a#nSc@sddlmZddlZddlZddlmZdefdYZdZedkrddl Z e\Z Z e j e ndS(i(tChemN(tRDConfigt SaltRemovercBs\eZejjejdZdZ dZ dddZ dZ e dZe dZRS(s Salts.txtcCs)|r||_n||_|jdS(N(t defnFilenametdefnDatat _initPatterns(tselfRR((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/SaltRemover.pyt__init__,s  cCstjd}|jr:ddlm}||j}nt|jd}g|_x|D]}|jj dd}|r\|j |}yt j |d}Wn&ddl }|j t|nX|jj|q\q\WdS(s >>> remover = SaltRemover() >>> len(remover.salts)>0 True >>> remover = SaltRemover(defnData="[Cl,Br]") >>> len(remover.salts) 1 s[\t ]+i(tStringIOtrs//iN(tretcompileRt cStringIORtfileRtsaltststriptsplitRt MolFromSmartst tracebackt print_exct ValueErrortappend(Rt whitespaceRtinFtlinetsplitLtsaltR((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/SaltRemover.pyR2s"       cCsd}|r.ttj|dkr.|St}xot|jD]^\}}||||}||k rD|}t}|rttj|dkrPqqDqDW|r|jdkrtj|n|S(s >>> remover = SaltRemover(defnData="[Cl,Br]") >>> len(remover.salts) 1 >>> mol = Chem.MolFromSmiles('CN(C)C.Cl') >>> res = remover.StripMol(mol) >>> res is not None True >>> res.GetNumAtoms() 4 Notice that all salts are removed: >>> mol = Chem.MolFromSmiles('CN(C)C.Cl.Cl.Br') >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 4 Matching (e.g. "salt-like") atoms in the molecule are unchanged: >>> mol = Chem.MolFromSmiles('CN(Br)Cl') >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 4 >>> mol = Chem.MolFromSmiles('CN(Br)Cl.Cl') >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 4 Charged salts are handled reasonably: >>> mol = Chem.MolFromSmiles('C[NH+](C)(C).[Cl-]') >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 4 Watch out for this case (everything removed): >>> remover = SaltRemover() >>> len(remover.salts)>1 True >>> mol = Chem.MolFromSmiles('CC(=O)O.[Na]') >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 0 dontRemoveEverything helps with this by leaving the last salt: >>> res = remover.StripMol(mol,dontRemoveEverything=True) >>> res.GetNumAtoms() 4 but in cases where the last salts are the same, it can't choose between them, so it returns all of them: >>> mol = Chem.MolFromSmiles('Cl.Cl') >>> res = remover.StripMol(mol,dontRemoveEverything=True) >>> res.GetNumAtoms() 2 cSs|j}|s|S|}tj||t}| sP|rT|jdkrT|S|}xe|jr||jkr|j}tj||t}|r|jdkrPq]|}q]W|S(Ni(t GetNumAtomsRtDeleteSubstructstTrue(tmRt notEverythingtnAtstrestt((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/SaltRemover.pyt _applyPatterns !  ii( tlenRt GetMolFragstFalset enumerateRRRt SanitizeMol(RtmoltdontRemoveEverythingR#tmodifiedtiRttMol((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/SaltRemover.pytStripMolQs< ! ! cCs|j|d|S(s >>> remover = SaltRemover(defnData="[Cl,Br]") >>> len(remover.salts) 1 >>> mol = Chem.MolFromSmiles('CN(C)C.Cl') >>> res = remover(mol) >>> res is not None True >>> res.GetNumAtoms() 4 R*(R.(RR)R*((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/SaltRemover.pyt__call__sN(t__name__t __module__tostpathtjoinRt RDDataDirRtNoneRRRRR&R.R/(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/SaltRemover.pyR(s  ^cCs,ddl}ddl}|j|jdS(Nit__main__(tdoctesttsysttestmodtmodules(R8R9((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/SaltRemover.pyt_testsR7( trdkitRR2R RtobjectRR<R0R9tfailedttriedtexit(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/SaltRemover.pyt#s