ó a#nSc@s†ddlmZddlmZddlmZdedd„Zd„Ze dkr‚ddl Z eƒ\Z Z e j e ƒndS(i˙˙˙˙(tChem(t rdDepictor(tGeometryc CsŚ|s|j|ƒ}n|s*td‚ni}|j|ƒ}xEt|ƒD]7\}}|j|ƒ} tj| j| jƒ||>> 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] s!no match between mol and templatet clearConfstcoordMap( tGetSubstructMatcht ValueErrort GetConformert enumeratetGetAtomPositionRtPoint2DtxtyRtCompute2DCoords( tmolttemplatetmatchRttemplateConfIdtatomMapt templateConftitidxtpt molConfId((sZ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/TemplateAlign.pytAlignMolToTemplate2Ds;  cCs,ddl}ddl}|j|jdƒS(Ni˙˙˙˙t__main__(tdoctesttsysttestmodtmodules(RR((sZ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/TemplateAlign.pyt_test\sRN(trdkitRt rdkit.ChemRRtNonetFalseRRt__name__Rtfailedttriedtexit(((sZ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/TemplateAlign.pyt s L