B ž3Rcè-ã§@sÌdZddlmZddlmZddlmZddddd d d d d ddddddddddddddddddd d!d"d#d$d%d&d'd(d)d*d+d,d-d.d/d0d1d2d3d4d5d6d7d8d9d:d;dd?d@dAdBdCdDdEdFdGdHdIdJdKdLdMdNdOdPdQdRdSdTdUdVdWdXdYdZd[d\d]d^d_d`dadbdcdddedfdgdhdidjdkdldmdndodpdqdrdsdtdudvdwdxdydzd{d|d}d~dd€ddd‚dƒd„d…d†d‡dˆd‰dŠd‹dŒddŽddd‘d’d“d”d•d–d—d˜d™dšd›dœddždŸd d¡d¢d£d¤d¥d¦d§d¨dd©œ¦Zdªad«d¬„Zd­d®„Z ej Z ej Z d¯d°„Z ed±krÈddªlZe ƒ\ZZe e¡dªS)²a£ SMARTS definitions for the publicly available MACCS keys and a MACCS fingerprinter I compared the MACCS fingerprints generated here with those from two other packages (not MDL, unfortunately). Of course there are disagreements between the various fingerprints still, but I think these definitions work pretty well. Some notes: 1) most of the differences have to do with aromaticity 2) there's a discrepancy sometimes because the current RDKit definitions do not require multiple matches to be distinct. e.g. the SMILES C(=O)CC(=O) can match the (hypothetical) key O=CC twice in my definition. It's not clear to me what the correct behavior is. 3) Some keys are not fully defined in the MDL documentation 4) Two keys, 125 and 166, have to be done outside of SMARTS. 5) Key 1 (ISOTOPE) isn't defined Rev history: 2006 (gl): Original open-source release May 2011 (gl): Update some definitions based on feedback from Andrew Dalke é)ÚChem)ÚrdMolDescriptors)Ú DataStructs)ú?r)z[#104]r)z%[#32,#33,#34,#50,#51,#52,#82,#83,#84]r)z-[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]r)z[Sc,Ti,Y,Zr,Hf]r)z.[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]r)z[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]r)z[!#6;!#1]1~*~*~*~1r)z[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]r)z[Be,Mg,Ca,Sr,Ba,Ra]r)z *1~*~*~*~1r)z[Cu,Zn,Ag,Cd,Au,Hg]r)z[#8]~[#7](~[#6])~[#6]r)z [#16]-[#16]r)z[#8]~[#6](~[#8])~[#8]r)z[!#6;!#1]1~*~*~1r)z [#6]#[#6]r)z[#5,#13,#31,#49,#81]r)z*1~*~*~*~*~*~*~1r)z[#14]r)z[#6]=[#6](~[!#6;!#1])~[!#6;!#1]r)z*1~*~*~1r)z[#7]~[#6](~[#8])~[#8]r)z 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*~[CH2]~[#7]r)a_[$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1)]r)z[!#6;!#1]~[#8]r)ZClr)z[!#6;!#1;!H0]~*~[CH2]~*r)z *@*(@*)@*r)z![!#6;!#1]~*(~[!#6;!#1])~[!#6;!#1]r)z[F,Cl,Br,I]~*(~*)~*r)z[CH3]~*~*~*~[CH2]~*r)z *~[CH2]~[#8]r)z[#7]~[#6]~[#8]r)z[#7]~*~[CH2]~*r)z *~*(~*)(~*)~*r)z [#8]!:*:*r)z [CH3]~[CH2]~*r)z[CH3]~*~[CH2]~*r)z+[$([CH3]~*~*~[CH2]~*),$([CH3]~*1~*~[CH2]1)]r)z [#7]~*~[#8]r)z'[$(*~[CH2]~[CH2]~*),$(*1~[CH2]~[CH2]1)]é)z[#7]=*r)z[!#6;R]r)z[#7;R]r)z *~[#7](~*)~*r)z[#8]~[#6]~[#8]r)z[!#6;!#1]~[!#6;!#1]r)z *!@[#8]!@*r)z *@*!@[#8]r)z[$(*~[CH2]~*~*~*~[CH2]~*),$([R]1@[CH2;R]@[R]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[R]@[CH2;R]1),$(*~[CH2]~*~[R]1@[R]@[CH2;R]1)]r)zT[$(*~[CH2]~*~*~[CH2]~*),$([R]1@[CH2]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[CH2;R]1)]r)z[!#6;!#1]~[!#6;!#1]r)z [!#6;!#1;!H0]r)z[#8]~*~[CH2]~*r)z *@*!@[#7]r)z [F,Cl,Br,I]r)z [#7]!:*:*r)z[#8]=*r)z [!C;!c;R]r)z[!#6;!#1]~[CH2]~*r)z[O;!H0]r)z[#8]é)z[CH3]é)z[#7]r)z *@*!@[#8]r)z *!:*:*!:*r)z*1~*~*~*~*~*~1r)z[#8]r )z-[$(*~[CH2]~[CH2]~*),$([R]1@[CH2;R]@[CH2;R]1)]r)z*~[!#6;!#1](~*)~*r)z [C;H3,H4]r)z *!@*@*!@*r)z[#7;!H0]r)z[#8]~[#6](~[#6])~[#6]r)z[!#6;!#1]~[CH2]~*r)z [#6]=[#8]r)z *!@[CH2]!@*r)z [#7]~*(~*)~*r)z [#6]-[#8]r)z [#6]-[#7]r)z[#8]r)z [C;H3,H4]r)z[#7]r)Úar)z*1~*~*~*~*~*~1r)z[#8]r)z[R]r)¦rr réééééé é é é é ééééééééééééééééééé é!é"é#é$é%é&é'é(é)é*é+é,é-é.é/é0é1é2é3é4é5é6é7é8é9é:é;é<é=é>é?é@éAéBéCéDéEéFéGéHéIéJéKéLéMéNéOéPéQéRéSéTéUéVéWéXéYéZé[é\é]é^é_é`éaébécédéeéfégéhéiéjékéléménéoépéqérésétéuévéwéxéyézé{é|é}é~éé€éé‚éƒé„é…é†é‡éˆé‰éŠé‹éŒééŽééé‘é’é“é”é•é–é—é˜é™éšé›éœééžéŸé é¡é¢é£é¤é¥é¦NcCsvt|ƒt| ¡ƒkstdƒ‚xT| ¡D]H}||\}}|dkr&t |¡}|s^td||fƒq&||f||d<q&WdS)zM *Internal Use Only* generates SMARTS patterns for the keys, run once zlength mismatchrz#SMARTS parser error for key #%d: %srN)ÚlenÚkeysÚAssertionErrorrZ MolFromSmartsÚprint)ZkeyListZkeyDictÚkeyÚpattÚcountZsma©rµú3lib/python3.7/site-packages/rdkit/Chem/MACCSkeys.pyÚ _InitKeysÜs  r·c KsTtdkr$dgtt ¡ƒatttƒ| dtj¡}|ttƒdƒ}x ttƒD]ü\}\}}|dk r¤|dkr€|  |¡||d<n"|  |¡}t|ƒ|kr¢d||d<qN|ddkr|  ¡}d} d|d<x„|  ¡D]H} d} x | D]} |  | ¡ ¡sÞd} PqÞW| rÐ| d7} | dkrÐd|d<PqÐWqN|dd krNd|d <tt |¡ƒdkrNd|d <qNW|S) a generates the MACCS fingerprint for a molecules **Arguments** - mol: the molecule to be fingerprinted - any extra keyword arguments are ignored **Returns** a _DataStructs.SparseBitVect_ containing the fingerprint. >>> m = Chem.MolFromSmiles('CNO') >>> bv = GenMACCSKeys(m) >>> tuple(bv.GetOnBits()) (24, 68, 69, 71, 93, 94, 102, 124, 131, 139, 151, 158, 160, 161, 164) >>> bv = GenMACCSKeys(Chem.MolFromSmiles('CCC')) >>> tuple(bv.GetOnBits()) (74, 114, 149, 155, 160) N)NrÚctorrrr„TFr­)Ú maccsKeysr®Ú smartsPattsr¯r·ÚgetrZ SparseBitVectÚ enumerateZHasSubstructMatchZGetSubstructMatchesZ GetRingInfoZ BondRingsZGetBondWithIdxZ GetIsAromaticrZ GetMolFrags) ZmolÚkwargsr¸ZresÚir³r´ZmatchesZriZnAromZringZisAromZbondIdxrµrµr¶Ú_pyGenMACCSKeysís@      r¿cCs ddl}ddl}| |jd¡S)NrÚ__main__)ÚdoctestÚsysZtestmodÚmodules)rÁrÂrµrµr¶Ú_test3srÄrÀ)Ú__doc__ZrdkitrZ rdkit.Chemrrrºr¹r·r¿ZGetMACCSKeysFingerprintZ GenMACCSKeysZFingerprintMolrÄÚ__name__rÂZfailedZtriedÚexitrµrµrµr¶Ú sf   >