B 3Rc @s^ddlmZddlmZddlmZd ddZd d Zed krZddlZe\Z Z e e dS) )Chem) rdDepictor)GeometryNFc Csp|s||}|stdi}||}x2t|D]&\}}||} t| j| j||<q2Wt j |||d} | S)a Arguments: - mol: the molecule to be aligned - template: the template to align to - match: If provided, this should be a sequence of integers containing the indices of the atoms in mol that match those in template. This is the result of calling: mol.GetSubstructMatch(template) - clearConfs: toggles removing any existing conformers on mol Returns the confId of the conformer containing the depiction >>> patt = Chem.MolFromSmiles('C1CC1') >>> rdDepictor.Compute2DCoords(patt) 0 >>> mol = Chem.MolFromSmiles('OC1CC1CC1CCC1') >>> rdDepictor.Compute2DCoords(mol) 0 >>> pc = patt.GetConformer(0) >>> mc = mol.GetConformer(0) We start out with the molecules not aligned: >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())] >>> [x<1e-4 for x in vs] [False, False, False] But then we can replace the conformer of mol: >>> AlignMolToTemplate2D(mol,patt,clearConfs=True) 0 >>> mol.GetNumConformers() 1 >>> pc = patt.GetConformer(0) >>> mc = mol.GetConformer(0) >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())] >>> [x<1e-4 for x in vs] [True, True, True] If we like, we can specify the atom map explicitly in order to align to the second matching ring in the probe molecule: >>> match = (5,6,7) >>> AlignMolToTemplate2D(mol,patt,clearConfs=True,match=match) 0 >>> mol.GetNumConformers() 1 >>> pc = patt.GetConformer(0) >>> mc = mol.GetConformer(0) >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())] >>> [x<1e-4 for x in vs] [False, False, False] >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+5).x) for i in range(pc.GetNumAtoms())] >>> [x<1e-4 for x in vs] [True, True, True] z!no match between mol and template) clearConfsZcoordMap) ZGetSubstructMatch ValueErrorZ GetConformer enumerateZGetAtomPositionrZPoint2DxyrZCompute2DCoords) ZmoltemplatematchrZtemplateConfIdZatomMapZ templateConfiidxpZ molConfIdr7lib/python3.7/site-packages/rdkit/Chem/TemplateAlign.pyAlignMolToTemplate2DsA   rcCs6ddl}ddl}ddlm}|d||jdS)Nr)rF__main__)doctestsys rdkit.ChemrZSetPreferCoordGenZtestmodmodules)rrrrrr_testcs  rr)NFr) Zrdkitrrrrrr__name__rZfailedZtriedexitrrrr s    O