double_quoted_string_re = re.compile(r'"([^"]*)"', re.M)
-# SCons' LaTeX scanner doesn't understand \asyfig{}, so keep track of
-# all Asymptote graphics for phony target creation.
+# SCons' LaTeX scanner doesn't understand \asyinclude{}, so keep track
+# of all Asymptote graphics for phony target creation.
asyfigs = []
def asymptote_scan(node, env, path, arg=None):
def asymptote_emitter(target, source, env):
assert str(source[0]).endswith('.asy'), str(source[0])
filebase = str(source[0])[:-len('.asy')]
- target.extend(['%s_%s' % (filebase, ext)
- for ext in ['.tex', '.pre', '0.pdf']])
- target.extend(['%s-comp.%s' % (filebase, ext)
- for ext in ['idx', 'log', 'nlo', 'pdf']])
+ target.extend(['%s%s' % (filebase, ext)
+ for ext in ['.tex', '.pre', '_0.pdf']])
source.append(SCons.Script.Alias('asytools'))
# side effect, keep track of all asymptote graphics.
asyfigs.append(target[0])
#pdf.generate(env)
env['BUILDERS']['Asymptote'] = SCons.Script.Builder(
- action=AsymptoteAction, suffix='_.tex', src_suffix = '.asy',
+ action=AsymptoteAction, suffix='.tex', src_suffix = '.asy',
emitter=asymptote_emitter)
- env['ASYMPTOTE'] = '../asy/asyprocess'
+
+ env['ASYMPTOTE'] = 'asy'
env['ASYMPTOTEFLAGS'] = SCons.Util.CLVar(
- "--texinputs=../..: "
- "--pretex='\documentclass{drexel-thesis} \input{packages}' "
- "--")
+ '-tex pdflatex -inlineimage -inlinetex')
env['ASYMPTOTECOM'] = 'cd ${TARGET.dir} && $ASYMPTOTE $ASYMPTOTEFLAGS ${SOURCE.filebase}'
env.Append(SCANNERS=SCons.Scanner.Base(
function=asymptote_scan,
force applied to the sample can be calculated.
\begin{figure}
- \asyfig{figures/schematic/afm}%
+ \asyinclude{figures/schematic/afm}%
\caption{Operating principle for an Atomic Force
Microscope\index{AFM}. A sharp tip integrated at the end of a
cantilever interacts with the sample. Cantilever bending is
\begin{figure}
\begin{center}
- \subfloat[][]{\asyfig{figures/schematic/unfolding}%
+ \subfloat[][]{\asyinclude{figures/schematic/unfolding}%
\label{fig:unfolding-schematic}}
% \hspace{.25in}%
- \subfloat[][]{\asyfig{figures/expt-sawtooth/expt-sawtooth}%
+ \subfloat[][]{\asyinclude{figures/expt-sawtooth/expt-sawtooth}%
\label{fig:expt-sawtooth}}
\caption{(a) Schematic of the experimental setup for mechanical
unfolding of proteins using an AFM (not to scale). An experiment
\href{http://www.ctan.org/}{CTAN}]
Typesetting.
\item[\href{http://sourceforge.net/projects/pgf/}{PGF}/%
- \href{http://asymptote.sourceforge.net/}{Asymptote}/%
- \href{http://github.com/wspr/asyfig/}{Asyfig}]
+ \href{http://asymptote.sourceforge.net/}{Asymptote}]
Graphical programming.
\item[\href{http://www.python.org/}{Python}]
General purpose scripting.
along the contour \C\ shown in \cref{fig:UHP-contour}.
\begin{figure}
- \asyfig{figures/contour/contour}
+ \asyinclude{figures/contour/contour}
\caption{Integral contour \C\ enclosing the upper half of the
complex plane. If the integrand $f(z)$ goes to zero ``quickly
enough'' as the radius of \C\ approaches infinity, then the only
produce \cref{fig:cant:v-dep}.
\begin{figure}
- \asyfig{figures/cantilever-data/v-dep}
+ \asyinclude{figures/cantilever-data/v-dep}
\caption{Pulling speed dependence of I27 for different cantilever
stiffnesses. The listed stiffnesses are averages across several
individual cantilevers and calibrations. Each box is the average
fit WLC\index{WLC} at unfolding.
\begin{figure}
- \asyfig{figures/cantilever-data/loading-rate}
+ \asyinclude{figures/cantilever-data/loading-rate}
\caption{Loading rate.\label{fig:cant:load-dep}}
\end{figure}
(\cref{fig:cant:sim:v-dep,fig:cant:sim:load-dep,fig:cant:sim:i-dep}).
\begin{figure}
- \asyfig{figures/cantilever-sim/v-dep}
+ \asyinclude{figures/cantilever-sim/v-dep}
\caption{Unfolding force velocity dependence for different
cantilevers.\label{fig:cant:sim:v-dep}}
\end{figure}
\begin{figure}
- \asyfig{figures/cantilever-sim/loading-rate}
+ \asyinclude{figures/cantilever-sim/loading-rate}
\caption{Unfolding force loading rate dependence simulations for
different cantilevers.\label{fig:cant:sim:load-dep}}
\end{figure}
\begin{figure}
- \asyfig{figures/cantilever-sim/i-dep}
+ \asyinclude{figures/cantilever-sim/i-dep}
\caption{Unfolding force peak index dependence simulations for
different cantilevers.\label{fig:cant:sim:i-dep}}
\end{figure}
\section{Theory}
\begin{figure}
- \asyfig{figures/schematic/landscape-cant}
+ \asyinclude{figures/schematic/landscape-cant}
\caption{Energy landscape schematic.\label{fig:landscape}}
\end{figure}
\usetikzlibrary{automata} % graph-theory library
\usetikzlibrary{calc} % coordinate-calculation library
-\usepackage{asyfig} % more fancy graphics ;).
+\usepackage[inline]{asymptote} % more fancy graphics ;).
\usepackage{epsdice} % dice-face font
\input{packages}
\begin{document}
+
+% Work-directory for Asymptote files (no spaces):
+\def\asydir{figures/scratch}
+\begin{asydef}
+// Global Asymptote definitions go here.
+//texpreamble("\documentclass{drexel-thesis}");
+//usepackage("packages");
+\end{asydef}
+
+
\begin{preamble}
\include{blurb/dedications}
\begin{figure}
\vspace{-1in}
\begin{center}
-\subfloat[][]{\asyfig{figures/sim-sawtooth/sim-sawtooth}%
+\subfloat[][]{\asyinclude{figures/sim-sawtooth/sim-sawtooth}%
\label{fig:sawsim:sim-sawtooth}%
}\\
-\subfloat[][]{\asyfig{figures/sim-hist/sim-hist}%
+\subfloat[][]{\asyinclude{figures/sim-hist/sim-hist}%
\label{fig:sawsim:sim-hist}%
}
\caption{(a) Three simulated force curves from pulling a polymer of
\begin{figure}
\begin{center}
- \asyfig{figures/order-dep/order-dep}
+ \asyinclude{figures/order-dep/order-dep}
\caption{The dependence of the unfolding force on the temporal
unfolding order for four polymers with $4$, $8$, $12$, and $16$
identical protein domains. Each point in the figure is the
\begin{figure}
\begin{center}
-\asyfig{figures/kappa-sawteeth/kappa-sawteeth}
+\asyinclude{figures/kappa-sawteeth/kappa-sawteeth}
\caption{Simulated force curves obtained from pulling a polymer with
eight protein molecules using cantilevers with different force
constants $\kappa_c$. Parameters used in generating these curves
\begin{figure}
\begin{center}
- \subfloat[][]{\asyfig{figures/v-dep/v-dep}%
+ \subfloat[][]{\asyinclude{figures/v-dep/v-dep}%
\label{fig:sawsim:v-dep}%
} \\
- \subfloat[][]{\asyfig{figures/v-dep/v-dep-sd}%
+ \subfloat[][]{\asyinclude{figures/v-dep/v-dep-sd}%
\label{fig:sawsim:width-v-dep}%
}
\caption{(a) The dependence of the unfolding forces on the pulling
\begin{figure}
\begin{center}
- \asyfig{figures/fit-space/fit-valley}
+ \asyinclude{figures/fit-space/fit-valley}
\caption{Fit quality between an experimental data set and simulated
data sets obtained using various values of unfolding rate
parameters $k_{u0}$ and $\Delta x_u$. The experimental data are
where the approximation is valid when $N_fP_1 \ll 1$.
\begin{figure}
- \asyfig{figures/schematic/monte-carlo}
+ \asyinclude{figures/schematic/monte-carlo}
\caption{Once the unfolding probability has been caculated, we need
to determine whether or not a domain should unfold. We do this by
generating a random number, and comparing that number to the