B 3Rc@@sdZddlZddlZddlZddlZddlZddlmZddlmZddl m Z ddl m Z ddl m Z dZeeZed Ze jjd e jjd e jjd iZd ZGdddejZejGdddejZejfeedddZ d7e j!j"eeeee#edddZ$ddZ%d8ddZ&ddZ'dd Z(d!d"Z)d9d$d%Z*d:d'd(Z+d)d*Z,d+d,Z-d-d.Z.d;d/d0Z/Gd1d2d2ejZ0d3d4Z1d5d6Z2dS)td|d }d }t|dkr~t|d }|r~dd t|d}|r|d |S|S)Ncss|]}|VqdS)N)strip).0prrr sz%GetCanonicalSmiles..|cSsg|] }|r|qSrr)r@rArrr sz&GetCanonicalSmiles..)r'r'z4Unexpected number of fragments in canonical CXSMILESrr', )splitlen ValueErrorENHANCED_STEREO_GROUP_REGEXfindalljoinsorted)r2Z smiles_partsr3Z stereo_groupsgroupsrrrr.s   r.cCsFt|}|dtj|t|tjj}t|tjj }||fS)NF) r(r;rr:ZRemoveStereochemistryrr*r+r>ZCanonicalSmiles)r1Z no_stereo_molr4r5rrrr0s   r0Tc Cs|dkrggfS|s(tt|}n\t|}|d}dd|dddD}dgt|}xt|D]\}}|||<qpWg}xH| D]<} || } || } | | kr| | } } | | | fqW||fS)a returns a 2-tuple with: 1. the canonical ranks of a molecule's atoms 2. the bonds expressed as (canonical_atom_rank_1,canonical_atom_rank_2) where canonical_atom_rank_1 < canonical_atom_rank_2 If useSmilesOrdering is True then the atom indices here correspond to the order of the atoms in the canonical SMILES, otherwise just the canonical atom order is used. useSmilesOrdering=True is a bit slower, but it allows the output to be linked to the canonical SMILES, which can be useful. rZ_smilesAtomOutputOrdercSsg|]}|rt|qSr)int)r@xrrrrDsz2_GetCanonicalAtomRanksAndBonds..rFrG) r<listrZCanonicalRankAtomsZ MolToSmilesGetProprIrJ enumerateGetBondsGetBeginAtomIdx GetEndAtomIdxappend) r1ZuseSmilesOrderingatRanksZsmiZordertxtZsmiOrderiidxbndOrderZbndZboZeorrr_GetCanonicalAtomRanksAndBondss$       r_Atropc s|ddks|dsdS|d}||kr2dS|d}t|dkrPtd|d}tfd d |D}|rtt|}tfd d |D}|rtt|}t ||||d } | S) z NOTES: if sortAtomAndBondOrder is true then the atom and bond lists will be sorted. This assumes that the order of the atoms in that list is not important TYPEDATZ FIELDNAMENZ DATAFIELDSrFz9cannot canonicalize data groups with multiple data fieldsrc3s|]}|VqdS)Nr)r@rR)r[rrrBsz*_CanonicalizeDataSGroup..c3s|]}|VqdS)Nr)r@rR)r^rrrBs) fieldNameZatombondsr) rUZHasPropZGetStringVectProprJrKrr7rOrWdict) sgr[r^Z fieldNamessortAtomAndBondOrderrddataatsbndsresr)r[r^r_CanonicalizeDataSGroups"     rmcCsJ|}|}||||ks8||||krB||krB||}}||fS)N)rXrY)ZbondZ atomRanksZaid1Zaid2rrr_GetCanononicalBondReps ( rnc s|ddkrdStfdd|D}tfdd|D}|rbtt|}tt|}|}td|||dd|d d |d d d }d |kr|d |d <d|krtfdd|dD} |rtt| } | |d<d|krtfdd|dD} t| dr"t d|rg} xRt dt| dD]>} | | | | d} }| |krl|| } }| | |fq>Wtt| } | |d<|S)z NOTES: if sortAtomAndBondOrder is true then the atom and bond lists will be sorted. This assumes that the ordering of those lists is not important rbSRUNc3s|]}|VqdS)Nr)r@rR)r[rrrB/sz)_CanonicalizeSRUSGroup..c3s|]}|VqdS)Nr)r@rR)r^rrrB0sindexrZCONNECTr'ZLABEL)typeatomsrerpZconnectZlabelPARENTZXBHEADc3s|]}t|VqdS)N)rnGetBondWithIdx)r@rR)r[r1rrrBAsZXBCORRc3s|]}t|VqdS)N)rnrt)r@rR)r[r1rrrBGsrEzXBCORR should have 2N bondsrF) rUrr7rWrOGetPropsAsDictrfgetrJrKrangerZ)r1rgr[r^rhrjrkpropsrlZxbhbondsZ xbcorrbondsZtmpr\Zb1Zb2r)r[r^r1r_CanonicalizeSRUSGroup'sL          rycs^|ddkrdStfdd|D}|r.rpr)rqrrrp)rUrr7rOrurfrv)rgr[rhrjrxrlr)r[r_CaonicalizeCOPSGroupWs r{c CsJ|pdg}t|\}}g}xt|D]t}d}|ddkrNt|||||}n:|ddkrnt|||||}n|ddkrt|||}|dk r&||q&Wt|dkr@t dd |D}t d d |D}i} x8t |D],\} } d | kr| d| | d <| d| d <qWx0t |D]$\} } d | kr| | d | d <qWt |S) z NOTES: if sortAtomAndBondOrder is true then the atom and bond lists will be sorted. This assumes that the ordering of those lists is not important raNrbrcrorzrFcss|]}t|VqdS)N)ritems)r@rRrrrrB|sz'_CanonicalizeSGroups..css|]}t|VqdS)N)rf)r@rRrrrrB}srprs)r_rZGetMolSubstanceGroupsrUrmryr{rZrJrOrrVjsondumps) r1r&rhr[r^rlrgZlresZtresZidxmapr\Zitmrrrr/gs2    r/c@seZdZeZeZdS)EnhancedStereoUpdateModeN)rr r r r ADD_WEIGHTSREMOVE_WEIGHTSrrrrrsrc Cs|tjkrd}n|tjkr d}ntdd}|}xv|D]n}|}|t|}xT|D]H}|} |tjkr| dkrtd| d| | | |d}q\Wq:W||fS) NrFrSz*Invalid Enhanced Stereo weight update modeFizQEnhanced stereo group canonicalization does not support isotopes above 999. Atom z is T) rrrrKGetStereoGroupsZ GetGroupTypeENHANCED_STEREO_GROUP_WEIGHTSr7Z GetIsotopeZGetIdxZ SetIsotope) r1modeZfactorisotopesModifiedZstgsZstgZstgtZweightr9Zisotoperrr!_UpdateEnhancedStereoGroupWeightss$     rc Cst|st||fSt|}t|t|tj\}}t }d|_ d|_ d}d}x6t ||D]&}t|}|dks||krh|}|}qhWt d}|d|}|rt|tj\}}||fS)a| Returns canonical CXSmiles and the corresponding molecule with the stereo groups canonicalized. The RDKit canonicalization code does not currently take stereo groups into account. We work around that by using EnumerateStereoisomers() to generate all possible instances of the molecule's stereogroups and then lexically compare the CXSMILES of those. TFNr'z#\[[1-3]0*([1-9]?[0-9]*[A-Z][a-z]?)@z[\1@)rJrrZ MolToCXSmilesMolZ FastFindRingsrrrrZStereoEnumerationOptionsZonlyStereoGroupsuniquerecompilesubr) r1rZoptsZ resultMolZresultCXSmilesZisomerZcxSmilesZextraIsotopeRemovalRegex_rrrr,s,        r,)NN)F)T)r`T)NT)3r r rr}ZloggingrtypingrrZrdkitrZ rdkit.Chemrrr8Z getLoggerrZloggerrrLZStereoGroupTypeZ STEREO_ANDZ STEREO_ORZSTEREO_ABSOLUTErr=Enumrrrrstrr!Zrdchemrsetr6r)r(r-r.r0r_rmrnryr{r/rrr,rrrrsL         &"  $ 0 $