B ž3RcO‹ã@sˆddlZddlZddlZddlZddlZddlmZddlmZdddddd d d d d d dddddddddœZ dddgdddddgddgdd d!d"d#gd$d%d&d'gd(gd)d*d+d,d-d.gd/d0d1d2gd3d4d5d6gd7d8d9d:gd;dd?d@gdAgdBgfZ e  e ¡Z x|e D]tZ xnee ƒD]b\ZZe\ZZZe dCeZe dCeZe dDdEe¡Ze dDdEe¡ZdFeeeeefZee e<qWqøWxVe D]NZ xFe D]>Zye e¡Ze ¡Wn ek rºeeƒ‚YnXq€WqvWiZx$e  ¡D]\ZZe  e¡ee<qÖWgZ!x|ee ƒD]p\Z"Z#gZ$xVe#D]N\Z%Z&Z'e dGe%Z(e dGe&Z)dHe(e'e)fZ*e  e*¡Z*e$ +e%e&e'e*f¡qWe! +e$¡qWe,dIdJ„e Dƒƒa-gZ.xxee ƒD]l\Z"Z/x`ee/ƒD]T\ZZe 0dK¡\Z1Z2dLe2e1fZe e¡Z3e 4dMe2¡Z5dNdJ„e5Dƒe3_6e. +e3¡q¦Wq”WdadQdR„Z7dbdSdT„Z8dcdVdW„Z9e :dX¡Z;dddZd[„Zd^kr„ddl?Z?Gd_d`„d`e?j@ƒZ@e=ƒ\ZAZBeAr|e CeA¡e? D¡dS)eéN)ÚChem)ÚrdChemReactionsz[C;D3]([#0,#6,#7,#8])(=O)z[O;D2]-;!@[#0,#6,#1]z[C;!D1;!$(C=*)]-;!@[#6]z:[N;!D1;!$(N=*);!$(N-[!#6;!#16;!#0;!#1]);!$([N;R]@[C;R]=O)]z[C;D3;!R](=O)-;!@[#0,#6,#7,#8]z[C;D2,D3]-[#6]z[C;!R;!D1]-;!@[#6]z[C;!R;!D1;!$(C!-*)]z![n;+0;$(n(:[c,n,o,s]):[c,n,o,s])]z[N;R;$(N(@C(=O))@[C,N,O,S])]z[S;D2](-;!@[#0,#6])z[S;D4]([#6,#0])(=O)(=O)z [C;$(C(-;@[C,N,O,S])-;@[N,O,S])]z[c;$(c(:[c,n,o,s]):[n,o,s])]z[C;$(C(-;@C)-;@C)]z[c;$(c(:c):c)])ZL1ZL3ZL4ZL5ZL6ZL7aZL7bz#L8ZL8ZL9ZL10ZL11ZL12ZL13ZL14ZL14bZL15ZL16ZL16b)Ú1Ú3ú-)rÚ5r)rÚ10r)rÚ4r)rÚ13r)rÚ14r)rÚ15r)rÚ16r)r rr)r Ú11r)rZ12r)rr r)rr r)rr r)rr r)Ú6r r)rr r)rr r)rr r)Z7aZ7bú=)Ú8Ú9r)rrr)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)rr r)r r r)r r r)r r r)r r r)r r r)r r r)r r r)r r rÚLz [a-z,A-Z]Úz0[$(%s):1]%s;!@[$(%s):2]>>[%s*]-[*:1].[%s*]-[*:2]zL%sz[$(%s)]%s;!@[$(%s)]cCsg|]}dd„|Dƒ‘qS)cSsg|]}t |¡‘qS©)Ú ReactionsÚReactionFromSmarts)Ú.0Úyrrú/lib/python3.7/site-packages/rdkit/Chem/BRICS.pyú ász.r)rÚxrrrrásrz>>z%s>>%sz\[([0-9]+?)\*\]cCsg|]}t d|¡‘qS)z[%s*])rÚ MolFromSmiles)rrrrrrésFTccs<t d¡}ttttƒƒƒ}tƒ}|r4tj|tjdi}x"t   ¡D]\}}|  |¡||<qBWxÚ|D]Ò} |rŒt| dd…} tj| tjdnt| } xž| D]–\} } } }|d| rš|d| sÀqš|  |¡}|  d| ¡} |  d| ¡} xL|D]D}||krè|d|df|krè| |¡|d|df| | ffVqèWqšWqbWdS)aö returns the bonds in a molecule that BRICS would cleave >>> from rdkit import Chem >>> m = Chem.MolFromSmiles('CCCOCC') >>> res = list(FindBRICSBonds(m)) >>> res [((3, 2), ('3', '4')), ((3, 4), ('3', '4'))] a more complicated case: >>> m = Chem.MolFromSmiles('CCCOCCC(=O)c1ccccc1') >>> res = list(FindBRICSBonds(m)) >>> res [((3, 2), ('3', '4')), ((3, 4), ('3', '4')), ((6, 8), ('6', '16'))] we can also randomize the order of the results: >>> random.seed(23) >>> res = list(FindBRICSBonds(m,randomizeOrder=True)) >>> sorted(res) [((3, 2), ('3', '4')), ((3, 4), ('3', '4')), ((6, 8), ('6', '16'))] Note that this is a generator function : >>> res = FindBRICSBonds(m) >>> res >>> next(res) ((3, 2), ('3', '4')) >>> m = Chem.MolFromSmiles('CC=CC') >>> res = list(FindBRICSBonds(m)) >>> sorted(res) [((1, 2), ('7', '7'))] make sure we don't match ring bonds: >>> m = Chem.MolFromSmiles('O=C1NCCC1') >>> list(FindBRICSBonds(m)) [] another nice one, make sure environment 8 doesn't match something connected to a ring atom: >>> m = Chem.MolFromSmiles('CC1(C)CCCCC1') >>> list(FindBRICSBonds(m)) [] z [a-z,A-Z])ÚrandomNrrér)ÚreÚcompileÚlistÚrangeÚlenÚ bondMatchersÚsetrÚshuffleÚenvironMatchersÚitemsÚHasSubstructMatchZGetSubstructMatchesÚsubÚadd)ÚmolZrandomizeOrderÚsilentZletterÚindicesZ bondsDoneZ envMatchesÚenvÚpattÚgpIdxÚcompatsÚi1Úi2ÚbTypeZmatchesÚmatchrrrÚFindBRICSBondsís.2       r8cCs–|s t |¡}|rt |¡|St |¡}| ¡}g}xð|D]è\}} |\} } | | | ¡} |  ¡} | | | ¡| \}}t d¡}|  t |ƒ¡|  d¡|}|d7}|  |¡|  | || ¡t d¡}|  t |ƒ¡|  d¡|}|d7}|  |¡|  | || ¡| ¡r<| || f¡| || f¡q>> from rdkit import Chem >>> m = Chem.MolFromSmiles('CCCOCC') >>> m2=BreakBRICSBonds(m) >>> Chem.MolToSmiles(m2,True) '[3*]O[3*].[4*]CC.[4*]CCC' a more complicated case: >>> m = Chem.MolFromSmiles('CCCOCCC(=O)c1ccccc1') >>> m2=BreakBRICSBonds(m) >>> Chem.MolToSmiles(m2,True) '[16*]c1ccccc1.[3*]O[3*].[4*]CCC.[4*]CCC([6*])=O' can also specify a limited set of bonds to work with: >>> m = Chem.MolFromSmiles('CCCOCC') >>> m2 = BreakBRICSBonds(m,[((3, 2), ('3', '4'))]) >>> Chem.MolToSmiles(m2,True) '[3*]OCC.[4*]CCC' this can be used as an alternate approach for doing a BRICS decomposition by following BreakBRICSBonds with a call to Chem.GetMolFrags: >>> m = Chem.MolFromSmiles('CCCOCC') >>> m2=BreakBRICSBonds(m) >>> frags = Chem.GetMolFrags(m2,asMols=True) >>> [Chem.MolToSmiles(x,True) for x in frags] ['[4*]CCC', '[3*]O[3*]', '[4*]CC'] rTr)rZFragmentOnBRICSBondsÚ SanitizeMolZ EditableMolÚ GetNumAtomsZGetBondBetweenAtomsZ GetBondTypeZ RemoveBondZAtomZ SetIsotopeÚintZ SetNoImplicitZAddAtomZAddBondÚGetNumConformersÚappendZGetMolZ GetConformersÚ GetConformerZGetIdZSetAtomPositionÚGetAtomPosition)r-ZbondsZsanitizer.ÚresZeMolZnAtsZdummyPositionsr/Z dummyTypesZiaZibZobondZbondTypeZdaZdbZatomaZidxaZatombZidxbZconfZresConfZparrrÚBreakBRICSBonds:sP"             rArc sft |d¡}|dkrtƒ}||kr(tƒS||i} | |¡||i} xÞttƒD]Ð\} } i} x¼| rd}tt| ƒƒ}|  |¡}x|t| ƒD]n\}}|r¨| |f|kr¨qŒ|sÄt dƒt t | |ƒ|  |f¡}|rŒ|sêt |dt |ƒdƒx|D]‰d}dd „tˆƒDƒ}|  ¡x~|D]v\}}ˆ|}yt |¡Wntk rTwYnXt |d¡}|d krŠ| d ¡}|||krŠd}P||_qW‡fd d „|Dƒ}|‰|ròd}xBˆD]:\}}|j}||krº|sà|| |<| |¡|| |<qºWqòWqŒW|s|s|s`|| |<q`W| } qNW|sN|sN|sDt|  ¡ƒ}n|  ¡}n|sZ|}n|  ¡}|S) a returns the BRICS decomposition for a molecule >>> from rdkit import Chem >>> m = Chem.MolFromSmiles('CCCOCc1cc(c2ncccc2)ccc1') >>> res = list(BRICSDecompose(m)) >>> sorted(res) ['[14*]c1ccccn1', '[16*]c1cccc([16*])c1', '[3*]O[3*]', '[4*]CCC', '[4*]C[8*]'] >>> res = list(BRICSDecompose(m,returnMols=True)) >>> res[0] >>> smis = [Chem.MolToSmiles(x,True) for x in res] >>> sorted(smis) ['[14*]c1ccccn1', '[16*]c1cccc([16*])c1', '[3*]O[3*]', '[4*]CCC', '[4*]C[8*]'] nexavar, an example from the paper (corrected): >>> m = Chem.MolFromSmiles('CNC(=O)C1=NC=CC(OC2=CC=C(NC(=O)NC3=CC(=C(Cl)C=C3)C(F)(F)F)C=C2)=C1') >>> res = list(BRICSDecompose(m)) >>> sorted(res) ['[1*]C([1*])=O', '[1*]C([6*])=O', '[14*]c1cc([16*])ccn1', '[16*]c1ccc(Cl)c([16*])c1', '[16*]c1ccc([16*])cc1', '[3*]O[3*]', '[5*]NC', '[5*]N[5*]', '[8*]C(F)(F)F'] it's also possible to keep pieces that haven't been fully decomposed: >>> m = Chem.MolFromSmiles('CCCOCC') >>> res = list(BRICSDecompose(m,keepNonLeafNodes=True)) >>> sorted(res) ['CCCOCC', '[3*]OCC', '[3*]OCCC', '[3*]O[3*]', '[4*]CC', '[4*]CCC'] >>> m = Chem.MolFromSmiles('CCCOCc1cc(c2ncccc2)ccc1') >>> res = list(BRICSDecompose(m,keepNonLeafNodes=True)) >>> sorted(res) ['CCCOCc1cccc(-c2ccccn2)c1', '[14*]c1ccccn1', '[16*]c1cccc(-c2ccccn2)c1', '[16*]c1cccc(COCCC)c1', '[16*]c1cccc([16*])c1', '[3*]OCCC', '[3*]OC[8*]', '[3*]OCc1cccc(-c2ccccn2)c1', '[3*]OCc1cccc([16*])c1', '[3*]O[3*]', '[4*]CCC', '[4*]C[8*]', '[4*]Cc1cccc(-c2ccccn2)c1', '[4*]Cc1cccc([16*])c1', '[8*]COCCC'] or to only do a single pass of decomposition: >>> m = Chem.MolFromSmiles('CCCOCc1cc(c2ncccc2)ccc1') >>> res = list(BRICSDecompose(m,singlePass=True)) >>> sorted(res) ['CCCOCc1cccc(-c2ccccn2)c1', '[14*]c1ccccn1', '[16*]c1cccc(-c2ccccn2)c1', '[16*]c1cccc(COCCC)c1', '[3*]OCCC', '[3*]OCc1cccc(-c2ccccn2)c1', '[4*]CCC', '[4*]Cc1cccc(-c2ccccn2)c1', '[8*]COCCC'] setting a minimum size for the fragments: >>> m = Chem.MolFromSmiles('CCCOCC') >>> res = list(BRICSDecompose(m,keepNonLeafNodes=True,minFragmentSize=2)) >>> sorted(res) ['CCCOCC', '[3*]OCC', '[3*]OCCC', '[4*]CC', '[4*]CCC'] >>> m = Chem.MolFromSmiles('CCCOCC') >>> res = list(BRICSDecompose(m,keepNonLeafNodes=True,minFragmentSize=3)) >>> sorted(res) ['CCCOCC', '[3*]OCC', '[4*]CCC'] >>> res = list(BRICSDecompose(m,minFragmentSize=2)) >>> sorted(res) ['[3*]OCC', '[3*]OCCC', '[4*]CC', '[4*]CCC'] rNFz--------z->ZproductsTcSs g|]\}}|jdd|f‘qS)T)Z onlyExplicit)r:)rÚidxÚprodrrrräsz"BRICSDecompose..rÚ*csg|]\}}|ˆ|f‘qSrr)rrr)ÚprodSeqrrrôs)rÚ MolToSmilesr&r,Ú enumerateÚ reactionsÚnextÚiterÚpopÚprintÚ smartsGpsÚ RunReactantsr$Úsortr9Ú ExceptionÚcountÚpSmiÚkeysÚvalues)r-ÚallNodesZminFragmentSizeZonlyUseReactionsr.ZkeepNonLeafNodesÚ singlePassZ returnMolsZmSmiZ activePoolZ foundMolsr2Z reactionGpZnewPoolZmatchedZnSmiZrxnIdxZreactionÚpsZseqOkZtSeqZnatsrBrCrRZnDummiesÚtsr@r)rErÚBRICSDecomposeŠs€<                 rYz[*]éc 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zTestCase.test7cCsRt d¡t d¡}t|ƒ}| t|ƒdk|¡dd„|Dƒ}tt|dddƒ}x|D]}t  |¡qVWd d„|Dƒ}|  t|ƒd ¡d d d ddg}dd„|Dƒ}x |D]}| ||k||f¡q¨Wtt|dddƒ}x|D]}t  |¡qÜWdd„|Dƒ}|  ||¡tt|dddƒ}x|D]}t  |¡q Wdd„|Dƒ}|  ||¡dS)Nézn1cncnc1OCC(C1CC1)OC1CNC1rwcSsg|]}t |¡‘qSr)rr)rrrrrrsz"TestCase.test8..rpF)r^r_cSsg|]}t |¡‘qSr)rrF)rrrrrr sé$zn1cnc(C2CNC2)nc1zn1cnc(-c2ncncn2)nc1zC(OC1CNC1)C(C1CC1)OC1CNC1zn1cnc(OC(COC2CNC2)C2CC2)nc1zn1cnc(OCC(OC2CNC2)C2CNC2)nc1cSsg|]}t t |¡d¡‘qS)T)rrFr)rrrrrrscSsg|]}t |¡‘qSr)rrF)rrrrrrsTcSsg|]}t |¡‘qSr)rrF)rrrrrrs) rrerrrYrqr$r"rcr9Ú assertEqualZassertNotEqual)rrÚbaseZcatalogZmsrsrXÚtZms2rrrÚtest8s2       zTestCase.test8cCszt d¡}t|ƒ}| t|ƒd¡| d|k¡| d|k¡t|dd}| t|ƒd¡| d|k¡| d|k¡dS) Nz$CCOc1ccccc1c1ncc(c2nc(NCCCC)ncn2)cc1éz [3*]O[3*]z[14*]c1ncnc(NCCCC)n1T)rVé z[3*]OCC)rrrYrˆr$rqr|)rrrsr@rrrÚtest9s  zTestCase.test9cCs(t d¡}t|ƒ}| t|ƒd|¡dS)NZC1CCCCN1c1ccccc1ro)rrrYrˆr$)rrrsr@rrrÚtest10*s zTestCase.test10c Csæd}t |¡}t|ƒ}tj|dd}| t|ƒd¡| |d ¡d¡| |d ¡d¡| |d ¡d¡| ¡}|d ¡}x8td ƒD],}|  |¡}|  |¡} | ||   ¡d ¡qŽW|  d ¡}|  d ¡} | ||   ¡d ¡|d ¡}xtdƒD]2}|  |d ¡}|  |¡} | ||   ¡d ¡qnW|  d ¡}|  d¡} | ||   ¡d ¡|  d ¡}|  d¡} | ||   ¡d ¡d }t |¡} |j |  ¡dd | |  ¡d¡t|ƒ}tj|dd}| t|ƒd¡| |d ¡d¡| |d ¡d¡| |d ¡d¡| |d  ¡d¡| |d  ¡d¡| |d  ¡d¡| d¡}|d d¡}x:td ƒD].}|  |¡}|  |¡} | ||   ¡d ¡qäW|  d ¡}|  d ¡} | ||   ¡d ¡|d d¡}x>td ƒD]2}|  |d¡}|  |¡} | ||   ¡d ¡qVW|  d ¡}|  d ¡} | ||   ¡d ¡|d d¡}x>tdƒD]2}|  |d ¡}|  |¡} | ||   ¡d ¡qÌW|  d ¡}|  d¡} | ||   ¡d ¡|  d ¡}|  d¡} | ||   ¡d ¡| d¡}|d d¡}x:td ƒD].}|  |¡}|  |¡} | ||   ¡d ¡qtW|  d ¡}|  d ¡} | ||   ¡d ¡|d d¡}x>td ƒD]2}|  |d¡}|  |¡} | ||   ¡d ¡qæW|  d ¡}|  d ¡} | ||   ¡d ¡|d d¡}x>tdƒD]2}|  |d ¡}|  |¡} | ||   ¡d ¡q\W|  d ¡}|  d¡} | ||   ¡d ¡|  d ¡}|  d¡} | ||   ¡d ¡dS)NaŒ RDKit 3D 13 14 0 0 0 0 0 0 0 0999 V2000 -1.2004 0.5900 0.6110 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2328 1.3173 0.0343 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4299 0.6533 -0.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3633 -0.7217 -0.3299 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1552 -1.3791 -0.2207 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1425 -0.7969 0.5335 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1458 -1.4244 0.4108 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2976 -0.7398 -0.1026 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4889 -0.7939 0.5501 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4615 0.1460 0.3535 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0116 1.4034 -0.0296 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9786 1.4264 -0.9435 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1399 0.3193 -0.9885 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 6 1 1 0 13 8 1 0 M END T)ZasMolsrZrrŒrrorygrwaŒ RDKit 2D 13 14 0 0 0 0 0 0 0 0999 V2000 -1.2990 -0.8654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.6154 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8971 -0.8654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8971 0.6346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2990 0.6346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.3846 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 0.6346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 -0.8654 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.6154 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8971 -0.8654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8971 0.6346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 6 1 1 0 13 8 1 0 M END )ZassignId) rZMolFromMolBlockrAZ GetMolFragsrˆr$r:r>r#r?ZLengthZ AddConformerr<) rrZmolblockrsÚpiecesrZc1Zc2ÚiZp1Zp2Zm2rrrÚtest11/sÒ"                #                           zTestCase.test11cCsRt d¡}tt|ƒƒ}| t|ƒd|¡dd„|Dƒ}| ¡| |ddg¡dS)NzCCS(=O)(=O)NCCrocSsg|] }|d‘qS)rr)rrrrrrìsz#TestCase.test12..)rwro)ryrw)rrr"r8rˆr$rO)rrrsr@ZatIdsrrrÚtest12ès   zTestCase.test12cCsRt d¡}t|ƒ}| t|ƒd¡| d|k¡t|ƒ}| tj|ddd¡dS)Nzc1ccccc1[C@H](C)NCrZz[4*][C@H]([8*])CT)ZisomericSmilesz%[16*]c1ccccc1.[4*][C@H]([8*])C.[5*]NC)rrrYrˆr$rqrArF)rrrsr@rrrÚtestGithub1734ðs zTestCase.testGithub1734N)Ú__name__Ú __module__Ú __qualname__rtrvrxr~rr‚r„r…r‹rŽrr’r“r”rrrrrn^s5  :rn)FT)NTT)NrNTFFF)TNTTrZ)ErÚcopyrjr ZrdkitrZ rdkit.ChemrrZenvironsZ reactionDefsÚdeepcopyrMZgprGÚjZdefnZg1Zg2ZbndZr1Zr2r+ZsmarrŠZ InitializerPrLr(r)r0Z MolFromSmartsr%r‘r3Ztmpr4r5r6Ze1Ze2r1r=ÚtuplerHr`ZrxnSetÚsplitZrsrWrfÚfindallÚlabelsrar8rArYrrbrcrmr•ZunittestrnZfailedZtriedÚexitÚmainrrrrÚ s                  M P   @