:
+we are putting the commands in a file.
+
+Once we have saved the file,
+we can ask the shell to execute the commands it contains.
+Our shell is called `bash`, so we run the following command:
+
+<div class="in" markdown="1">
+~~~
+$ bash middle.sh
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ATOM 14 C 1 -1.463 -0.666 1.001 1.00 0.00
+ATOM 15 C 1 0.762 -0.929 0.295 1.00 0.00
+ATOM 16 C 1 0.771 -0.937 1.840 1.00 0.00
+ATOM 17 C 1 -0.664 -0.610 2.293 1.00 0.00
+ATOM 18 C 1 -4.705 2.108 -0.396 1.00 0.00
+~~~
+</div>
+
+Sure enough,
+our script's output is exactly what we would get if we ran that pipeline directly.
+
+> #### Text vs. Whatever
+>
+> We usually call programs like Microsoft Word or LibreOffice Writer "text
+> editors", but we need to be a bit more careful when it comes to
+> programming. By default, Microsoft Word uses `.docx` files to store not
+> only text, but also formatting information about fonts, headings, and so
+> on. This extra information isn't stored as characters, and doesn't mean
+> anything to tools like `head`: they expect input files to contain
+> nothing but the letters, digits, and punctuation on a standard computer
+> keyboard. When editing programs, therefore, you must either use a plain
+> text editor, or be careful to save files as plain text.
+
+What if we want to select lines from an arbitrary file?
+We could edit `middle.sh` each time to change the filename,
+but that would probably take longer than just retyping the command.
+Instead,
+let's edit `middle.sh` and replace `cholesterol.pdb` with a special variable called `$1`:
+
+<div class="in" markdown="1">
+~~~
+$ cat middle.sh
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+head -20 $1 | tail -5
+~~~
+</div>
+
+Inside a shell script,
+`$1` means "the first filename (or other parameter) on the command line".
+We can now run our script like this:
+
+<div class="in" markdown="1">
+~~~
+$ bash middle.sh cholesterol.pdb
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ATOM 14 C 1 -1.463 -0.666 1.001 1.00 0.00
+ATOM 15 C 1 0.762 -0.929 0.295 1.00 0.00
+ATOM 16 C 1 0.771 -0.937 1.840 1.00 0.00
+ATOM 17 C 1 -0.664 -0.610 2.293 1.00 0.00
+ATOM 18 C 1 -4.705 2.108 -0.396 1.00 0.00
+~~~
+</div>
+
+or on a different file like this:
+
+<div class="in" markdown="1">
+~~~
+$ bash middle.sh vitamin-a.pdb
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ATOM 14 C 1 1.788 -0.987 -0.861
+ATOM 15 C 1 2.994 -0.265 -0.829
+ATOM 16 C 1 4.237 -0.901 -1.024
+ATOM 17 C 1 5.406 -0.117 -1.087
+ATOM 18 C 1 -0.696 -2.628 -0.641
+~~~
+</div>
+
+We still need to edit `middle.sh` each time we want to adjust the range of lines,
+though.
+Let's fix that by using the special variables `$2` and `$3`:
+
+<div class="in" markdown="1">
+~~~
+$ cat middle.sh
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+head $2 $1 | tail $3
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ bash middle.sh vitamin-a.pdb -20 -5
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ATOM 14 C 1 1.788 -0.987 -0.861
+ATOM 15 C 1 2.994 -0.265 -0.829
+ATOM 16 C 1 4.237 -0.901 -1.024
+ATOM 17 C 1 5.406 -0.117 -1.087
+ATOM 18 C 1 -0.696 -2.628 -0.641
+~~~
+</div>
+
+This works,
+but it may take the next person who reads `middle.sh` a moment to figure out what it does.
+We can improve our script by adding some [comments](../../gloss.html#comment) at the top:
+
+<div class="in" markdown="1">
+~~~
+$ cat middle.sh
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+# Select lines from the middle of a file.
+# Usage: middle.sh filename -end_line -num_lines
+head $2 $1 | tail $3
+~~~
+</div>
+
+A comment starts with a `#` character and runs to the end of the line.
+The computer ignores comments,
+but they're invaluable for helping people understand and use scripts.
+
+What if we want to process many files in a single pipeline?
+For example, if we want to sort our `.pdb` files by length, we would type:
+
+<div class="in" markdown="1">
+~~~
+$ wc -l *.pdb | sort -n
+~~~
+</div>
+
+because `wc -l` lists the number of lines in the files
+and `sort -n` sorts things numerically.
+We could put this in a file,
+but then it would only ever sort a list of `.pdb` files in the current directory.
+If we want to be able to get a sorted list of other kinds of files,
+we need a way to get all those names into the script.
+We can't use `$1`, `$2`, and so on
+because we don't know how many files there are.
+Instead, we use the special variable `$*`,
+which means,
+"All of the command-line parameters to the shell script."
+Here's an example:
+
+<div class="in" markdown="1">
+~~~
+$ cat sorted.sh
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+wc -l $* | sort -n
+~~~
+</div>
+<div class="in" markdown="1">
+~~~
+$ bash sorted.sh *.dat backup/*.dat
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+ 29 chloratin.dat
+ 89 backup/chloratin.dat
+ 91 sphagnoi.dat
+ 156 sphag2.dat
+ 172 backup/sphag-merged.dat
+ 182 girmanis.dat
+~~~
+</div>
+
+> #### Why Isn't It Doing Anything?
+>
+> What happens if a script is supposed to process a bunch of files, but we
+> don't give it any filenames? For example, what if we type:
+>
+> $ bash sorted.sh
+>
+> but don't say `*.dat` (or anything else)? In this case, `$*` expands to
+> nothing at all, so the pipeline inside the script is effectively:
+>
+> wc -l | sort -n
+>
+> Since it doesn't have any filenames, `wc` assumes it is supposed to
+> process standard input, so it just sits there and waits for us to give
+> it some data interactively. From the outside, though, all we see is it
+> sitting there: the script doesn't appear to do anything.
+
+We have two more things to do before we're finished with our simple shell scripts.
+If you look at a script like:
+
+<div class="file" markdown="1">
+~~~
+wc -l $* | sort -n
+~~~
+</div>
+
+you can probably puzzle out what it does.
+On the other hand,
+if you look at this script:
+
+<div class="file" markdown="1">
+~~~
+# List files sorted by number of lines.
+wc -l $* | sort -n
+~~~
+</div>
+
+you don't have to puzzle it out—the comment at the top tells you what it does.
+A line or two of documentation like this make it much easier for other people
+(including your future self)
+to re-use your work.
+The only caveat is that each time you modify the script,
+you should check that the comment is still accurate:
+an explanation that sends the reader in the wrong direction is worse than none at all.
+
+Second,
+suppose we have just run a series of commands that did something useful—for example,
+that created a graph we'd like to use in a paper.
+We'd like to be able to re-create the graph later if we need to,
+so we want to save the commands in a file.
+Instead of typing them in again
+(and potentially getting them wrong)
+we can do this:
+
+<div class="in" markdown="1">
+~~~
+$ history | tail -4 > redo-figure-3.sh
+~~~
+</div>
+
+The file `redo-figure-3.sh` now contains:
+
+<div class="file" markdown="1">
+~~~
+297 goostats -r NENE01729B.txt stats-NENE01729B.txt
+298 goodiff stats-NENE01729B.txt /data/validated/01729.txt > 01729-differences.txt
+299 cut -d ',' -f 2-3 01729-differences.txt > 01729-time-series.txt
+300 ygraph --format scatter --color bw --borders none 01729-time-series.txt figure-3.png
+~~~
+</div>
+
+After a moment's work in an editor to remove the serial numbers on the commands,
+we have a completely accurate record of how we created that figure.
+
+> #### Unnumbering
+>
+> Nelle could also use `colrm` (short for "column removal") to remove the
+> serial numbers on her previous commands.
+> Its parameters are the range of characters to strip from its input:
+>
+> ~~~
+> $ history | tail -5
+> 173 cd /tmp
+> 174 ls
+> 175 mkdir bakup
+> 176 mv bakup backup
+> 177 history | tail -5
+> $ history | tail -5 | colrm 1 7
+> cd /tmp
+> ls
+> mkdir bakup
+> mv bakup backup
+> history | tail -5
+> history | tail -5 | colrm 1 7
+> ~~~
+
+In practice, most people develop shell scripts by running commands at the shell prompt a few times
+to make sure they're doing the right thing,
+then saving them in a file for re-use.
+This style of work allows people to recycle
+what they discover about their data and their workflow with one call to `history`
+and a bit of editing to clean up the output
+and save it as a shell script.
+
+#### Nelle's Pipeline: Creating a Script
+
+An off-hand comment from her supervisor has made Nelle realize that
+she should have provided a couple of extra parameters to `goostats` when she processed her files.
+This might have been a disaster if she had done all the analysis by hand,
+but thanks to for loops,
+it will only take a couple of hours to re-do.
+
+But experience has taught her that if something needs to be done twice,
+it will probably need to be done a third or fourth time as well.
+She runs the editor and writes the following:
+
+<div class="file" markdown="1">
+~~~
+# Calculate reduced stats for data files at J = 100 c/bp.
+for datafile in $*
+do
+ echo $datafile
+ goostats -J 100 -r $datafile stats-$datafile
+done
+~~~
+</div>
+
+(The parameters `-J 100` and `-r` are the ones her supervisor said she should have used.)
+She saves this in a file called `do-stats.sh`
+so that she can now re-do the first stage of her analysis by typing:
+
+<div class="in" markdown="1">
+~~~
+$ bash do-stats.sh *[AB].txt
+~~~
+</div>
+
+She can also do this:
+
+<div class="in" markdown="1">
+~~~
+$ bash do-stats.sh *[AB].txt | wc -l
+~~~
+</div>
+
+so that the output is just the number of files processed
+rather than the names of the files that were processed.
+
+One thing to note about Nelle's script is that
+it lets the person running it decide what files to process.
+She could have written it as:
+
+<div class="file" markdown="1">
+~~~
+# Calculate reduced stats for A and Site B data files at J = 100 c/bp.
+for datafile in *[AB].txt
+do
+ echo $datafile
+ goostats -J 100 -r $datafile stats-$datafile
+done
+~~~
+</div>
+
+The advantage is that this always selects the right files:
+she doesn't have to remember to exclude the 'Z' files.
+The disadvantage is that it *always* selects just those files—she can't run it on all files
+(including the 'Z' files),
+or on the 'G' or 'H' files her colleagues in Antarctica are producing,
+without editing the script.
+If she wanted to be more adventurous,
+she could modify her script to check for command-line parameters,
+and use `*[AB].txt` if none were provided.
+Of course, this introduces another tradeoff between flexibility and complexity.
+
+<div class="keypoints" markdown="1">
+
+#### Key Points
+* Save commands in files (usually called shell scripts) for re-use.
+* `bash filename` runs the commands saved in a file.
+* `$*` refers to all of a shell script's command-line parameters.
+* `$1`, `$2`, etc., refer to specified command-line parameters.
+* Letting users decide what files to process is more flexible and more consistent with built-in Unix commands.
+
+</div>
+
+<div class="challenges" markdown="1">
+
+#### Challenges
+
+1. Leah has several hundred data files, each of which is formatted like this:
+
+ ~~~
+ 2013-11-05,deer,5
+ 2013-11-05,rabbit,22
+ 2013-11-05,raccoon,7
+ 2013-11-06,rabbit,19
+ 2013-11-06,deer,2
+ 2013-11-06,fox,1
+ 2013-11-07,rabbit,18
+ 2013-11-07,bear,1
+ ~~~
+
+ Write a shell script called `species.sh` that takes any number of
+ filenames as command-line parameters, and uses `cut`, `sort`, and
+ `uniq` to print a list of the unique species appearing in each of
+ those files separately.
+
+2. Write a shell script called `longest.sh` that takes the name of a
+ directory and a filename extension as its parameters, and prints out
+ the name of the most recently modified file in that directory with
+ that extension. For example:
+
+ ~~~
+ $ bash largest.sh /tmp/data pdb
+ ~~~
+
+ would print the name of the `.pdb` file in `/tmp/data` that has been
+ changed most recently.
+
+3. If you run the command:
+
+ ~~~
+ history | tail -5 > recent.sh
+ ~~~
+
+ the last command in the file is the `history` command itself, i.e.,
+ the shell has added `history` to the command log before actually
+ running it. In fact, the shell *always* adds commands to the log
+ before running them. Why do you think it does this?
+
+4. Joel's `data` directory contains three files: `fructose.dat`,
+ `glucose.dat`, and `sucrose.dat`. Explain what a script called
+ `example.sh` would when run as `bash example.sh *.dat`
+ if it contained the following lines:
+
+<table>
+ <tr>
+ <td valign="top">1.</td>
+ <td valign="top">
+<pre>
+echo *.*
+</pre>
+ </td>
+ </tr>
+ <tr>
+ <td valign="top">2.</td>
+ <td valign="top">
+<pre>
+for filename in $1 $2 $3
+do
+ cat $filename
+done
+</pre>
+ </td>
+ </tr>
+ <tr>
+ <td valign="top">3.</td>
+ <td valign="top">
+<pre>
+echo $*.dat
+</pre>
+ </td>
+ </tr>
+</table>
+
+</div>
--- /dev/null
+---
+layout: lesson
+root: ../..
+title: Finding Things
+---
+<div class="objectives" markdown="1">
+
+#### Objectives
+* Use `grep` to select lines from text files that match simple patterns.
+* Use `find` to find files whose names match simple patterns.
+* Use the output of one command as the command-line parameters to another command.
+* Explain what is meant by "text" and "binary" files, and why many common tools don't handle the latter well.
+
+</div>
+
+You can guess someone's age by how they talk about search:
+young people use "Google" as a verb,
+while crusty old Unix programmers use "grep".
+The word is a contraction of "global/regular expression/print",
+a common sequence of operations in early Unix text editors.
+It is also the name of a very useful command-line program.
+
+`grep` finds and prints lines in files that match a pattern.
+For our examples,
+we will use a file that contains three haikus taken from a
+1998 competition in *Salon* magazine:
+
+<div class="in" markdown="1">
+~~~
+$ cat haiku.txt
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+The Tao that is seen
+Is not the true Tao, until
+You bring fresh toner.
+
+With searching comes loss
+and the presence of absence:
+"My Thesis" not found.
+
+Yesterday it worked
+Today it is not working
+Software is like that.
+~~~
+</div>
+
+> #### Forever, or Five Years
+>
+> We haven't linked to the original haikus because they don't appear to be on *Salon*'s site any longer.
+> As [Jeff Rothenberg said](http://www.clir.org/pubs/archives/ensuring.pdf),
+> "Digital information lasts forever—or five years, whichever comes first."
+
+Let's find lines that contain the word "not":
+
+<div class="in" markdown="1">
+~~~
+$ grep not haiku.txt
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+Is not the true Tao, until
+"My Thesis" not found
+Today it is not working
+~~~
+</div>
+
+Here, `not` is the pattern we're searching for.
+It's pretty simple:
+every alphanumeric character matches against itself.
+After the pattern comes the name or names of the files we're searching in.
+The output is the three lines in the file that contain the letters "not".
+
+Let's try a different pattern: "day".
+
+<div class="in" markdown="1">
+~~~
+$ grep day haiku.txt
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+Yesterday it worked
+Today it is not working
+~~~
+</div>
+
+This time,
+the output is lines containing the words "Yesterday" and "Today",
+which both have the letters "day".
+If we give `grep` the `-w` flag,
+it restricts matches to word boundaries,
+so that only lines with the word "day" will be printed:
+
+<div class="in" markdown="1">
+~~~
+$ grep -w day haiku.txt
+~~~
+</div>
+
+In this case, there aren't any, so `grep`'s output is empty.
+
+Another useful option is `-n`, which numbers the lines that match:
+
+<div class="in" markdown="1">
+~~~
+$ grep -n it haiku.txt
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+5:With searching comes loss
+9:Yesterday it worked
+10:Today it is not working
+~~~
+</div>
+
+Here, we can see that lines 5, 9, and 10 contain the letters "it".
+
+We can combine flags as we do with other Unix commands.
+For example,
+since `-i` makes matching case-insensitive and `-v` inverts the match,
+using them both only prints lines that *don't* match the pattern
+in any mix of upper and lower case:
+
+<div class="in" markdown="1">
+~~~
+$ grep -i -v the haiku.txt
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+You bring fresh toner.
+
+With searching comes loss
+
+Yesterday it worked
+Today it is not working
+Software is like that.
+~~~
+</div>
+
+`grep` has lots of other options.
+To find out what they are, we can type `man grep`.
+`man` is the Unix "manual" command:
+it prints a description of a command and its options,
+and (if you're lucky) provides a few examples of how to use it:
+
+<div class="in" markdown="1">
+~~~
+$ man grep
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+GREP(1) GREP(1)
+
+NAME
+grep, egrep, fgrep - print lines matching a pattern
+
+SYNOPSIS
+grep [OPTIONS] PATTERN [FILE...]
+grep [OPTIONS] [-e PATTERN | -f FILE] [FILE...]
+
+DESCRIPTION
+grep searches the named input FILEs (or standard input if no files are named, or if a single hyphen-
+minus (-) is given as file name) for lines containing a match to the given PATTERN. By default, grep
+prints the matching lines.
+... ... ...
+
+OPTIONS
+Generic Program Information
+--help Print a usage message briefly summarizing these command-line options and the bug-reporting
+address, then exit.
+
+-V, --version
+Print the version number of grep to the standard output stream. This version number should be
+included in all bug reports (see below).
+
+Matcher Selection
+-E, --extended-regexp
+Interpret PATTERN as an extended regular expression (ERE, see below). (-E is specified by
+POSIX.)
+
+-F, --fixed-strings
+Interpret PATTERN as a list of fixed strings, separated by newlines, any of which is to be
+matched. (-F is specified by POSIX.)
+... ... ...
+~~~
+</div>
+
+> #### Wildcards
+>
+> `grep`'s real power doesn't come from its options, though; it comes from
+> the fact that patterns can include wildcards. (The technical name for
+> these is [regular expressions](../../gloss.html#regular-expression), which
+> is what the "re" in "grep" stands for.) Regular expressions are both complex
+> and powerful; if you want to do complex searches, please look at the lesson
+> on [our website](http://software-carpentry.org). As a taster, we can
+> find lines that have an 'o' in the second position like this:
+>
+> $ grep -E '^.o' haiku.txt
+> You bring fresh toner.
+> Today it is not working
+> Software is like that.
+>
+> We use the `-E` flag and put the pattern in quotes to prevent the shell
+> from trying to interpret it. (If the pattern contained a '\*', for
+> example, the shell would try to expand it before running `grep`.) The
+> '\^' in the pattern anchors the match to the start of the line. The '.'
+> matches a single character (just like '?' in the shell), while the 'o'
+> matches an actual 'o'.
+
+While `grep` finds lines in files,
+the `find` command finds files themselves.
+Again,
+it has a lot of options;
+to show how the simplest ones work, we'll use the directory tree shown below.
+
+<img src="img/find-file-tree.svg" alt="File Tree for Find Example" />
+
+Vlad's home directory contains one file called `notes.txt` and four subdirectories:
+`thesis` (which is sadly empty),
+`data` (which contains two files `one.txt` and `two.txt`),
+a `tools` directory that contains the programs `format` and `stats`,
+and an empty subdirectory called `old`.
+
+For our first command,
+let's run `find . -type d -print`.
+As always,
+the `.` on its own means the current working directory,
+which is where we want our search to start;
+`-type d` means "things that are directories",
+and (unsurprisingly) `-print` means "print what's found".
+Sure enough,
+`find`'s output is the names of the five directories in our little tree
+(including `.`):
+
+<div class="in" markdown="1">
+~~~
+$ find . -type d -print
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./
+./data
+./thesis
+./tools
+./tools/old
+~~~
+</div>
+
+If we change `-type d` to `-type f`,
+we get a listing of all the files instead:
+
+<div class="in" markdown="1">
+~~~
+$ find . -type f -print
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./data/one.txt
+./data/two.txt
+./notes.txt
+./tools/format
+./tools/stats
+~~~
+</div>
+
+`find` automatically goes into subdirectories,
+their subdirectories,
+and so on to find everything that matches the pattern we've given it.
+If we don't want it to,
+we can use `-maxdepth` to restrict the depth of search:
+
+<div class="in" markdown="1">
+~~~
+$ find . -maxdepth 1 -type f -print
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./notes.txt
+~~~
+</div>
+
+The opposite of `-maxdepth` is `-mindepth`,
+which tells `find` to only report things that are at or below a certain depth.
+`-mindepth 2` therefore finds all the files that are two or more levels below us:
+
+<div class="in" markdown="1">
+~~~
+$ find . -mindepth 2 -type f -print
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./data/one.txt
+./data/two.txt
+./tools/format
+./tools/stats
+~~~
+</div>
+
+Another option is `-empty`,
+which restricts matches to empty files and directories:
+
+<div class="in" markdown="1">
+~~~
+$ find . -empty -print
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./thesis
+./tools/old
+~~~
+</div>
+
+Now let's try matching by name:
+
+<div class="in" markdown="1">
+~~~
+$ find . -name *.txt -print
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./notes.txt
+~~~
+</div>
+
+We expected it to find all the text files,
+but it only prints out `./notes.txt`.
+The problem is that the shell expands wildcard characters like `*` *before* commands run.
+Since `*.txt` in the current directory expands to `notes.txt`,
+the command we actually ran was:
+
+<div class="in" markdown="1">
+~~~
+$ find . -name notes.txt -print
+~~~
+</div>
+
+`find` did what we asked; we just asked for the wrong thing.
+
+To get what we want,
+let's do what we did with `grep`:
+put `*.txt` in single quotes to prevent the shell from expanding the `*` wildcard.
+This way,
+`find` actually gets the pattern `*.txt`, not the expanded filename `notes.txt`:
+
+<div class="in" markdown="1">
+~~~
+$ find . -name '*.txt' -print
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./data/one.txt
+./data/two.txt
+./notes.txt
+~~~
+</div>
+
+> #### Listing vs. Finding
+>
+> `ls` and `find` can be made to do similar things given the right options,
+> but under normal circumstances,
+> `ls` lists everything it can,
+> while `find` searches for things with certain properties and shows them.
+
+As we said earlier,
+the command line's power lies in combining tools.
+We've seen how to do that with pipes;
+let's look at another technique.
+As we just saw,
+`find . -name '*.txt' -print` gives us a list of all text files in or below the current directory.
+How can we combine that with `wc -l` to count the lines in all those files?
+
+The simplest way is to put the `find` command inside `$()`:
+
+<div class="in" markdown="1">
+~~~
+$ wc -l $(find . -name '*.txt' -print)
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+70 ./data/one.txt
+420 ./data/two.txt
+30 ./notes.txt
+520 total
+~~~
+</div>
+
+When the shell executes this command,
+the first thing it does is run whatever is inside the `$()`.
+It then replaces the `$()` expression with that command's output.
+Since the output of `find` is the three filenames `./data/one.txt`, `./data/two.txt`, and `./notes.txt`,
+the shell constructs the command:
+
+<div class="in" markdown="1">
+~~~
+$ wc -l ./data/one.txt ./data/two.txt ./notes.txt
+~~~
+</div>
+
+which is what we wanted.
+This expansion is exactly what the shell does when it expands wildcards like `*` and `?`,
+but lets us use any command we want as our own "wildcard".
+
+It's very common to use `find` and `grep` together.
+The first finds files that match a pattern;
+the second looks for lines inside those files that match another pattern.
+Here, for example, we can find PDB files that contain iron atoms
+by looking for the string "FE" in all the `.pdb` files below the current directory:
+
+<div class="in" markdown="1">
+~~~
+$ grep FE $(find . -name '*.pdb' -print)
+~~~
+</div>
+<div class="out" markdown="1">
+~~~
+./human/heme.pdb:ATOM 25 FE 1 -0.924 0.535 -0.518
+~~~
+</div>
+
+> #### Binary Files
+>
+> We have focused exclusively on finding things in text files. What if
+> your data is stored as images, in databases, or in some other format?
+> One option would be to extend tools like `grep` to handle those formats.
+> This hasn't happened, and probably won't, because there are too many
+> formats to support.
+>
+> The second option is to convert the data to text, or extract the
+> text-ish bits from the data. This is probably the most common approach,
+> since it only requires people to build one tool per data format (to
+> extract information). On the one hand, it makes simple things easy to
+> do. On the negative side, complex things are usually impossible. For
+> example, it's easy enough to write a program that will extract X and Y
+> dimensions from image files for `grep` to play with, but how would you
+> write something to find values in a spreadsheet whose cells contained
+> formulas?
+>
+> The third choice is to recognize that the shell and text processing have
+> their limits, and to use a programming language such as Python instead.
+> When the time comes to do this, don't be too hard on the shell: many
+> modern programming languages, Python included, have borrowed a lot of
+> ideas from it, and imitation is also the sincerest form of praise.
+
+#### Conclusion
+
+The Unix shell is older than most of the people who use it. It has
+survived so long because it is one of the most productive programming
+environments ever created—maybe even *the* most productive. Its syntax
+may be cryptic, but people who have mastered it can experiment with
+different commands interactively, then use what they have learned to
+automate their work. Graphical user interfaces may be better at the
+first, but the shell is still unbeaten at the second. And as Alfred
+North Whitehead wrote in 1911, "Civilization advances by extending the
+number of important operations which we can perform without thinking
+about them."
+
+<div class="keypoints" markdown="1">
+
+#### Key Points
+* Use `find` to find files and directories, and `grep` to find text patterns in files.
+* `$(command)` inserts a command's output in place.
+* `man command` displays the manual page for a given command.
+
+</div>
+
+<div class="challenges" markdown="1">
+
+#### Challenges
+
+1. Write a short explanatory comment for the following shell script:
+
+ <div class="file" markdown="1">
+ ~~~
+ find . -name '*.dat' -print | wc -l | sort -n
+ ~~~
+ </div>
+
+2. The `-v` flag to `grep` inverts pattern matching, so that only lines
+ which do *not* match the pattern are printed. Given that, which of
+ the following commands will find all files in `/data` whose names
+ end in `ose.dat` (e.g., `sucrose.dat` or `maltose.dat`), but do
+ *not* contain the word `temp`?
+
+ 1. `find /data -name '*.dat' -print | grep ose | grep -v temp`
+
+ 2. `find /data -name ose.dat -print | grep -v temp`
+
+ 3. `grep -v temp $(find /data -name '*ose.dat' -print)`
+
+ 4. None of the above.
+
+</div>
--- /dev/null
+# Resources
+
+* `filesystem`: filesystem used in "Files and Directories"
+* `creatures`: DNA data used in "Loops"
+* `finding`: data using in "Finding Things"
+* `molecules`: PDB files used in "Pipes and Filters"
+* `scripting`: files and directories used in "Shell Scripts"
--- /dev/null
+COMMON NAME: basilisk
+CLASSIFICATION: basiliscus vulgaris
+UPDATED: 1745-05-02
+CCCCAACGAG
+GAAACAGATC
+ATTAGAAGAT
+CTGTCGCGAA
+CCGCACCTCT
+CCTATCTACA
+TGTTTGTCTC
+TGGGTGGGGA
+TCCATAGGCA
+GCATTACCAG
+CACCCTACGA
+TAAGGACTTC
+CGTCAGAGAT
+TTCCTGGTAT
+TATACAGCTC
+CTAGTGTTAT
+CCAGTTTGTG
+TCGTCCCATA
+GCCAGCAAGA
+GCCAAACAAA
+AGCCGGGTCG
+CTTTACCTTA
+AAGCCGAGGG
+GGGTGGTACG
+CCGAACATAA
+ACGCTTTAAC
+GTCCCTCCAG
+GCTGATAATC
+GTTTAAGCAC
+ACGTGGTCTA
+GAGTTGCGCT
+TACCGGACAA
+ACCTGCGCGT
+TGAAAGGGTT
+ACGCCTGGTA
+CGAAATAAGA
+CGAACCCCAG
+GACCCAGCAG
+ACAAAGGAAC
+GTGCTAGGCC
+CATATAATCA
+GGTAGATCGA
+TCTCTCTCCT
+AAGTTGTGGT
+CAAACAGGCG
+CGCGCTAGTT
+GGGTATGCCC
+GCCCAATAAC
+TGGTGGGGCC
+TGTGTGTAAA
+CTTCGATCAA
+TTTTGCAATT
+TATGTGCAGC
+TAACTGAATA
+TGTGATGTGT
+TGGAACCCGG
+ACTTCCTTTA
+CATTTCGCGC
+CCTAGTGTTT
+CAAGCGTCGC
+TGAGGTTATG
+ATTTATAGGA
+CACACTCAGC
+CGCGAACACA
+CAGTGTCATG
+ACTAAGTAGA
+ATCACCCATA
+TTCTCGTTAG
+TGCGATTGTA
+CCGCTTGAAC
+CTCGTATGCC
+TGGACCCGCT
+TCGATTTACA
+GCAATTCGAC
+TGGTGGTGAT
+TAACTTGAAG
+GATATGGTTT
+CGGTACCGAA
+AAGGGTCGCG
+CAAGTGTTCC
+CGGGACAATA
+GTTCTGCTAA
+GATAAGTATG
+TGCCGACTTA
+CCCGACCGTC
+TAGGTTATAA
+GGCACAACCG
+CTTCACTGTA
+GAGGTGTACA
+AGGATCCGTT
+GCGCGGGCGG
+CAGTCTATGT
+TTTTCGACAC
+TGGACTGCTT
+CCCTTTGAGG
+GTGGATTTTT
+CGTAACGGGT
+GAGTCCCTTG
+TGATTCCAGA
+CACGGGTTGC
+CGGGCGCTAC
+CCGCCGACGC
+CAGGCTTGGC
+AAGAGCGGTA
+TAAGGGCTCG
+CTACCACTTG
+TACTAGACTG
+ATTTGCGGAC
+GGTAGTAGCG
+CGGTGATCCC
+TATCATACGG
+GGTTTGGTGT
+ATGAGCCCTG
+CTGTCTTTTC
+TAGCGTACCA
+CAGATTGAAC
+TCCTCTTCTC
+GCGTTTCAGC
+GGTTAAAATT
+GCGATCCTCT
+CAGACCTTTG
+GTTGCCTTCG
+GTCCTTCCAC
+GCCTTCCTAT
+GATAGTAGCC
+TCACCTTCCA
+TCTCAAATCC
+CTCCCGCGAC
+CTTTGATTGT
+ACCGTTCAAG
+CCCTGACATA
+CCCACTCAAT
+ATTGACCCCT
+GCCGTATAGA
+CGTTGTCGGG
+ATAGCCAGAA
+CCAGTACTCT
+CTATCGGAAG
+CGTGACAGGC
+CCAAATACCT
+CGTTTAAAGC
+TGGACGCATC
+ACACTTGCTT
+GACTAACAGA
+GTGCTGGCCC
+GTGTTATTCA
+GCTAATGCAT
+CATGGGATCA
+GACGCCTGTA
+TATACAATTT
+TCAACTGCTC
+GAACTACTCG
+CCAAAACACT
+TTCGACTAGG
+CGATCGACCA
+AGAAAAGAGA
+CTGGACTGCT
+TACAGAGGTT
+TGAACTTTAC
+CGCGCCCACC
--- /dev/null
+COMMON NAME: unicorn
+CLASSIFICATION: equus monoceros
+UPDATED: 1738-11-24
+AGCCGGGTCG
+CTTTACCTTA
+AAGCCGAGGG
+GGGTGGTACG
+CCGAACATAA
+ACGCTTTAAC
+GTCCCTCCAG
+GCTGATAATC
+GTTTAAGCAC
+ACGTGGTCTA
+GAGTTGCGCT
+TACCGGACAA
+ACCTGCGCGT
+TGAAAGGGTT
+ACGCCTGGTA
+CGAAATAAGA
+CGAACCCCAG
+GACCCAGCAG
+ACAAAGGAAC
+GTGCTAGGCC
+AGCCGGGTCG
+CTTTACCTTA
+AAGCCGAGGG
+GGGTGGTACG
+CCGAACATAA
+ACGCTTTAAC
+GTCCCTCCAG
+GCTGATAATC
+GTTTAAGCAC
+ACGTGGTCTA
+GAGTTGCGCT
+TACCGGACAA
+ACCTGCGCGT
+TGAAAGGGTT
+ACGCCTGGTA
+CGAAATAAGA
+CGAACCCCAG
+GACCCAGCAG
+ACAAAGGAAC
+GTGCTAGGCC
+CATATAATCA
+GGTAGATCGA
+TCTCTCTCCT
+AAGTTGTGGT
+CAAACAGGCG
+CGCGCTAGTT
+GGGTATGCCC
+GCCCAATAAC
+TGGTGGGGCC
+TGTGTGTAAA
+CTTCGATCAA
+TTTTGCAATT
+TATGTGCAGC
+TAACTGAATA
+TGTGATGTGT
+TGGAACCCGG
+ACTTCCTTTA
+CATTTCGCGC
+CCTAGTGTTT
+CAAGCGTCGC
+TGAGGTTATG
+ATTTATAGGA
+CACACTCAGC
+CGCGAACACA
+CAGTGTCATG
+ACTAAGTAGA
+ATCACCCATA
+TTCTCGTTAG
+TGCGATTGTA
+CCGCTTGAAC
+CTCGTATGCC
+TGGACCCGCT
+TCGATTTACA
+GCAATTCGAC
+TGGTGGTGAT
+TAACTTGAAG
+GATATGGTTT
+CGGTACCGAA
+AAGGGTCGCG
+CAAGTGTTCC
+CGGGACAATA
+GTTCTGCTAA
+GATAAGTATG
+TGCCGACTTA
+CCCGACCGTC
+TAGGTTATAA
+GGCACAACCG
+CTTCACTGTA
+GAGGTGTACA
+AGGATCCGTT
+GCGCGGGCGG
+CAGTCTATGT
+TTTTCGACAC
+TGGACTGCTT
+CCCTTTGAGG
+GTGGATTTTT
+CGTAACGGGT
+GAGTCCCTTG
+TGATTCCAGA
+CACGGGTTGC
+CGGGCGCTAC
+CCGCCGACGC
+CAGGCTTGGC
+AAGAGCGGTA
+TAAGGGCTCG
+CTACCACTTG
+TACTAGACTG
+ATTTGCGGAC
+GGTAGTAGCG
+CGGTGATCCC
+TATCATACGG
+GGTTTGGTGT
+ATGAGCCCTG
+CTGTCTTTTC
+TAGCGTACCA
+CAGATTGAAC
+TCCTCTTCTC
+GCGTTTCAGC
+GGTTAAAATT
+GCGATCCTCT
+CAGACCTTTG
+GTTGCCTTCG
+GTCCTTCCAC
+GCCTTCCTAT
+GATAGTAGCC
+TCACCTTCCA
+TCTCAAATCC
+CTCCCGCGAC
+CTTTGATTGT
+ACCGTTCAAG
+CCCTGACATA
+CCCACTCAAT
+ATTGACCCCT
+GCCGTATAGA
+CGTTGTCGGG
+ATAGCCAGAA
+CCAGTACTCT
+CTATCGGAAG
+CGTGACAGGC
+CCAAATACCT
+CGTTTAAAGC
+TGGACGCATC
+ACACTTGCTT
+GACTAACAGA
+GTGCTGGCCC
+GTGTTATTCA
+GCTAATGCAT
+CATGGGATCA
+GACGCCTGTA
+TATACAATTT
+TCAACTGCTC
+GAACTACTCG
+CCAAAACACT
+TTCGACTAGG
+CGATCGACCA
+AGAAAAGAGA
+CTGGACTGCT
+TACAGAGGTT
+TGAACTTTAC
+CGCGCCCACC
--- /dev/null
+Access forbidden.
--- /dev/null
+offset: off
+color: off
--- /dev/null
+speed: high
--- /dev/null
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--- /dev/null
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--- /dev/null
+# difference of two input files
+# demo version, just return a random number or "files are identical"
+if [ "$1" == "$2" ]
+then
+ echo "files are identical"
+else
+ echo 0.$RANDOM
+fi
--- /dev/null
+sleep 2
+head -3 $1 | cut -d , -f 1 | sort | uniq > $2
--- /dev/null
+Alanine Ala
+Arginine Arg
+Asparagine Asn
+Aspartic acid Asp
+Cysteine Cys
+Glutamic acid Glu
+Glutamine Gln
+Glycine Gly
+Histidine His
+Isoleucine Ile
+Leucine Leu
+Lysine Lys
+Methionine Met
+Phenylalanine Phe
+Proline Pro
+Serine Ser
+Threonine Thr
+Tryptophan Trp
+Tyrosine Tyr
+Valine Val
--- /dev/null
+<element name="Actinium"/>
+ <symbol>Ac</symbol>
+ <atomic-number>89</atomic-number>
+ <atomic-weight>227.0278</atomic-weight>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1320</melting-point>
+ <boiling-point>3470</boiling-point>
+</element>
--- /dev/null
+<element name="Silver"/>
+ <symbol>Ag</symbol>
+ <atomic-number>47</atomic-number>
+ <atomic-weight>107.8682</atomic-weight>
+ <oxidation-states>+1</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1235.1</melting-point>
+ <boiling-point>2485</boiling-point>
+</element>
--- /dev/null
+<element name="Aluminum"/>
+ <symbol>Al</symbol>
+ <atomic-number>13</atomic-number>
+ <atomic-weight>26.981539</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>933.5</melting-point>
+ <boiling-point>2740</boiling-point>
+</element>
--- /dev/null
+<element name="Americium"/>
+ <symbol>Am</symbol>
+ <atomic-number>95</atomic-number>
+ <atomic-weight>243.0614</atomic-weight>
+ <oxidation-states>+3, +4, +5, +6</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1267</melting-point>
+ <boiling-point>2880</boiling-point>
+</element>
--- /dev/null
+<element name="Argon"/>
+ <symbol>Ar</symbol>
+ <atomic-number>18</atomic-number>
+ <atomic-weight>39.948</atomic-weight>
+ <oxidation-states>0</oxidation-states>
+ <state-at-room-temp>gas, nonmetal</state-at-room-temp>
+ <melting-point>83.8</melting-point>
+ <boiling-point>87.3</boiling-point>
+</element>
--- /dev/null
+<element name="Arsenic"/>
+ <symbol>As</symbol>
+ <atomic-number>33</atomic-number>
+ <atomic-weight>74.92159</atomic-weight>
+ <oxidation-states>+3,+5,-3</oxidation-states>
+ <state-at-room-temp>solid, metalloid</state-at-room-temp>
+ <melting-point>1090</melting-point>
+ <boiling-point>889 (sub)</boiling-point>
+</element>
--- /dev/null
+<element name="Astatine"/>
+ <symbol>At</symbol>
+ <atomic-number>85</atomic-number>
+ <atomic-weight>209.9871</atomic-weight>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>575</melting-point>
+ <boiling-point>610</boiling-point>
+</element>
--- /dev/null
+<element name="Gold"/>
+ <symbol>Au</symbol>
+ <atomic-number>79</atomic-number>
+ <atomic-weight>196.96654</atomic-weight>
+ <oxidation-states>+1,+3</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>1337.58</melting-point>
+ <boiling-point>3080</boiling-point>
+</element>
--- /dev/null
+<element name="Boron"/>
+ <symbol>B</symbol>
+ <atomic-number>5</atomic-number>
+ <atomic-weight>10.811</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metalloid</state-at-room-temp>
+ <melting-point>2573</melting-point>
+ <boiling-point>3931</boiling-point>
+</element>
--- /dev/null
+<element name="Barium"/>
+ <symbol>Ba</symbol>
+ <atomic-number>56</atomic-number>
+ <atomic-weight>137.327</atomic-weight>
+ <oxidation-states>+2</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>1002</melting-point>
+ <boiling-point>1910</boiling-point>
+</element>
--- /dev/null
+<element name="Beryllium"/>
+ <symbol>Be</symbol>
+ <atomic-number>4</atomic-number>
+ <atomic-weight>9.01218</atomic-weight>
+ <oxidation-states>+2</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1551</melting-point>
+ <boiling-point>3243</boiling-point>
+</element>
--- /dev/null
+<element name="Bismuth"/>
+ <symbol>Bi</symbol>
+ <atomic-number>83</atomic-number>
+ <atomic-weight>208.98037</atomic-weight>
+ <oxidation-states>+3,+5</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>544.5</melting-point>
+ <boiling-point>1883</boiling-point>
+</element>
--- /dev/null
+<element name="Berkelium"/>
+ <symbol>Bk</symbol>
+ <atomic-number>97</atomic-number>
+ <atomic-weight>247.0703</atomic-weight>
+ <oxidation-states>+3, +4</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+</element>
--- /dev/null
+<element name="Bromine"/>
+ <symbol>Br</symbol>
+ <atomic-number>35</atomic-number>
+ <atomic-weight>79.904</atomic-weight>
+ <oxidation-states>+1,+5,-1</oxidation-states>
+ <state-at-room-temp>liquid, nonmetal</state-at-room-temp>
+ <melting-point>265.9</melting-point>
+ <boiling-point>331.9</boiling-point>
+</element>
--- /dev/null
+<element name="Carbon"/>
+ <symbol>C</symbol>
+ <atomic-number>6</atomic-number>
+ <atomic-weight>12.011</atomic-weight>
+ <oxidation-states>+2, +4, -4</oxidation-states>
+ <state-at-room-temp>solid, nonmetal</state-at-room-temp>
+ <melting-point>3820</melting-point>
+ <boiling-point>5100</boiling-point>
+</element>
--- /dev/null
+<element name="Calcium"/>
+ <symbol>Ca</symbol>
+ <atomic-number>20</atomic-number>
+ <atomic-weight>40.078</atomic-weight>
+ <oxidation-states>+2</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1112</melting-point>
+ <boiling-point>1757</boiling-point>
+</element>
--- /dev/null
+<element name="Cadmium"/>
+ <symbol>Cd</symbol>
+ <atomic-number>48</atomic-number>
+ <atomic-weight>112.411</atomic-weight>
+ <oxidation-states>+2</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>594.1</melting-point>
+ <boiling-point>1038</boiling-point>
+</element>
--- /dev/null
+<element name="Cerium"/>
+ <symbol>Ce</symbol>
+ <atomic-number>58</atomic-number>
+ <atomic-weight>140.115</atomic-weight>
+ <oxidation-states>+3, +4</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1072</melting-point>
+ <boiling-point>3699</boiling-point>
+</element>
--- /dev/null
+<element name="Californium"/>
+ <symbol>Cf</symbol>
+ <atomic-number>98</atomic-number>
+ <atomic-weight>251.0796</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+</element>
--- /dev/null
+<element name="Chlorine"/>
+ <symbol>Cl</symbol>
+ <atomic-number>17</atomic-number>
+ <atomic-weight>35.4527</atomic-weight>
+ <oxidation-states>+1,+5,+7,-1</oxidation-states>
+ <state-at-room-temp>gas, nonmetal</state-at-room-temp>
+ <melting-point>172.2</melting-point>
+ <boiling-point>238.6</boiling-point>
+</element>
--- /dev/null
+<element name="Curium"/>
+ <symbol>Cm</symbol>
+ <atomic-number>96</atomic-number>
+ <atomic-weight>247.0703</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+</element>
--- /dev/null
+<element name="Cobalt"/>
+ <symbol>Co</symbol>
+ <atomic-number>27</atomic-number>
+ <atomic-weight>58.9332</atomic-weight>
+ <oxidation-states>+2,+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1768</melting-point>
+ <boiling-point>3143</boiling-point>
+</element>
--- /dev/null
+<element name="Chromium"/>
+ <symbol>Cr</symbol>
+ <atomic-number>24</atomic-number>
+ <atomic-weight>51.9961</atomic-weight>
+ <oxidation-states>+2,+3,+6</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2130</melting-point>
+ <boiling-point>2945</boiling-point>
+</element>
--- /dev/null
+<element name="Cesium"/>
+ <symbol>Cs</symbol>
+ <atomic-number>55</atomic-number>
+ <atomic-weight>132.90543</atomic-weight>
+ <oxidation-states>+1</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>301.6</melting-point>
+ <boiling-point>951.6</boiling-point>
+</element>
--- /dev/null
+<element name="Copper"/>
+ <symbol>Cu</symbol>
+ <atomic-number>29</atomic-number>
+ <atomic-weight>63.546</atomic-weight>
+ <oxidation-states>+1,+2</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1356.6</melting-point>
+ <boiling-point>2840</boiling-point>
+</element>
--- /dev/null
+<element name="Dysprosium"/>
+ <symbol>Dy</symbol>
+ <atomic-number>66</atomic-number>
+ <atomic-weight>162.50</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1685</melting-point>
+ <boiling-point>2835</boiling-point>
+</element>
--- /dev/null
+<element name="Erbium"/>
+ <symbol>Er</symbol>
+ <atomic-number>68</atomic-number>
+ <atomic-weight>167.26</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1802</melting-point>
+ <boiling-point>3136</boiling-point>
+</element>
--- /dev/null
+<element name="Einsteinium"/>
+ <symbol>Es</symbol>
+ <atomic-number>99</atomic-number>
+ <atomic-weight>252.083</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+</element>
--- /dev/null
+<element name="Europium"/>
+ <symbol>Eu</symbol>
+ <atomic-number>63</atomic-number>
+ <atomic-weight>151.965</atomic-weight>
+ <oxidation-states>+2, +3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1095</melting-point>
+ <boiling-point>1870</boiling-point>
+</element>
--- /dev/null
+<element name="Fluorine"/>
+ <symbol>F</symbol>
+ <atomic-number>9</atomic-number>
+ <atomic-weight>18.998403</atomic-weight>
+ <oxidation-states>-1</oxidation-states>
+ <state-at-room-temp>gas, nonmetal</state-at-room-temp>
+ <melting-point>53.53</melting-point>
+ <boiling-point>85.01</boiling-point>
+</element>
--- /dev/null
+<element name="Iron"/>
+ <symbol>Fe</symbol>
+ <atomic-number>26</atomic-number>
+ <atomic-weight>55.847</atomic-weight>
+ <oxidation-states>+2,+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1808</melting-point>
+ <boiling-point>3023</boiling-point>
+</element>
--- /dev/null
+<element name="Fermium"/>
+ <symbol>Fm</symbol>
+ <atomic-number>100</atomic-number>
+ <atomic-weight>257.0951</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+</element>
--- /dev/null
+<element name="Francium"/>
+ <symbol>Fr</symbol>
+ <atomic-number>87</atomic-number>
+ <atomic-weight>223.0197</atomic-weight>
+ <oxidation-states>+1</oxidation-states>
+ <state-at-room-temp>liquid, metal</state-at-room-temp>
+ <melting-point>300</melting-point>
+ <boiling-point>950</boiling-point>
+</element>
--- /dev/null
+<element name="Gallium"/>
+ <symbol>Ga</symbol>
+ <atomic-number>31</atomic-number>
+ <atomic-weight>69.723</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>302.93</melting-point>
+ <boiling-point>2676</boiling-point>
+</element>
--- /dev/null
+<element name="Gadolinium"/>
+ <symbol>Gd</symbol>
+ <atomic-number>64</atomic-number>
+ <atomic-weight>157.25</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1586</melting-point>
+ <boiling-point>3539</boiling-point>
+</element>
--- /dev/null
+<element name="Germanium"/>
+ <symbol>Ge</symbol>
+ <atomic-number>32</atomic-number>
+ <atomic-weight>72.61</atomic-weight>
+ <oxidation-states>+2,+4</oxidation-states>
+ <state-at-room-temp>solid, metalloid</state-at-room-temp>
+ <melting-point>1210.6</melting-point>
+ <boiling-point>3103</boiling-point>
+</element>
--- /dev/null
+<element name="Hydrogen"/>
+ <symbol>H</symbol>
+ <atomic-number>1</atomic-number>
+ <atomic-weight>1.00794</atomic-weight>
+ <oxidation-states>+1, -1</oxidation-states>
+ <state-at-room-temp>gas, non-metal</state-at-room-temp>
+ <melting-point>14.01</melting-point>
+ <boiling-point>20.28</boiling-point>
+</element>
--- /dev/null
+<element name="Helium"/>
+ <symbol>He</symbol>
+ <atomic-number>2</atomic-number>
+ <atomic-weight>4.002602</atomic-weight>
+ <oxidation-states>0</oxidation-states>
+ <state-at-room-temp>gas, non-metal</state-at-room-temp>
+ <melting-point>0.95</melting-point>
+ <boiling-point>4.216</boiling-point>
+</element>
--- /dev/null
+<element name="Hafnium"/>
+ <symbol>Hf</symbol>
+ <atomic-number>72</atomic-number>
+ <atomic-weight>178.49</atomic-weight>
+ <oxidation-states>+4</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>2503</melting-point>
+ <boiling-point>5470</boiling-point>
+</element>
--- /dev/null
+<element name="Mercury"/>
+ <symbol>Hg</symbol>
+ <atomic-number>80</atomic-number>
+ <atomic-weight>200.59</atomic-weight>
+ <oxidation-states>+1,+2</oxidation-states>
+ <state-at-room-temp>liquid</state-at-room-temp>
+ <melting-point>234.28</melting-point>
+ <boiling-point>629.73</boiling-point>
+</element>
--- /dev/null
+<element name="Holmium"/>
+ <symbol>Ho</symbol>
+ <atomic-number>67</atomic-number>
+ <atomic-weight>164.93032</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1747</melting-point>
+ <boiling-point>2968</boiling-point>
+</element>
--- /dev/null
+<element name="Iodine"/>
+ <symbol>I</symbol>
+ <atomic-number>53</atomic-number>
+ <atomic-weight>126.90447</atomic-weight>
+ <oxidation-states>+1,+5,+7,-1</oxidation-states>
+ <state-at-room-temp>solid, nonmetal</state-at-room-temp>
+ <melting-point>386.7</melting-point>
+ <boiling-point>457.5</boiling-point>
+</element>
--- /dev/null
+<element name="Indium"/>
+ <symbol>In</symbol>
+ <atomic-number>49</atomic-number>
+ <atomic-weight>114.818</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>429.32</melting-point>
+ <boiling-point>2353</boiling-point>
+</element>
--- /dev/null
+<element name="Iridium"/>
+ <symbol>Ir</symbol>
+ <atomic-number>77</atomic-number>
+ <atomic-weight>192.22</atomic-weight>
+ <oxidation-states>+3,+4</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>2683</melting-point>
+ <boiling-point>4403</boiling-point>
+</element>
--- /dev/null
+<element name="Potassium"/>
+ <symbol>K</symbol>
+ <atomic-number>19</atomic-number>
+ <atomic-weight>39.0983</atomic-weight>
+ <oxidation-states>+1</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>336.8</melting-point>
+ <boiling-point>1047</boiling-point>
+</element>
--- /dev/null
+<element name="Krypton"/>
+ <symbol>Kr</symbol>
+ <atomic-number>36</atomic-number>
+ <atomic-weight>83.8</atomic-weight>
+ <oxidation-states>0</oxidation-states>
+ <state-at-room-temp>gas, nonmetal</state-at-room-temp>
+ <melting-point>116.6</melting-point>
+ <boiling-point>120.85</boiling-point>
+</element>
--- /dev/null
+<element name="Lanthanum"/>
+ <symbol>La</symbol>
+ <atomic-number>57</atomic-number>
+ <atomic-weight>138.9055</atomic-weight>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1194</melting-point>
+ <boiling-point>3730</boiling-point>
+</element>
--- /dev/null
+<element name="Lithium"/>
+ <symbol>Li</symbol>
+ <atomic-number>3</atomic-number>
+ <atomic-weight>6.941</atomic-weight>
+ <oxidation-states>+1</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>553.69</melting-point>
+ <boiling-point>1118.15</boiling-point>
+</element>
--- /dev/null
+<element name="Lawrencium"/>
+ <symbol>Lr</symbol>
+ <atomic-number>103</atomic-number>
+ <atomic-weight>262.11</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+</element>
--- /dev/null
+<element name="Lutetium"/>
+ <symbol>Lu</symbol>
+ <atomic-number>71</atomic-number>
+ <atomic-weight>174.967</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1936</melting-point>
+ <boiling-point>3668</boiling-point>
+</element>
--- /dev/null
+<element name="Mendelevium"/>
+ <symbol>Md</symbol>
+ <atomic-number>101</atomic-number>
+ <atomic-weight>258.1</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+</element>
--- /dev/null
+<element name="Magnesium"/>
+ <symbol>Mg</symbol>
+ <atomic-number>12</atomic-number>
+ <atomic-weight>24.305</atomic-weight>
+ <oxidation-states>+2</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>922</melting-point>
+ <boiling-point>1363</boiling-point>
+</element>
--- /dev/null
+<element name="Manganese"/>
+ <symbol>Mn</symbol>
+ <atomic-number>25</atomic-number>
+ <atomic-weight>54.93805</atomic-weight>
+ <oxidation-states>+2,+3,+4,+7</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1517</melting-point>
+ <boiling-point>2235</boiling-point>
+</element>
--- /dev/null
+<element name="Molybdenum"/>
+ <symbol>Mo</symbol>
+ <atomic-number>42</atomic-number>
+ <atomic-weight>95.94</atomic-weight>
+ <oxidation-states>+6</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2890</melting-point>
+ <boiling-point>4885</boiling-point>
+</element>
--- /dev/null
+<element name="Nitrogen"/>
+ <symbol>N</symbol>
+ <atomic-number>7</atomic-number>
+ <atomic-weight>14.00674</atomic-weight>
+ <oxidation-states>+1,+2,+3,+4,+5,-1,-2,-3</oxidation-states>
+ <state-at-room-temp>gas, nonmetal</state-at-room-temp>
+ <melting-point>63.29</melting-point>
+ <boiling-point>77.4</boiling-point>
+</element>
--- /dev/null
+<element name="Sodium"/>
+ <symbol>Na</symbol>
+ <atomic-number>11</atomic-number>
+ <atomic-weight>22.989768</atomic-weight>
+ <oxidation-states>+1</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>370.96</melting-point>
+ <boiling-point>1156.1</boiling-point>
+</element>
--- /dev/null
+<element name="Niobium"/>
+ <symbol>Nb</symbol>
+ <atomic-number>41</atomic-number>
+ <atomic-weight>92.90638</atomic-weight>
+ <oxidation-states>+3,+5</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2741</melting-point>
+ <boiling-point>5015</boiling-point>
+</element>
--- /dev/null
+<element name="Neodymium"/>
+ <symbol>Nd</symbol>
+ <atomic-number>60</atomic-number>
+ <atomic-weight>144.24</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1294</melting-point>
+ <boiling-point>3341</boiling-point>
+</element>
--- /dev/null
+<element name="Neon"/>
+ <symbol>Ne</symbol>
+ <atomic-number>10</atomic-number>
+ <atomic-weight>20.1797</atomic-weight>
+ <oxidation-states>0</oxidation-states>
+ <state-at-room-temp>gas, nonmetal</state-at-room-temp>
+ <melting-point>24,48</melting-point>
+ <boiling-point>27.1</boiling-point>
+</element>
--- /dev/null
+<element name="Nickel"/>
+ <symbol>Ni</symbol>
+ <atomic-number>28</atomic-number>
+ <atomic-weight>58.6934</atomic-weight>
+ <oxidation-states>+2,+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1726</melting-point>
+ <boiling-point>3005</boiling-point>
+</element>
--- /dev/null
+<element name="Nobelium"/>
+ <symbol>No</symbol>
+ <atomic-number>102</atomic-number>
+ <atomic-weight>259.1009</atomic-weight>
+ <oxidation-states>+2, +3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+</element>
--- /dev/null
+<element name="Neptunium"/>
+ <symbol>Np</symbol>
+ <atomic-number>93</atomic-number>
+ <atomic-weight>237.048</atomic-weight>
+ <oxidation-states>+3, +4, +5, +6</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>913</melting-point>
+ <boiling-point>4175</boiling-point>
+</element>
--- /dev/null
+<element name="Oxygen"/>
+ <symbol>O</symbol>
+ <atomic-number>8</atomic-number>
+ <atomic-weight>15.9994</atomic-weight>
+ <oxidation-states>-2</oxidation-states>
+ <state-at-room-temp>gas, nonmetal</state-at-room-temp>
+ <melting-point>54.8</melting-point>
+ <boiling-point>90.19</boiling-point>
+</element>
--- /dev/null
+<element name="Osmium"/>
+ <symbol>Os</symbol>
+ <atomic-number>76</atomic-number>
+ <atomic-weight>190.23</atomic-weight>
+ <oxidation-states>+3,+4</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>3327</melting-point>
+ <boiling-point>5300</boiling-point>
+</element>
--- /dev/null
+<element name="Phosphorus"/>
+ <symbol>P</symbol>
+ <atomic-number>15</atomic-number>
+ <atomic-weight>30.973762</atomic-weight>
+ <oxidation-states>+3, +5, -3</oxidation-states>
+ <state-at-room-temp>solid, nonmetal</state-at-room-temp>
+ <melting-point>317.3</melting-point>
+ <boiling-point>553</boiling-point>
+</element>
--- /dev/null
+<element name="Protactinium"/>
+ <symbol>Pa</symbol>
+ <atomic-number>91</atomic-number>
+ <atomic-weight>231.03588</atomic-weight>
+ <oxidation-states>+4, +5</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2113</melting-point>
+ <boiling-point>4300</boiling-point>
+</element>
--- /dev/null
+<element name="Lead"/>
+ <symbol>Pb</symbol>
+ <atomic-number>82</atomic-number>
+ <atomic-weight>207.2</atomic-weight>
+ <oxidation-states>+2,+4</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>600.65</melting-point>
+ <boiling-point>2013</boiling-point>
+</element>
--- /dev/null
+<element name="Palladium"/>
+ <symbol>Pd</symbol>
+ <atomic-number>46</atomic-number>
+ <atomic-weight>106.42</atomic-weight>
+ <oxidation-states>+2,+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1825</melting-point>
+ <boiling-point>3413</boiling-point>
+</element>
--- /dev/null
+<element name="Promethium"/>
+ <symbol>Pm</symbol>
+ <atomic-number>61</atomic-number>
+ <atomic-weight>144.9127</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1441</melting-point>
+ <boiling-point>3000</boiling-point>
+</element>
--- /dev/null
+<element name="Polonium"/>
+ <symbol>Po</symbol>
+ <atomic-number>84</atomic-number>
+ <atomic-weight>208.9824</atomic-weight>
+ <oxidation-states>+2,+4</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>527</melting-point>
+ <boiling-point>1235</boiling-point>
+</element>
--- /dev/null
+<element name="Praseodymium"/>
+ <symbol>Pr</symbol>
+ <atomic-number>59</atomic-number>
+ <atomic-weight>140.90765</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1204</melting-point>
+ <boiling-point>3785</boiling-point>
+</element>
--- /dev/null
+<element name="Platinum"/>
+ <symbol>Pt</symbol>
+ <atomic-number>78</atomic-number>
+ <atomic-weight>195.08</atomic-weight>
+ <oxidation-states>+2,+4</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>2045</melting-point>
+ <boiling-point>4100</boiling-point>
+</element>
--- /dev/null
+<element name="Plutonium"/>
+ <symbol>Pu</symbol>
+ <atomic-number>94</atomic-number>
+ <atomic-weight>244.0642</atomic-weight>
+ <oxidation-states>+3, +4, +5, +6</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>914</melting-point>
+ <boiling-point>3505</boiling-point>
+</element>
--- /dev/null
+<element name="Radium"/>
+ <symbol>Ra</symbol>
+ <atomic-number>88</atomic-number>
+ <atomic-weight>226.0254</atomic-weight>
+ <oxidation-states>+2</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>973</melting-point>
+ <boiling-point>1413</boiling-point>
+</element>
--- /dev/null
+<element name="Rubidium"/>
+ <symbol>Rb</symbol>
+ <atomic-number>37</atomic-number>
+ <atomic-weight>85.4678</atomic-weight>
+ <oxidation-states>+1</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>312.2</melting-point>
+ <boiling-point>961</boiling-point>
+</element>
--- /dev/null
+<element name="Rhenium"/>
+ <symbol>Re</symbol>
+ <atomic-number>75</atomic-number>
+ <atomic-weight>186.207</atomic-weight>
+ <oxidation-states>+4,+6,+7</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>3453</melting-point>
+ <boiling-point>5900</boiling-point>
+</element>
--- /dev/null
+<element name="Rhodium"/>
+ <symbol>Rh</symbol>
+ <atomic-number>45</atomic-number>
+ <atomic-weight>102.9055</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2239</melting-point>
+ <boiling-point>4000</boiling-point>
+</element>
--- /dev/null
+<element name="Radon"/>
+ <symbol>Rn</symbol>
+ <atomic-number>86</atomic-number>
+ <atomic-weight>222.0176</atomic-weight>
+ <oxidation-states>0</oxidation-states>
+ <state-at-room-temp>gas</state-at-room-temp>
+ <melting-point>202</melting-point>
+ <boiling-point>211.4</boiling-point>
+</element>
--- /dev/null
+<element name="Ruthenium"/>
+ <symbol>Ru</symbol>
+ <atomic-number>44</atomic-number>
+ <atomic-weight>101.07</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2583</melting-point>
+ <boiling-point>4173</boiling-point>
+</element>
--- /dev/null
+<element name="Sulfur"/>
+ <symbol>S</symbol>
+ <atomic-number>16</atomic-number>
+ <atomic-weight>32.068</atomic-weight>
+ <oxidation-states>+4,+6,-2</oxidation-states>
+ <state-at-room-temp>solid, nonmetal</state-at-room-temp>
+ <melting-point>386</melting-point>
+ <boiling-point>717.824</boiling-point>
+</element>
--- /dev/null
+<element name="Antimony"/>
+ <symbol>Sb</symbol>
+ <atomic-number>51</atomic-number>
+ <atomic-weight>121.757</atomic-weight>
+ <oxidation-states>+3,+5,-3</oxidation-states>
+ <state-at-room-temp>solid, metalloid</state-at-room-temp>
+ <melting-point>903.9</melting-point>
+ <boiling-point>1908</boiling-point>
+</element>
--- /dev/null
+<element name="Scandium"/>
+ <symbol>Sc</symbol>
+ <atomic-number>21</atomic-number>
+ <atomic-weight>44.95591</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1814</melting-point>
+ <boiling-point>3104</boiling-point>
+</element>
--- /dev/null
+<element name="Selenium"/>
+ <symbol>Se</symbol>
+ <atomic-number>34</atomic-number>
+ <atomic-weight>78.96</atomic-weight>
+ <oxidation-states>+4,+6,-2</oxidation-states>
+ <state-at-room-temp>solid, nonmetal</state-at-room-temp>
+ <melting-point>490</melting-point>
+ <boiling-point>958.1</boiling-point>
+</element>
--- /dev/null
+<element name="Silicon"/>
+ <symbol>Si</symbol>
+ <atomic-number>14</atomic-number>
+ <atomic-weight>28.0855</atomic-weight>
+ <oxidation-states>+2,+4,-4</oxidation-states>
+ <state-at-room-temp>solid, metalloid</state-at-room-temp>
+ <melting-point>1683</melting-point>
+ <boiling-point>2628</boiling-point>
+</element>
--- /dev/null
+<element name="Samarium"/>
+ <symbol>Sm</symbol>
+ <atomic-number>62</atomic-number>
+ <atomic-weight>150.36</atomic-weight>
+ <oxidation-states>+2, +3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1350</melting-point>
+ <boiling-point>2064</boiling-point>
+</element>
--- /dev/null
+<element name="Tin"/>
+ <symbol>Sn</symbol>
+ <atomic-number>50</atomic-number>
+ <atomic-weight>118.71</atomic-weight>
+ <oxidation-states>+2,+4</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>505.1</melting-point>
+ <boiling-point>2543</boiling-point>
+</element>
--- /dev/null
+<element name="Strontium"/>
+ <symbol>Sr</symbol>
+ <atomic-number>38</atomic-number>
+ <atomic-weight>87.62</atomic-weight>
+ <oxidation-states>+2</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1042</melting-point>
+ <boiling-point>1657</boiling-point>
+</element>
--- /dev/null
+<element name="Tantalum"/>
+ <symbol>Ta</symbol>
+ <atomic-number>73</atomic-number>
+ <atomic-weight>180.9479</atomic-weight>
+ <oxidation-states>+5</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>3269</melting-point>
+ <boiling-point>5698</boiling-point>
+</element>
--- /dev/null
+<element name="Terbium"/>
+ <symbol>Tb</symbol>
+ <atomic-number>65</atomic-number>
+ <atomic-weight>158.92534</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1629</melting-point>
+ <boiling-point>3296</boiling-point>
+</element>
--- /dev/null
+<element name="Technetium"/>
+ <symbol>Tc</symbol>
+ <atomic-number>43</atomic-number>
+ <atomic-weight>97.9072</atomic-weight>
+ <oxidation-states>+4,+6,+7</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2445</melting-point>
+ <boiling-point>5150</boiling-point>
+</element>
--- /dev/null
+<element name="Tellurium"/>
+ <symbol>Te</symbol>
+ <atomic-number>52</atomic-number>
+ <atomic-weight>127.6</atomic-weight>
+ <oxidation-states>+4,+6,-2</oxidation-states>
+ <state-at-room-temp>solid, metalloid</state-at-room-temp>
+ <melting-point>722.7</melting-point>
+ <boiling-point>1263</boiling-point>
+</element>
--- /dev/null
+<element name="Thorium"/>
+ <symbol>Th</symbol>
+ <atomic-number>90</atomic-number>
+ <atomic-weight>232.0381</atomic-weight>
+ <oxidation-states>+3, +4</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1842</melting-point>
+ <boiling-point>---</boiling-point>
+</element>
--- /dev/null
+<element name="Titanium"/>
+ <symbol>Ti</symbol>
+ <atomic-number>22</atomic-number>
+ <atomic-weight>47.88</atomic-weight>
+ <oxidation-states>+2,+3,+4</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1933</melting-point>
+ <boiling-point>3560</boiling-point>
+</element>
--- /dev/null
+<element name="Thallium"/>
+ <symbol>Tl</symbol>
+ <atomic-number>81</atomic-number>
+ <atomic-weight>204.3833</atomic-weight>
+ <oxidation-states>+1,+3</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>576.6</melting-point>
+ <boiling-point>1730</boiling-point>
+</element>
--- /dev/null
+<element name="Thulium"/>
+ <symbol>Tm</symbol>
+ <atomic-number>69</atomic-number>
+ <atomic-weight>168.93421</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1818</melting-point>
+ <boiling-point>2220</boiling-point>
+</element>
--- /dev/null
+<element name="Uranium"/>
+ <symbol>U</symbol>
+ <atomic-number>92</atomic-number>
+ <atomic-weight>238.0289</atomic-weight>
+ <oxidation-states>+3, +4, +5, +6</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1405.5</melting-point>
+ <boiling-point>4018</boiling-point>
+</element>
--- /dev/null
+<element name="Vanadium"/>
+ <symbol>V</symbol>
+ <atomic-number>23</atomic-number>
+ <atomic-weight>50.9415</atomic-weight>
+ <oxidation-states>+2,+3,+4.+5</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2160</melting-point>
+ <boiling-point>3650</boiling-point>
+</element>
--- /dev/null
+<element name="Tungsten"/>
+ <symbol>W</symbol>
+ <atomic-number>74</atomic-number>
+ <atomic-weight>183.84</atomic-weight>
+ <oxidation-states>+6</oxidation-states>
+ <state-at-room-temp>solid</state-at-room-temp>
+ <melting-point>3680</melting-point>
+ <boiling-point>5930</boiling-point>
+</element>
--- /dev/null
+<element name="Xenon"/>
+ <symbol>Xe</symbol>
+ <atomic-number>54</atomic-number>
+ <atomic-weight>131.29</atomic-weight>
+ <oxidation-states>0</oxidation-states>
+ <state-at-room-temp>gas, nonmetal</state-at-room-temp>
+ <melting-point>161.3</melting-point>
+ <boiling-point>166.1</boiling-point>
+</element>
--- /dev/null
+<element name="Yttrium"/>
+ <symbol>Y</symbol>
+ <atomic-number>39</atomic-number>
+ <atomic-weight>88.90585</atomic-weight>
+ <oxidation-states>+3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1795</melting-point>
+ <boiling-point>3611</boiling-point>
+</element>
--- /dev/null
+<element name="Ytterbium"/>
+ <symbol>Yb</symbol>
+ <atomic-number>70</atomic-number>
+ <atomic-weight>173.04</atomic-weight>
+ <oxidation-states>+2, +3</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>1097</melting-point>
+ <boiling-point>1466</boiling-point>
+</element>
--- /dev/null
+<element name="Zinc"/>
+ <symbol>Zn</symbol>
+ <atomic-number>30</atomic-number>
+ <atomic-weight>65.39</atomic-weight>
+ <oxidation-states>+2</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>692.73</melting-point>
+ <boiling-point>1180</boiling-point>
+</element>
--- /dev/null
+<element name="Zirconium"/>
+ <symbol>Zr</symbol>
+ <atomic-number>40</atomic-number>
+ <atomic-weight>91.224</atomic-weight>
+ <oxidation-states>+4</oxidation-states>
+ <state-at-room-temp>solid, metal</state-at-room-temp>
+ <melting-point>2125</melting-point>
+ <boiling-point>4650</boiling-point>
+</element>
--- /dev/null
+0 -----
+1 .----
+2 ..---
+3 ...--
+4 ....-
+5 .....
+6 -....
+7 --...
+8 ---..
+9 ----.
+A .-
+B -...
+C -.-.
+D -..
+E .
+F ..-.
+G --.
+H ....
+I ..
+J .---
+K -.-
+L .-..
+M --
+N -.
+O ---
+P .--.
+Q --.-
+R .-.
+S ...
+T -
+U ..-
+V ...-
+W .--
+X -..-
+Y -.--
+Z --..
+
+. .-.-.-
+, --..--
+: ---...
+? ..--..
+' .----.
+- -....-
+/ -..-.
+() -.--.-
+" .-..-.
+
+Dots and intra-character spaces are 1 unit long. Dashes and
+inter-character spaces are 3 units long. Inter-word spaces are 7
+units long.
--- /dev/null
+COMPND ALDRIN
+AUTHOR DAVE WOODCOCK 97 08 06
+ATOM 1 C 1 -0.888 0.654 -1.753
+ATOM 2 C 1 0.276 1.404 -1.135
+ATOM 3 C 1 1.381 0.453 -0.730
+ATOM 4 C 1 0.786 -0.400 0.372
+ATOM 5 C 1 -0.640 0.143 0.522
+ATOM 6 C 1 -1.451 -0.124 -0.733
+ATOM 7 CL 1 -1.479 -0.191 2.029
+ATOM 8 CL 1 -2.844 -1.216 -0.888
+ATOM 9 CL 1 -1.450 0.743 -3.432
+ATOM 10 CL 1 0.737 2.870 -1.987
+ATOM 11 C 1 -0.369 1.633 0.244
+ATOM 12 CL 1 -1.860 2.599 0.158
+ATOM 13 CL 1 0.735 2.363 1.410
+ATOM 14 C 1 1.037 -1.812 -0.091
+ATOM 15 C 1 0.994 -1.782 -1.608
+ATOM 16 C 1 1.937 -0.617 -1.697
+ATOM 17 C 1 2.584 -2.004 0.033
+ATOM 18 C 1 3.113 -1.214 -1.046
+ATOM 19 H 1 2.231 1.006 -0.328
+ATOM 20 H 1 1.320 -0.204 1.301
+ATOM 21 H 1 0.442 -2.597 0.378
+ATOM 22 H 1 0.002 -1.636 -2.012
+ATOM 23 H 1 1.441 -2.681 -2.039
+ATOM 24 H 1 2.104 -0.212 -2.687
+ATOM 25 H 1 2.985 -2.347 0.999
+ATOM 26 H 1 4.160 -0.911 -0.708
+TER 27 1
+END
--- /dev/null
+COMPND Ammonia
+AUTHOR DAVE WOODCOCK 97 10 31
+ATOM 1 N 1 0.257 -0.363 0.000
+ATOM 2 H 1 0.257 0.727 0.000
+ATOM 3 H 1 0.771 -0.727 0.890
+ATOM 4 H 1 0.771 -0.727 -0.890
+TER 5 1
+END
\ No newline at end of file
--- /dev/null
+COMPND ASCORBIC ACID, VITAMIN C
+AUTHOR DAVE WOODCOCK 96 05 24
+ATOM 1 C 1 0.182 0.119 -0.645 1.00 0.00
+ATOM 2 C 1 0.591 -1.187 0.091 1.00 0.00
+ATOM 3 C 1 1.908 -1.150 0.401 1.00 0.00
+ATOM 4 C 1 2.407 0.104 0.031 1.00 0.00
+ATOM 5 O 1 1.453 0.978 -0.535 1.00 0.00
+ATOM 6 O 1 3.677 0.478 0.175 1.00 0.00
+ATOM 7 O 1 2.621 -2.174 1.011 1.00 0.00
+ATOM 8 O 1 -0.324 -2.236 0.293 1.00 0.00
+ATOM 9 H 1 -0.030 -0.160 -1.688 1.00 0.00
+ATOM 10 C 1 -1.084 0.762 0.207 1.00 0.00
+ATOM 11 H 1 -1.959 0.100 0.315 1.00 0.00
+ATOM 12 O 1 -0.591 1.195 1.590 1.00 0.00
+ATOM 13 C 1 -1.585 2.076 -0.581 1.00 0.00
+ATOM 14 O 1 -2.771 2.432 0.067 1.00 0.00
+ATOM 15 H 1 1.946 -2.997 1.192 1.00 0.00
+ATOM 16 H 1 -0.747 -2.497 -0.666 1.00 0.00
+ATOM 17 H 1 0.118 2.004 1.470 1.00 0.00
+ATOM 18 H 1 -1.839 1.784 -1.606 1.00 0.00
+ATOM 19 H 1 -0.831 2.856 -0.721 1.00 0.00
+ATOM 20 H 1 -2.572 2.906 1.016 1.00 0.00
+TER 21 1
+END
--- /dev/null
+COMPND BENZALDEHYDE
+AUTHOR DAVE WOODCOCK 96 07 05
+ATOM 1 C 1 1.819 1.228 0.002 1.00 0.00
+ATOM 2 O 1 1.819 2.598 0.002 1.00 0.00
+ATOM 3 C 1 0.606 0.528 0.002 1.00 0.00
+ATOM 4 C 1 -0.606 1.228 0.002 1.00 0.00
+ATOM 5 C 1 -1.819 0.528 0.000 1.00 0.00
+ATOM 6 C 1 -1.819 -0.872 -0.002 1.00 0.00
+ATOM 7 C 1 -0.606 -1.572 -0.002 1.00 0.00
+ATOM 8 C 1 0.606 -0.872 0.000 1.00 0.00
+ATOM 9 H 1 2.754 0.688 0.002 1.00 0.00
+ATOM 10 H 1 -0.606 2.308 0.003 1.00 0.00
+ATOM 11 H 1 -2.754 1.068 0.000 1.00 0.00
+ATOM 12 H 1 -2.754 -1.412 -0.003 1.00 0.00
+ATOM 13 H 1 -0.606 -2.652 -0.003 1.00 0.00
+ATOM 14 H 1 1.542 -1.412 0.000 1.00 0.00
+TER 15 1
+END
--- /dev/null
+COMPND CAMPHENE
+AUTHOR DAVE WOODCOCK 96 02 06
+ATOM 1 C 1 1.603 -1.641 0.934 1.00 0.00
+ATOM 2 C 1 0.611 -0.661 0.656 1.00 0.00
+ATOM 3 C 1 -0.722 -0.538 1.432 1.00 0.00
+ATOM 4 C 1 -0.619 0.968 1.694 1.00 0.00
+ATOM 5 C 1 -0.489 1.334 0.209 1.00 0.00
+ATOM 6 C 1 0.772 0.533 -0.254 1.00 0.00
+ATOM 7 H 1 -0.723 -1.135 2.380 1.00 0.00
+ATOM 8 C 1 2.059 1.326 0.041 1.00 0.00
+ATOM 9 C 1 0.751 0.131 -1.743 1.00 0.00
+ATOM 10 H 1 1.453 -2.410 1.680 1.00 0.00
+ATOM 11 H 1 2.544 -1.611 0.385 1.00 0.00
+ATOM 12 H 1 0.202 1.272 2.276 1.00 0.00
+ATOM 13 H 1 -1.592 1.363 2.135 1.00 0.00
+ATOM 14 H 1 -0.420 2.410 0.015 1.00 0.00
+ATOM 15 H 1 2.126 1.567 1.099 1.00 0.00
+ATOM 16 H 1 2.086 2.255 -0.535 1.00 0.00
+ATOM 17 H 1 2.926 0.726 -0.229 1.00 0.00
+ATOM 18 H 1 0.583 0.988 -2.380 1.00 0.00
+ATOM 19 H 1 -0.047 -0.622 -1.933 1.00 0.00
+ATOM 20 H 1 1.700 -0.320 -1.998 1.00 0.00
+ATOM 21 C 1 -1.778 0.698 -0.317 1.00 0.00
+ATOM 22 C 1 -1.823 -0.673 0.487 1.00 0.00
+ATOM 23 H 1 -1.800 0.572 -1.405 1.00 0.00
+ATOM 24 H 1 -2.634 1.317 -0.053 1.00 0.00
+ATOM 25 H 1 -1.745 -1.462 -0.361 1.00 0.00
+ATOM 26 H 1 -2.926 -0.663 0.899 1.00 0.00
+TER 27 1
+END
--- /dev/null
+COMPND CHOLESTEROL
+AUTHOR DAVE WOODCOCK 96 07 31
+ATOM 1 C 1 -4.816 0.580 -0.559 1.00 0.00
+ATOM 2 C 1 -5.376 0.265 -1.962 1.00 0.00
+ATOM 3 C 1 -6.876 0.502 -2.096 1.00 0.00
+ATOM 4 C 1 -7.610 -0.380 -1.092 1.00 0.00
+ATOM 5 C 1 -7.266 0.081 0.324 1.00 0.00
+ATOM 6 C 1 -5.750 0.070 0.543 1.00 0.00
+ATOM 7 C 1 -5.245 -0.289 1.805 1.00 0.00
+ATOM 8 C 1 -3.765 -0.603 2.034 1.00 0.00
+ATOM 9 C 1 -2.834 0.035 0.981 1.00 0.00
+ATOM 10 C 1 -3.453 -0.147 -0.423 1.00 0.00
+ATOM 11 C 1 -2.479 0.245 -1.546 1.00 0.00
+ATOM 12 C 1 -1.136 -0.444 -1.410 1.00 0.00
+ATOM 13 C 1 -0.490 -0.120 -0.042 1.00 0.00
+ATOM 14 C 1 -1.463 -0.666 1.001 1.00 0.00
+ATOM 15 C 1 0.762 -0.929 0.295 1.00 0.00
+ATOM 16 C 1 0.771 -0.937 1.840 1.00 0.00
+ATOM 17 C 1 -0.664 -0.610 2.293 1.00 0.00
+ATOM 18 C 1 -4.705 2.108 -0.396 1.00 0.00
+ATOM 19 C 1 -0.225 1.386 0.115 1.00 0.00
+ATOM 20 O 1 -9.006 -0.295 -1.302 1.00 0.00
+ATOM 21 C 1 2.101 -0.421 -0.305 1.00 0.00
+ATOM 22 C 1 3.285 -1.303 0.107 1.00 0.00
+ATOM 23 C 1 4.613 -0.560 -0.129 1.00 0.00
+ATOM 24 C 1 5.829 -1.420 0.234 1.00 0.00
+ATOM 25 C 1 7.126 -0.805 -0.329 1.00 0.00
+ATOM 26 C 1 8.312 -1.688 0.030 1.00 0.00
+ATOM 27 C 1 7.353 0.610 0.201 1.00 0.00
+ATOM 28 C 1 2.018 -0.382 -1.851 1.00 0.00
+ATOM 29 H 1 -5.175 -0.780 -2.201 1.00 0.00
+ATOM 30 H 1 -4.873 0.890 -2.700 1.00 0.00
+ATOM 31 H 1 -7.180 0.235 -3.108 1.00 0.00
+ATOM 32 H 1 -7.114 1.551 -1.920 1.00 0.00
+ATOM 33 H 1 -7.301 -1.419 -1.220 1.00 0.00
+ATOM 34 H 1 -7.742 -0.592 1.039 1.00 0.00
+ATOM 35 H 1 -7.638 1.093 0.484 1.00 0.00
+ATOM 36 H 1 -5.941 -0.503 2.602 1.00 0.00
+ATOM 37 H 1 -3.637 -1.685 1.986 1.00 0.00
+ATOM 38 H 1 -3.462 -0.257 3.023 1.00 0.00
+ATOM 39 H 1 -2.721 1.087 1.229 1.00 0.00
+ATOM 40 H 1 -3.657 -1.214 -0.535 1.00 0.00
+ATOM 41 H 1 -2.313 1.319 -1.556 1.00 0.00
+ATOM 42 H 1 -2.870 -0.071 -2.512 1.00 0.00
+ATOM 43 H 1 -0.444 -0.140 -2.205 1.00 0.00
+ATOM 44 H 1 -1.215 -1.526 -1.511 1.00 0.00
+ATOM 45 H 1 -1.640 -1.720 0.776 1.00 0.00
+ATOM 46 H 1 0.617 -1.959 -0.036 1.00 0.00
+ATOM 47 H 1 1.454 -0.183 2.232 1.00 0.00
+ATOM 48 H 1 1.062 -1.923 2.204 1.00 0.00
+ATOM 49 H 1 -0.699 0.387 2.733 1.00 0.00
+ATOM 50 H 1 -1.021 -1.347 3.012 1.00 0.00
+ATOM 51 H 1 -5.692 2.560 -0.486 1.00 0.00
+ATOM 15 H 1 -4.058 2.530 -1.163 1.00 0.00
+ATOM 53 H 1 -4.308 2.360 0.586 1.00 0.00
+ATOM 54 H 1 -1.147 1.962 0.111 1.00 0.00
+ATOM 55 H 1 0.399 1.737 -0.704 1.00 0.00
+ATOM 56 H 1 0.302 1.581 1.047 1.00 0.00
+ATOM 57 H 1 -9.260 -0.705 -2.269 1.00 0.00
+ATOM 58 H 1 2.272 0.601 0.041 1.00 0.00
+ATOM 59 H 1 3.286 -2.231 -0.468 1.00 0.00
+ATOM 60 H 1 3.233 -1.528 1.173 1.00 0.00
+ATOM 61 H 1 4.637 0.338 0.483 1.00 0.00
+ATOM 62 H 1 4.771 -0.279 -1.183 1.00 0.00
+ATOM 63 H 1 5.715 -2.416 -0.199 1.00 0.00
+ATOM 64 H 1 5.912 -1.519 1.317 1.00 0.00
+ATOM 65 H 1 7.019 -0.764 -1.416 1.00 0.00
+ATOM 66 H 1 8.153 -2.690 -0.370 1.00 0.00
+ATOM 67 H 1 8.422 -1.741 1.114 1.00 0.00
+ATOM 68 H 1 9.216 -1.265 -0.409 1.00 0.00
+ATOM 69 H 1 7.340 0.601 1.292 1.00 0.00
+ATOM 70 H 1 6.578 1.277 -0.175 1.00 0.00
+ATOM 71 H 1 8.324 0.961 -0.149 1.00 0.00
+ATOM 72 H 1 1.483 0.513 -2.162 1.00 0.00
+ATOM 73 H 1 1.515 -1.282 -2.203 1.00 0.00
+ATOM 74 H 1 3.013 -0.348 -2.301 1.00 0.00
+TER 75 1
+END
--- /dev/null
+COMPND TRANS-CINNAMALDEHYDE
+AUTHOR DAVE WOODCOCK 97 06 04
+ATOM 1 C 1 -1.004 1.164 -0.187
+ATOM 2 C 1 -2.392 1.257 -0.390
+ATOM 3 C 1 -3.182 0.100 -0.439
+ATOM 4 C 1 -2.571 -1.153 -0.281
+ATOM 5 C 1 -1.187 -1.249 -0.079
+ATOM 6 C 1 -0.390 -0.085 -0.032
+ATOM 7 C 1 1.001 -0.253 0.173
+ATOM 8 C 1 1.935 0.799 0.220
+ATOM 9 C 1 3.299 0.530 0.439
+ATOM 10 O 1 4.195 1.563 0.481
+ATOM 11 H 1 -0.430 2.073 -0.148
+ATOM 12 H 1 -2.859 2.224 -0.509
+ATOM 13 H 1 -4.249 0.171 -0.595
+ATOM 14 H 1 -3.171 -2.049 -0.317
+ATOM 15 H 1 -0.734 -2.224 0.041
+ATOM 16 H 1 1.360 -1.265 0.300
+ATOM 17 H 1 1.598 1.813 0.082
+ATOM 18 H 1 3.615 -0.496 0.573
+TER 19 1
+END
--- /dev/null
+COMPND (R)-(+)-CITRONELLAL
+AUTHOR DAVE WOODCOCK 96 12 20
+ATOM 1 C 1 -1.048 0.968 -0.164
+ATOM 2 C 1 0.094 0.028 0.266
+ATOM 3 C 1 1.449 0.551 -0.209
+ATOM 4 C 1 2.612 -0.216 -0.038
+ATOM 5 C 1 3.943 0.305 -0.590
+ATOM 6 C 1 2.557 -1.568 0.683
+ATOM 7 C 1 -2.405 0.526 0.379
+ATOM 8 C 1 -3.440 1.610 0.039
+ATOM 9 C 1 -2.832 -0.825 -0.214
+ATOM 10 C 1 -4.143 -1.344 0.374
+ATOM 11 O 1 -4.689 -2.508 -0.102
+ATOM 12 H 1 -0.818 1.958 0.231
+ATOM 13 H 1 -1.072 1.018 -1.254
+ATOM 14 H 1 0.091 -0.062 1.353
+ATOM 15 H 1 -0.072 -0.960 -0.157
+ATOM 16 H 1 1.503 1.511 -0.701
+ATOM 17 H 1 3.861 0.420 -1.671
+ATOM 18 H 1 4.163 1.273 -0.138
+ATOM 19 H 1 4.742 -0.399 -0.356
+ATOM 20 H 1 2.116 -1.434 1.671
+ATOM 21 H 1 1.947 -2.263 0.106
+ATOM 22 H 1 3.563 -1.974 0.785
+ATOM 23 H 1 -2.352 0.435 1.465
+ATOM 24 H 1 -3.082 2.562 0.437
+ATOM 25 H 1 -3.536 1.697 -1.044
+ATOM 26 H 1 -4.401 1.338 0.477
+ATOM 27 H 1 -2.924 -0.730 -1.296
+ATOM 28 H 1 -2.062 -1.560 -0.003
+ATOM 29 H 1 -4.609 -0.825 1.198
+TER 30 1
+END
--- /dev/null
+COMPND CODEINE
+AUTHOR DAVE WOODCOCK 97 05 26
+ATOM 1 C 1 0.060 1.042 -0.046
+ATOM 2 C 1 1.341 1.395 0.169
+ATOM 3 C 1 2.213 0.515 0.696
+ATOM 4 C 1 1.819 -0.712 1.064
+ATOM 5 C 1 0.557 -1.075 0.825
+ATOM 6 C 1 -0.276 -0.221 0.241
+ATOM 7 C 1 -1.653 -0.835 0.088
+ATOM 8 C 1 -2.753 0.235 0.113
+ATOM 9 C 1 -2.334 1.337 -0.880
+ATOM 10 C 1 -1.030 2.047 -0.441
+ATOM 11 C 1 -1.619 -1.845 1.257
+ATOM 12 C 1 -1.707 -1.572 -1.266
+ATOM 13 C 1 -1.345 -0.591 -2.399
+ATOM 14 N 1 -2.115 0.716 -2.256
+ATOM 15 C 1 -2.334 1.567 -3.497
+ATOM 16 H 1 -3.696 -0.211 -0.208
+ATOM 17 C 1 -2.964 0.802 1.542
+ATOM 18 C 1 -2.739 0.091 2.611
+ATOM 19 C 1 -1.849 -1.184 2.635
+ATOM 20 H 1 -2.326 -2.660 1.095
+ATOM 21 O 1 -0.175 -2.315 1.279
+ATOM 22 H 1 -2.302 -1.916 3.305
+ATOM 23 O 1 -0.511 -0.791 3.186
+ATOM 24 O 1 2.771 -1.646 1.758
+ATOM 25 H 1 1.653 2.416 -0.055
+ATOM 26 H 1 3.239 0.837 0.866
+ATOM 27 H 1 -3.130 2.079 -0.948
+ATOM 28 H 1 -1.247 2.672 0.425
+ATOM 29 H 1 -0.672 2.680 -1.252
+ATOM 30 H 1 -2.712 -1.964 -1.426
+ATOM 31 H 1 -0.995 -2.398 -1.268
+ATOM 32 H 1 -1.576 -1.049 -3.360
+ATOM 33 H 1 -0.277 -0.373 -2.362
+ATOM 34 H 1 -2.839 0.977 -4.262
+ATOM 35 H 1 -1.370 1.904 -3.878
+ATOM 36 H 1 -2.946 2.434 -3.249
+ATOM 37 H 1 -3.476 1.759 1.606
+ATOM 38 H 1 -3.044 0.458 3.587
+ATOM 39 H 1 3.029 -1.160 3.154
+ATOM 40 H 1 3.668 -1.874 3.673
+ATOM 41 H 1 2.082 -1.068 3.686
+ATOM 42 H 1 3.523 -0.189 3.122
+ATOM 43 H 1 -0.614 -0.398 4.155
+TER 44 1
+END
--- /dev/null
+COMPND CUBANE
+AUTHOR DAVE WOODCOCK 95 12 06
+ATOM 1 C 1 0.789 -0.852 0.504 1.00 0.00
+ATOM 2 C 1 -0.161 -1.104 -0.624 1.00 0.00
+ATOM 3 C 1 -1.262 -0.440 0.160 1.00 0.00
+ATOM 4 C 1 -0.289 -0.202 1.284 1.00 0.00
+ATOM 5 C 1 1.203 0.513 -0.094 1.00 0.00
+ATOM 6 C 1 0.099 1.184 0.694 1.00 0.00
+ATOM 7 C 1 -0.885 0.959 -0.460 1.00 0.00
+ATOM 8 C 1 0.236 0.283 -1.269 1.00 0.00
+ATOM 9 H 1 1.410 -1.631 0.942 1.00 0.00
+ATOM 10 H 1 -0.262 -2.112 -1.024 1.00 0.00
+ATOM 11 H 1 -2.224 -0.925 0.328 1.00 0.00
+ATOM 12 H 1 -0.468 -0.501 2.315 1.00 0.00
+ATOM 13 H 1 2.224 0.892 -0.134 1.00 0.00
+ATOM 14 H 1 0.240 2.112 1.251 1.00 0.00
+ATOM 15 H 1 -1.565 1.730 -0.831 1.00 0.00
+ATOM 16 H 1 0.472 0.494 -2.315 1.00 0.00
+TER 17 1
+END
--- /dev/null
+COMPND CYCLOBUTANE
+AUTHOR DAVE WOODCOCK 96 02 23
+ATOM 1 C 1 -0.750 0.452 -0.417 1.00 0.00
+ATOM 2 C 1 -0.696 -0.588 0.609 1.00 0.00
+ATOM 3 C 1 0.820 -0.678 0.537 1.00 0.00
+ATOM 4 C 1 0.892 0.417 -0.428 1.00 0.00
+ATOM 5 H 1 -1.285 1.273 0.066 1.00 0.00
+ATOM 6 H 1 -1.328 0.080 -1.263 1.00 0.00
+ATOM 7 H 1 -1.225 -1.507 0.366 1.00 0.00
+ATOM 8 H 1 -1.029 -0.162 1.555 1.00 0.00
+ATOM 9 H 1 1.158 -1.594 0.054 1.00 0.00
+ATOM 10 H 1 1.310 -0.477 1.488 1.00 0.00
+ATOM 11 H 1 1.432 0.009 -1.290 1.00 0.00
+ATOM 12 H 1 1.506 1.236 -0.056 1.00 0.00
+TER 13 1
+END
--- /dev/null
+COMPND CYCLOHEXANOL, CHAIR, EQUATORIAL
+AUTHOR DAVE WOODCOCK 96 06 28
+ATOM 1 C 1 1.159 -0.600 -0.143 1.00 0.00
+ATOM 2 C 1 0.728 0.390 -1.220 1.00 0.00
+ATOM 3 C 1 -0.790 0.367 -1.363 1.00 0.00
+ATOM 4 C 1 -1.439 0.739 -0.033 1.00 0.00
+ATOM 5 C 1 -1.008 -0.250 1.044 1.00 0.00
+ATOM 6 C 1 0.510 -0.228 1.188 1.00 0.00
+ATOM 7 O 1 2.561 -0.563 -0.004 1.00 0.00
+ATOM 8 H 1 0.848 -1.605 -0.427 1.00 0.00
+ATOM 9 H 1 1.184 0.113 -2.171 1.00 0.00
+ATOM 10 H 1 1.049 1.393 -0.941 1.00 0.00
+ATOM 11 H 1 -1.113 -0.632 -1.655 1.00 0.00
+ATOM 12 H 1 -1.094 1.085 -2.125 1.00 0.00
+ATOM 13 H 1 -2.524 0.710 -0.137 1.00 0.00
+ATOM 14 H 1 -1.128 1.744 0.255 1.00 0.00
+ATOM 15 H 1 -1.330 -1.254 0.766 1.00 0.00
+ATOM 16 H 1 -1.464 0.026 1.995 1.00 0.00
+ATOM 17 H 1 0.814 -0.946 1.950 1.00 0.00
+ATOM 18 H 1 0.833 0.771 1.480 1.00 0.00
+ATOM 19 H 1 2.869 0.433 0.278 1.00 0.00
+TER 20 1
+END
--- /dev/null
+COMPND CYCLOPROPANE
+AUTHOR DAVE WOODCOCK 96 02 23
+ATOM 1 C 1 -0.776 -0.483 0.641 1.00 0.00
+ATOM 2 C 1 0.748 -0.414 0.598 1.00 0.00
+ATOM 3 C 1 -0.080 0.342 -0.437 1.00 0.00
+ATOM 4 H 1 -1.250 0.088 1.439 1.00 0.00
+ATOM 5 H 1 -1.214 -1.423 0.306 1.00 0.00
+ATOM 6 H 1 1.250 -1.311 0.235 1.00 0.00
+ATOM 7 H 1 1.214 0.201 1.368 1.00 0.00
+ATOM 8 H 1 -0.089 -0.088 -1.439 1.00 0.00
+ATOM 9 H 1 -0.126 1.423 -0.306 1.00 0.00
+TER 10 1
+END
--- /dev/null
+COMPND ETHANE
+AUTHOR DAVE WOODCOCK 95 12 18
+ATOM 1 C 1 -0.752 0.001 -0.141 1.00 0.00
+ATOM 2 C 1 0.752 -0.001 0.141 1.00 0.00
+ATOM 3 H 1 -1.158 0.991 0.070 1.00 0.00
+ATOM 4 H 1 -1.240 -0.737 0.496 1.00 0.00
+ATOM 5 H 1 -0.924 -0.249 -1.188 1.00 0.00
+ATOM 6 H 1 1.158 -0.991 -0.070 1.00 0.00
+ATOM 7 H 1 0.924 0.249 1.188 1.00 0.00
+ATOM 8 H 1 1.240 0.737 -0.496 1.00 0.00
+TER 9 1
+END
--- /dev/null
+COMPND METHANOL
+AUTHOR DAVE WOODCOCK 96 01 03
+ATOM 1 C 1 -0.426 -0.115 -0.147 1.00 0.00
+ATOM 2 O 1 -0.599 1.244 -0.481 1.00 0.00
+ATOM 3 H 1 -0.750 -0.738 -0.981 1.00 0.00
+ATOM 4 H 1 -1.022 -0.351 0.735 1.00 0.00
+ATOM 5 H 1 -1.642 1.434 -0.689 1.00 0.00
+ATOM 6 C 1 1.047 -0.383 0.147 1.00 0.00
+ATOM 7 H 1 1.370 0.240 0.981 1.00 0.00
+ATOM 8 H 1 1.642 -0.147 -0.735 1.00 0.00
+ATOM 9 H 1 1.180 -1.434 0.405 1.00 0.00
+TER 10 1
+END
--- /dev/null
+COMPND c8h16-c6-e
+AUTHOR Created by Dave Woodcock at Okanagan University College
+AUTHOR email:woodcock@okanagan.bc.ca
+AUTHOR GENERATED BY BABEL 1.6
+ATOM 1 C UNK 1 0.000 0.000 0.000 1.00 0.00
+ATOM 2 C UNK 1 1.537 0.000 0.000 1.00 0.00
+ATOM 3 C UNK 1 2.118 1.420 0.000 1.00 0.00
+ATOM 4 C UNK 1 1.794 2.165 1.305 1.00 0.00
+ATOM 5 C UNK 1 2.423 3.561 1.295 1.00 0.00
+ATOM 6 C UNK 1 3.939 3.459 1.119 1.00 0.00
+ATOM 7 C UNK 1 4.262 2.729 -0.186 1.00 0.00
+ATOM 8 C UNK 1 3.639 1.333 -0.171 1.00 0.00
+ATOM 9 H UNK 1 -0.371 0.393 0.945 1.00 0.00
+ATOM 10 H UNK 1 -0.348 -1.028 -0.111 1.00 0.00
+ATOM 11 H UNK 1 -0.361 0.621 -0.821 1.00 0.00
+ATOM 12 H UNK 1 1.871 -0.522 -0.898 1.00 0.00
+ATOM 13 H UNK 1 1.884 -0.540 0.882 1.00 0.00
+ATOM 14 H UNK 1 1.705 1.979 -0.841 1.00 0.00
+ATOM 15 H UNK 1 2.184 1.598 2.151 1.00 0.00
+ATOM 16 H UNK 1 0.714 2.281 1.393 1.00 0.00
+ATOM 17 H UNK 1 2.202 4.059 2.240 1.00 0.00
+ATOM 18 H UNK 1 2.001 4.143 0.474 1.00 0.00
+ATOM 19 H UNK 1 4.364 2.905 1.957 1.00 0.00
+ATOM 20 H UNK 1 4.369 4.461 1.088 1.00 0.00
+ATOM 21 H UNK 1 5.345 2.637 -0.287 1.00 0.00
+ATOM 22 H UNK 1 3.864 3.297 -1.028 1.00 0.00
+ATOM 23 H UNK 1 4.066 0.753 0.649 1.00 0.00
+ATOM 24 H UNK 1 3.861 0.841 -1.120 1.00 0.00
+CONECT 1 2 9 10 11
+CONECT 2 1 3 12 13
+CONECT 3 2 4 8 14
+CONECT 4 3 5 15 16
+CONECT 5 4 6 17 18
+CONECT 6 5 7 19 20
+CONECT 7 6 8 21 22
+CONECT 8 3 7 23 24
+CONECT 9 1
+CONECT 10 1
+CONECT 11 1
+CONECT 12 2
+CONECT 13 2
+CONECT 14 3
+CONECT 15 4
+CONECT 16 4
+CONECT 17 5
+CONECT 18 5
+CONECT 19 6
+CONECT 20 6
+CONECT 21 7
+CONECT 22 7
+CONECT 23 8
+CONECT 24 8
+MASTER 0 0 0 0 0 0 0 0 24 0 24 0
+END
--- /dev/null
+COMPND ETHANE-1,2-DIOL
+AUTHOR DAVE WOODCOCK 96 06 28
+ATOM 1 C 1 0.000 -0.763 0.000 1.00 0.00
+ATOM 2 C 1 0.000 0.763 0.000 1.00 0.00
+ATOM 3 O 1 -1.329 1.233 0.000 1.00 0.00
+ATOM 4 O 1 1.329 -1.233 0.000 1.00 0.00
+ATOM 5 H 1 -0.514 -1.126 -0.890 1.00 0.00
+ATOM 6 H 1 -0.514 -1.126 0.890 1.00 0.00
+ATOM 7 H 1 0.514 1.126 -0.890 1.00 0.00
+ATOM 8 H 1 0.514 1.126 0.890 1.00 0.00
+ATOM 9 H 1 -1.838 0.873 0.882 1.00 0.00
+ATOM 10 H 1 1.838 -0.873 0.882 1.00 0.00
+TER 11 1
+END
--- /dev/null
+COMPND HEME
+AUTHOR DAVE WOODCOCK 97 05 31
+ATOM 1 C 1 -1.978 3.340 -0.709
+ATOM 2 C 1 -3.116 4.078 -0.849
+ATOM 3 C 1 -4.168 3.145 -0.909
+ATOM 4 C 1 -3.582 1.914 -0.799
+ATOM 5 N 1 -2.214 1.991 -0.679
+ATOM 6 C 1 -4.313 0.722 -0.812
+ATOM 7 C 1 -3.758 -0.525 -0.700
+ATOM 8 C 1 -4.460 -1.668 -0.716
+ATOM 9 C 1 -3.525 -2.738 -0.591
+ATOM 10 C 1 -2.330 -2.115 -0.510
+ATOM 11 N 1 -2.359 -0.771 -0.568
+ATOM 12 C 1 -1.151 -2.884 -0.401
+ATOM 13 C 1 0.199 -2.298 -0.327
+ATOM 14 C 1 1.224 -3.020 -0.246
+ATOM 15 C 1 2.324 -2.015 -0.223
+ATOM 16 C 1 1.783 -0.894 -0.293
+ATOM 17 N 1 0.325 -0.902 -0.373
+ATOM 18 C 1 2.501 0.336 -0.306
+ATOM 19 C 1 1.900 1.621 -0.383
+ATOM 20 C 1 2.616 2.712 -0.378
+ATOM 21 C 1 1.672 3.804 -0.456
+ATOM 22 C 1 0.481 3.242 -0.512
+ATOM 23 N 1 0.525 1.808 -0.469
+ATOM 24 C 1 -0.722 3.948 -0.617
+ATOM 25 FE 1 -0.924 0.535 -0.518
+ATOM 26 C 1 1.072 -4.553 -0.200
+ATOM 27 C 1 3.791 -2.466 -0.128
+ATOM 28 C 1 4.264 -2.377 1.335
+ATOM 29 C 1 5.336 -3.455 1.605
+ATOM 30 O 1 5.954 -3.576 2.949
+ATOM 31 O 1 5.749 -4.381 0.493
+ATOM 32 C 1 4.151 2.620 -0.299
+ATOM 33 C 1 4.735 2.549 -1.722
+ATOM 34 C 1 5.955 3.491 -1.831
+ATOM 35 O 1 6.053 4.462 -2.949
+ATOM 36 O 1 7.041 3.415 -0.793
+ATOM 37 C 1 2.168 5.260 -0.459
+ATOM 38 C 1 -3.036 5.615 -0.908
+ATOM 39 C 1 -5.433 3.562 -1.047
+ATOM 40 C 1 -6.434 2.676 -1.104
+ATOM 41 C 1 -3.949 -4.008 -0.578
+ATOM 42 C 1 -3.075 -5.014 -0.461
+ATOM 43 C 1 -5.994 -1.630 -0.852
+ATOM 44 H 1 3.566 0.310 -0.263
+ATOM 45 H 1 -0.699 5.018 -0.634
+ATOM 46 H 1 1.091 -4.951 -1.214
+ATOM 47 H 1 0.149 -4.834 0.287
+ATOM 48 H 1 1.894 -4.979 0.374
+ATOM 49 H 1 4.416 -1.827 -0.752
+ATOM 50 H 1 3.870 -3.498 -0.473
+ATOM 51 H 1 3.416 -2.537 2.002
+ATOM 52 H 1 4.689 -1.390 1.519
+ATOM 53 H 1 6.143 -3.822 -0.304
+ATOM 54 H 1 4.452 1.749 0.265
+ATOM 55 H 1 4.540 3.501 0.210
+ATOM 56 H 1 3.978 2.860 -2.443
+ATOM 57 H 1 5.044 1.526 -1.939
+ATOM 58 H 1 7.460 2.453 -0.791
+ATOM 59 H 1 2.346 5.581 -1.486
+ATOM 60 H 1 3.098 5.325 0.108
+ATOM 61 H 1 1.419 5.905 -0.001
+ATOM 62 H 1 -2.919 5.934 -1.944
+ATOM 63 H 1 -2.197 5.969 -0.321
+ATOM 64 H 1 -3.949 6.044 -0.497
+ATOM 65 H 1 -5.648 4.629 -1.115
+ATOM 66 H 1 -7.460 3.019 -1.217
+ATOM 67 H 1 -6.445 1.815 -1.069
+ATOM 68 H 1 -5.015 -4.224 -0.664
+ATOM 69 H 1 -3.425 -6.044 -0.451
+ATOM 70 H 1 -2.218 -5.052 -0.374
+ATOM 71 H 1 -6.266 -1.661 -1.907
+ATOM 72 H 1 -6.386 -0.722 -0.402
+ATOM 73 H 1 -6.425 -2.488 -0.340
+ATOM 74 H 1 -5.388 0.748 -0.916
+ATOM 75 H 1 -1.211 -3.962 -0.369
+TER 76 1
+END
--- /dev/null
+COMPND (R)-2-HYDROXYPROPANOIC ACID, LACTIC ACID
+AUTHOR DAVE WOODCOCK 98 02 11
+ATOM 1 C 1 -1.341 -1.213 0.672 1.00 0.00
+ATOM 2 C 1 -1.058 0.086 -0.108 1.00 0.00
+ATOM 3 C 1 0.268 0.009 -0.870 1.00 0.00
+ATOM 4 O 1 0.644 1.052 -1.679 1.00 0.00
+ATOM 5 O 1 1.086 -1.141 -0.801 1.00 0.00
+ATOM 6 O 1 -1.032 1.177 0.781 1.00 0.00
+ATOM 7 H 1 -1.409 -2.042 -0.033 1.00 0.00
+ATOM 8 H 1 -2.322 -1.111 1.146 1.00 0.00
+ATOM 9 H 1 -0.506 -1.385 1.360 1.00 0.00
+ATOM 10 H 1 -1.869 0.235 -0.821 1.00 0.00
+ATOM 11 H 1 0.849 -1.803 -1.621 1.00 0.00
+ATOM 12 H 1 -0.243 1.052 1.509 1.00 0.00
+TER
--- /dev/null
+COMPND LACTOSE
+AUTHOR DAVE WOODCOCK 96 10 11
+ATOM 1 C 1 -1.751 2.307 -0.863
+ATOM 2 C 1 -2.630 2.467 0.383
+ATOM 3 C 1 -2.354 1.287 1.317
+ATOM 4 C 1 -0.856 1.212 1.630
+ATOM 5 C 1 -0.037 1.165 0.327
+ATOM 6 O 1 -0.394 2.268 -0.481
+ATOM 7 O 1 1.349 1.250 0.639
+ATOM 8 C 1 2.229 1.267 -0.481
+ATOM 9 C 1 3.443 0.371 -0.159
+ATOM 10 C 1 2.748 2.703 -0.740
+ATOM 11 C 1 3.885 2.679 -1.789
+ATOM 12 C 1 4.966 1.700 -1.351
+ATOM 13 O 1 4.397 0.413 -1.204
+ATOM 14 O 1 5.980 1.622 -2.337
+ATOM 15 O 1 4.402 3.981 -1.939
+ATOM 16 O 1 1.762 3.565 -1.242
+ATOM 17 O 1 -0.573 0.084 2.433
+ATOM 18 O 1 -3.092 1.426 2.514
+ATOM 19 O 1 -2.358 3.677 1.057
+ATOM 20 C 1 -1.929 3.473 -1.847
+ATOM 21 O 1 -1.074 3.308 -2.962
+ATOM 22 C 1 3.012 -1.094 0.030
+ATOM 23 O 1 4.146 -1.902 0.275
+ATOM 24 H 1 -2.017 1.377 -1.368
+ATOM 25 H 1 -3.681 2.450 0.091
+ATOM 26 H 1 -2.664 0.368 0.817
+ATOM 27 H 1 -0.563 2.106 2.184
+ATOM 28 H 1 -0.248 0.235 -0.202
+ATOM 29 H 1 1.751 0.899 -1.387
+ATOM 30 H 1 3.886 0.712 0.779
+ATOM 31 H 1 3.169 3.081 0.182
+ATOM 32 H 1 3.437 2.343 -2.729
+ATOM 33 H 1 5.420 2.015 -0.410
+ATOM 34 H 1 6.555 2.537 -2.352
+ATOM 35 H 1 4.825 4.336 -1.010
+ATOM 36 H 1 1.352 4.184 -0.425
+ATOM 37 H 1 -0.842 -0.825 1.914
+ATOM 38 H 1 -4.151 1.407 2.300
+ATOM 39 H 1 -2.880 4.492 0.578
+ATOM 40 H 1 -1.664 4.411 -1.360
+ATOM 41 H 1 -2.965 3.522 -2.183
+ATOM 42 H 1 -1.345 2.417 -3.510
+ATOM 43 H 1 2.521 -1.441 -0.879
+ATOM 44 H 1 2.316 -1.185 0.866
+ATOM 45 H 1 4.617 -1.610 1.202
+TER 46 1
+END
--- /dev/null
+COMPND lanoxin
+AUTHOR Created by Dave Woodcock at Okanagan University College
+AUTHOR email:woodcock@okanagan.bc.ca
+AUTHOR GENERATED BY BABEL 1.6
+ATOM 1 C UNK 1 0.000 0.000 0.000 1.00 0.00
+ATOM 2 C UNK 1 1.552 0.000 0.000 1.00 0.00
+ATOM 3 C UNK 1 2.060 1.441 0.000 1.00 0.00
+ATOM 4 C UNK 1 1.613 2.260 1.212 1.00 0.00
+ATOM 5 C UNK 1 0.070 2.226 1.213 1.00 0.00
+ATOM 6 C UNK 1 -0.523 0.789 1.215 1.00 0.00
+ATOM 7 O UNK 1 -0.541 -1.323 0.139 1.00 0.00
+ATOM 8 H UNK 1 1.635 1.911 -0.887 1.00 0.00
+ATOM 9 C UNK 1 3.556 1.471 -0.171 1.00 0.00
+ATOM 10 C UNK 1 4.003 2.898 -0.423 1.00 0.00
+ATOM 11 C UNK 1 3.598 3.813 0.738 1.00 0.00
+ATOM 12 C UNK 1 2.093 3.737 1.001 1.00 0.00
+ATOM 13 C UNK 1 2.136 1.687 2.553 1.00 0.00
+ATOM 14 H UNK 1 1.560 4.101 0.124 1.00 0.00
+ATOM 15 H UNK 1 4.130 3.480 1.629 1.00 0.00
+ATOM 16 C UNK 1 4.057 5.279 0.447 1.00 0.00
+ATOM 17 C UNK 1 3.619 6.326 1.509 1.00 0.00
+ATOM 18 C UNK 1 2.105 6.113 1.845 1.00 0.00
+ATOM 19 C UNK 1 1.759 4.644 2.191 1.00 0.00
+ATOM 20 O UNK 1 5.483 5.295 0.383 1.00 0.00
+ATOM 21 C UNK 1 3.737 7.680 0.780 1.00 0.00
+ATOM 22 C UNK 1 4.414 6.244 2.808 1.00 0.00
+ATOM 23 C UNK 1 3.757 7.373 -0.713 1.00 0.00
+ATOM 24 C UNK 1 3.495 5.876 -0.862 1.00 0.00
+ATOM 25 H UNK 1 2.850 8.277 0.993 1.00 0.00
+ATOM 26 C UNK 1 4.907 8.603 1.130 1.00 0.00
+ATOM 27 C UNK 1 6.250 8.296 1.016 1.00 0.00
+ATOM 28 C UNK 1 6.957 9.503 1.071 1.00 0.00
+ATOM 29 O UNK 1 8.326 9.615 0.895 1.00 0.00
+ATOM 30 O UNK 1 6.101 10.641 1.259 1.00 0.00
+ATOM 31 C UNK 1 4.774 10.096 1.342 1.00 0.00
+ATOM 32 C UNK 1 -0.628 -2.144 -1.030 1.00 0.00
+ATOM 33 C UNK 1 -1.485 -1.532 -2.165 1.00 0.00
+ATOM 34 C UNK 1 -0.612 -1.229 -3.376 1.00 0.00
+ATOM 35 C UNK 1 0.035 -2.526 -3.859 1.00 0.00
+ATOM 36 C UNK 1 0.620 -3.312 -2.660 1.00 0.00
+ATOM 37 O UNK 1 0.662 -2.505 -1.495 1.00 0.00
+ATOM 38 O UNK 1 -1.385 -0.646 -4.394 1.00 0.00
+ATOM 39 C UNK 1 2.073 -3.766 -2.921 1.00 0.00
+ATOM 40 O UNK 1 2.122 -4.691 -3.993 1.00 0.00
+ATOM 41 O UNK 1 -0.970 -3.298 -4.513 1.00 0.00
+ATOM 42 H UNK 1 0.168 -0.522 -3.087 1.00 0.00
+ATOM 43 H UNK 1 0.836 -2.253 -4.546 1.00 0.00
+ATOM 44 C UNK 1 -0.588 -3.896 -5.749 1.00 0.00
+ATOM 45 C UNK 1 -1.808 -4.580 -6.376 1.00 0.00
+ATOM 46 C UNK 1 -1.397 -5.278 -7.671 1.00 0.00
+ATOM 47 C UNK 1 -0.662 -4.304 -8.609 1.00 0.00
+ATOM 48 C UNK 1 0.410 -3.510 -7.846 1.00 0.00
+ATOM 49 O UNK 1 -0.136 -2.920 -6.680 1.00 0.00
+ATOM 50 H UNK 1 -2.288 -5.651 -8.175 1.00 0.00
+ATOM 51 O UNK 1 -0.566 -6.381 -7.370 1.00 0.00
+ATOM 52 H UNK 1 -1.380 -3.601 -9.030 1.00 0.00
+ATOM 53 O UNK 1 -0.026 -5.076 -9.625 1.00 0.00
+ATOM 54 C UNK 1 0.976 -2.374 -8.700 1.00 0.00
+ATOM 55 O UNK 1 1.741 -2.864 -9.774 1.00 0.00
+ATOM 56 C UNK 1 -0.596 -5.080 -10.937 1.00 0.00
+ATOM 57 C UNK 1 -2.109 -5.455 -10.956 1.00 0.00
+ATOM 58 C UNK 1 -2.560 -5.484 -12.419 1.00 0.00
+ATOM 59 C UNK 1 -2.219 -4.162 -13.110 1.00 0.00
+ATOM 60 C UNK 1 -0.722 -3.864 -12.944 1.00 0.00
+ATOM 61 O UNK 1 -0.395 -3.801 -11.564 1.00 0.00
+ATOM 62 H UNK 1 -3.642 -5.615 -12.434 1.00 0.00
+ATOM 63 O UNK 1 -1.989 -6.561 -13.094 1.00 0.00
+ATOM 64 H UNK 1 -2.804 -3.369 -12.642 1.00 0.00
+ATOM 65 O UNK 1 -2.572 -4.252 -14.480 1.00 0.00
+ATOM 66 C UNK 1 -0.329 -2.526 -13.579 1.00 0.00
+ATOM 67 O UNK 1 1.046 -2.259 -13.359 1.00 0.00
+ATOM 68 H UNK 1 -0.370 0.475 -0.907 1.00 0.00
+ATOM 69 H UNK 1 1.927 -0.484 -0.901 1.00 0.00
+ATOM 70 H UNK 1 1.966 -0.568 0.832 1.00 0.00
+ATOM 71 H UNK 1 -0.369 2.812 0.402 1.00 0.00
+ATOM 72 H UNK 1 -0.283 2.663 2.146 1.00 0.00
+ATOM 73 H UNK 1 -1.620 0.817 1.240 1.00 0.00
+ATOM 74 H UNK 1 -0.109 0.298 2.093 1.00 0.00
+ATOM 75 H UNK 1 3.843 0.849 -1.017 1.00 0.00
+ATOM 76 H UNK 1 4.061 1.067 0.707 1.00 0.00
+ATOM 77 H UNK 1 3.608 3.249 -1.376 1.00 0.00
+ATOM 78 H UNK 1 5.088 2.869 -0.492 1.00 0.00
+ATOM 79 H UNK 1 3.201 1.832 2.731 1.00 0.00
+ATOM 80 H UNK 1 1.912 0.623 2.608 1.00 0.00
+ATOM 81 H UNK 1 1.740 2.265 3.393 1.00 0.00
+ATOM 82 H UNK 1 1.552 6.327 0.916 1.00 0.00
+ATOM 83 H UNK 1 1.909 6.716 2.750 1.00 0.00
+ATOM 84 H UNK 1 0.686 4.634 2.387 1.00 0.00
+ATOM 85 H UNK 1 2.298 4.329 3.085 1.00 0.00
+ATOM 86 H UNK 1 5.842 4.973 -0.584 1.00 0.00
+ATOM 87 H UNK 1 5.498 6.282 2.692 1.00 0.00
+ATOM 88 H UNK 1 4.369 5.247 3.258 1.00 0.00
+ATOM 89 H UNK 1 4.089 7.026 3.497 1.00 0.00
+ATOM 90 H UNK 1 4.711 7.620 -1.177 1.00 0.00
+ATOM 91 H UNK 1 2.997 7.955 -1.235 1.00 0.00
+ATOM 92 H UNK 1 3.998 5.490 -1.749 1.00 0.00
+ATOM 93 H UNK 1 2.425 5.712 -0.976 1.00 0.00
+ATOM 94 H UNK 1 6.662 7.349 0.713 1.00 0.00
+ATOM 95 H UNK 1 4.108 10.544 0.606 1.00 0.00
+ATOM 96 H UNK 1 4.332 10.297 2.317 1.00 0.00
+ATOM 97 H UNK 1 -1.130 -3.063 -0.725 1.00 0.00
+ATOM 98 H UNK 1 -1.936 -0.603 -1.816 1.00 0.00
+ATOM 99 H UNK 1 -2.242 -2.263 -2.457 1.00 0.00
+ATOM 100 H UNK 1 0.005 -4.192 -2.459 1.00 0.00
+ATOM 101 H UNK 1 -0.747 -0.378 -5.224 1.00 0.00
+ATOM 102 H UNK 1 2.455 -4.258 -2.020 1.00 0.00
+ATOM 103 H UNK 1 2.650 -2.884 -3.210 1.00 0.00
+ATOM 104 H UNK 1 3.144 -4.997 -4.165 1.00 0.00
+ATOM 105 H UNK 1 0.189 -4.635 -5.562 1.00 0.00
+ATOM 106 H UNK 1 -2.576 -3.837 -6.592 1.00 0.00
+ATOM 107 H UNK 1 -2.268 -5.284 -5.683 1.00 0.00
+ATOM 108 H UNK 1 1.230 -4.171 -7.562 1.00 0.00
+ATOM 109 H UNK 1 -1.121 -7.120 -6.810 1.00 0.00
+ATOM 110 H UNK 1 1.642 -1.782 -8.071 1.00 0.00
+ATOM 111 H UNK 1 0.168 -1.743 -9.073 1.00 0.00
+ATOM 112 H UNK 1 2.110 -2.034 -10.358 1.00 0.00
+ATOM 113 H UNK 1 -0.046 -5.836 -11.501 1.00 0.00
+ATOM 114 H UNK 1 -2.651 -4.618 -10.513 1.00 0.00
+ATOM 115 H UNK 1 -2.290 -6.434 -10.488 1.00 0.00
+ATOM 116 H UNK 1 -0.139 -4.651 -13.424 1.00 0.00
+ATOM 117 H UNK 1 -2.329 -7.482 -12.643 1.00 0.00
+ATOM 118 H UNK 1 -2.674 -3.265 -14.907 1.00 0.00
+ATOM 119 H UNK 1 -0.904 -1.743 -13.080 1.00 0.00
+ATOM 120 H UNK 1 -0.505 -2.570 -14.657 1.00 0.00
+ATOM 121 H UNK 1 1.659 -3.001 -13.851 1.00 0.00
+CONECT 1 2 6 7 68
+CONECT 2 1 3 69 70
+CONECT 3 2 4 8 9
+CONECT 4 3 5 12 13
+CONECT 5 4 6 71 72
+CONECT 6 1 5 73 74
+CONECT 7 1 32
+CONECT 8 3
+CONECT 9 3 10 75 76
+CONECT 10 9 11 77 78
+CONECT 11 10 12 15 16
+CONECT 12 4 11 14 19
+CONECT 13 4 79 80 81
+CONECT 14 12
+CONECT 15 11
+CONECT 16 11 17 20 24
+CONECT 17 16 18 21 22
+CONECT 18 17 19 82 83
+CONECT 19 12 18 84 85
+CONECT 20 16 86
+CONECT 21 17 23 25 26
+CONECT 22 17 87 88 89
+CONECT 23 21 24 90 91
+CONECT 24 16 23 92 93
+CONECT 25 21
+CONECT 26 21 27 31
+CONECT 27 26 28 94
+CONECT 28 27 29 30
+CONECT 29 28
+CONECT 30 28 31
+CONECT 31 26 30 95 96
+CONECT 32 7 33 37 97
+CONECT 33 32 34 98 99
+CONECT 34 33 35 38 42
+CONECT 35 34 36 41 43
+CONECT 36 35 37 39 100
+CONECT 37 32 36
+CONECT 38 34 101
+CONECT 39 36 40 102 103
+CONECT 40 39 104
+CONECT 41 35 44
+CONECT 42 34
+CONECT 43 35
+CONECT 44 41 45 49 105
+CONECT 45 44 46 106 107
+CONECT 46 45 47 50 51
+CONECT 47 46 48 52 53
+CONECT 48 47 49 54 108
+CONECT 49 44 48
+CONECT 50 46
+CONECT 51 46 109
+CONECT 52 47
+CONECT 53 47 56
+CONECT 54 48 55 110 111
+CONECT 55 54 112
+CONECT 56 53 57 61 113
+CONECT 57 56 58 114 115
+CONECT 58 57 59 62 63
+CONECT 59 58 60 64 65
+CONECT 60 59 61 66 116
+CONECT 61 56 60
+CONECT 62 58
+CONECT 63 58 117
+CONECT 64 59
+CONECT 65 59 118
+CONECT 66 60 67 119 120
+CONECT 67 66 121
+CONECT 68 1
+CONECT 69 2
+CONECT 70 2
+CONECT 71 5
+CONECT 72 5
+CONECT 73 6
+CONECT 74 6
+CONECT 75 9
+CONECT 76 9
+CONECT 77 10
+CONECT 78 10
+CONECT 79 13
+CONECT 80 13
+CONECT 81 13
+CONECT 82 18
+CONECT 83 18
+CONECT 84 19
+CONECT 85 19
+CONECT 86 20
+CONECT 87 22
+CONECT 88 22
+CONECT 89 22
+CONECT 90 23
+CONECT 91 23
+CONECT 92 24
+CONECT 93 24
+CONECT 94 27
+CONECT 95 31
+CONECT 96 31
+CONECT 97 32
+CONECT 98 33
+CONECT 99 33
+CONECT 100 36
+CONECT 101 38
+CONECT 102 39
+CONECT 103 39
+CONECT 104 40
+CONECT 105 44
+CONECT 106 45
+CONECT 107 45
+CONECT 108 48
+CONECT 109 51
+CONECT 110 54
+CONECT 111 54
+CONECT 112 55
+CONECT 113 56
+CONECT 114 57
+CONECT 115 57
+CONECT 116 60
+CONECT 117 63
+CONECT 118 65
+CONECT 119 66
+CONECT 120 66
+CONECT 121 67
+MASTER 0 0 0 0 0 0 0 0 121 0 121 0
+END
--- /dev/null
+COMPND LSD, LYSERGIC ACID, DIETHYLAMIDE
+AUTHOR DAVE WOODCOCK 95 12 12
+ATOM 1 C 1 -2.697 -1.271 1.437 1.00 0.00
+ATOM 2 C 1 -2.126 -0.717 0.282 1.00 0.00
+ATOM 3 C 1 -3.021 -0.234 -0.708 1.00 0.00
+ATOM 4 C 1 -4.413 -0.428 -0.556 1.00 0.00
+ATOM 5 C 1 -4.949 -1.119 0.554 1.00 0.00
+ATOM 6 C 1 -4.059 -1.516 1.553 1.00 0.00
+ATOM 7 N 1 -4.241 -2.471 2.497 1.00 0.00
+ATOM 8 C 1 -3.036 -2.857 2.960 1.00 0.00
+ATOM 9 C 1 -2.037 -2.106 2.326 1.00 0.00
+ATOM 10 C 1 -0.615 -2.577 1.977 1.00 0.00
+ATOM 11 C 1 0.119 -1.421 1.282 1.00 0.00
+ATOM 12 C 1 -0.710 -0.753 0.162 1.00 0.00
+ATOM 13 H 1 0.300 -0.639 2.094 1.00 0.00
+ATOM 14 N 1 1.388 -1.914 0.749 1.00 0.00
+ATOM 15 C 1 -0.013 -0.114 -0.876 1.00 0.00
+ATOM 16 C 1 1.519 -0.062 -0.921 1.00 0.00
+ATOM 17 C 1 2.188 -0.766 0.268 1.00 0.00
+ATOM 18 H 1 1.852 -0.599 -1.846 1.00 0.00
+ATOM 19 C 1 1.972 1.398 -0.946 1.00 0.00
+ATOM 20 O 1 1.227 2.309 -0.252 1.00 0.00
+ATOM 21 N 1 3.346 1.735 -1.342 1.00 0.00
+ATOM 22 C 1 3.754 3.060 -0.781 1.00 0.00
+ATOM 21 C 1 5.214 3.412 -1.048 1.00 0.00
+ATOM 24 C 1 3.538 1.630 -2.822 1.00 0.00
+ATOM 25 C 1 4.848 0.923 -3.149 1.00 0.00
+ATOM 26 H 1 -2.661 0.224 -1.617 1.00 0.00
+ATOM 27 H 1 -5.075 -0.101 -1.344 1.00 0.00
+ATOM 28 H 1 -5.995 -1.385 0.616 1.00 0.00
+ATOM 29 H 1 -5.144 -3.055 2.631 1.00 0.00
+ATOM 30 H 1 -2.844 -3.801 3.451 1.00 0.00
+ATOM 31 H 1 -0.701 -3.442 1.316 1.00 0.00
+ATOM 32 H 1 -0.110 -2.884 2.898 1.00 0.00
+ATOM 33 H 1 -0.558 0.396 -1.651 1.00 0.00
+ATOM 34 H 1 2.320 -0.064 1.092 1.00 0.00
+ATOM 35 H 1 3.179 -1.115 -0.035 1.00 0.00
+ATOM 36 H 1 3.590 3.043 0.289 1.00 0.00
+ATOM 37 H 1 3.115 3.833 -1.214 1.00 0.00
+ATOM 38 H 1 5.370 3.618 -2.167 1.00 0.00
+ATOM 39 H 1 5.888 2.566 -0.704 1.00 0.00
+ATOM 40 H 1 5.482 4.388 -0.447 1.00 0.00
+ATOM 41 H 1 3.515 2.632 -3.251 1.00 0.00
+ATOM 42 H 1 2.713 1.085 -3.258 1.00 0.00
+ATOM 43 H 1 4.872 -0.106 -2.644 1.00 0.00
+ATOM 44 H 1 5.750 1.550 -2.790 1.00 0.00
+ATOM 45 H 1 4.922 0.787 -4.320 1.00 0.00
+ATOM 46 C 1 1.690 -3.403 0.759 1.00 0.00
+ATOM 47 H 1 0.936 -3.931 0.174 1.00 0.00
+ATOM 48 H 1 1.675 -3.770 1.786 1.00 0.00
+ATOM 49 H 1 2.674 -3.578 0.325 1.00 0.00
+TER 50 1
+END
--- /dev/null
+COMPND mALTOSE
+AUTHOR DAVE WOODCOCK 96 10 11
+ATOM 1 C 1 -1.194 0.890 0.052
+ATOM 2 C 1 -2.033 1.672 1.075
+ATOM 3 C 1 -3.272 0.905 1.549
+ATOM 4 C 1 -4.036 0.377 0.329
+ATOM 5 C 1 -3.071 -0.476 -0.504
+ATOM 6 C 1 -3.796 -1.094 -1.710
+ATOM 7 O 1 -2.020 0.354 -0.981
+ATOM 8 O 1 -2.902 -1.888 -2.464
+ATOM 9 O 1 -1.243 2.038 2.192
+ATOM 10 O 1 -4.095 1.764 2.313
+ATOM 11 O 1 -5.143 -0.398 0.750
+ATOM 12 O 1 -0.402 -0.165 0.587
+ATOM 13 C 1 1.000 0.108 0.705
+ATOM 14 C 1 1.607 -0.955 1.647
+ATOM 15 C 1 3.108 -0.693 1.825
+ATOM 16 C 1 3.796 -0.629 0.456
+ATOM 17 C 1 1.797 0.015 -0.620
+ATOM 18 C 1 1.358 0.980 -1.728
+ATOM 19 O 1 2.268 0.945 -2.813
+ATOM 20 O 1 3.154 0.334 -0.351
+ATOM 21 O 1 5.146 -0.233 0.596
+ATOM 22 O 1 3.696 -1.708 2.619
+ATOM 23 O 1 0.985 -0.941 2.915
+ATOM 24 H 1 -0.600 1.629 -0.378
+ATOM 25 H 1 -2.380 2.596 0.603
+ATOM 26 H 1 -2.959 0.061 2.167
+ATOM 27 H 1 -4.391 1.212 -0.277
+ATOM 28 H 1 -2.676 -1.283 0.116
+ATOM 29 H 1 -4.179 -0.296 -2.347
+ATOM 30 H 1 -4.629 -1.716 -1.381
+ATOM 31 H 1 -2.567 -2.730 -1.874
+ATOM 32 H 1 -0.480 2.739 1.883
+ATOM 33 H 1 -4.441 2.594 1.712
+ATOM 34 H 1 -5.911 0.238 1.166
+ATOM 35 H 1 1.142 1.091 1.156
+ATOM 36 H 1 1.467 -1.939 1.194
+ATOM 37 H 1 3.242 0.265 2.331
+ATOM 38 H 1 3.758 -1.604 -0.032
+ATOM 39 H 1 1.727 -1.001 -1.014
+ATOM 40 H 1 1.343 2.007 -1.355
+ATOM 41 H 1 0.376 0.718 -2.121
+ATOM 42 H 1 2.263 -0.038 -3.263
+ATOM 43 H 1 5.721 -1.020 1.062
+ATOM 44 H 1 3.590 -2.670 2.138
+ATOM 45 H 1 -0.006 -1.367 2.855
+TER 46 1
+END
--- /dev/null
+COMPND MENTHOL
+AUTHOR DAVE WOODCOCK 95 11 02
+ATOM 1 C 1 2.007 0.837 -0.426 1.00 0.00
+ATOM 2 C 1 1.103 1.677 -1.313 1.00 0.00
+ATOM 3 C 1 0.026 0.777 -1.900 1.00 0.00
+ATOM 4 C 1 -0.811 0.124 -0.800 1.00 0.00
+ATOM 5 C 1 0.068 -0.698 0.172 1.00 0.00
+ATOM 6 C 1 1.197 0.205 0.701 1.00 0.00
+ATOM 7 H 1 2.781 1.477 0.009 1.00 0.00
+ATOM 8 H 1 2.483 0.053 -1.023 1.00 0.00
+ATOM 9 H 1 0.647 2.475 -0.725 1.00 0.00
+ATOM 10 H 1 0.491 0.005 -2.518 1.00 0.00
+ATOM 11 H 1 -0.639 1.383 -2.522 1.00 0.00
+ATOM 12 H 1 -1.350 0.878 -0.223 1.00 0.00
+ATOM 13 H 1 0.520 -1.524 -0.381 1.00 0.00
+ATOM 14 H 1 1.899 -0.397 1.296 1.00 0.00
+ATOM 15 H 1 0.769 0.991 1.338 1.00 0.00
+ATOM 16 C 1 1.920 2.324 -2.436 1.00 0.00
+ATOM 17 H 1 2.396 1.556 -3.045 1.00 0.00
+ATOM 18 H 1 2.689 2.970 -2.010 1.00 0.00
+ATOM 19 H 1 1.265 2.925 -3.069 1.00 0.00
+ATOM 20 C 1 -0.738 -1.284 1.368 1.00 0.00
+ATOM 21 C 1 0.178 -2.060 2.327 1.00 0.00
+ATOM 22 C 1 -1.848 -2.234 0.936 1.00 0.00
+ATOM 23 O 1 -1.759 -0.703 -1.456 1.00 0.00
+ATOM 24 H 1 -1.172 -0.448 1.922 1.00 0.00
+ATOM 25 H 1 0.842 -1.380 2.861 1.00 0.00
+ATOM 26 H 1 0.768 -2.793 1.770 1.00 0.00
+ATOM 27 H 1 -0.427 -2.583 3.069 1.00 0.00
+ATOM 28 H 1 -1.468 -2.970 0.149 1.00 0.00
+ATOM 29 H 1 -2.781 -1.610 0.492 1.00 0.00
+ATOM 30 H 1 -2.240 -2.828 1.850 1.00 0.00
+ATOM 31 H 1 -2.445 -0.089 -2.008 1.00 0.00
+TER 32 1
+END
--- /dev/null
+COMPND METHANE
+AUTHOR DAVE WOODCOCK 95 12 18
+ATOM 1 C 1 0.257 -0.363 0.000 1.00 0.00
+ATOM 2 H 1 0.257 0.727 0.000 1.00 0.00
+ATOM 3 H 1 0.771 -0.727 0.890 1.00 0.00
+ATOM 4 H 1 0.771 -0.727 -0.890 1.00 0.00
+ATOM 5 H 1 -0.771 -0.727 0.000 1.00 0.00
+TER 6 1
+END
--- /dev/null
+COMPND METHANOL
+AUTHOR DAVE WOODCOCK 96 01 03
+ATOM 1 C 1 -0.748 -0.015 0.024 1.00 0.00
+ATOM 2 O 1 0.558 0.420 -0.278 1.00 0.00
+ATOM 3 H 1 -1.293 -0.202 -0.901 1.00 0.00
+ATOM 4 H 1 -1.263 0.754 0.600 1.00 0.00
+ATOM 5 H 1 -0.699 -0.934 0.609 1.00 0.00
+ATOM 6 H 1 0.716 1.404 0.137 1.00 0.00
+TER 6 1
+END
--- /dev/null
+COMPND (R)-HYDROXYDIHYDROCITRONELLAL
+AUTHOR DAVE WOODCOCK 97 06 03
+ATOM 1 C 1 4.705 -0.311 -0.346
+ATOM 2 C 1 3.370 -0.064 0.370
+ATOM 3 C 1 2.226 -0.448 -0.585
+ATOM 4 C 1 0.837 -0.285 0.057
+ATOM 5 C 1 -0.260 -0.677 -0.940
+ATOM 6 C 1 -1.654 -0.501 -0.320
+ATOM 7 C 1 -2.726 -1.010 -1.291
+ATOM 8 C 1 -4.118 -0.952 -0.653
+ATOM 9 C 1 3.292 1.423 0.769
+ATOM 10 C 1 -1.912 0.971 0.007
+ATOM 11 O 1 -5.235 -1.111 -1.430
+ATOM 12 O 1 3.312 -0.870 1.530
+ATOM 13 H 1 4.515 -0.693 -1.349
+ATOM 14 H 1 5.289 -1.041 0.215
+ATOM 15 H 1 5.261 0.624 -0.413
+ATOM 16 H 1 2.335 -1.491 -0.882
+ATOM 17 H 1 2.261 0.188 -1.469
+ATOM 18 H 1 0.694 0.754 0.353
+ATOM 19 H 1 0.766 -0.927 0.935
+ATOM 20 H 1 -0.134 -1.721 -1.226
+ATOM 21 H 1 -0.189 -0.046 -1.826
+ATOM 22 H 1 -1.712 -1.068 0.609
+ATOM 23 H 1 -2.509 -2.043 -1.562
+ATOM 24 H 1 -2.728 -0.391 -2.188
+ATOM 25 H 1 -4.219 -0.787 0.409
+ATOM 26 H 1 3.353 2.043 -0.125
+ATOM 27 H 1 4.120 1.664 1.436
+ATOM 28 H 1 2.348 1.613 1.279
+ATOM 29 H 1 -1.854 1.562 -0.907
+ATOM 30 H 1 -1.162 1.323 0.716
+ATOM 31 H 1 -2.904 1.077 0.446
+ATOM 32 H 1 4.130 -0.614 2.188
+TER 33 1
+END
--- /dev/null
+COMPND MORPHINE
+AUTHOR DAVE WOODCOCK 97 03 17
+ATOM 1 C 1 0.205 1.266 -1.134
+ATOM 2 C 1 -0.284 2.165 -2.099
+ATOM 3 C 1 -1.562 2.753 -1.945
+ATOM 4 C 1 -2.380 2.407 -0.841
+ATOM 5 C 1 -1.872 1.519 0.115
+ATOM 6 C 1 -0.603 1.008 -0.018
+ATOM 7 C 1 -0.361 -0.061 0.993
+ATOM 8 C 1 0.589 -1.141 0.497
+ATOM 9 C 1 1.826 -0.446 -0.092
+ATOM 10 C 1 1.457 0.410 -1.353
+ATOM 11 C 1 -1.842 -0.443 1.259
+ATOM 12 C 1 0.304 0.606 2.203
+ATOM 13 C 1 1.641 1.260 1.781
+ATOM 14 N 1 2.490 0.319 1.002
+ATOM 15 C 1 3.778 0.959 0.609
+ATOM 16 H 1 0.915 -1.733 1.353
+ATOM 17 C 1 -0.061 -2.116 -0.469
+ATOM 18 C 1 -1.376 -2.518 -0.226
+ATOM 19 C 1 -2.410 -1.521 0.299
+ATOM 20 H 1 -1.939 -0.801 2.284
+ATOM 21 O 1 -2.606 0.768 1.078
+ATOM 22 H 1 -3.177 -2.075 0.841
+ATOM 23 O 1 -3.025 -0.945 -0.842
+ATOM 24 O 1 -3.711 2.880 -0.762
+ATOM 25 H 1 0.305 2.369 -2.981
+ATOM 26 H 1 -1.932 3.421 -2.710
+ATOM 27 H 1 2.513 -1.220 -0.440
+ATOM 28 H 1 1.218 -0.302 -2.155
+ATOM 29 H 1 2.299 1.087 -1.531
+ATOM 30 H 1 0.493 -0.137 2.981
+ATOM 31 H 1 -0.345 1.389 2.599
+ATOM 32 H 1 2.169 1.555 2.692
+ATOM 33 H 1 1.412 2.124 1.155
+ATOM 34 H 1 4.341 1.151 1.530
+ATOM 35 H 1 3.556 1.822 -0.030
+ATOM 36 H 1 4.369 0.275 0.003
+ATOM 37 H 1 0.580 -2.741 -1.073
+ATOM 38 H 1 -1.727 -3.421 -0.703
+ATOM 39 H 1 -3.565 -1.698 -1.399
+ATOM 40 H 1 -4.369 2.204 -1.290
+TER 41 1
+END
--- /dev/null
+COMPND SINIGRIN
+AUTHOR DAVE WOODCOCK 96 10 11
+ATOM 1 C 1 -3.194 1.453 -0.615
+ATOM 2 C 1 -4.200 1.391 0.546
+ATOM 3 C 1 -3.614 0.567 1.701
+ATOM 4 C 1 -2.247 1.146 2.079
+ATOM 5 C 1 -1.362 1.173 0.828
+ATOM 6 O 1 -1.958 1.986 -0.166
+ATOM 7 O 1 -1.648 0.356 3.089
+ATOM 8 O 1 -4.466 0.605 2.829
+ATOM 9 O 1 -5.420 0.820 0.110
+ATOM 10 C 1 -3.732 2.343 -1.742
+ATOM 11 O 1 -2.786 2.441 -2.787
+ATOM 12 H 1 -1.263 0.157 0.450
+ATOM 13 S 1 0.271 1.835 1.238
+ATOM 14 C 1 1.358 0.821 0.205
+ATOM 15 N 1 2.408 1.393 -0.407
+ATOM 16 O 1 3.386 0.528 -1.148
+ATOM 17 S 1 4.564 1.406 -1.776
+ATOM 18 O 1 5.498 0.470 -2.581
+ATOM 19 O 1 5.372 2.081 -0.641
+ATOM 20 C 1 1.258 -0.708 0.267
+ATOM 21 C 1 0.769 -1.246 -1.077
+ATOM 22 C 1 0.552 -2.614 -1.258
+ATOM 23 H 1 -3.031 0.448 -1.010
+ATOM 24 H 1 -4.396 2.404 0.900
+ATOM 25 H 1 -3.489 -0.469 1.380
+ATOM 26 H 1 -2.375 2.163 2.452
+ATOM 27 H 1 -1.505 -0.657 2.741
+ATOM 28 H 1 -5.370 0.046 2.634
+ATOM 29 H 1 -5.258 -0.185 -0.252
+ATOM 30 H 1 -3.933 3.342 -1.354
+ATOM 31 H 1 -4.656 1.922 -2.140
+ATOM 32 H 1 -2.620 1.468 -3.228
+ATOM 33 H 1 0.555 -1.008 1.048
+ATOM 34 H 1 2.235 -1.142 0.494
+ATOM 35 H 1 0.591 -0.533 -1.949
+ATOM 36 H 1 0.214 -2.992 -2.221
+ATOM 37 H 1 0.718 -3.300 -0.438
+TER 38 1
+END
--- /dev/null
+COMPND NEROL
+AUTHOR DAVE WOODCOCK 96 12 20
+ATOM 1 C 1 3.275 -1.876 -0.001
+ATOM 2 C 1 3.290 -0.347 -0.003
+ATOM 3 C 1 2.099 0.401 -0.001
+ATOM 4 C 1 2.235 1.941 -0.001
+ATOM 5 C 1 0.744 -0.317 0.002
+ATOM 6 C 1 -0.464 0.627 0.000
+ATOM 7 C 1 -1.781 -0.150 0.000
+ATOM 8 C 1 -3.014 0.522 0.000
+ATOM 9 C 1 -4.311 -0.290 0.000
+ATOM 10 C 1 -3.067 2.051 0.000
+ATOM 11 O 1 4.600 -2.373 0.001
+ATOM 12 H 1 2.763 -2.241 -0.892
+ATOM 13 H 1 2.757 -2.241 0.886
+ATOM 14 H 1 4.235 0.178 -0.010
+ATOM 15 H 1 2.817 2.219 -0.882
+ATOM 16 H 1 2.820 2.219 0.879
+ATOM 17 H 1 1.237 2.381 0.000
+ATOM 18 H 1 0.683 -0.947 0.890
+ATOM 19 H 1 0.682 -0.953 -0.881
+ATOM 20 H 1 -0.419 1.275 -0.875
+ATOM 21 H 1 -0.420 1.278 0.872
+ATOM 22 H 1 -1.758 -1.230 0.001
+ATOM 23 H 1 -4.341 -0.921 0.889
+ATOM 24 H 1 -4.341 -0.921 -0.889
+ATOM 25 H 1 -5.171 0.380 0.000
+ATOM 26 H 1 -2.562 2.432 -0.888
+ATOM 27 H 1 -2.564 2.432 0.889
+ATOM 28 H 1 -4.104 2.386 -0.001
+ATOM 29 H 1 5.094 -2.106 0.924
+TER 30 1
+END
--- /dev/null
+COMPND Norethindrone
+AUTHOR DAVE WOODCOCK 97 07 26
+ATOM 1 C 1 -1.594 -1.694 0.363
+ATOM 2 C 1 -2.334 -1.616 1.720
+ATOM 3 C 1 -3.753 -2.210 1.582
+ATOM 4 C 1 -4.473 -1.398 0.442
+ATOM 5 C 1 -3.796 -0.974 -0.653
+ATOM 6 C 1 -2.468 -1.131 -0.767
+ATOM 7 C 1 -1.821 -0.885 -2.125
+ATOM 8 C 1 -0.531 -0.093 -1.939
+ATOM 9 C 1 0.399 -0.853 -0.963
+ATOM 10 C 1 -0.271 -0.894 0.440
+ATOM 11 C 1 0.676 -1.490 1.526
+ATOM 12 C 1 2.043 -0.761 1.534
+ATOM 13 C 1 2.684 -0.790 0.159
+ATOM 14 C 1 1.740 -0.095 -0.797
+ATOM 15 C 1 3.910 0.103 -0.005
+ATOM 16 C 1 4.010 0.362 -1.558
+ATOM 17 C 1 2.562 0.131 -2.096
+ATOM 18 C 1 3.068 -2.198 -0.259
+ATOM 19 O 1 -5.767 -1.223 0.533
+ATOM 20 C 1 3.753 1.463 0.709
+ATOM 21 C 1 3.587 2.510 1.272
+ATOM 22 O 1 5.172 -0.566 0.483
+ATOM 23 H 1 -1.375 -2.735 0.125
+ATOM 24 H 1 -2.410 -0.575 2.038
+ATOM 25 H 1 -1.782 -2.185 2.467
+ATOM 26 H 1 -4.293 -2.189 2.532
+ATOM 27 H 1 -3.638 -3.244 1.257
+ATOM 28 H 1 -4.345 -0.525 -1.483
+ATOM 29 H 1 -1.630 -1.826 -2.643
+ATOM 30 H 1 -2.490 -0.266 -2.719
+ATOM 31 H 1 -0.737 0.925 -1.603
+ATOM 32 H 1 -0.059 -0.066 -2.920
+ATOM 33 H 1 0.554 -1.860 -1.349
+ATOM 34 H 1 -0.511 0.132 0.720
+ATOM 35 H 1 0.246 -1.457 2.527
+ATOM 36 H 1 0.848 -2.529 1.265
+ATOM 37 H 1 2.720 -1.274 2.216
+ATOM 38 H 1 1.917 0.270 1.863
+ATOM 39 H 1 1.524 0.872 -0.345
+ATOM 40 H 1 4.708 -0.317 -2.054
+ATOM 41 H 1 4.322 1.391 -1.732
+ATOM 42 H 1 2.564 -0.841 -2.578
+ATOM 43 H 1 2.174 0.891 -2.782
+ATOM 44 H 1 2.190 -2.833 -0.301
+ATOM 45 H 1 3.761 -2.594 0.480
+ATOM 46 H 1 3.550 -2.197 -1.232
+ATOM 47 H 1 3.459 3.468 1.774
+ATOM 48 H 1 5.259 -0.805 1.503
+TER 49 1
--- /dev/null
+COMPND OCTANE
+AUTHOR DAVE WOODCOCK 96 01 05
+ATOM 1 C 1 -4.397 0.370 -0.255 1.00 0.00
+ATOM 2 C 1 -3.113 -0.447 -0.421 1.00 0.00
+ATOM 3 C 1 -1.896 0.386 -0.007 1.00 0.00
+ATOM 4 C 1 -0.611 -0.426 -0.198 1.00 0.00
+ATOM 5 C 1 0.608 0.405 0.216 1.00 0.00
+ATOM 6 C 1 1.892 -0.400 0.001 1.00 0.00
+ATOM 7 C 1 3.113 0.429 0.414 1.00 0.00
+ATOM 8 C 1 4.397 -0.374 0.199 1.00 0.00
+ATOM 9 H 1 -4.502 0.681 0.785 1.00 0.00
+ATOM 10 H 1 -5.254 -0.243 -0.537 1.00 0.00
+ATOM 11 H 1 -4.357 1.252 -0.895 1.00 0.00
+ATOM 12 H 1 -3.009 -0.741 -1.467 1.00 0.00
+ATOM 13 H 1 -3.172 -1.337 0.206 1.00 0.00
+ATOM 14 H 1 -1.992 0.668 1.044 1.00 0.00
+ATOM 15 H 1 -1.849 1.286 -0.621 1.00 0.00
+ATOM 16 H 1 -0.515 -0.707 -1.248 1.00 0.00
+ATOM 17 H 1 -0.659 -1.326 0.417 1.00 0.00
+ATOM 18 H 1 0.520 0.671 1.270 1.00 0.00
+ATOM 19 H 1 0.645 1.314 -0.386 1.00 0.00
+ATOM 20 H 1 1.979 -0.666 -1.054 1.00 0.00
+ATOM 21 H 1 1.855 -1.309 0.604 1.00 0.00
+ATOM 22 H 1 3.030 0.696 1.467 1.00 0.00
+ATOM 23 H 1 3.155 1.337 -0.188 1.00 0.00
+ATOM 24 H 1 4.493 -0.641 -0.854 1.00 0.00
+ATOM 25 H 1 4.368 -1.282 0.801 1.00 0.00
+ATOM 26 H 1 5.254 0.230 0.498 1.00 0.00
+TER 27 1
+END
--- /dev/null
+COMPND PENTANE
+AUTHOR DAVE WOODCOCK 95 12 18
+ATOM 1 C 1 2.484 -0.389 0.322 1.00 0.00
+ATOM 2 C 1 1.261 0.350 -0.243 1.00 0.00
+ATOM 3 C 1 -0.027 -0.348 0.199 1.00 0.00
+ATOM 4 C 1 -1.249 0.421 -0.326 1.00 0.00
+ATOM 5 C 1 -2.536 -0.311 0.047 1.00 0.00
+ATOM 6 H 1 2.471 -1.420 -0.033 1.00 0.00
+ATOM 7 H 1 2.443 -0.371 1.412 1.00 0.00
+ATOM 8 H 1 3.393 0.112 -0.016 1.00 0.00
+ATOM 9 H 1 1.324 0.350 -1.332 1.00 0.00
+ATOM 10 H 1 1.271 1.378 0.122 1.00 0.00
+ATOM 11 H 1 -0.074 -0.384 1.288 1.00 0.00
+ATOM 12 H 1 -0.048 -1.362 -0.205 1.00 0.00
+ATOM 13 H 1 -1.183 0.500 -1.412 1.00 0.00
+ATOM 14 H 1 -1.259 1.420 0.112 1.00 0.00
+ATOM 15 H 1 -2.608 -0.407 1.130 1.00 0.00
+ATOM 16 H 1 -2.540 -1.303 -0.404 1.00 0.00
+ATOM 17 H 1 -3.393 0.254 -0.321 1.00 0.00
+TER 18 1
+END
--- /dev/null
+COMPND Piperine
+AUTHOR DAVE WOODCOCK 97 10 28
+ATOM 1 C 1 -4.603 -1.688 0.777
+ATOM 2 C 1 -3.225 -1.468 0.876
+ATOM 3 C 1 -2.651 -0.365 0.203
+ATOM 4 C 1 -3.497 0.506 -0.541
+ATOM 5 C 1 -4.880 0.263 -0.631
+ATOM 6 C 1 -5.413 -0.841 0.036
+ATOM 7 O 1 -6.747 -1.261 0.094
+ATOM 8 C 1 -6.709 -2.420 0.937
+ATOM 9 O 1 -5.366 -2.707 1.354
+ATOM 10 C 1 -1.258 -0.172 0.317
+ATOM 11 C 1 -0.531 0.773 -0.435
+ATOM 12 C 1 0.850 0.926 -0.242
+ATOM 13 C 1 1.582 1.845 -1.017
+ATOM 14 C 1 2.962 2.047 -0.845
+ATOM 15 O 1 3.657 1.304 0.073
+ATOM 16 N 1 3.657 3.047 -1.625
+ATOM 17 C 1 3.262 4.452 -1.275
+ATOM 18 C 1 3.860 5.430 -2.325
+ATOM 19 C 1 5.390 5.265 -2.442
+ATOM 20 C 1 5.681 3.803 -2.882
+ATOM 21 C 1 5.108 2.784 -1.844
+ATOM 22 H 1 -2.619 -2.146 1.458
+ATOM 23 H 1 -3.100 1.387 -1.021
+ATOM 24 H 1 -5.519 0.926 -1.192
+ATOM 25 H 1 -7.105 -3.276 0.389
+ATOM 26 H 1 -7.327 -2.242 1.818
+ATOM 27 H 1 -0.699 -0.805 0.993
+ATOM 28 H 1 -0.987 1.381 -1.204
+ATOM 29 H 1 1.390 0.353 0.499
+ATOM 30 H 1 1.086 2.442 -1.769
+ATOM 31 H 1 3.714 4.674 -0.302
+ATOM 32 H 1 2.168 4.534 -1.290
+ATOM 33 H 1 3.644 6.447 -1.994
+ATOM 34 H 1 3.395 5.262 -3.298
+ATOM 35 H 1 5.811 5.398 -1.445
+ATOM 36 H 1 5.827 5.997 -3.127
+ATOM 37 H 1 6.763 3.669 -2.935
+ATOM 38 H 1 5.229 3.624 -3.861
+ATOM 39 H 1 5.619 2.941 -0.891
+ATOM 40 H 1 5.249 1.758 -2.200
+TER 41 1
+END
\ No newline at end of file
--- /dev/null
+COMPND PROPANE
+AUTHOR DAVE WOODCOCK 95 12 18
+ATOM 1 C 1 1.241 0.444 0.349 1.00 0.00
+ATOM 2 C 1 -0.011 -0.441 0.333 1.00 0.00
+ATOM 3 C 1 -1.176 0.296 -0.332 1.00 0.00
+ATOM 4 H 1 1.516 0.699 -0.675 1.00 0.00
+ATOM 5 H 1 2.058 -0.099 0.827 1.00 0.00
+ATOM 6 H 1 1.035 1.354 0.913 1.00 0.00
+ATOM 7 H 1 -0.283 -0.691 1.359 1.00 0.00
+ATOM 8 H 1 0.204 -1.354 -0.225 1.00 0.00
+ATOM 9 H 1 -0.914 0.551 -1.359 1.00 0.00
+ATOM 10 H 1 -1.396 1.211 0.219 1.00 0.00
+ATOM 11 H 1 -2.058 -0.345 -0.332 1.00 0.00
+TER 12 1
+END
--- /dev/null
+COMPND PYRIDOXAL, VITAMIN B6
+AUTHOR DAVE WOODCOCK 97 08 13
+ATOM 1 C 1 -1.057 -0.975 -0.516
+ATOM 2 C 1 -1.050 0.386 -0.392
+ATOM 3 C 1 0.103 1.044 -0.177
+ATOM 4 C 1 1.259 0.336 -0.094
+ATOM 5 C 1 1.224 -1.016 -0.244
+ATOM 6 N 1 0.096 -1.616 -0.438
+ATOM 7 C 1 0.164 2.365 -0.038
+ATOM 8 O 1 1.333 2.917 0.193
+ATOM 9 C 1 -2.426 1.134 -0.482
+ATOM 10 O 1 -2.902 1.495 0.840
+ATOM 11 O 1 2.533 1.039 0.137
+ATOM 12 C 1 2.541 -1.789 -0.182
+ATOM 13 H 1 -1.998 -1.512 -0.677
+ATOM 14 H 1 -0.698 3.029 -0.088
+ATOM 15 H 1 -3.199 0.485 -0.888
+ATOM 16 H 1 -2.386 2.043 -1.081
+ATOM 17 H 1 -2.154 2.076 1.288
+ATOM 18 H 1 2.694 1.081 1.173
+ATOM 19 H 1 3.005 -1.628 0.791
+ATOM 20 H 1 3.207 -1.430 -0.967
+ATOM 21 H 1 2.335 -2.850 -0.325
+TER 22 1
+END
--- /dev/null
+COMPND QUININE
+AUTHOR DAVE WOODCOCK 95 11 02
+ATOM 1 C 1 -3.080 -1.899 0.133 1.00 0.00
+ATOM 2 C 1 -2.208 -0.876 -0.337 1.00 0.00
+ATOM 3 C 1 -2.543 0.466 -0.048 1.00 0.00
+ATOM 4 C 1 -3.745 0.777 0.615 1.00 0.00
+ATOM 5 C 1 -4.618 -0.245 1.033 1.00 0.00
+ATOM 6 C 1 -4.275 -1.585 0.808 1.00 0.00
+ATOM 7 O 1 -4.122 2.122 0.826 1.00 0.00
+ATOM 8 C 1 -1.052 -1.254 -1.082 1.00 0.00
+ATOM 9 C 1 -0.856 -2.634 -1.300 1.00 0.00
+ATOM 10 C 1 -1.709 -3.594 -0.743 1.00 0.00
+ATOM 11 N 1 -2.801 -3.200 -0.072 1.00 0.00
+ATOM 12 C 1 -0.209 -0.308 -1.981 1.00 0.00
+ATOM 13 C 1 1.057 0.340 -1.355 1.00 0.00
+ATOM 14 O 1 -1.026 0.697 -2.556 1.00 0.00
+ATOM 15 C 1 2.184 0.473 -2.405 1.00 0.00
+ATOM 16 N 1 1.614 -0.307 -0.133 1.00 0.00
+ATOM 17 C 1 2.571 0.651 0.485 1.00 0.00
+ATOM 18 C 1 3.713 1.021 -0.485 1.00 0.00
+ATOM 19 C 1 3.545 0.185 -1.756 1.00 0.00
+ATOM 20 C 1 2.355 -1.553 -0.445 1.00 0.00
+ATOM 21 C 1 3.574 -1.285 -1.332 1.00 0.00
+ATOM 22 C 1 3.748 2.514 -0.840 1.00 0.00
+ATOM 23 C 1 4.814 3.033 -1.590 1.00 0.00
+ATOM 24 C 1 -5.435 2.165 1.550 1.00 0.00
+ATOM 25 H 1 -5.727 3.203 1.712 1.00 0.00
+ATOM 26 H 1 -1.868 1.271 -0.339 1.00 0.00
+ATOM 27 H 1 -5.556 0.007 1.527 1.00 0.00
+ATOM 28 H 1 -4.947 -2.381 1.129 1.00 0.00
+ATOM 29 H 1 -0.024 -2.976 -1.916 1.00 0.00
+ATOM 30 H 1 -1.484 -4.655 -0.857 1.00 0.00
+ATOM 31 H 1 0.151 -0.858 -2.851 1.00 0.00
+ATOM 32 H 1 0.808 1.332 -0.979 1.00 0.00
+ATOM 33 H 1 -1.474 1.263 -1.793 1.00 0.00
+ATOM 34 H 1 2.186 1.485 -2.808 1.00 0.00
+ATOM 35 H 1 2.014 -0.240 -3.212 1.00 0.00
+ATOM 36 H 1 3.010 0.203 1.377 1.00 0.00
+ATOM 37 H 1 2.045 1.565 0.759 1.00 0.00
+ATOM 38 H 1 4.673 0.803 -0.016 1.00 0.00
+ATOM 39 H 1 4.331 0.272 -2.506 1.00 0.00
+ATOM 40 H 1 1.697 -2.246 -0.970 1.00 0.00
+ATOM 41 H 1 2.701 -2.012 0.481 1.00 0.00
+ATOM 42 H 1 4.252 -0.603 -0.819 1.00 0.00
+ATOM 43 H 1 4.088 -2.224 -1.536 1.00 0.00
+ATOM 44 H 1 2.944 3.172 -0.510 1.00 0.00
+ATOM 45 H 1 4.837 4.094 -1.842 1.00 0.00
+ATOM 46 H 1 5.618 2.377 -1.921 1.00 0.00
+ATOM 47 H 1 -5.337 1.660 2.511 1.00 0.00
+ATOM 48 H 1 -6.196 1.663 0.952 1.00 0.00
+TER 50 1
+END
--- /dev/null
+COMPND STRYCHNINE
+AUTHOR DAVE WOODCOCK 97 03 17
+ATOM 1 C 1 -1.533 0.399 0.458
+ATOM 2 C 1 -0.808 -0.182 1.500
+ATOM 3 C 1 -1.463 -0.793 2.582
+ATOM 4 C 1 -2.869 -0.791 2.619
+ATOM 5 C 1 -3.605 -0.212 1.565
+ATOM 6 C 1 -2.942 0.378 0.472
+ATOM 7 C 1 0.640 -0.437 1.085
+ATOM 8 N 1 -0.711 0.708 -0.561
+ATOM 9 C 1 -0.949 1.596 -1.557
+ATOM 10 O 1 -2.133 2.285 -1.623
+ATOM 11 C 1 0.649 0.270 -0.292
+ATOM 12 C 1 0.213 2.126 -2.433
+ATOM 13 C 1 1.634 1.872 -1.881
+ATOM 14 H 1 0.933 -0.424 -1.080
+ATOM 15 C 1 1.521 1.522 -0.393
+ATOM 16 H 1 2.212 2.791 -1.992
+ATOM 17 O 1 2.246 0.843 -2.652
+ATOM 18 C 1 3.632 0.672 -2.408
+ATOM 19 C 1 3.863 -0.325 -1.272
+ATOM 20 C 1 3.502 -0.009 0.045
+ATOM 21 C 1 3.781 -0.997 1.191
+ATOM 22 C 1 2.829 1.329 0.367
+ATOM 23 H 1 1.002 2.357 0.081
+ATOM 24 H 1 3.507 2.160 0.172
+ATOM 25 C 1 2.432 1.320 1.837
+ATOM 26 C 1 1.703 0.007 2.124
+ATOM 27 C 1 0.879 -1.949 0.914
+ATOM 28 C 1 1.850 -2.311 2.023
+ATOM 29 N 1 2.679 -1.104 2.185
+ATOM 30 H 1 -0.900 -1.316 3.340
+ATOM 31 H 1 -3.387 -1.276 3.433
+ATOM 32 H 1 -4.684 -0.260 1.575
+ATOM 33 H 1 -3.516 0.712 -0.378
+ATOM 34 H 1 0.079 3.203 -2.529
+ATOM 35 H 1 0.120 1.700 -3.433
+ATOM 36 H 1 4.114 1.622 -2.176
+ATOM 37 H 1 4.095 0.278 -3.313
+ATOM 38 H 1 4.333 -1.274 -1.484
+ATOM 39 H 1 4.684 -0.667 1.705
+ATOM 40 H 1 4.017 -1.974 0.771
+ATOM 41 H 1 1.786 2.165 2.074
+ATOM 42 H 1 3.319 1.399 2.467
+ATOM 43 H 1 1.232 0.084 3.104
+ATOM 44 H 1 1.356 -2.190 -0.036
+ATOM 45 H 1 -0.035 -2.539 0.978
+ATOM 46 H 1 2.429 -3.203 1.787
+ATOM 47 H 1 1.308 -2.520 2.946
+TER 48 1
+END
--- /dev/null
+COMPND STYRENE
+AUTHOR DAVE WOODCOCK 96 07 05
+ATOM 1 C 1 1.195 0.373 -0.084 1.00 0.00
+ATOM 2 C 1 1.241 1.771 -0.210 1.00 0.00
+ATOM 3 C 1 0.052 2.516 -0.242 1.00 0.00
+ATOM 4 C 1 -1.182 1.856 -0.149 1.00 0.00
+ATOM 5 C 1 -1.231 0.457 -0.022 1.00 0.00
+ATOM 6 C 1 -0.042 -0.301 0.012 1.00 0.00
+ATOM 7 C 1 -0.016 -1.708 0.139 1.00 0.00
+ATOM 8 C 1 -1.157 -2.523 0.242 1.00 0.00
+ATOM 9 H 1 2.121 -0.184 -0.062 1.00 0.00
+ATOM 10 H 1 2.194 2.275 -0.283 1.00 0.00
+ATOM 11 H 1 0.086 3.591 -0.339 1.00 0.00
+ATOM 12 H 1 -2.099 2.426 -0.175 1.00 0.00
+ATOM 13 H 1 -2.194 -0.020 0.050 1.00 0.00
+ATOM 14 H 1 0.946 -2.202 0.160 1.00 0.00
+ATOM 15 H 1 -1.031 -3.591 0.337 1.00 0.00
+ATOM 16 H 1 -2.153 -2.112 0.229 1.00 0.00
+TER 17 1
+END
--- /dev/null
+COMPND SUCROSE
+AUTHOR DAVE WOODCOCK 96 10 15
+ATOM 1 C 1 -1.757 1.179 0.017
+ATOM 2 C 1 -2.934 1.259 0.995
+ATOM 3 C 1 -2.689 0.344 2.205
+ATOM 4 C 1 -1.373 0.737 2.882
+ATOM 5 C 1 -0.218 0.668 1.879
+ATOM 6 O 1 -0.485 1.553 0.704
+ATOM 7 H 1 0.663 1.023 2.398
+ATOM 8 O 1 -0.070 -0.757 1.449
+ATOM 9 C 1 1.268 -1.259 0.961
+ATOM 10 C 1 1.080 -1.839 -0.458
+ATOM 11 C 1 2.471 -0.289 0.991
+ATOM 12 O 1 1.716 -2.382 1.846
+ATOM 13 C 1 3.195 -2.544 1.624
+ATOM 14 C 1 3.694 -1.234 0.957
+ATOM 15 H 1 -1.668 0.153 -0.335
+ATOM 16 H 1 -3.033 2.285 1.347
+ATOM 17 H 1 -2.619 -0.690 1.870
+ATOM 18 H 1 -1.452 1.757 3.255
+ATOM 19 H 1 0.580 -1.102 -1.086
+ATOM 20 H 1 2.039 -2.099 -0.902
+ATOM 21 H 1 2.456 0.400 0.146
+ATOM 22 H 1 3.374 -3.389 0.958
+ATOM 23 H 1 4.532 -0.796 1.500
+ATOM 24 C 1 3.862 -2.819 2.989
+ATOM 25 O 1 5.311 -3.228 2.781
+ATOM 26 O 1 4.102 -1.521 -0.458
+ATOM 27 O 1 2.579 0.469 2.282
+ATOM 28 O 1 0.242 -3.076 -0.372
+ATOM 29 C 1 -1.998 2.070 -1.194
+ATOM 30 O 1 -0.904 1.923 -2.173
+ATOM 31 O 1 -4.207 0.882 0.314
+ATOM 32 O 1 -3.816 0.466 3.183
+ATOM 33 O 1 -1.096 -0.190 4.027
+ATOM 34 H 1 3.321 -3.626 3.486
+ATOM 35 H 1 3.807 -1.926 3.611
+ATOM 36 H 1 5.879 -2.443 2.375
+ATOM 37 H 1 4.441 -0.641 -0.920
+ATOM 38 H 1 2.511 -0.188 3.097
+ATOM 39 H 1 -0.685 -2.836 0.060
+ATOM 40 H 1 -1.962 3.102 -0.851
+ATOM 41 H 1 -2.964 1.864 -1.657
+ATOM 42 H 1 -1.138 2.578 -2.959
+ATOM 43 H 1 -4.159 -0.104 -0.041
+ATOM 44 H 1 -4.710 0.189 2.707
+ATOM 45 H 1 -0.979 -1.176 3.684
+TER 46 1
+END
--- /dev/null
+COMPND TESTOSTERONE
+AUTHOR DAVE WOODCOCK 97 08 06
+ATOM 1 C 1 -1.694 0.623 -0.129
+ATOM 2 C 1 -2.422 1.241 -1.367
+ATOM 3 C 1 -3.967 1.285 -1.174
+ATOM 4 C 1 -4.400 -0.211 -0.803
+ATOM 5 C 1 -3.591 -1.066 -0.107
+ATOM 6 C 1 -2.336 -0.714 0.242
+ATOM 7 C 1 -1.570 -1.599 1.216
+ATOM 8 C 1 -0.153 -1.802 0.721
+ATOM 9 C 1 0.538 -0.468 0.552
+ATOM 10 C 1 -0.200 0.372 -0.512
+ATOM 11 C 1 0.528 1.686 -0.918
+ATOM 12 C 1 2.004 1.407 -1.294
+ATOM 13 C 1 2.699 0.676 -0.125
+ATOM 14 C 1 1.983 -0.638 0.108
+ATOM 15 C 1 4.116 0.144 -0.488
+ATOM 16 C 1 4.351 -0.991 0.553
+ATOM 17 C 1 2.926 -1.387 1.034
+ATOM 18 C 1 -1.836 1.597 1.079
+ATOM 19 C 1 2.800 1.586 1.130
+ATOM 20 O 1 -5.611 -0.584 -1.156
+ATOM 21 O 1 5.194 1.214 -0.436
+ATOM 22 H 1 -2.185 0.675 -2.269
+ATOM 23 H 1 -2.074 2.265 -1.491
+ATOM 24 H 1 -4.475 1.695 -2.053
+ATOM 25 H 1 -4.166 1.941 -0.327
+ATOM 26 H 1 -3.960 -2.056 0.175
+ATOM 27 H 1 -1.662 -1.308 2.269
+ATOM 28 H 1 -1.972 -2.585 1.011
+ATOM 29 H 1 -0.145 -2.408 -0.187
+ATOM 30 H 1 0.345 -2.332 1.528
+ATOM 31 H 1 0.527 0.034 1.515
+ATOM 32 H 1 -0.210 -0.251 -1.405
+ATOM 33 H 1 0.033 2.194 -1.746
+ATOM 34 H 1 0.540 2.348 -0.058
+ATOM 35 H 1 2.508 2.364 -1.426
+ATOM 36 H 1 2.069 0.827 -2.216
+ATOM 37 H 1 1.974 -1.178 -0.838
+ATOM 38 H 1 4.083 -0.295 -1.487
+ATOM 39 H 1 4.911 -0.596 1.401
+ATOM 40 H 1 4.878 -1.845 0.122
+ATOM 41 H 1 2.754 -2.448 0.859
+ATOM 42 H 1 2.762 -1.128 2.081
+ATOM 43 H 1 -2.874 1.668 1.403
+ATOM 44 H 1 -1.502 2.585 0.767
+ATOM 45 H 1 -1.231 1.265 1.922
+ATOM 46 H 1 1.824 1.847 1.534
+ATOM 47 H 1 3.322 2.497 0.836
+ATOM 48 H 1 3.380 1.091 1.907
+ATOM 49 H 1 5.388 1.514 0.551
+TER 50 1
+END
--- /dev/null
+COMPND THIAMIN CATION, VITAMIN B1
+AUTHOR DAVE WOODCOCK 97 08 06
+ATOM 1 C 1 -2.282 -1.745 -1.009
+ATOM 2 C 1 -1.930 -0.705 -0.131
+ATOM 3 C 1 -2.871 0.333 0.072
+ATOM 4 N 1 -4.082 0.243 -0.522
+ATOM 5 C 1 -4.417 -0.817 -1.284
+ATOM 6 N 1 -3.516 -1.784 -1.551
+ATOM 7 C 1 -5.837 -0.923 -1.849
+ATOM 8 N 1 -2.553 1.511 0.872
+ATOM 9 C 1 -0.616 -0.794 0.634
+ATOM 10 N 1 0.443 0.160 0.303
+ATOM 11 C 1 1.588 0.205 0.935
+ATOM 12 C 1 2.536 1.106 0.375
+ATOM 13 S 1 1.835 2.031 -0.997
+ATOM 14 C 1 0.350 0.982 -0.770
+ATOM 15 C 1 1.942 -0.673 2.157
+ATOM 16 C 1 3.982 1.223 0.821
+ATOM 17 C 1 4.910 1.609 -0.347
+ATOM 18 O 1 6.257 1.588 0.073
+ATOM 19 H 1 -1.599 -2.557 -1.212
+ATOM 20 H 1 -4.812 1.025 -0.370
+ATOM 21 H 1 -3.785 -2.614 -2.189
+ATOM 22 H 1 -5.908 -0.329 -2.760
+ATOM 23 H 1 -6.551 -0.549 -1.115
+ATOM 24 H 1 -6.073 -1.963 -2.078
+ATOM 25 H 1 -2.012 2.231 0.258
+ATOM 26 H 1 -1.966 1.257 1.754
+ATOM 27 H 1 -3.462 1.973 1.257
+ATOM 28 H 1 -0.164 -1.783 0.539
+ATOM 29 H 1 -0.805 -0.652 1.696
+ATOM 30 H 1 -0.515 1.001 -1.421
+ATOM 31 H 1 2.283 -1.643 1.789
+ATOM 32 H 1 1.038 -0.774 2.760
+ATOM 33 H 1 2.744 -0.203 2.730
+ATOM 34 H 1 4.337 0.278 1.231
+ATOM 35 H 1 4.072 1.973 1.606
+ATOM 36 H 1 4.660 2.614 -0.691
+ATOM 37 H 1 4.775 0.898 -1.163
+ATOM 38 H 1 6.551 0.579 0.327
+TER 39 1
+END
--- /dev/null
+COMPND 2,4,6-TRINITROTOLUENE
+AUTHOR DAVE WOODCOCK 96 07 05
+ATOM 1 C 1 1.183 -0.757 -0.174 1.00 0.00
+ATOM 2 C 1 1.212 0.643 -0.175 1.00 0.00
+ATOM 3 C 1 0.015 1.368 -0.204 1.00 0.00
+ATOM 4 C 1 -1.211 0.693 -0.232 1.00 0.00
+ATOM 5 C 1 -1.240 -0.706 -0.231 1.00 0.00
+ATOM 6 C 1 -0.043 -1.431 -0.201 1.00 0.00
+ATOM 7 N 1 -0.071 -2.771 -0.200 1.00 0.00
+ATOM 8 O 1 1.126 -3.496 -0.171 1.00 0.00
+ATOM 9 O 1 -1.297 -3.446 -0.228 1.00 0.00
+ATOM 10 N 1 2.386 1.289 -0.148 1.00 0.00
+ATOM 11 O 1 2.415 2.689 -0.150 1.00 0.00
+ATOM 12 O 1 3.583 0.564 -0.119 1.00 0.00
+ATOM 13 N 1 -2.357 1.387 -0.260 1.00 0.00
+ATOM 14 O 1 -3.583 0.713 -0.288 1.00 0.00
+ATOM 15 O 1 -2.328 2.787 -0.262 1.00 0.00
+ATOM 16 C 1 0.047 2.894 -0.206 1.00 0.00
+ATOM 17 H 1 2.107 -1.316 -0.150 1.00 0.00
+ATOM 18 H 1 -2.187 -1.227 -0.252 1.00 0.00
+ATOM 19 H 1 0.995 3.237 -0.619 1.00 0.00
+ATOM 20 H 1 -0.059 3.260 0.816 1.00 0.00
+ATOM 21 H 1 -0.773 3.273 -0.816 1.00 0.00
+TER 22 1
+END
--- /dev/null
+COMPND c10h11no2
+AUTHOR Created by Dave Woodcock at Okanagan University College
+AUTHOR email:woodcock@okanagan.bc.ca
+AUTHOR GENERATED BY BABEL 1.6
+ATOM 1 C UNK 1 0.000 0.000 0.000 1.00 0.00
+ATOM 2 C UNK 1 1.406 0.000 0.000 1.00 0.00
+ATOM 3 C UNK 1 2.129 1.211 0.000 1.00 0.00
+ATOM 4 C UNK 1 1.414 2.425 0.000 1.00 0.00
+ATOM 5 C UNK 1 0.007 2.425 0.000 1.00 0.00
+ATOM 6 C UNK 1 -0.712 1.215 0.000 1.00 0.00
+ATOM 7 O UNK 1 -2.136 1.303 0.000 1.00 0.00
+ATOM 8 C UNK 1 -2.848 0.078 0.000 1.00 0.00
+ATOM 9 C UNK 1 3.543 1.136 0.000 1.00 0.00
+ATOM 10 C UNK 1 4.403 2.250 0.000 1.00 0.00
+ATOM 11 N UNK 1 5.740 2.075 0.000 1.00 0.00
+ATOM 12 C UNK 1 6.578 3.126 0.000 1.00 0.00
+ATOM 13 O UNK 1 7.928 2.916 0.000 1.00 0.00
+ATOM 14 H UNK 1 -0.518 -0.945 0.000 1.00 0.00
+ATOM 15 H UNK 1 1.937 -0.942 0.000 1.00 0.00
+ATOM 16 H UNK 1 1.921 3.375 0.000 1.00 0.00
+ATOM 17 H UNK 1 -0.529 3.363 0.000 1.00 0.00
+ATOM 18 H UNK 1 -2.581 -0.527 0.867 1.00 0.00
+ATOM 19 H UNK 1 -2.581 -0.527 -0.867 1.00 0.00
+ATOM 20 H UNK 1 -3.914 0.315 0.000 1.00 0.00
+ATOM 21 H UNK 1 3.988 0.151 0.000 1.00 0.00
+ATOM 22 H UNK 1 3.978 3.241 0.000 1.00 0.00
+ATOM 23 H UNK 1 6.096 1.051 0.000 1.00 0.00
+ATOM 24 H UNK 1 6.154 4.122 0.000 1.00 0.00
+CONECT 1 2 6 14
+CONECT 2 1 3 15
+CONECT 3 2 4 9
+CONECT 4 3 5 16
+CONECT 5 4 6 17
+CONECT 6 1 5 7
+CONECT 7 6 8
+CONECT 8 7 18 19 20
+CONECT 9 3 10 21
+CONECT 10 9 11 22
+CONECT 11 10 12 23
+CONECT 12 11 13 24
+CONECT 13 12
+CONECT 14 1
+CONECT 15 2
+CONECT 16 4
+CONECT 17 5
+CONECT 18 8
+CONECT 19 8
+CONECT 20 8
+CONECT 21 9
+CONECT 22 10
+CONECT 23 11
+CONECT 24 12
+MASTER 0 0 0 0 0 0 0 0 24 0 24 0
+END
--- /dev/null
+COMPND TYRIAN PURPLE
+AUTHOR DAVE WOODCOCK 95 11 01
+ATOM 1 C 1 -2.842 -0.519 -0.133 1.00 0.00
+ATOM 2 C 1 -2.777 0.808 -0.163 1.00 0.00
+ATOM 3 C 1 -3.921 1.680 -0.135 1.00 0.00
+ATOM 4 C 1 -5.160 1.044 -0.070 1.00 0.00
+ATOM 5 C 1 -5.277 -0.381 -0.049 1.00 0.00
+ATOM 6 C 1 -4.125 -1.208 -0.079 1.00 0.00
+ATOM 7 C 1 -1.613 -1.051 -0.144 1.00 0.00
+ATOM 8 O 1 -1.280 -2.408 -0.113 1.00 0.00
+ATOM 9 C 1 -0.683 -0.007 -0.186 1.00 0.00
+ATOM 10 C 1 0.692 0.010 -0.194 1.00 0.00
+ATOM 11 N 1 -1.425 1.156 -0.200 1.00 0.00
+ATOM 12 N 1 1.434 -1.154 -0.155 1.00 0.00
+ATOM 13 C 1 1.624 1.050 -0.234 1.00 0.00
+ATOM 14 O 1 1.293 2.409 -0.269 1.00 0.00
+ATOM 15 C 1 2.853 0.519 -0.210 1.00 0.00
+ATOM 16 C 1 2.783 -0.811 -0.157 1.00 0.00
+ATOM 17 C 1 3.922 -1.682 -0.085 1.00 0.00
+ATOM 18 C 1 5.166 -1.048 -0.067 1.00 0.00
+ATOM 19 C 1 5.291 0.375 -0.141 1.00 0.00
+ATOM 20 C 1 4.138 1.201 -0.213 1.00 0.00
+ATOM 21 H 1 -3.799 2.759 -0.152 1.00 0.00
+ATOM 22 H 1 -6.274 -0.806 0.001 1.00 0.00
+ATOM 23 H 1 -4.349 -2.285 -0.050 1.00 0.00
+ATOM 24 H 1 -1.115 2.205 -0.216 1.00 0.00
+ATOM 25 H 1 1.121 -2.199 -0.096 1.00 0.00
+ATOM 26 H 1 3.797 -2.759 -0.029 1.00 0.00
+ATOM 27 H 1 6.288 0.802 -0.126 1.00 0.00
+ATOM 28 H 1 4.362 2.277 -0.250 1.00 0.00
+ATOM 29 BR 1 -6.747 2.106 0.006 1.00 0.00
+ATOM 30 BR 1 6.747 -2.112 0.082 1.00 0.00
+TER 31 1
+END
--- /dev/null
+COMPND VANILLIN
+AUTHOR DAVE WOODCOCK 95 11 01
+ATOM 1 C 1 1.032 0.073 -0.001 1.00 0.00
+ATOM 2 C 1 1.032 1.473 -0.001 1.00 0.00
+ATOM 3 C 1 -0.181 2.173 -0.003 1.00 0.00
+ATOM 4 C 1 -1.393 1.473 -0.005 1.00 0.00
+ATOM 5 C 1 -1.393 0.073 -0.005 1.00 0.00
+ATOM 6 C 1 -0.181 -0.627 -0.003 1.00 0.00
+ATOM 7 O 1 -0.181 -2.037 -0.003 1.00 0.00
+ATOM 8 C 1 1.148 -2.507 -0.001 1.00 0.00
+ATOM 9 O 1 -2.614 -0.632 -0.007 1.00 0.00
+ATOM 10 C 1 2.244 2.173 0.001 1.00 0.00
+ATOM 11 O 1 2.244 3.543 0.001 1.00 0.00
+ATOM 12 H 1 1.967 -0.467 0.000 1.00 0.00
+ATOM 13 H 1 -0.181 3.253 -0.003 1.00 0.00
+ATOM 14 H 1 -2.329 2.013 -0.006 1.00 0.00
+ATOM 15 H 1 1.661 -2.143 0.890 1.00 0.00
+ATOM 16 H 1 1.664 -2.143 -0.890 1.00 0.00
+ATOM 17 H 1 1.148 -3.597 -0.001 1.00 0.00
+ATOM 18 H 1 -3.179 -0.371 -0.890 1.00 0.00
+ATOM 19 H 1 3.179 1.633 0.002 1.00 0.00
+TER 29 1
+END
--- /dev/null
+COMPND CHLOROETHENE
+AUTHOR JENNI WOODCOCK 97 07 31
+ATOM 1 C 1 -0.958 -0.216 0.345
+ATOM 2 C 1 0.268 0.216 -0.173
+ATOM 3 Cl 1 1.570 -0.940 -0.434
+ATOM 4 H 1 -1.106 -1.259 0.585
+ATOM 5 H 1 -1.757 0.493 0.505
+ATOM 6 H 1 0.416 1.259 -0.413
+TER 7 1
+END
--- /dev/null
+COMPND VITAMIN A
+AUTHOR DAVE WOODCOCK 97 03 17
+ATOM 1 C 1 -4.322 -0.225 -0.083
+ATOM 2 C 1 -5.496 -1.028 0.032
+ATOM 3 C 1 -6.900 -0.427 0.103
+ATOM 4 C 1 -6.894 1.007 0.608
+ATOM 5 C 1 -5.886 1.795 -0.219
+ATOM 6 C 1 -4.438 1.332 0.029
+ATOM 7 C 1 -4.019 1.807 1.437
+ATOM 8 C 1 -3.629 2.059 -1.044
+ATOM 9 C 1 -5.409 -2.558 0.048
+ATOM 10 C 1 -3.108 -0.890 -0.360
+ATOM 11 C 1 -1.819 -0.374 -0.094
+ATOM 12 C 1 -0.646 -1.096 -0.404
+ATOM 13 C 1 0.579 -0.383 -0.468
+ATOM 14 C 1 1.788 -0.987 -0.861
+ATOM 15 C 1 2.994 -0.265 -0.829
+ATOM 16 C 1 4.237 -0.901 -1.024
+ATOM 17 C 1 5.406 -0.117 -1.087
+ATOM 18 C 1 -0.696 -2.628 -0.641
+ATOM 19 C 1 4.311 -2.434 -1.137
+ATOM 20 C 1 6.794 -0.746 -1.278
+ATOM 21 O 1 7.789 0.254 -1.348
+ATOM 22 H 1 -7.522 -1.026 0.767
+ATOM 23 H 1 -7.342 -0.450 -0.893
+ATOM 24 H 1 -6.641 1.037 1.667
+ATOM 25 H 1 -7.887 1.439 0.484
+ATOM 26 H 1 -5.987 2.853 0.025
+ATOM 27 H 1 -6.135 1.668 -1.274
+ATOM 28 H 1 -4.520 1.220 2.206
+ATOM 29 H 1 -4.277 2.859 1.560
+ATOM 30 H 1 -2.950 1.704 1.600
+ATOM 31 H 1 -3.901 3.112 -1.116
+ATOM 32 H 1 -3.751 1.596 -2.024
+ATOM 33 H 1 -2.555 2.106 -0.869
+ATOM 34 H 1 -4.653 -2.892 0.760
+ATOM 35 H 1 -5.152 -2.930 -0.944
+ATOM 36 H 1 -6.372 -2.973 0.342
+ATOM 37 H 1 -3.181 -1.872 -0.798
+ATOM 38 H 1 -1.717 0.575 0.399
+ATOM 39 H 1 0.592 0.669 -0.212
+ATOM 40 H 1 1.791 -2.011 -1.198
+ATOM 41 H 1 2.966 0.797 -0.625
+ATOM 42 H 1 5.328 0.958 -1.004
+ATOM 43 H 1 -0.807 -2.839 -1.705
+ATOM 44 H 1 -1.523 -3.081 -0.095
+ATOM 45 H 1 0.211 -3.112 -0.282
+ATOM 46 H 1 3.849 -2.752 -2.072
+ATOM 47 H 1 3.779 -2.888 -0.300
+ATOM 48 H 1 5.340 -2.786 -1.119
+ATOM 49 H 1 6.808 -1.319 -2.206
+ATOM 50 H 1 7.018 -1.407 -0.440
+ATOM 51 H 1 7.867 0.766 -0.400
+TER 52 1
+END
--- /dev/null
+"Planet Name","Pl. Mass","Pl. Radius","Pl. Period",\r
+"55 Cnc e","0.027","0.194","0.7365449",\r
+"CoRoT-1 b","1.03","1.49","1.5089557",\r
+"CoRoT-10 b","2.75","0.97","13.2406",\r
+"CoRoT-11 b","2.33","1.43","2.99433",\r
+"CoRoT-12 b","0.917","1.44","2.828042",\r
+"CoRoT-13 b","1.308","0.885","4.03519",\r
+"CoRoT-14 b","7.6","1.09","1.51214",\r
+"CoRoT-16 b","0.535","1.17","5.35227",\r
+"CoRoT-17 b","2.45","1.02","3.768125",\r
+"CoRoT-18 b","3.47","1.31","1.9000693",\r
+"CoRoT-19 b","1.11","1.45","3.89713",\r
+"CoRoT-2 b","3.31","1.465","1.7429964",\r
+"CoRoT-20 b","4.24","0.84","9.2",\r
+"CoRoT-21 b","2.26","1.3","2.72474",\r
+"CoRoT-23 b","2.8","1.05","3.6314",\r
+"CoRoT-3 b","21.66","1.01","4.2568",\r
+"CoRoT-4 b","0.72","1.19","9.20205",\r
+"CoRoT-5 b","0.467","1.388","4.0378962",\r
+"CoRoT-6 b","2.96","1.166","8.886593",\r
+"CoRoT-7 b","0.0151","0.15","0.853585",\r
+"CoRoT-8 b","0.22","0.57","6.21229",\r
+"CoRoT-9 b","0.84","1.05","95.2738",\r
+"GJ 1214 b","0.02","0.245","1.58040482",\r
+"GJ 436 b","0.0737","0.365","2.6438986",\r
+"HAT-P-1 b","0.524","1.217","4.4652934",\r
+"HAT-P-11 b","0.081","0.452","4.887804",\r
+"HAT-P-12 b","0.211","0.959","3.2130598",\r
+"HAT-P-13 b","0.85","1.28","2.916243",\r
+"HAT-P-14 b","2.2","1.2","4.627657",\r
+"HAT-P-15 b","1.946","1.072","10.863502",\r
+"HAT-P-16 b","4.193","1.289","2.77596",\r
+"HAT-P-17 b","0.53","1.01","10.338523",\r
+"HAT-P-18 b","0.197","0.995","5.508023",\r
+"HAT-P-19 b","0.292","1.132","4.008778",\r
+"HAT-P-2 b","8.74","0.951","5.6334729",\r
+"HAT-P-20 b","7.246","0.867","2.875317",\r
+"HAT-P-21 b","4.063","1.024","4.124461",\r
+"HAT-P-22 b","2.147","1.08","3.21222",\r
+"HAT-P-23 b","2.09","1.368","1.212884",\r
+"HAT-P-24 b","0.685","1.242","3.35524",\r
+"HAT-P-25 b","0.567","1.19","3.652836",\r
+"HAT-P-26 b","0.059","0.565","4.234516",\r
+"HAT-P-27/WASP-40 b","0.66","1.055","3.0395721",\r
+"HAT-P-28 b","0.626","1.212","3.257215",\r
+"HAT-P-29 b","0.778","1.107","5.72318",\r
+"HAT-P-3 b","0.591","0.827","2.899703",\r
+"HAT-P-30/WASP-51 b","0.711","1.34","2.810595",\r
+"HAT-P-31 b","2.171","1.07","5.005425",\r
+"HAT-P-32 b","0.941","2.037","2.150009",\r
+"HAT-P-33 b","0.763","1.827","3.474474",\r
+"HAT-P-34 b","3.328","1.107","5.452654",\r
+"HAT-P-35 b","1.054","1.332","3.646706",\r
+"HAT-P-36 b","1.832","1.264","1.327347",\r
+"HAT-P-37 b","1.169","1.178","2.797436",\r
+"HAT-P-38 b","0.267","0.825","4.640382",\r
+"HAT-P-4 b","0.68","1.27","3.0565114",\r
+"HAT-P-5 b","1.06","1.26","2.788491",\r
+"HAT-P-6 b","1.057","1.33","3.853003",\r
+"HAT-P-7 b","1.8","1.421","2.2047298",\r
+"HAT-P-8 b","1.34","1.5","3.0763402",\r
+"HAT-P-9 b","0.67","1.4","3.922814",\r
+"HD 149026 b","0.356","0.718","2.8758916",\r
+"HD 17156 b","3.191","1.095","21.2163979",\r
+"HD 189733 b","1.138","1.138","2.21857312",\r
+"HD 209458 b","0.714","1.38","3.52474859",\r
+"HD 80606 b","3.94","0.921","111.43637",\r
+"HD 97658 b","0.02","0.262","9.4957",\r
+"Kepler-10 b","0.0143","0.127","0.837495",\r
+"Kepler-10 c","0.063","0.199","45.29485",\r
+"Kepler-11 b","0.01353","0.1762","10.30375",\r
+"Kepler-11 c","0.0425","0.28175","13.02502",\r
+"Kepler-11 d","0.01919","0.3068","22.68719",\r
+"Kepler-11 e","0.02643","0.4043","31.9959",\r
+"Kepler-11 f","0.007237","0.2335","46.68876",\r
+"Kepler-11 g","0.95","0.3274","118.37774",\r
+"Kepler-12 b","0.431","1.695","4.4379637",\r
+"Kepler-14 b","8.4","1.136","6.790123",\r
+"Kepler-15 b","0.66","0.96","4.942782",\r
+"Kepler-16 (AB) b","0.333","0.7538","228.776",\r
+"Kepler-17 b","2.45","1.312","1.4857108",\r
+"Kepler-18 b","0.0217","0.179","3.504725",\r
+"Kepler-18 c","0.054","0.49","7.64159",\r
+"Kepler-18 d","0.052","0.62","14.85888",\r
+"Kepler-19 b","0.064","0.198","9.2869944",\r
+"Kepler-20 b","0.027","0.17","3.6961219",\r
+"Kepler-20 c","0.051","0.27","10.854092",\r
+"Kepler-20 d","0.06","0.25","77.61185",\r
+"Kepler-20 e","0.0097","0.078","6.098493",\r
+"Kepler-20 f","0.045","0.09","19.57706",\r
+"Kepler-21 b","0.033","0.1459","2.785755",\r
+"Kepler-22 b","0.11","0.21","289.8623",\r
+"Kepler-23 b","0.8","0.17","7.1073",\r
+"Kepler-23 c","2.7","0.29","10.7421",\r
+"Kepler-24 b","1.6","0.21","8.1453",\r
+"Kepler-24 c","1.6","0.25","12.3335",\r
+"Kepler-25 b","12.7","0.23","6.2385",\r
+"Kepler-25 c","4.16","0.4","12.7204",\r
+"Kepler-26 b","0.38","0.32","12.2829",\r
+"Kepler-26 c","0.375","0.32","17.2513",\r
+"Kepler-27 b","9.11","0.36","15.3348",\r
+"Kepler-27 c","13.8","0.44","31.3309",\r
+"Kepler-28 b","1.51","0.32","5.9123",\r
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+"KIC 10905746 b",,"0.237","9.8844",\r
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+"WASP-1 b","0.86","1.484","2.5199464",\r
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+"WASP-32 b","3.6","1.18","2.71865",\r
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+"WASP-34 b","0.59","1.22","4.3176782",\r
+"WASP-35 b","0.72","1.32","3.161575",\r
+"WASP-36 b","2.279","1.269","1.5373653",\r
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+"WASP-38 b","2.712","1.079","6.871815",\r
+"WASP-39 b","0.28","1.27","4.055259",\r
+"WASP-4 b","1.1215","1.363","1.33823187",\r
+"WASP-41 b","0.92","1.21","3.052394",\r
+"WASP-42 b","0.6","1","5",\r
+"WASP-43 b","1.78","0.93","0.813475",\r
+"WASP-44 b","0.889","1.14","2.4238039",\r
+"WASP-45 b","1.007","1.16","3.1260876",\r
+"WASP-46 b","2.101","1.31","1.43037",\r
+"WASP-47 b","1.1","1.2","4.1",\r
+"WASP-48 b","0.98","1.67","2.143634",\r
+"WASP-49 b","0.4","1.3","2.8",\r
+"WASP-5 b","1.637","1.171","1.6284246",\r
+"WASP-50 b","1.468","1.153","1.9550959",\r
+"WASP-52 b","0.5","1.3","1.7",\r
+"WASP-53 b","2.5","1.2","3.3",\r
+"WASP-54 b","0.6","1.4","3.7",\r
+"WASP-55 b","0.6","1.4","4.5",\r
+"WASP-56 b","0.6","1.2","4.6",\r
+"WASP-57 b","0.8","1.1","2.8",\r
+"WASP-58 b","1.1","1.3","5",\r
+"WASP-59 b","0.7","0.9","7.9",\r
+"WASP-6 b","0.503","1.224","3.361006",\r
+"WASP-60 b","0.5","0.9","4.3",\r
+"WASP-61 b","1.7","1.4","3.8",\r
+"WASP-62 b","0.5","1.5","4.4",\r
+"WASP-63 b","0.3","1","4.4",\r
+"WASP-64 b","1.2","0.7","1.6",\r
+"WASP-65 b","1.6","1.3","2.3",\r
+"WASP-66 b","1.9","1.5","4.1",\r
+"WASP-67 b","0.4","1.7","4.6",\r
+"WASP-68 b","0.8","0.9","5.1",\r
+"WASP-69 b","0.3","1","3.9",\r
+"WASP-7 b","0.96","1.33","4.9546416",\r
+"WASP-70 b","0.6","0.8","3.7",\r
+"WASP-8 b","2.244","1.038","8.158715",\r
+"XO-1 b","0.9","1.184","3.9415128",\r
+"XO-2 b","0.62","0.973","2.615838",\r
+"XO-3 b","11.79","1.217","3.1915239",\r
+"XO-4 b","1.72","1.34","4.1250823",\r
+"XO-5 b","1.077","1.03","4.1877537",\r
--- /dev/null
+(* Sunspot data collected by Robin McQuinn from *)
+(* http://sidc.oma.be/html/sunspot.html *)
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+
+(* Month: 1864 10 *) 34
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+(* Month: 1915 03 *) 39
+(* Month: 1915 04 *) 41
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+(* Month: 1915 07 *) 72
+(* Month: 1915 08 *) 70
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+(* Month: 1916 07 *) 54
+(* Month: 1916 08 *) 35
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+(* Month: 1917 06 *) 115
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+(* Month: 1919 09 *) 55
+(* Month: 1919 10 *) 53
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+(* Month: 1919 12 *) 35
+(* Month: 1920 01 *) 51
+(* Month: 1920 02 *) 54
+(* Month: 1920 03 *) 70
+(* Month: 1920 04 *) 15
+(* Month: 1920 05 *) 33
+(* Month: 1920 06 *) 39
+(* Month: 1920 07 *) 28
+(* Month: 1920 08 *) 19
+(* Month: 1920 09 *) 36
+(* Month: 1920 10 *) 50
+(* Month: 1920 11 *) 27
+(* Month: 1920 12 *) 30
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+(* Month: 1921 02 *) 28
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+(* Month: 1921 04 *) 32
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+(* Month: 1921 07 *) 42
+(* Month: 1921 08 *) 23
+(* Month: 1921 09 *) 18
+(* Month: 1921 10 *) 18
+(* Month: 1921 11 *) 18
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+(* Month: 1922 03 *) 55
+(* Month: 1922 04 *) 11
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+(* Month: 1923 01 *) 5
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+(* Month: 1923 05 *) 3
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+(* Month: 1923 07 *) 4
+(* Month: 1923 08 *) 1
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+(* Month: 1923 10 *) 12
+(* Month: 1923 11 *) 10
+(* Month: 1923 12 *) 3
+(* Month: 1924 01 *) 1
+(* Month: 1924 02 *) 5
+(* Month: 1924 03 *) 2
+(* Month: 1924 04 *) 11
+(* Month: 1924 05 *) 21
+(* Month: 1924 06 *) 24
+(* Month: 1924 07 *) 28
+(* Month: 1924 08 *) 19
+(* Month: 1924 09 *) 25
+(* Month: 1924 10 *) 26
+(* Month: 1924 11 *) 23
+(* Month: 1924 12 *) 17
+(* Month: 1925 01 *) 6
+(* Month: 1925 02 *) 23
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+(* Month: 1925 04 *) 32
+(* Month: 1925 05 *) 43
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+(* Month: 1925 07 *) 39
+(* Month: 1925 08 *) 38
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+(* Month: 1925 11 *) 59
+(* Month: 1925 12 *) 99
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+(* Month: 1926 02 *) 70
+(* Month: 1926 03 *) 63
+(* Month: 1926 04 *) 39
+(* Month: 1926 05 *) 64
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+(* Month: 1926 09 *) 61
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+(* Month: 1931 01 *) 15
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+(* Month: 1931 03 *) 30
+(* Month: 1931 04 *) 31
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+(* Month: 1931 06 *) 15
+(* Month: 1931 07 *) 17
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+(* Month: 1931 12 *) 18
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+(* Month: 1932 02 *) 11
+(* Month: 1932 03 *) 11
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+(* Month: 1932 05 *) 18
+(* Month: 1932 06 *) 22
+(* Month: 1932 07 *) 10
+(* Month: 1932 08 *) 7
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+(* Month: 1932 12 *) 11
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+(* Month: 1933 02 *) 22
+(* Month: 1933 03 *) 10
+(* Month: 1933 04 *) 3
+(* Month: 1933 05 *) 3
+(* Month: 1933 06 *) 5
+(* Month: 1933 07 *) 3
+(* Month: 1933 08 *) 0
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+(* Month: 1934 03 *) 4
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+(* Month: 1934 05 *) 20
+(* Month: 1934 06 *) 7
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+(* Month: 1934 12 *) 15
+(* Month: 1935 01 *) 19
+(* Month: 1935 02 *) 21
+(* Month: 1935 03 *) 23
+(* Month: 1935 04 *) 12
+(* Month: 1935 05 *) 27
+(* Month: 1935 06 *) 46
+(* Month: 1935 07 *) 34
+(* Month: 1935 08 *) 30
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+(* Month: 1938 06 *) 98
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+(* Month: 1938 12 *) 93
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+(* Month: 1939 05 *) 118
+(* Month: 1939 06 *) 101
+(* Month: 1939 07 *) 98
+(* Month: 1939 08 *) 106
+(* Month: 1939 09 *) 113
+(* Month: 1939 10 *) 88
+(* Month: 1939 11 *) 68
+(* Month: 1939 12 *) 42
+(* Month: 1940 01 *) 51
+(* Month: 1940 02 *) 59
+(* Month: 1940 03 *) 83
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+(* Month: 1940 05 *) 54
+(* Month: 1940 06 *) 84
+(* Month: 1940 07 *) 68
+(* Month: 1940 08 *) 106
+(* Month: 1940 09 *) 67
+(* Month: 1940 10 *) 55
+(* Month: 1940 11 *) 58
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+(* Month: 1941 01 *) 46
+(* Month: 1941 02 *) 45
+(* Month: 1941 03 *) 46
+(* Month: 1941 04 *) 33
+(* Month: 1941 05 *) 30
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+(* Month: 1942 05 *) 25
+(* Month: 1942 06 *) 11
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+(* Month: 1942 08 *) 20
+(* Month: 1942 09 *) 17
+(* Month: 1942 10 *) 19
+(* Month: 1942 11 *) 31
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+(* Month: 1943 04 *) 26
+(* Month: 1943 05 *) 14
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+(* Month: 1943 09 *) 10
+(* Month: 1943 10 *) 8
+(* Month: 1943 11 *) 10
+(* Month: 1943 12 *) 19
+(* Month: 1944 01 *) 4
+(* Month: 1944 02 *) 1
+(* Month: 1944 03 *) 11
+(* Month: 1944 04 *) 0
+(* Month: 1944 05 *) 3
+(* Month: 1944 06 *) 5
+(* Month: 1944 07 *) 5
+(* Month: 1944 08 *) 17
+(* Month: 1944 09 *) 14
+(* Month: 1944 10 *) 17
+(* Month: 1944 11 *) 11
+(* Month: 1944 12 *) 28
+(* Month: 1945 01 *) 19
+(* Month: 1945 02 *) 13
+(* Month: 1945 03 *) 22
+(* Month: 1945 04 *) 32
+(* Month: 1945 05 *) 31
+(* Month: 1945 06 *) 36
+(* Month: 1945 07 *) 43
+(* Month: 1945 08 *) 26
+(* Month: 1945 09 *) 35
+(* Month: 1945 10 *) 69
+(* Month: 1945 11 *) 46
+(* Month: 1945 12 *) 27
+(* Month: 1946 01 *) 48
+(* Month: 1946 02 *) 86
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+(* Month: 1946 04 *) 76
+(* Month: 1946 05 *) 85
+(* Month: 1946 06 *) 74
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+(* Month: 1948 01 *) 109
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+(* Month: 1948 05 *) 174
+(* Month: 1948 06 *) 168
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+(* Month: 1948 08 *) 158
+(* Month: 1948 09 *) 143
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+(* Month: 1948 11 *) 96
+(* Month: 1948 12 *) 138
+(* Month: 1949 01 *) 119
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+(* Month: 1949 05 *) 106
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+(* Month: 1950 06 *) 84
+(* Month: 1950 07 *) 91
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+(* Month: 1950 09 *) 51
+(* Month: 1950 10 *) 61
+(* Month: 1950 11 *) 55
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+(* Month: 1951 02 *) 60
+(* Month: 1951 03 *) 56
+(* Month: 1951 04 *) 93
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+(* Month: 1951 08 *) 61
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+(* Month: 1951 10 *) 52
+(* Month: 1951 11 *) 52
+(* Month: 1951 12 *) 46
+(* Month: 1952 01 *) 41
+(* Month: 1952 02 *) 23
+(* Month: 1952 03 *) 22
+(* Month: 1952 04 *) 29
+(* Month: 1952 05 *) 23
+(* Month: 1952 06 *) 36
+(* Month: 1952 07 *) 39
+(* Month: 1952 08 *) 55
+(* Month: 1952 09 *) 28
+(* Month: 1952 10 *) 24
+(* Month: 1952 11 *) 22
+(* Month: 1952 12 *) 34
+(* Month: 1953 01 *) 27
+(* Month: 1953 02 *) 4
+(* Month: 1953 03 *) 10
+(* Month: 1953 04 *) 28
+(* Month: 1953 05 *) 13
+(* Month: 1953 06 *) 22
+(* Month: 1953 07 *) 9
+(* Month: 1953 08 *) 24
+(* Month: 1953 09 *) 19
+(* Month: 1953 10 *) 8
+(* Month: 1953 11 *) 2
+(* Month: 1953 12 *) 3
+(* Month: 1954 01 *) 0
+(* Month: 1954 02 *) 1
+(* Month: 1954 03 *) 11
+(* Month: 1954 04 *) 2
+(* Month: 1954 05 *) 1
+(* Month: 1954 06 *) 0
+(* Month: 1954 07 *) 5
+(* Month: 1954 08 *) 8
+(* Month: 1954 09 *) 2
+(* Month: 1954 10 *) 7
+(* Month: 1954 11 *) 9
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+(* Month: 1955 01 *) 23
+(* Month: 1955 02 *) 21
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+(* Month: 1955 06 *) 32
+(* Month: 1955 07 *) 27
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+(* Month: 1955 09 *) 43
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+(* Month: 1955 11 *) 89
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+(* Month: 1956 02 *) 124
+(* Month: 1956 03 *) 118
+(* Month: 1956 04 *) 111
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+(* Month: 1956 06 *) 117
+(* Month: 1956 07 *) 129
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+(* Month: 1957 03 *) 157
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+(* Month: 1957 06 *) 201
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+(* Month: 1957 08 *) 158
+(* Month: 1957 09 *) 236
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+(* Month: 1958 02 *) 165
+(* Month: 1958 03 *) 191
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+(* Month: 1958 05 *) 175
+(* Month: 1958 06 *) 172
+(* Month: 1958 07 *) 191
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+(* Month: 1958 09 *) 201
+(* Month: 1958 10 *) 182
+(* Month: 1958 11 *) 152
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+(* Month: 1959 03 *) 186
+(* Month: 1959 04 *) 163
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+(* Month: 1959 07 *) 150
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+(* Month: 1959 09 *) 145
+(* Month: 1959 10 *) 111
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+(* Month: 1959 12 *) 125
+(* Month: 1960 01 *) 146
+(* Month: 1960 02 *) 106
+(* Month: 1960 03 *) 102
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+(* Month: 1961 08 *) 56
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+(* Month: 1961 12 *) 40
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+(* Month: 1962 04 *) 46
+(* Month: 1962 05 *) 44
+(* Month: 1962 06 *) 42
+(* Month: 1962 07 *) 22
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+(* Month: 1962 09 *) 51
+(* Month: 1962 10 *) 40
+(* Month: 1962 11 *) 27
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+(* Month: 1963 02 *) 24
+(* Month: 1963 03 *) 17
+(* Month: 1963 04 *) 29
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+(* Month: 1963 07 *) 20
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+(* Month: 1963 10 *) 35
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+(* Month: 1963 12 *) 15
+(* Month: 1964 01 *) 15
+(* Month: 1964 02 *) 18
+(* Month: 1964 03 *) 17
+(* Month: 1964 04 *) 9
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+(* Month: 1965 02 *) 14
+(* Month: 1965 03 *) 12
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+(* Month: 1965 06 *) 16
+(* Month: 1965 07 *) 12
+(* Month: 1965 08 *) 9
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+(* Month: 1965 10 *) 20
+(* Month: 1965 11 *) 16
+(* Month: 1965 12 *) 17
+(* Month: 1966 01 *) 28
+(* Month: 1966 02 *) 24
+(* Month: 1966 03 *) 25
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+(* Month: 1966 06 *) 48
+(* Month: 1966 07 *) 57
+(* Month: 1966 08 *) 51
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+(* Month: 1966 10 *) 57
+(* Month: 1966 11 *) 57
+(* Month: 1966 12 *) 70
+(* Month: 1967 01 *) 111
+(* Month: 1967 02 *) 94
+(* Month: 1967 03 *) 112
+(* Month: 1967 04 *) 70
+(* Month: 1967 05 *) 87
+(* Month: 1967 06 *) 67
+(* Month: 1967 07 *) 92
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+(* Month: 1967 09 *) 77
+(* Month: 1967 10 *) 88
+(* Month: 1967 11 *) 94
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+(* Month: 1968 01 *) 122
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+(* Month: 1968 08 *) 109
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+(* Month: 1968 10 *) 108
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+(* Month: 1969 01 *) 104
+(* Month: 1969 02 *) 121
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+(* Month: 1969 04 *) 107
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+(* Month: 1969 06 *) 106
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+(* Month: 1970 07 *) 113
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+(* Month: 1973 09 *) 59
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+(* Month: 1973 12 *) 23
+(* Month: 1974 01 *) 28
+(* Month: 1974 02 *) 26
+(* Month: 1974 03 *) 21
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+(* Month: 1974 05 *) 40
+(* Month: 1974 06 *) 36
+(* Month: 1974 07 *) 56
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+(* Month: 1974 09 *) 40
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+
+(* Month: 1976 11 *) 5
+(* Month: 1976 12 *) 15
+(* Month: 1977 01 *) 16
+(* Month: 1977 02 *) 23
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+(* Month: 1977 04 *) 13
+(* Month: 1977 05 *) 19
+(* Month: 1977 06 *) 39
+(* Month: 1977 07 *) 21
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+(* Month: 1981 06 *) 91
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+(* Month: 1982 03 *) 154
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+(* Month: 1982 05 *) 82
+(* Month: 1982 06 *) 110
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+(* Month: 1982 09 *) 119
+(* Month: 1982 10 *) 95
+(* Month: 1982 11 *) 98
+(* Month: 1982 12 *) 127
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--- /dev/null
+- finish experiments
+- write thesis
+- get post-doc position (pref. with Dr. Horrible)
--- /dev/null
+alpha: 0.5
+beta: 0.2
+gamma: off
--- /dev/null
+The Tao that is seen
+Is not the true Tao, until
+You bring fresh toner.
+
+With searching comes loss
+and the presence of absence:
+"My Thesis" not found.
+
+Yesterday it worked
+Today it is not working
+Software is like that.
--- /dev/null
+First file.
--- /dev/null
+Second file.
--- /dev/null
+A file full of notes.
--- /dev/null
+Formats supported.
--- /dev/null
+Statistics calculated.
--- /dev/null
+#!/usr/bin/env python\r
+\r
+'''Generate random data for files in `filesystem/users/nelle/north-pacific-gyre/2012-07-03/NENE*.txt`.'''\r
+\r
+import sys\r
+import os\r
+import random\r
+\r
+assert len(sys.argv) >= 5, \\r
+ 'Usage: {0} mean length output_directory filenames'.format(sys.argv[0])\r
+\r
+mean, length, output_directory, filenames = \\r
+ float(sys.argv[1]), int(sys.argv[2]), sys.argv[3], sys.argv[4:]\r
+\r
+assert mean > 0.0, \\r
+ 'Mean {0} must be positive'.format(mean)\r
+assert length > 0, \\r
+ 'File length {0} must be positive'.format(length)\r
+assert os.path.isdir(output_directory), \\r
+ 'Output directory "{0}" does not exist'.format(output_directory)\r
+assert len(filenames) > 0, \\r
+ 'No filenames provided'\r
+\r
+for f in filenames:\r
+ with open(os.path.join(output_directory, f), 'w') as writer:\r
+ for i in range(length):\r
+ print >> writer, random.expovariate(1.0/mean)\r
--- /dev/null
+#!/usr/bin/env python
+
+'''Generate random seuqence data for files in `creatures` directory.'''
+
+import sys
+import random
+
+assert len(sys.argv) == 3, 'Usage: gen-sequence lines seed'
+num_lines = int(sys.argv[1])
+random.seed(sys.argv[2])
+for i in range(num_lines):
+ print ''.join(random.choice('ACGT') for j in range(10))
--- /dev/null
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--- /dev/null
+---
+layout: lesson
+root: ../..
+title: The Unix Shell
+---
+The Unix shell has been around longer than most of its users have been alive.
+It has survived so long because it's a power tool
+that allows people to do complex things with just a few keystrokes.
+More importantly,
+it helps them combine existing programs in new ways
+and automate repetitive tasks
+so that they don't have to type the same things over and over again.
+
+<div class="toc" markdown="1">
+
+1. [Introducing the Shell](00-intro.html)
+2. [Files and Directories](01-filedir.html)
+3. [Creating Things](02-create.html)
+4. [Pipes and Filters](03-pipefilter.html)
+5. [Loops](04-loop.html)
+6. [Shell Scripts](05-script.html)
+7. [Finding Things](06-find.html)
+
+</div>
--- /dev/null
+COMPND CUBANE
+AUTHOR DAVE WOODCOCK 95 12 06
+ATOM 1 C 1 0.789 -0.852 0.504 1.00 0.00
+ATOM 2 C 1 -0.161 -1.104 -0.624 1.00 0.00
+ATOM 3 C 1 -1.262 -0.440 0.160 1.00 0.00
+ATOM 4 C 1 -0.289 -0.202 1.284 1.00 0.00
+ATOM 5 C 1 1.203 0.513 -0.094 1.00 0.00
+ATOM 6 C 1 0.099 1.184 0.694 1.00 0.00
+ATOM 7 C 1 -0.885 0.959 -0.460 1.00 0.00
+ATOM 8 C 1 0.236 0.283 -1.269 1.00 0.00
+ATOM 9 H 1 1.410 -1.631 0.942 1.00 0.00
+ATOM 10 H 1 -0.262 -2.112 -1.024 1.00 0.00
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+ATOM 15 H 1 -1.565 1.730 -0.831 1.00 0.00
+ATOM 16 H 1 0.472 0.494 -2.315 1.00 0.00
+TER 17 1
+END
--- /dev/null
+COMPND ETHANE
+AUTHOR DAVE WOODCOCK 95 12 18
+ATOM 1 C 1 -0.752 0.001 -0.141 1.00 0.00
+ATOM 2 C 1 0.752 -0.001 0.141 1.00 0.00
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+ATOM 7 H 1 0.924 0.249 1.188 1.00 0.00
+ATOM 8 H 1 1.240 0.737 -0.496 1.00 0.00
+TER 9 1
+END
--- /dev/null
+COMPND METHANE
+AUTHOR DAVE WOODCOCK 95 12 18
+ATOM 1 C 1 0.257 -0.363 0.000 1.00 0.00
+ATOM 2 H 1 0.257 0.727 0.000 1.00 0.00
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+ATOM 4 H 1 0.771 -0.727 -0.890 1.00 0.00
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+TER 6 1
+END
--- /dev/null
+COMPND OCTANE
+AUTHOR DAVE WOODCOCK 96 01 05
+ATOM 1 C 1 -4.397 0.370 -0.255 1.00 0.00
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+TER 27 1
+END
--- /dev/null
+COMPND PENTANE
+AUTHOR DAVE WOODCOCK 95 12 18
+ATOM 1 C 1 2.484 -0.389 0.322 1.00 0.00
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+TER 18 1
+END
--- /dev/null
+COMPND PROPANE
+AUTHOR DAVE WOODCOCK 95 12 18
+ATOM 1 C 1 1.241 0.444 0.349 1.00 0.00
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+ATOM 11 H 1 -2.058 -0.345 -0.332 1.00 0.00
+TER 12 1
+END
--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
+COMPND CHOLESTEROL
+AUTHOR DAVE WOODCOCK 96 07 31
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+TER 75 1
+END
--- /dev/null
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--- /dev/null
+COMPND VITAMIN A
+AUTHOR DAVE WOODCOCK 97 03 17
+ATOM 1 C 1 -4.322 -0.225 -0.083
+ATOM 2 C 1 -5.496 -1.028 0.032
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+ATOM 50 H 1 7.018 -1.407 -0.440
+ATOM 51 H 1 7.867 0.766 -0.400
+TER 52 1
+END
projects / swc-modular-shell.git / commitdiff
