B ž3Rc› ã@s.ddlmZddlmZddlZddd„ZdS) é)ÚChem)ÚrdFMCSNTútmp.pdbcCs^t |¡}t |¡}| ¡ ¡}| ¡ ¡}t ||g¡}t |j¡}t|  |¡ƒ}|j |dd} ||}g} x@| D]8} |t| ƒ} | |} |   t   | |  ¡t| ƒ¡¡qtWt| ƒ}|rZ| t  | ¡}tt||ƒƒ}dd„| ¡Dƒ}| ¡d ¡ ¡}xLt| ¡ƒD]<\}}| ¡ |¡|| ¡kr| ¡ |||¡qWt ||¡|S)a Calculate the Root-mean-square deviation (RMSD) between two prealigned ligands, even when atom names between the two ligands are not matching. The symmetry of the molecules is taken into consideration (e.g. tri-methyl groups). Moreover, if one ligand structure has missing atoms (e.g. undefined electron density in the crystal structure), the RMSD is calculated for the maximum common substructure (MCS). Parameters ---------- lig1 : RDKit molecule lig2 : RDKit molecule rename_lig2 : bool, optional True to rename the atoms of lig2 according to the atom names of lig1 output_filename : str, optional If rename_lig2 is set to True, a PDB file with the renamed lig2 atoms is written as output. This may be useful to check that the RMSD has been "properly" calculated, i.e. that the atoms have been properly matched for the calculation of the RMSD. Returns ------- rmsd : float Root-mean-square deviation between the two input molecules F)ZuniquifycSsg|]}| ¡ ¡‘qS©)ÚGetPDBResidueInfoZGetName)Ú.0Úatom1rrú.share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.pyú DszCalcLigRMSD..r)rZRemoveHsZ GetConformerZ GetPositionsrZFindMCSZ MolFromSmartsZ smartsStringÚlistZGetSubstructMatchZGetSubstructMatchesÚappendÚnpZsqrtÚsumÚlenÚminZargminÚdictÚzipZGetAtomsrZGetResidueNameÚ enumerateZSetResidueNameÚkeysZSetNameZ MolToPDBFile)Zlig1Zlig2Z rename_lig2Zoutput_filenameZcoordinates_lig2Zcoordinates_lig1ZresZref_molZmas1Z mas2_listZ list_rmsdZmatch1Zcoordinates_lig2_tmpZdiffZlig_rmsdZmas2Zcorrespondence_key2_item1Zatom_names_lig1Z lig1_ResNameÚirrrr Ú CalcLigRMSDs4       $ r)Tr)ZrdkitrZ rdkit.ChemrZnumpyr rrrrr Ú s