From 5c9e831f851ddb1cb9d0b06ff18c9d63ddf02aea Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Thu, 17 Dec 2009 14:19:40 -0500 Subject: [PATCH] Added README and reorganized directory structure (breaks code) --- README | 49 ++++++++++++++++++ convfilt.conf => conf/convfilt.conf | 0 hooke.conf => conf/hooke.conf | 0 pca_config.txt => conf/pca_config.txt | 0 hooke.jpg => doc/hooke.jpg | Bin csvdriver.py => hooke/driver/csvdriver.py | 0 hemingclamp.py => hooke/driver/hemingclamp.py | 0 jpk.py => hooke/driver/jpk.py | 0 mcs.py => hooke/driver/mcs.py | 0 mfp1dexport.py => hooke/driver/mfp1dexport.py | 0 picoforce.py => hooke/driver/picoforce.py | 0 .../driver/picoforcealt.py | 0 .../driver/tutorialdriver.py | 0 hooke.py => hooke/hooke.py | 0 hooke_cli.py => hooke/hooke_cli.py | 0 libhooke.py => hooke/libhooke.py | 0 libhookecurve.py => hooke/libhookecurve.py | 0 libinput.py => hooke/libinput.py | 0 liboutlet.py => hooke/liboutlet.py | 0 libpeakspot.py => hooke/libpeakspot.py | 0 libviewer.py => hooke/libviewer.py | 0 autopeak.py => hooke/plugin/autopeak.py | 0 cut.py => hooke/plugin/cut.py | 0 fit.py => hooke/plugin/fit.py | 0 flatfilts.py => hooke/plugin/flatfilts.py | 0 .../plugin/generalclamp.py | 0 generaltccd.py => hooke/plugin/generaltccd.py | 0 .../plugin/generalvclamp.py | 0 macro.py => hooke/plugin/macro.py | 0 .../plugin/massanalysis.py | 0 .../plugin/multidistance.py | 0 pcluster.py => hooke/plugin/pcluster.py | 0 procplots.py => hooke/plugin/procplots.py | 0 superimpose.py => hooke/plugin/superimpose.py | 0 tutorial.py => hooke/plugin/tutorial.py | 0 viewer.py => hooke/plugin/viewer.py | 0 default.000 => hooke/test/default.000 | 0 test.hkp => hooke/test/test.hkp | 0 38 files changed, 49 insertions(+) create mode 100644 README rename convfilt.conf => conf/convfilt.conf (100%) rename hooke.conf => conf/hooke.conf (100%) rename pca_config.txt => conf/pca_config.txt (100%) rename hooke.jpg => doc/hooke.jpg (100%) rename csvdriver.py => hooke/driver/csvdriver.py (100%) rename hemingclamp.py => hooke/driver/hemingclamp.py (100%) rename jpk.py => hooke/driver/jpk.py (100%) rename mcs.py => hooke/driver/mcs.py (100%) rename mfp1dexport.py => hooke/driver/mfp1dexport.py (100%) rename picoforce.py => hooke/driver/picoforce.py (100%) rename picoforcealt.py => hooke/driver/picoforcealt.py (100%) rename tutorialdriver.py => hooke/driver/tutorialdriver.py (100%) rename hooke.py => hooke/hooke.py (100%) rename hooke_cli.py => hooke/hooke_cli.py (100%) rename libhooke.py => hooke/libhooke.py (100%) rename libhookecurve.py => hooke/libhookecurve.py (100%) rename libinput.py => hooke/libinput.py (100%) rename liboutlet.py => hooke/liboutlet.py (100%) rename libpeakspot.py => hooke/libpeakspot.py (100%) rename libviewer.py => hooke/libviewer.py (100%) rename autopeak.py => hooke/plugin/autopeak.py (100%) rename cut.py => hooke/plugin/cut.py (100%) rename fit.py => hooke/plugin/fit.py (100%) rename flatfilts.py => hooke/plugin/flatfilts.py (100%) rename generalclamp.py => hooke/plugin/generalclamp.py (100%) rename generaltccd.py => hooke/plugin/generaltccd.py (100%) rename generalvclamp.py => hooke/plugin/generalvclamp.py (100%) rename macro.py => hooke/plugin/macro.py (100%) rename massanalysis.py => hooke/plugin/massanalysis.py (100%) rename multidistance.py => hooke/plugin/multidistance.py (100%) rename pcluster.py => hooke/plugin/pcluster.py (100%) rename procplots.py => hooke/plugin/procplots.py (100%) rename superimpose.py => hooke/plugin/superimpose.py (100%) rename tutorial.py => hooke/plugin/tutorial.py (100%) rename viewer.py => hooke/plugin/viewer.py (100%) rename default.000 => hooke/test/default.000 (100%) rename test.hkp => hooke/test/test.hkp (100%) diff --git a/README b/README new file mode 100644 index 0000000..3ab3fa9 --- /dev/null +++ b/README @@ -0,0 +1,49 @@ +What is it? +=========== + +It is a software for the (semiautomatic) analysis and filtering of +force curves. Force curves are the output of an analytical technique +called force spectroscopy. A force spectroscopy experiment usually +requires the analysis of thousands of force curves at a time. As of +today, there is no standard, free software for the analysis of force +curves. Hooke aims to solve that. + +What it does? +============= + + * View, annotate, measure force curves + * Worm-like chain and freely-jointed chain fit of force peaks + * Automatic convolution-based filtering of empty curves + * Automatic fit and measurement of multiple force peaks + * Handles force-clamp force experiments (experimental) + * It is extensible by users by mean of plugins and drivers + +See the Google Code website for more details + http://code.google.com/p/hooke/ + +Is this published in some peer-reviewed journal? +================================================ + +Sandal M, Benedetti F, Brucale M, Gomez-Casado A, Samorì B. +"Hooke: an open software platform for force spectroscopy." +Bioinformatics, 2009 25(11):1428-1430. +doi:10.1093/bioinformatics/btp180 + +Please cite Hooke if you use it. + +Troubleshooting +=============== + +If you have troubles in using it, before throwing it in the trash: + 1) try look at the TroubleShooting page or in the discussion group + 2) ask a question in the discussion group! +http://groups.google.com/group/hookesoftware + +Disclaimer +========== + +Remember that Hooke is still experimental software! It has been mostly +done to fit the needs of its authors, and there is no guarantee it +will do what you need. However, you can write us/help us improve it so +that it does. We aim to make of Hooke a little, universal tool that +can help your research. diff --git a/convfilt.conf b/conf/convfilt.conf similarity index 100% rename from convfilt.conf rename to conf/convfilt.conf diff --git a/hooke.conf b/conf/hooke.conf similarity index 100% rename from hooke.conf rename to conf/hooke.conf diff --git a/pca_config.txt b/conf/pca_config.txt similarity index 100% rename from pca_config.txt rename to conf/pca_config.txt diff --git a/hooke.jpg b/doc/hooke.jpg similarity index 100% rename from hooke.jpg rename to doc/hooke.jpg diff --git a/csvdriver.py b/hooke/driver/csvdriver.py similarity index 100% rename from csvdriver.py rename to hooke/driver/csvdriver.py diff --git a/hemingclamp.py b/hooke/driver/hemingclamp.py similarity index 100% rename from hemingclamp.py rename to hooke/driver/hemingclamp.py diff --git a/jpk.py b/hooke/driver/jpk.py similarity index 100% rename from jpk.py rename to hooke/driver/jpk.py diff --git a/mcs.py b/hooke/driver/mcs.py similarity index 100% rename from mcs.py rename to hooke/driver/mcs.py diff --git a/mfp1dexport.py b/hooke/driver/mfp1dexport.py similarity index 100% rename from mfp1dexport.py rename to hooke/driver/mfp1dexport.py diff --git a/picoforce.py b/hooke/driver/picoforce.py similarity index 100% rename from picoforce.py rename to hooke/driver/picoforce.py diff --git a/picoforcealt.py b/hooke/driver/picoforcealt.py similarity index 100% rename from picoforcealt.py rename to hooke/driver/picoforcealt.py diff --git a/tutorialdriver.py b/hooke/driver/tutorialdriver.py similarity index 100% rename from tutorialdriver.py rename to hooke/driver/tutorialdriver.py diff --git a/hooke.py b/hooke/hooke.py similarity index 100% rename from hooke.py rename to hooke/hooke.py diff --git a/hooke_cli.py b/hooke/hooke_cli.py similarity index 100% rename from hooke_cli.py rename to hooke/hooke_cli.py diff --git a/libhooke.py b/hooke/libhooke.py similarity index 100% rename from libhooke.py rename to hooke/libhooke.py diff --git a/libhookecurve.py b/hooke/libhookecurve.py similarity index 100% rename from libhookecurve.py rename to hooke/libhookecurve.py diff --git a/libinput.py b/hooke/libinput.py similarity index 100% rename from libinput.py rename to hooke/libinput.py diff --git a/liboutlet.py b/hooke/liboutlet.py similarity index 100% rename from liboutlet.py rename to hooke/liboutlet.py diff --git a/libpeakspot.py b/hooke/libpeakspot.py similarity index 100% rename from libpeakspot.py rename to hooke/libpeakspot.py diff --git a/libviewer.py b/hooke/libviewer.py similarity index 100% rename from libviewer.py rename to hooke/libviewer.py diff --git a/autopeak.py b/hooke/plugin/autopeak.py similarity index 100% rename from autopeak.py rename to hooke/plugin/autopeak.py diff --git a/cut.py b/hooke/plugin/cut.py similarity index 100% rename from cut.py rename to hooke/plugin/cut.py diff --git a/fit.py b/hooke/plugin/fit.py similarity index 100% rename from fit.py rename to hooke/plugin/fit.py diff --git a/flatfilts.py b/hooke/plugin/flatfilts.py similarity index 100% rename from flatfilts.py rename to hooke/plugin/flatfilts.py diff --git a/generalclamp.py b/hooke/plugin/generalclamp.py similarity index 100% rename from generalclamp.py rename to hooke/plugin/generalclamp.py diff --git a/generaltccd.py b/hooke/plugin/generaltccd.py similarity index 100% rename from generaltccd.py rename to hooke/plugin/generaltccd.py diff --git a/generalvclamp.py b/hooke/plugin/generalvclamp.py similarity index 100% rename from generalvclamp.py rename to hooke/plugin/generalvclamp.py diff --git a/macro.py b/hooke/plugin/macro.py similarity index 100% rename from macro.py rename to hooke/plugin/macro.py diff --git a/massanalysis.py b/hooke/plugin/massanalysis.py similarity index 100% rename from massanalysis.py rename to hooke/plugin/massanalysis.py diff --git a/multidistance.py b/hooke/plugin/multidistance.py similarity index 100% rename from multidistance.py rename to hooke/plugin/multidistance.py diff --git a/pcluster.py b/hooke/plugin/pcluster.py similarity index 100% rename from pcluster.py rename to hooke/plugin/pcluster.py diff --git a/procplots.py b/hooke/plugin/procplots.py similarity index 100% rename from procplots.py rename to hooke/plugin/procplots.py diff --git a/superimpose.py b/hooke/plugin/superimpose.py similarity index 100% rename from superimpose.py rename to hooke/plugin/superimpose.py diff --git a/tutorial.py b/hooke/plugin/tutorial.py similarity index 100% rename from tutorial.py rename to hooke/plugin/tutorial.py diff --git a/viewer.py b/hooke/plugin/viewer.py similarity index 100% rename from viewer.py rename to hooke/plugin/viewer.py diff --git a/default.000 b/hooke/test/default.000 similarity index 100% rename from default.000 rename to hooke/test/default.000 diff --git a/test.hkp b/hooke/test/test.hkp similarity index 100% rename from test.hkp rename to hooke/test/test.hkp -- 2.26.2