Merge devel branch to master

.gitignore

@@ -70,6 +70,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/api/autogenerated/
 
 # PyBuilder
 target/

MANIFEST.in

@@ -1,2 +1,2 @@
 include versioneer.py
-include offPELE/_version.py
+include offpele/_version.py

README.md

@@ -1,2 +1,2 @@
-# Open Force Field toolkit for PELE
-The Open Force Field toolkit for PELE is a Python package that builds PELE-compatible force field templates using the Open Force Field toolkit.
+# Open Force Field to PELE
+The Open Force Field to PELE is a Python package that builds PELE-compatible force field templates using the Open Force Field toolkit.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_templates/class.rst

@@ -0,0 +1,24 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   {% if methods %}
+   {% for item in methods %}
+      .. automethod:: {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/conf.py

@@ -0,0 +1,96 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+import sphinx
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Open Force Field for PELE'
+copyright = '2020, Barcelona Supercomputing Center'
+author = 'Martí Municoy'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'm2r',
+              'sphinx.ext.napoleon', 'sphinx.ext.viewcode', ]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+def monkeypatch(cls):
+    """ decorator to monkey-patch methods """
+    def decorator(f):
+        method = f.__name__
+        old_method = getattr(cls, method)
+        setattr(cls, method, lambda self, *args, **kwargs: f(old_method, self, *args, **kwargs))
+    return decorator
+
+
+# workaround until https://github.com/miyakogi/m2r/pull/55 is merged
+@monkeypatch(sphinx.registry.SphinxComponentRegistry)
+def add_source_parser(_old_add_source_parser, self, *args, **kwargs):
+    # signature is (parser: Type[Parser], **kwargs), but m2r expects
+    # the removed (str, parser: Type[Parser], **kwargs).
+    if isinstance(args[0], str):
+        args = args[1:]
+    return _old_add_source_parser(self, *args, **kwargs)
+
+
+# Custom options
+autosummary_generate = True
+#autoclass_content = "class"
+#autodoc_default_flags = ['members', 'inherited-members']
+autodoc_member_order = 'bysource'
+#numpydoc_class_members_toctree = False
+source_suffix = ['.rst', '.md']
+master_doc = 'index'
+
+import offpele
+version = offpele.__version__
+
+pygments_style = 'sphinx'
+
+html_theme = 'sphinx_rtd_theme'
+
+napoleon_google_docstring = False
+napoleon_use_param = False
+napoleon_use_ivar = True
+#html_theme = 'bootstrap'
+#html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()

docs/index.rst

@@ -0,0 +1,25 @@
+Open Force Field for PELE
+=========================
+
+The Open Force Field for PELE is a Python package that builds
+PELE-compatible force field templates using the Open Force Field
+toolkit.
+
+
+User guide
+----------
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+API documentation
+-----------------
+
+.. toctree::
+  :maxdepth: 1
+
+  topology
+  template
+  solvent

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/solvent.rst

@@ -0,0 +1,20 @@
+.. _solvent ::
+
+Solvent models
+==============
+
+This module provides different methods to parameterize solvent models
+for PELE.
+
+.. currentmodule:: offpele.solvent
+
+Primary objects
+---------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    OBC1
+    OBC2

docs/template.rst

@@ -0,0 +1,35 @@
+.. _template ::
+
+Template handlers
+=================
+
+This module provides a toolkit to generate parameter templates for PELE.
+
+.. currentmodule:: offpele.template
+
+Primary objects
+---------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    Impact
+
+
+Secondary objects
+-----------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    impact.WritableWrapper
+    impact.WritableAtom
+    impact.WritableBond
+    impact.WritableAngle
+    impact.WritableProper
+    impact.WritableImproper
+

docs/topology.rst

@@ -0,0 +1,44 @@
+.. _topology ::
+
+Topology representations
+========================
+
+This module provides different topological representations to
+translate from external toolkits the different molecular parameters
+for PELE.
+
+.. currentmodule:: offpele.topology
+
+Primary objects
+---------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    Molecule
+
+
+Secondary objects
+-----------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    Atom
+    Bond
+    Angle
+    Dihedral
+    Proper
+    Improper
+    molecule.DummyAtom
+    topology.OFFDihedral
+    topology.OFFProper
+    topology.OFFImproper
+    ZMatrix
+    rotamer.Rotamer
+    rotamer.RotamerLibrary
+    rotamer.MolecularGraph

offpele/__init__.py

@@ -0,0 +1,3 @@
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions

offPELE/_version.py → offpele/_version.py

@@ -42,8 +42,8 @@ def get_config():
     cfg.VCS = "git"
     cfg.style = "pep440"
     cfg.tag_prefix = ""
-    cfg.parentdir_prefix = "offPELE-"
-    cfg.versionfile_source = "offPELE/_version.py"
+    cfg.parentdir_prefix = "offpele-"
+    cfg.versionfile_source = "offpele/_version.py"
     cfg.verbose = False
     return cfg
 

offpele/data/benchmarks/README.md

@@ -0,0 +1,17 @@
+# Benchmarks
+Datasets to be used in benchmarking studies for offpele.
+
+## Content
+_Content under construction_
+- GPCRs
+- PPI (Protein-protein inhibitors)
+- Small molecule set
+- Small molecule set with experimental hydration free energies
+
+## Analysis features
+_Content under construction_
+- Rotamer library comparison between offpele and PlopRotTemp
+- Experimental hydration free energies comparison _(inside the PELE-platform)_
+- Comparison of parameters between offpele and PlopRotTemp (bonds, angles, dihedrals, nonbonding and OBC)
+- Structural comparison between PELE's OPLS and OFF implementations
+- Energetic profile comparison in gold-standard systems (previously published)