pdbeccdutils 0.5.9__tar.gz

Users/lpravda/anaconda3/envs/rdkit-env/bin/process_components_cif

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+#!/Users/lpravda/anaconda3/envs/rdkit-env/bin/python
+# EASY-INSTALL-ENTRY-SCRIPT: 'pdbeccdutils==0.5.9','console_scripts','process_components_cif'
+import re
+import sys
+
+# for compatibility with easy_install; see #2198
+__requires__ = 'pdbeccdutils==0.5.9'
+
+try:
+    from importlib.metadata import distribution
+except ImportError:
+    try:
+        from importlib_metadata import distribution
+    except ImportError:
+        from pkg_resources import load_entry_point
+
+
+def importlib_load_entry_point(spec, group, name):
+    dist_name, _, _ = spec.partition('==')
+    matches = (
+        entry_point
+        for entry_point in distribution(dist_name).entry_points
+        if entry_point.group == group and entry_point.name == name
+    )
+    return next(matches).load()
+
+
+globals().setdefault('load_entry_point', importlib_load_entry_point)
+
+
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
+    sys.exit(load_entry_point('pdbeccdutils==0.5.9', 'console_scripts', 'process_components_cif')())

Users/lpravda/anaconda3/envs/rdkit-env/bin/setup_pubchem_library

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+#!/Users/lpravda/anaconda3/envs/rdkit-env/bin/python
+# EASY-INSTALL-ENTRY-SCRIPT: 'pdbeccdutils==0.5.9','console_scripts','setup_pubchem_library'
+import re
+import sys
+
+# for compatibility with easy_install; see #2198
+__requires__ = 'pdbeccdutils==0.5.9'
+
+try:
+    from importlib.metadata import distribution
+except ImportError:
+    try:
+        from importlib_metadata import distribution
+    except ImportError:
+        from pkg_resources import load_entry_point
+
+
+def importlib_load_entry_point(spec, group, name):
+    dist_name, _, _ = spec.partition('==')
+    matches = (
+        entry_point
+        for entry_point in distribution(dist_name).entry_points
+        if entry_point.group == group and entry_point.name == name
+    )
+    return next(matches).load()
+
+
+globals().setdefault('load_entry_point', importlib_load_entry_point)
+
+
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
+    sys.exit(load_entry_point('pdbeccdutils==0.5.9', 'console_scripts', 'setup_pubchem_library')())

Users/lpravda/anaconda3/envs/rdkit-env/lib/python3.7/site-packages/doc/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/stable/config
+
+# -- 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.
+#
+from recommonmark.transform import AutoStructify
+import pdbeccdutils
+
+# region Project information
+project = "pdbeccdutils"
+copyright = "2020, Protein Data Bank in Europe"
+author = "Protein Data Bank in Europe"
+
+# The short X.Y version
+version = pdbeccdutils.__version__
+# The full version, including alpha/beta/rc tags
+release = pdbeccdutils.__version__
+
+# endregion
+
+# region General configuration
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.napoleon",
+    "sphinx.ext.todo",
+    "sphinx_markdown_tables",
+    "sphinx.ext.coverage",
+    "sphinx.ext.intersphinx",
+    "recommonmark",
+]
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "rdkit": ("https://www.rdkit.org/docs/", None),
+}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+source_parsers = {".rst": "restructuredtext", ".txt": "markdown", ".md": "markdown"}
+
+# The master toctree document.
+master_doc = "index"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# 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"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# endregion
+
+# region 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 = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {
+    "collapse_navigation": False,
+    "sticky_navigation": True,
+    "navigation_depth": 4,
+    "logo_only": False,
+    "display_version": True,
+    "prev_next_buttons_location": "bottom",
+}
+html_logo = "logo.png"
+# 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"]
+# html_css_files = ["css/styles.css"]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+# end region
+
+# region Options for HTMLHelp output
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "pdbeccdutilsdoc"
+
+# endregion
+
+# region Options for LaTeX output
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (
+        master_doc,
+        "pdbeccdutils.tex",
+        "pdbeccdutils Documentation",
+        "Protein Data Bank in Europe",
+        "manual",
+    ),
+]
+# endregion
+
+# region Options for manual page output
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "pdbeccdutils", "pdbeccdutils Documentation", [author], 1)]
+# endregion
+
+# region Options for Texinfo output
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "pdbeccdutils",
+        "pdbeccdutils Documentation",
+        author,
+        "pdbeccdutils",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
+]
+
+# endregion
+
+# region Extension configuration
+github_doc_root = "https://github.com/rtfd/recommonmark/tree/master/doc/"
+
+
+def setup(app):
+    app.add_config_value(
+        "recommonmark_config",
+        {
+            "url_resolver": lambda url: github_doc_root + url,
+            "auto_toc_tree_section": "Contents",
+        },
+        True,
+    )
+    app.add_transform(AutoStructify)
+    app.connect(
+        "autodoc-process-docstring",
+        no_namedtuple_attrib_docstring,
+    )
+
+
+def no_namedtuple_attrib_docstring(app, what, name, obj, options, lines):
+    is_namedtuple_docstring = len(lines) == 1 and lines[0].startswith(
+        "Alias for field number"
+    )
+    if is_namedtuple_docstring:
+        # We don't return, so we need to purge in-place
+        del lines[:]
+
+
+# endregion

Users/lpravda/anaconda3/envs/rdkit-env/lib/python3.7/site-packages/pdbeccdutils/__init__.py

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+__version__ = "0.5.9"

Users/lpravda/anaconda3/envs/rdkit-env/lib/python3.7/site-packages/pdbeccdutils/computations/parity_method.py

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+"""Lightweight implementation of the `parity method <https://doi.org/10.1016/j.str.2018.02.009>`_ provided by
+Jon Tyzack.
+"""
+
+from rdkit import Chem
+from rdkit.Chem import rdFMCS
+
+from pdbeccdutils.core.models import ParityResult
+
+
+def _get_matches(mol, smarts):
+    """Gets the subgraph match for the parity method.
+
+    Args:
+        mol (rdkit.Chem.rdchem.Mol): Molecule to be queried
+        smarts (str): Molecule representation in SMARTS.
+
+    Returns:
+        int: Molecular subgraph matches.
+    """
+
+    patt = Chem.MolFromSmarts(smarts)
+    matches = mol.GetSubstructMatches(patt, uniquify=False)
+    return matches
+
+
+def _generate_sim_score(template, query, smarts):
+    """Given the two moleculs and their common subgraph represented as
+    smarts string returns similarity score.
+
+    Args:
+        template (rdkit.Chem.rdchem.Mol): template molecule.
+        query (rdkit.Chem.Mol): query molecule.
+        smarts (str): common subgraph in the SMARTS format.
+
+    Returns:
+        tuple[dict[int, int], float]: atom id mapping for a common
+        subgraph and the similarity score.
+    """
+
+    if template.GetNumAtoms() == 1:
+        smarts = Chem.MolToSmarts(template)
+    elif query.GetNumAtoms() == 1:
+        smarts = Chem.MolToSmarts(query)
+    if smarts is None:
+        substructure = {}
+        best_sim_score = 0.0
+    else:
+        matches_1 = _get_matches(template, smarts)
+        matches_2 = _get_matches(query, smarts)
+        best_matches = 0
+        substructure = {}
+        size_1 = template.GetNumAtoms()
+        size_2 = query.GetNumAtoms()
+
+        for match_1 in matches_1:
+            for match_2 in matches_2:
+                matches = 0
+                for i, value in enumerate(match_1):
+                    atom_1 = template.GetAtomWithIdx(value)
+                    atom_2 = query.GetAtomWithIdx(match_2[i])
+                    symbol_1 = atom_1.GetSymbol()
+                    symbol_2 = atom_2.GetSymbol()
+                    if symbol_1 == symbol_2:
+                        matches += 1
+                if matches > best_matches:
+                    best_matches = matches
+                    substructure = dict(zip(match_1, match_2))
+        best_sim_score = float(best_matches) / float(size_1 + size_2 - best_matches)
+
+    return (substructure, best_sim_score)
+
+
+def compare_molecules(template, query, thresh=0.01, exact_match=False):
+    """Given the two molecules calculates their similarity score.
+    If expected similarity score is lower than the threshold nothing
+    is calculated.
+
+    Args:
+        template (rdkit.Chem.rdchem.Mol): Template molecule
+        query (rdkit.Chem.rdchem.Mol): Query molecule
+        thresh (float, optional): Threshold score for
+            the match to be considered. Defaults to 0.01.
+        exact_match (bool, optional): Controls whether atom type and
+            bond order should be checked too. Defaults to False.
+
+    Returns:
+        ParityResult: Result of the PARITY comparison.
+    """
+
+    template_atoms = template.GetNumAtoms()
+    query_atoms = query.GetNumAtoms()
+
+    min_num_atoms = min(template_atoms, query_atoms)
+    max_sim_score = float(min_num_atoms) / float(
+        template_atoms + query_atoms - min_num_atoms
+    )
+
+    if max_sim_score < thresh:
+        return ParityResult({}, 0.0)
+
+    if not exact_match:
+        mcs_graph = rdFMCS.FindMCS(
+            [template, query],
+            bondCompare=rdFMCS.BondCompare.CompareAny,
+            atomCompare=rdFMCS.AtomCompare.CompareAny,
+            timeout=40,
+            completeRingsOnly=True,
+        )
+    else:
+        mcs_graph = rdFMCS.FindMCS(
+            [template, query],
+            bondCompare=rdFMCS.BondCompare.CompareOrderExact,
+            atomCompare=rdFMCS.AtomCompare.CompareElements,
+            timeout=40,
+            completeRingsOnly=True,
+        )
+
+    substructure, sim_score = _generate_sim_score(
+        template, query, mcs_graph.smartsString
+    )
+
+    return ParityResult(substructure, sim_score)