Commit 0e50f032 authored by jdurrant's avatar jdurrant

Adding version 1.0.0.mda

parent 5f8a5a57
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Scoria
======
What is it?
-----------
The scoria library is a lightweight python code base designed for
importing, manipulating, and exporting molecular models.
The Latest Version
------------------
Visit [https://durrantlab.com/scoria/](https://durrantlab.com/scoria/) to:
* download the latest version
* read the documenation
* suggest an improvement
* point out a bug
* ask a question about usage
Installation
------------
The scoria libarary can be installed via pip as
```bash
# for python 2
pip install scoria
# for python 3
pip3 install scoria
```
Scoria runs best with NumPy and SciPy. It can also use the MDAnalysis library
for additional import methods. The first two dependancies should be
automatically installed alongside the package.
Licensing
---------
Scoria is released under the MIT License. See LICENCE.txt for details.
Authors and Contacts
--------------------
This library was produced by Jacob Durrant (durrantj@pitt.edu) with
the assistance of Patrick Ropp and Aaron Friedman.
# Scoria MDA is a program for manipulating 3D molecular models
# that includes MDAnalysis support.
#
# Copyright (C) 2017 Jacob D. Durrant
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Note that this version of Scoria (with MDAnalysis integration) is
# derived from the original Scoria source code, which retains its
# Apache 2.0 license.
import scoria
import numpy as np
# Load in a DCD/PSF trajectory.
print("Loading Molecule...")
mol = scoria.Molecule(
"../scoria/sample-files/test_sim.psf",
"../scoria/sample-files/test_sim.dcd"
)
# Create two new trajectories, corresponding to the shroom2
# protein and the rock1 dimer, respectively. Shroom2 is
# resid 1 to 181, and the rock1 dimer is 182 to 297.
print("Splitting trajectory into shroom2 and rock1...")
shroom2 = mol.get_molecule_from_selection(
mol.select_atoms({
"resseq": range(1, 181)
})
)
rock1 = mol.get_molecule_from_selection(
mol.select_atoms({
"resseq": range(182, 297)
})
)
# Create numpy arrays to store the number of times each
# atom of shroom2 comes within 3.0 A of the atoms of rock1,
# and vice versa.
print("Calculating contacts...")
shroom2_counts = np.zeros(
shroom2.get_total_number_of_atoms()
)
rock1_counts = np.zeros(
rock1.get_total_number_of_atoms()
)
# Go through each frame and compare shroom2 and rock1
# atoms, keeping track of close-contact counts.
traj_length = mol.get_trajectory_frame_count()
for frame in range(0, traj_length):
# Set the current trajectoyr frame for each model.
shroom2.set_default_trajectory_frame(frame)
rock1.set_default_trajectory_frame(frame)
# Find the indices of the atoms that come in close
# contact with atoms of the other model.
shroom2_indx, rock1_indx = shroom2.select_close_atoms_from_different_molecules(
rock1, 3.0
)
# Update the counts
shroom2_counts[shroom2_indx] += 1
rock1_counts[rock1_indx] += 1
# Normalize the counts so the range extends from 0.0 to at
# most 1.0.
shroom2_counts = shroom2_counts / traj_length
rock1_counts = rock1_counts / traj_length
# Replace the occupancies with these normalized count
# values.
shroom2_atom_info = shroom2.get_atom_information()
rock1_atom_info = rock1.get_atom_information()
shroom2_atom_info["occupancy"] = shroom2_counts
rock1_atom_info["occupancy"] = rock1_counts
shroom2.set_atom_information(shroom2_atom_info)
rock1.set_atom_information(rock1_atom_info)
# Save the first frame of each trajectory, with the updated
# occupancies.
print("Writing output files...")
shroom2.save_pdb("./shroom2_contacts.pdb", frame = 0)
rock1.save_pdb("./rock1_contacts.pdb", frame = 0)
# This bash script works in Linux and macOS, assuming the python executable is
# in the path. It creates a symbolic link to the scoria directory from this
# one.
# A very similar command should work in Windows. Just copy the scoria directory to
# this one before running.
# Make the symbolic link (Linux and macOS).
ln -s ../scoria ./
# Run footprint.py using the python executable, which should be in the path.
python footprint.py
\ No newline at end of file
# 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) source
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
.PHONY: help
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 " applehelp to make an Apple Help Book"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " epub3 to make an epub3"
@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 " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
@echo " coverage to run coverage check of the documentation (if enabled)"
@echo " dummy to check syntax errors of document sources"
.PHONY: clean
clean:
rm -rf $(BUILDDIR)/*
.PHONY: html
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
.PHONY: dirhtml
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
.PHONY: singlehtml
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
.PHONY: pickle
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
.PHONY: json
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
.PHONY: htmlhelp
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."
.PHONY: qthelp
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/scoria0.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/scoria0.qhc"
.PHONY: applehelp
applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~/Library/Documentation/Help or install it in your application" \
"bundle."
.PHONY: devhelp
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/scoria0"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/scoria0"
@echo "# devhelp"
.PHONY: epub
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
.PHONY: epub3
epub3:
$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
@echo
@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
.PHONY: latex
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)."
.PHONY: latexpdf
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."
.PHONY: latexpdfja
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
.PHONY: text
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
.PHONY: man
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
.PHONY: texinfo
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
.PHONY: info
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
.PHONY: gettext
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
.PHONY: changes
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
.PHONY: linkcheck
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."
.PHONY: doctest
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
.PHONY: coverage
coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)/coverage/python.txt."
.PHONY: xml
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
.PHONY: pseudoxml
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
.PHONY: dummy
dummy:
$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
@echo
@echo "Build finished. Dummy builder generates no files."
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The AtomsAndBonds Class
=======================
Rationale of the AtomsAndBonds functions
----------------------------------------
The functions within the AtomsAndBonds framework all involve the
addition, deletion, and manipulation of individual atoms and their
bonds within the molecular framework.
Other Classes
^^^^^^^^^^^^^
To make modifications to the coordinate set of all atoms, use the
functions within the :class:`~scoria.Manipulation` class. To look
at groups of atoms with similar properties, use the functions within
the :class:`~scoria.Selections` class.
Function Definitions
--------------------
.. automodule:: scoria.AtomsAndBonds
:members:
:undoc-members:
:show-inheritance:
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The FileIO Class
========================
File Types and Formats
----------------------
Scoria can naitvely read and write PDB, PDBQT, and PYM files. It
can also read multiframe PDB and PDBQT files. It also has the ability
to import information from :any:`MDAnalysis
<MDAnalysis.core.AtomGroup>` objects.
Function Definitions
--------------------
.. automodule:: scoria.FileIO
:members:
:undoc-members:
:show-inheritance:
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