Merge branch 'dev'

.github/workflows/documentation.yml

@@ -4,44 +4,42 @@ name: ccdutils documentation
 
 on:
   push:
-    branches: 
+    branches:
       - master
 
   pull_request:
-    branches: 
+    branches:
       - master
 
-  
 jobs:
   documentation:
     name: Generate documentation
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-      with:
-        persist-credentials: false    
-    
-    - name: Set up python
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.7
-    
-    - name: Set up environment and generate docs
-      uses: s-weigand/setup-conda@v1
-      with:
-        activate-conda: true
-        conda-channels: conda-forge 
-    - run: |
+      - uses: actions/checkout@v2
+        with:
+          persist-credentials: false
+
+      - name: Set up python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+
+      - name: Set up environment and generate docs
+        uses: s-weigand/setup-conda@v1
+        with:
+          activate-conda: true
+          conda-channels: conda-forge
+      - run: |
           conda install rdkit=2020.03.6
-          pip install -e ".[docs]"    
-    - run: |
+          pip install -e ".[docs]"
+      - run: |
           cd doc
           make html
-    
-        
-    - name: Deploy pages
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./doc/_build/html
+
+      - name: Deploy pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/_build/html

.github/workflows/tests.yml

@@ -18,21 +18,21 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-      with:
-        persist-credentials: false    
-    
-    - name: Set up python
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.7
-    
-    - name: Set up environment and run pytest
-      uses: s-weigand/setup-conda@v1
-      with:
-        activate-conda: true
-        conda-channels: conda-forge 
-    - run: |
-        conda install rdkit=2020.03.6
-        pip install -e ".[tests]"
-    - run: pytest --cov=pdbeccdutils
+      - uses: actions/checkout@v2
+        with:
+          persist-credentials: false
+
+      - name: Set up python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+
+      - name: Set up environment and run pytest
+        uses: s-weigand/setup-conda@v1
+        with:
+          activate-conda: true
+          conda-channels: conda-forge
+      - run: |
+          conda install rdkit=2020.03.6
+          pip install -e ".[tests]"
+      - run: pytest --cov=pdbeccdutils

.gitlab-ci.yml

@@ -9,20 +9,19 @@ before_script:
 
 test:
   script:
-  - pytest --cov=pdbeccdutils
+    - pytest --cov=pdbeccdutils
 
   only:
-  - master
+    - master
 
 pages:
   script:
-  - cd doc
-  - make html
-  - mv _build/html/ ../public/
-  
+    - cd doc
+    - make html
+    - mv _build/html/ ../public/
+
   artifacts:
     paths:
-    - public
+      - public
   only:
-  - master
-
+    - master

README.md

-![GitHub](https://img.shields.io/github/license/pdbeurope/ccdutils) ![ccdutils documentation](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20documentation/badge.svg) ![ccdutils tests](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20tests/badge.svg)
+[![CodeFactor](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/badge/master)](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/overview/master)  ![PYPi](https://img.shields.io/pypi/v/pdbeccdutils?color=green&style=flat)  ![GitHub](https://img.shields.io/github/license/pdbeurope/ccdutils)   ![ccdutils documentation](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20documentation/badge.svg) ![ccdutils tests](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20tests/badge.svg)
 
 # pdbeccdutils
 
@@ -43,8 +43,7 @@
 
 ## TODO list
 
-* Port rest of the important functionality implemented by Oliver
-* Add more unit/regression tests to get at least higher code coverage.
+* Add more unit/regression tests to get higher code coverage.
 * Further improvements of the documentation.
 
 ## Notes
@@ -65,7 +64,7 @@ Otherwise it cannot pick `rdkit` module. `sphinx_rtd_theme` is a theme providing
 
 * Generate *.rst* files to be included as a part of the documentation. Inside the directory `pdbeccdutils/doc` run the following commands to generate documentation.
 * Alternatively, use the `recommonmark` package along with the proper configuration to get the Markdown working.
-  
+
  Use the following to generate initial markup files to be used by sphinx.  This needs to be used when adding another sub-packages.
 
 ```console

doc/conf.py

@@ -99,7 +99,7 @@ html_logo = "logo.png"
 # 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"]
+# html_css_files = ["css/styles.css"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -191,7 +191,8 @@ def setup(app):
     )
     app.add_transform(AutoStructify)
     app.connect(
-        "autodoc-process-docstring", no_namedtuple_attrib_docstring,
+        "autodoc-process-docstring",
+        no_namedtuple_attrib_docstring,
     )
 
 
@@ -205,4 +206,3 @@ def no_namedtuple_attrib_docstring(app, what, name, obj, options, lines):
 
 
 # endregion
-

pdbeccdutils/core/ccd_reader.py

@@ -26,17 +26,20 @@ of molecules. The basic use can be as easy as this:
 """
 
 import os
-import sys
 from datetime import date
 from typing import Dict, List, NamedTuple
 
 import rdkit
-from pdbecif.mmcif_io import MMCIF2Dict
-
 from pdbeccdutils.core.component import Component
 from pdbeccdutils.core.exceptions import CCDUtilsError
-from pdbeccdutils.core.models import CCDProperties, Descriptor, ReleaseStatus
-from pdbeccdutils.helpers import collection_ext, conversions
+from pdbeccdutils.core.models import (
+    CCDProperties,
+    ConformerType,
+    Descriptor,
+    ReleaseStatus,
+)
+from pdbeccdutils.helpers import collection_ext, conversions, mol_tools, logging
+from pdbecif.mmcif_io import MMCIF2Dict
 
 
 class CCDReaderResult(NamedTuple):
@@ -52,11 +55,13 @@ class CCDReaderResult(NamedTuple):
         warnings (list[str]): A list of any warnings
             found while reading the CCD. If no warnings found `warnings`
             will be empty.
+        sanitized (bool): Whether or not the molecule was sanitized
     """
 
     warnings: List[str]
     errors: List[str]
     component: Component
+    sanitized: bool
 
 
 def read_pdb_cif_file(path_to_cif: str, sanitize: bool = True) -> CCDReaderResult:
@@ -110,11 +115,10 @@ def read_pdb_components_file(
 
     for k, v in MMCIF2Dict().parse(path_to_cif).items():
         try:
-            result_bag[k] = _parse_pdb_mmcif(v)
+            result_bag[k] = _parse_pdb_mmcif(v, sanitize)
         except CCDUtilsError as e:
-            print(
-                f"ERROR: Data block {k} not processed. Reason: ({str(e)}).",
-                file=sys.stderr,
+            logging.logger.error(
+                f"ERROR: Data block {k} not processed. Reason: ({str(e)})."
             )
 
     return result_bag
@@ -134,8 +138,9 @@ def _parse_pdb_mmcif(cif_dict, sanitize=True):
         CCDReaderResult: internal representation with the results
             of parsing and Mol object.
     """
-    warnings = list()
-    errors = list()
+    warnings = []
+    errors = []
+    sanitized = False
     mol = rdkit.Chem.RWMol()
 
     atoms_dict = _preprocess_pdb_parser_output(cif_dict, "_chem_comp_atom", warnings)
@@ -153,12 +158,17 @@ def _parse_pdb_mmcif(cif_dict, sanitize=True):
     _parse_pdb_bonds(mol, bonds_dict, atoms_dict, errors)
     _handle_implicit_hydrogens(mol)
 
+    if sanitize:
+        sanitized = mol_tools.sanitize(mol)
+
     descriptors = _parse_pdb_descriptors(descriptors_dict, "descriptor")
     descriptors += _parse_pdb_descriptors(identifiers_dict, "identifier")
     properties = _parse_pdb_properties(properties_dict)
 
-    comp = Component(mol.GetMol(), cif_dict, properties, descriptors, sanitize=sanitize)
-    reader_result = CCDReaderResult(warnings=warnings, errors=errors, component=comp)
+    comp = Component(mol.GetMol(), cif_dict, properties, descriptors)
+    reader_result = CCDReaderResult(
+        warnings=warnings, errors=errors, component=comp, sanitized=sanitized
+    )
 
     return reader_result
 
@@ -212,20 +222,23 @@ def _parse_pdb_conformers(mol, atoms):
     if not atoms:
         return
 
-    ideal = _setup_pdb_conformer(atoms, "pdbx_model_Cartn_{}_ideal")
-    model = _setup_pdb_conformer(atoms, "model_Cartn_{}")
+    ideal = _setup_pdb_conformer(
+        atoms, "pdbx_model_Cartn_{}_ideal", ConformerType.Ideal.name
+    )
+    model = _setup_pdb_conformer(atoms, "model_Cartn_{}", ConformerType.Model.name)
 
     mol.AddConformer(ideal, assignId=True)
     mol.AddConformer(model, assignId=True)
 
 
-def _setup_pdb_conformer(atoms, label):
+def _setup_pdb_conformer(atoms, label, name):
     """
     Setup a conformer
 
     Args:
         atoms (dict): mmcif category with the atom info.
         label (str): Namespace with the [x,y,z] coordinates.
+        name (str): Conformer name.
 
     Returns:
         rdkit.Chem.rdchem.Conformer: Conformer of the component.
@@ -243,6 +256,8 @@ def _setup_pdb_conformer(atoms, label):
         atom_position = rdkit.Chem.rdGeometry.Point3D(x, y, z)
         conformer.SetAtomPosition(i, atom_position)
 
+    conformer.SetProp("name", name)
+
     return conformer
 
 
@@ -352,6 +367,11 @@ def _parse_pdb_properties(chem_comp):
 
         rel_status = chem_comp["pdbx_release_status"][0]
         rel_status = ReleaseStatus.from_str(chem_comp["pdbx_release_status"][0])
+        weight = (
+            0.0
+            if chem_comp["formula_weight"][0] == "?"
+            else float(chem_comp["formula_weight"][0])
+        )
 
         properties = CCDProperties(
             id=chem_comp["id"][0],
@@ -359,9 +379,7 @@ def _parse_pdb_properties(chem_comp):
             formula=chem_comp["formula"][0],
             modified_date=d,
             pdbx_release_status=rel_status,
-            weight=0.0
-            if chem_comp["formula_weight"][0] == "?"
-            else float(chem_comp["formula_weight"][0]),
+            weight=weight,
         )
     return properties
 

pdbeccdutils/core/ccd_writer.py

@@ -28,15 +28,15 @@ import math
 import xml.etree.ElementTree as ET
 from collections import OrderedDict
 from typing import List
-from xml.dom import minidom
 
+import pdbeccdutils
 import pdbecif.mmcif_io as mmcif
 import rdkit
-
-import pdbeccdutils
+from defusedxml import minidom
 from pdbeccdutils.core.component import Component
 from pdbeccdutils.core.exceptions import CCDUtilsError
 from pdbeccdutils.core.models import ConformerType
+from pdbeccdutils.helpers.logging import logger
 
 
 def write_molecule(
@@ -165,24 +165,24 @@ def to_sdf_str(
     Returns:
         str: String representation of the component in the SDF format
     """
-    (mol_to_save, conf_id, conf_type) = _prepate_structure(
-        component, remove_hs, conf_type
-    )
+    (mol_to_save, _, conf_type) = _prepate_structure(component, remove_hs, conf_type)
 
     mol_block = []
-    mappings = {}
+
     if conf_type == ConformerType.AllConformers:
         conformers = [ConformerType.Model, ConformerType.Ideal, ConformerType.Computed]
     else:
         conformers = [conf_type]
     try:
-        for conf in conformers:
+        for c in conformers:
             try:
+                conf_id = -1
+                if c != ConformerType.AllConformers:
+                    conf_id = component.get_conformer(c).GetId()
+
                 block = [
-                    f"{component.id} - {conf.name} conformer",
-                    rdkit.Chem.MolToMolBlock(
-                        mol_to_save, confId=component.conformers_mapping[conf]
-                    ).strip(),
+                    f"{component.id} - {c.name} conformer",
+                    rdkit.Chem.MolToMolBlock(mol_to_save, confId=conf_id).strip(),
                     "$$$$\n",
                 ]
                 mol_block += block
@@ -192,8 +192,7 @@ def to_sdf_str(
                 else:
                     raise CCDUtilsError(f"Error writing SDF file - {e}")
     except Exception:
-        mappings = {m.name: component.conformers_mapping[m] for m in conformers}
-        mol_block = _to_sdf_str_fallback(mol_to_save, component.id, mappings)
+        mol_block = _to_sdf_str_fallback(mol_to_save, component.id, conformers)
 
     return "\n".join(mol_block)
 
@@ -544,11 +543,16 @@ def _prepate_structure(component, remove_hs, conf_type):
         tuple(rdkit.Mol,int,ConformerType): mol along with properties
         to be exported.
     """
-    conf_id = (
-        0
-        if conf_type == ConformerType.Depiction
-        else component.conformers_mapping[conf_type]
-    )
+    conf_id = -1  # this is AllConformers options
+
+    if conf_type == ConformerType.Depiction:
+        conf_id = 0
+    else:
+        for c in component.mol.GetConformers():
+            if c.GetProp("name") == conf_type.name:
+                conf_id = c.GetId()
+                break
+
     mol_to_save = (
         component.mol2D if conf_type == ConformerType.Depiction else component.mol
     )
@@ -794,11 +798,14 @@ def _get_cml_bond_type(bond_order):
     """
     if bond_order == rdkit.Chem.rdchem.BondType.SINGLE:
         return "1"
-    elif bond_order == rdkit.Chem.rdchem.BondType.DOUBLE:
+
+    if bond_order == rdkit.Chem.rdchem.BondType.DOUBLE:
         return "2"
-    elif bond_order == rdkit.Chem.rdchem.BondType.TRIPLE:
+
+    if bond_order == rdkit.Chem.rdchem.BondType.TRIPLE:
         return "3"
-    elif bond_order == rdkit.Chem.rdchem.BondType.AROMATIC:
+
+    if bond_order == rdkit.Chem.rdchem.BondType.AROMATIC:
         return "A"
     else:
         return str(bond_order)
@@ -823,13 +830,14 @@ def _get_ccd_cif_bond_stereo(bond):
         rdkit.Chem.rdchem.BondStereo.STEREOCIS,
     ):
         return "E"
-    elif stereo in (
+
+    if stereo in (
         rdkit.Chem.rdchem.BondStereo.STEREOZ,
         rdkit.Chem.rdchem.BondStereo.STEREOTRANS,
     ):
         return "Z"
-    else:
-        return "N"
+
+    return "N"
 
 
 def _get_ccd_cif_bond_type(bond):
@@ -848,16 +856,20 @@ def _get_ccd_cif_bond_type(bond):
 
     if bond_order == rdkit.Chem.rdchem.BondType.SINGLE:
         return "SING"
-    elif bond_order == rdkit.Chem.rdchem.BondType.DOUBLE:
+
+    if bond_order == rdkit.Chem.rdchem.BondType.DOUBLE:
         return "DOUB"
-    elif bond_order == rdkit.Chem.rdchem.BondType.TRIPLE:
+
+    if bond_order == rdkit.Chem.rdchem.BondType.TRIPLE:
         return "TRIP"
-    elif bond_order == rdkit.Chem.rdchem.BondType.AROMATIC:
+
+    if bond_order == rdkit.Chem.rdchem.BondType.AROMATIC:
         return "AROM"
-    elif bond_order == rdkit.Chem.rdchem.BondType.QUADRUPLE:
+
+    if bond_order == rdkit.Chem.rdchem.BondType.QUADRUPLE:
         return "QUAD"
-    else:
-        return "SING"
+
+    return "SING"
 
 
 def _get_ccd_cif_chiral_type(atom):
@@ -877,10 +889,11 @@ def _get_ccd_cif_chiral_type(atom):
 
     if chiral_type == rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW:
         return "R"
-    elif chiral_type == rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW:
+
+    if chiral_type == rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW:
         return "S"
-    else:
-        return "N"
+
+    return "N"
 
 
 def _get_atom_coord(component, at_id, conformer_type):
@@ -895,39 +908,49 @@ def _get_atom_coord(component, at_id, conformer_type):
     Returns:
         rdkit.Geometry.rdGeometry.Point3D: 3D coordinates of the atom.
     """
-    conf_id = component.conformers_mapping[conformer_type]
+    conformer = None
+    for c in component.mol.GetConformers():
+        if c.GetProp("name") == conformer_type.name:
+            conformer = c
+            break
 
-    return component.mol.GetConformer(conf_id).GetAtomPosition(at_id)
+    return conformer.GetAtomPosition(at_id)
 
 
 # region fallbacks
 
 
-def _to_sdf_str_fallback(mol, ccd_id, mappings):
+def _to_sdf_str_fallback(mol, ccd_id, conformers):
     """Fallback method to generate SDF file in case the default one in
     RDKit fails.
 
     Args:
         mol (rdkit.Chem.rdchem.Mol): rdkit mol to be exported
         id (str): component id.
-        mappings (dict of str): Deemed mappings to be exported
+        conformers (list of of ConformerType): List of conformer types
+            to be exported.
 
     Returns:
         list of str: SDF representation of the component
     """
     content = []
 
-    for k, v in mappings.items():
-        try:
-            rdkit_conformer = mol.GetConformer(v)
-        except ValueError:
-            continue
+    for c in conformers:
+        rdkit_conformer = None
+
+        if c == ConformerType.AllConformers:
+            rdkit_conformer = mol.GetConformer()
+        else:
+            for conf in mol.GetConformers():
+                if conf.GetProp("name") == c.name:
+                    rdkit_conformer = conf
+                    break
 
         atom_count = mol.GetNumAtoms()
         bond_count = mol.GetNumBonds()
 
         content += [
-            f"{ccd_id} - {k} conformer",
+            f"{ccd_id} - {c.name} conformer",
             "    RDKit   3D",
             "\n" f"{atom_count:>3}{bond_count:3}  0  0  0  0  0  0  0  0999 V2000",
         ]
@@ -1041,20 +1064,20 @@ def __charge_to_sdf(charge):
     """
     if charge == -3:
         return "7"
-    elif charge == -2:
+    if charge == -2:
         return "6"
-    elif charge == -1:
+    if charge == -1:
         return "5"
-    elif charge == 0:
+    if charge == 0:
         return "0"
-    elif charge == 1:
+    if charge == 1:
         return "+1"
-    elif charge == 2:
+    if charge == 2:
         return "+2"
-    elif charge == 3:
+    if charge == 3:
         return "+4"
-    else:
-        return "0"
+
+    return "0"
 
 
 def __bond_stereo_to_sdf(bond):
@@ -1095,14 +1118,14 @@ def __bond_type_to_sdf(bond):
 
     if bond_order == rdkit.Chem.rdchem.BondType.SINGLE:
         return "1"
-    elif bond_order == rdkit.Chem.rdchem.BondType.DOUBLE:
+    if bond_order == rdkit.Chem.rdchem.BondType.DOUBLE:
         return "2"
-    elif bond_order == rdkit.Chem.rdchem.BondType.TRIPLE:
+    if bond_order == rdkit.Chem.rdchem.BondType.TRIPLE:
         return "3"
-    elif bond_order == rdkit.Chem.rdchem.BondType.AROMATIC:
+    if bond_order == rdkit.Chem.rdchem.BondType.AROMATIC:
         return "A"
-    else:
-        return "0"
+
+    return "0"
 
 
 def __post_process_cif_category(cif_copy, category_name):
@@ -1382,11 +1405,11 @@ def _add_rdkit_conformer_cif(component, cif_copy, remove_hs):
         the CIF file.
     remove_hs (boolean): Whether or not hydrogen atoms should be written
     """
+
     try:
-        conformer = component.mol.GetConformer(
-            component.conformers_mapping[ConformerType.Computed]
-        )
+        conformer = component.get_conformer(ConformerType.Computed)
     except ValueError:
+        logger.warning("Computed conformer does not exist.")
         return  # no conformer nothing to write, we quit
 
     category = "_pdbe_chem_comp_rdkit_conformer"

pdbeccdutils/core/component.py

@@ -17,9 +17,7 @@
 
 import json
 import re
-import sys
 from datetime import date