Merge branch 'master' of https://github.com/shirtsgroup/intermol

.gitignore

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+# GROMACS #
+\#*\#
+*.trr
+*.edr
+*.xvg
+
+# VIM #
+*.swp
+*.swo
+*.swn
+*.swm
+
+# OS Stuff #
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# python #
+*.pyc

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2013 Michael Shirts
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+InterMol
+========
+
+[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/shirtsgroup/InterMol?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
+Conversion tool for molecular simulations. 
+
+We are currently in alpha testing phase, debugging Desmond<=>Gromacs<=>Lammps conversions. 
+
+To check out how it works, use the ````convert.py```` script found in the ````testing```` directory:
+
+````
+$ python convert.py -h
+usage: convert.py [-h] [--des_in file] [--gro_in file file] [--lmp_in file]
+                  [--desmond] [--gromacs] [--lammps] [--odir directory]
+                  [--oname prefix] [-e] [--efile EFILE] [-d path] [-g path]
+                  [-l path] [-f]
+
+Perform a file conversion
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Choose input conversion format:
+  --des_in file         .cms file for conversion from DESMOND file format
+  --gro_in file file    .gro and .top file for conversion from GROMACS file
+                        format
+  --lmp_in file         .lmp file for conversion from LAMMPS file format
+                        (expects matching .input file)
+
+Choose output conversion format(s):
+  --desmond             convert to DESMOND
+  --gromacs             convert to GROMACS
+  --lammps              convert to LAMMPS
+
+Other optional arguments:
+  --odir directory      specification of output directory (default: ./)
+  --oname prefix        specification of prefix for output filenames (default:
+                        inputprefix_converted)
+  -e, --energy          evaluate energy of input and output files for
+                        comparison
+  --efile EFILE         optional run file for energy evaluation (e.g. .cfg,
+                        .mdp, .input)
+  -d path, --despath path
+                        path for DESMOND binary, needed for energy evaluation
+  -g path, --gropath path
+                        path for GROMACS binary, needed for energy evaluation
+  -l path, --lmppath path
+                        path for LAMMPS binary, needed for energy evaluation
+  -f, --force           ignore warnings 
+````
+
+For example, to convert from desmond to gromacs and evalutate the energy of the input and output files:
+
+````
+# current working directory is Intermol/testing
+mkdir test_output
+python convert.py --des_in Inputs/Desmond/UnitTest/frag_opls2001/frag_opls2001.cms --gromacs --odir test_output -e
+````
+
+Note that the program may not give the same ASCII output; the goal is to produce the same energy output, and there are frequently multiple ways to express the same molecular potential energy function using differently formatted files.

docs/Makefile

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/ctools.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/ctools.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/ctools"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/ctools"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	make -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."

docs/_build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: bcc43d84dd26921841d194d2fbf5d5f9
+tags: fbb0d17656682115ca4d033fb2f83ba1

docs/_build/html/_sources/atom.txt

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+Atom
+====
+
+.. module:: ctools.Atom
+
+.. autoclass:: Atom
+   :show-inheritance:
+   :members:
+   :undoc-members:
+

docs/_build/html/_sources/converter.txt

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+Converter
+=========
+
+.. module:: ctools.Converter
+
+.. automodule:: ctools.Converter 
+   :show-inheritance:
+   :members:
+   :undoc-members:
+

docs/_build/html/_sources/hashMap.txt

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+HashMap
+=======
+
+.. module:: ctools.HashMap
+
+.. autoclass:: HashMap
+   :show-inheritance:
+   :members:
+   :undoc-members:
+

docs/_build/html/_sources/index.txt

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+.. ctools documentation master file, created by
+   sphinx-quickstart on Wed Mar 23 16:11:26 2011.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ctools's documentation!
+====================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   testfiles/example
+   system
+   molecule
+   moleculeType
+   atom
+   hashMap
+   orderedSet
+   converter
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/_build/html/_sources/molecule.txt

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+Molecule
+========
+
+.. module:: ctools.Molecule
+
+.. autoclass:: Molecule
+   :show-inheritance:
+   :members:
+   :undoc-members:
+

docs/_build/html/_sources/moleculeType.txt

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+MoleculeType
+============
+
+.. module:: ctools.MoleculeType
+
+.. autoclass:: MoleculeType
+   :show-inheritance:
+   :members:
+   :undoc-members:
+

docs/_build/html/_sources/orderedSet.txt

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+OrderedSet
+==========
+
+.. module:: ctools.OrderedSet
+
+.. autoclass:: OrderedSet
+   :show-inheritance:
+   :members:
+   :undoc-members:
+

docs/_build/html/_sources/system.txt

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+System
+======
+
+.. module:: ctools.System
+
+.. autoclass:: System
+   :show-inheritance:
+   :members:
+   :undoc-members:

docs/_build/html/_sources/testfiles/example.txt

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+Example
+=======
+
+>>> Driver.initSystem("Solvated GMX")
+>>> # Reading
+>>> Driver.loadctools("system_GMX.top")
+>>> Driver.loadStructure("system_GMX.gro")
+>>> # Writing
+>>> Driver.writeStructure("system_GMX_out.gro")
+>>> Driver.writectools("system_GMX_out.top")