ib3dZddlZddlZddlZddlmZddlmZm Z m Z m Z m Z m Z mZmZmZmZmZmZmZmZmZmZmZmZddlmZmZejdZdZGd d eZ dS) a RDKit topology parser --- :mod:`MDAnalysis.converters.RDKitParser` ================================================================== Converts an `RDKit `_ :class:`rdkit.Chem.rdchem.Mol` into a :class:`MDAnalysis.core.Topology`. See Also -------- :mod:`MDAnalysis.converters.RDKit` Classes ------- .. autoclass:: RDKitParser :members: :inherited-members: N)Topology)AltLocs AromaticitiesAtomids Atomnames AtomtypesBondsChainIDsChargesElementsICodesMasses OccupanciesResidsResnamesResnums RSChiralitySegids Tempfactors)TopologyReaderBase change_squashz!MDAnalysis.converters.RDKitParsercP |dS#t$rYdSwxYw)zFetches RDKit chiral tags_CIPCode)GetPropKeyError)atoms k/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/converters/RDKitParser.py_rdkit_atom_to_RSr Ls;||J''' rrs  %%c2eZdZdZdZedZdZdS) RDKitParserao For RDKit structures Creates the following Attributes: - Atomids - Atomnames - Aromaticities - Elements - Types - Masses - Bonds - Resids - Resnums - RSChirality - Segids Depending on RDKit's input, the following Attributes might be present: - Charges - Resnames - AltLocs - ChainIDs - ICodes - Occupancies - Tempfactors Attributes table: +---------------------------------------------+-------------------------+ | RDKit attribute | MDAnalysis equivalent | +=============================================+=========================+ | atom.GetMonomerInfo().GetAltLoc() | altLocs | +---------------------------------------------+-------------------------+ | atom.GetIsAromatic() | aromaticities | +---------------------------------------------+-------------------------+ | atom.GetMonomerInfo().GetChainId() | chainIDs | +---------------------------------------------+-------------------------+ | atom.GetDoubleProp('_GasteigerCharge') | charges | | atom.GetDoubleProp('_TriposPartialCharge') | | +---------------------------------------------+-------------------------+ | atom.GetSymbol() | elements | +---------------------------------------------+-------------------------+ | atom.GetMonomerInfo().GetInsertionCode() | icodes | +---------------------------------------------+-------------------------+ | atom.GetIdx() | indices | +---------------------------------------------+-------------------------+ | atom.GetMass() | masses | +---------------------------------------------+-------------------------+ | atom.GetMonomerInfo().GetName() | names | | atom.GetProp('_TriposAtomName') | | +---------------------------------------------+-------------------------+ | atom.GetProp('_CIPCode') | chiralities | +---------------------------------------------+-------------------------+ | atom.GetMonomerInfo().GetOccupancy() | occupancies | +---------------------------------------------+-------------------------+ | atom.GetMonomerInfo().GetResidueName() | resnames | +---------------------------------------------+-------------------------+ | atom.GetMonomerInfo().GetResidueNumber() | resnums | +---------------------------------------------+-------------------------+ | atom.GetMonomerInfo().GetTempFactor() | tempfactors | +---------------------------------------------+-------------------------+ | atom.GetProp('_TriposAtomType') | types | +---------------------------------------------+-------------------------+ Raises ------ ValueError If only part of the atoms have MonomerInfo available .. versionadded:: 2.0.0 .. versionchanged:: 2.1.0 Added R/S chirality support .. versionchanged:: 2.8.0 Removed type guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API). If atoms types is not present in the input rdkit molecule as a _TriposAtomType property, the type attribute get the same values as the element attribute. RDKITc^ ddlm}n#t$rYdSwxYwt||jS)z$Can this Parser read object *thing*?r)ChemF)rdkitr% ImportError isinstanceMol)thingr%s r _format_hintzRDKitParser._format_hintsP  " " " " " " "   55 %***s  c j|j}g}g}g}g}g}g}g} g} g} g} g} g}g}g}g}g} |d}n'#t$rtdddddd}|cYSwxYw|dr)|drt jd|D]i}| | || || | | |t||}|r||||||| ||||||||||| ||dn#t4$rYnwxYw | |dn#t4$rYnwxYw | |d #t4$r> | |dn#t4$rYnwxYwYgwxYwg}t9| }|r"t9||krt;d | t<t>j f|tBtDf|tFt>j$f| tJtLf|tNd ffD]8\}}}||t?j(|| 9g}g}g}|)D]}||*|+f||,|t[|.|t_||| |r<|tat?j(|tD n|D]A}| | }||B|tat?j(|tD | r<|tct?j(| tD nt>j23|} | rA|tit?j(| t>j$ n |tjtDf|tltDf|tnt>j$f|tpt>j$ffD]:\}}}|r2||t?j(|| ;ts|rJtsd |Ds0t?j(|t>j }t?j(|tD }t?j(| tD } t?j(|tD }tu|||| f|||| f\} \}}}} t9|}!|tvt>j f|<tzt>j f|t|tDf|t~tDffD]8\}}}||t?j(|| 9nn|twt?j(dg|t{t?j(dgd} d}!ts| rbtsd| DsItu| f| f\}"\} t9| }#|t| n@d}#|tt?j(dgtD d}"t||!|#|| |"}|S)zfParse RDKit into Topology Returns ------- MDAnalysis Topology object rN)n_atomsn_resn_segattrs atom_resindexresidue_segindex_GasteigerCharge_TriposPartialChargezjBoth _GasteigerCharge and _TriposPartialCharge properties are present. Using Gasteiger charges by default._TriposAtomName_TriposAtomTypezResidueInfo is only partially available in the molecule. If you have added hydrogens to the input RDKit molecule with `Chem.AddHs(mol)`, consider using `Chem.AddHs(mol, addResidueInfo=True)` insteadU1)dtype)typesorderc3K|]}|duV dSN.0vals r z$RDKitParser.parse..Ps&#C#CCC4K#C#C#C#C#C#Cc3K|]}|duV dSr<r=r>s rrAz$RDKitParser.parse..hs&"A"A33$;"A"A"A"A"A"ArBSYSTEM)r0r1r2)AfilenameGetAtomWithIdx RuntimeErrorrHasPropwarningswarnGetAtomsappendGetIdx GetSymbolGetMass GetIsAromaticr GetMonomerInfoGetNamestripGetResidueNumberGetResidueNameGetSegmentNumber GetAltLoc GetChainIdGetInsertionCode GetOccupancy GetTempFactorrr GetDoubleProplen ValueErrorrnpint32r objectrfloat32rboolrarrayGetBondsGetBeginAtomIdx GetEndAtomIdxGetBondTypeAsDoublestr GetBondTyper rr charupperr rr rranyrrcopyrrrr)$selfkwargsmolnames chiralitiesresnumsresnameselementsmassescharges aromaticsids atomtypessegidsaltlocschainidsicodes occupancies tempfactorsrtopmir0r-valsAttrr8bonds bond_types bond_ordersbondnameresidx n_residuessegidx n_segmentss$ rparsezRDKitParser.parses m      %%a((DD   "!% CJJJ  <<* + +  LL/ 0 0  MC    LLNN( ( D JJt{{}} % % % OODNN,, - - - MM$,,.. ) ) )   T//11 2 2 2   066 7 7 7$$&&B!  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