def compute_2d(self,
manager: DepictionManager,
remove_hs: bool = True) -> DepictionResult:
"""Compute 2d depiction of the component using DepictionManager
instance.
Args:
manager (DepictionManager): Instance of the ligand depiction
class.
remove_hs (bool, optional): Defaults to True. Remove
hydrogens prior to depiction.
Returns:
DepictionResult: Object with the details about depiction process.
"""
mol_copy = rdkit.Chem.RWMol(self.mol)
if remove_hs:
mol_copy = rdkit.Chem.RemoveHs(mol_copy,
updateExplicitCount=True,
sanitize=False)
rdkit.Chem.SanitizeMol(mol_copy, catchErrors=True)
result_log = manager.depict_molecule(self.id, mol_copy)
self.mol2D = result_log.mol
return result_log
def __init__(
self,
pubchem_templates="",
general_templates=config.general_templates,
library_path=config.fragment_library,
):
"""Initialize manager
Args:
pubchem_templates (str): Path to the pubchem templates
general_templates (str, optional): Path to the general templates.
Defaults to config.general_templates.
library_path (str, optional): Path to the fragments library:
Defaults to config.fragment_library.
"""
# helper class to download templates if needed
self.pubchem = (PubChemDownloader(pubchem_templates)
if pubchem_templates else None)
# helper class to get nice depictions
self.depictions = DepictionManager(pubchem_templates,
general_templates)
# Fragments library to get substructure matches
self.fragment_library = FragmentLibrary(library_path)
def test_collision_template_picked(expected_template, names):
"""Test if expected templates are picked for certain compounds
Args:
expected_template (str): template name.
names (list of str): list of ids matching this template.
"""
d = DepictionManager()
for ccd_id in names:
mol = load_molecule(ccd_id)
response = mol.compute_2d(d)
assert response.source == DepictionSource.Template
assert response.score > 0
assert response.template_name == expected_template
def _init(self, args):
"""Initialize PDBeChem pipeline and necessary objects.
Args:
args (argparse.Namespace): Verified application arguments
"""
self.logger.debug('Initializing calculation...')
self.output_dir = args.output_dir
self.depictions = DepictionManager(args.pubchem_templates,
args.general_templates)
self.pubchem = PubChemDownloader(
args.pubchem_templates) if os.path.isdir(
args.pubchem_templates) else None
self.fragment_library = FragmentLibrary(args.library)
self.logger.debug(f'Reading in {args.components_cif} file...')
self.compounds = ccd_reader.read_pdb_components_file(
args.components_cif)
self.ligands_to_process = len(
self.compounds) if args.test_first is None else args.test_first
self.logger.debug('Initialization finished.')
import pytest
from pdbeccdutils.core import ccd_reader
from pdbeccdutils.core.component import Component
from pdbeccdutils.core.depictions import DepictionManager, DepictionSource
from pdbeccdutils.tests.tst_utilities import cif_filename
collision_free_templates = [
('hem', ['HEM', 'HEA', 'HEB', 'HEC', 'HDD', 'HEG']),
('porphycene', ['HNN', 'HME']),
('ru_complex', ['11R']),
]
collision_templates = [('cube', ['SF4', '0KA', '1CL']),
('adamantane', ['ADM'])]
depictions = DepictionManager()
def load_molecule(id_):
c = ccd_reader.read_pdb_cif_file(cif_filename(id_)).component
c.compute_2d(depictions)
return c
class TestWriteImg:
@staticmethod
def test_file_generated(
tmpdir): # tmpdir is a fixture with temporary directory
mol = load_molecule('ATP')
path = str(tmpdir.join('atp_test.svg'))