from ccdc.molecule import Molecule
from ccdc.io import _CSDDatabaseLocator
from ccdc.utilities import _private_importer
with _private_importer():
import ChemicalAnalysisLib
import ConformerGeneratorLib
def ccdc_mol_from_smiles(smiles, identifier=None, generate_initial_sites=True):
"""
Pete's function for making a ccdc molecule with initial coordinates from a smiles string.
:param identifier:
:param generate_initial_sites:
:return:
"""
if identifier is None:
identifier = smiles
if generate_initial_sites:
parameter_files = _CSDDatabaseLocator.get_conformer_parameter_file_location()
molmaker = ConformerGeneratorLib.MoleculeTo3D(parameter_files)
mol = Molecule(identifier, molmaker.create_conformation(smiles))
else:
molmaker = ChemicalAnalysisLib.SMILESMoleculeMaker()
mol = Molecule(identifier, _molecule=molmaker.siteless_atoms(smiles))
return mol
from ccdc.pharmacophore import Pharmacophore
from ccdc.io import csd_directory, CrystalReader, MoleculeWriter, MoleculeReader
from ccdc.molecule import Molecule, Atom, Coordinates
from ccdc.descriptors import GeometricDescriptors
from ccdc import utilities
from ccdc.utilities import PushDir
from hotspots.grid_extension import Grid
from hotspots.wrapper_pdb import PDBResult
from hotspots.wrapper_arpeggio import Arpeggio
from hotspots.protein_extension import Protein
from hotspots.wrapper_pymol import PyMOLCommands, PyMOLFile
with utilities._private_importer():
import MotifPharmacophoreLib
import SubstructureSearchLib
import ChemistryLib
import MathsLib
import UtilitiesLib
def _coordinate_str(coord, digits=4):
return f"{round(coord[0], digits)}_{round(coord[1], digits)}_{round(coord[2], digits)}"
def to_array(t):
return np.array([float(t[0]), float(t[1]), float(t[2])])