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Support writing CX extensions in reactions #7340
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Original file line number | Diff line number | Diff line change |
---|---|---|
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@@ -91,8 +91,35 @@ std::string chemicalReactionTemplatesToString( | |
return res; | ||
} | ||
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void insertTemplates(const RDKit::ChemicalReaction &rxn, | ||
RDKit::RWMol &rwmol, std::vector<unsigned int> &atomOrdering, | ||
std::vector<unsigned int> &bondOrdering, RDKit::ReactionMoleculeType type) { | ||
auto at_count = rwmol.getNumAtoms(); | ||
auto bnd_count = rwmol.getNumBonds(); | ||
std::vector<unsigned int> prevAtomOrdering; | ||
std::vector<unsigned int> prevBondOrdering; | ||
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for (auto begin = getStartIterator(rxn, type); | ||
begin != getEndIterator(rxn, type); ++begin) { | ||
rwmol.insertMol(**begin); | ||
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std::vector<unsigned int> prevAtomOrdering; | ||
std::vector<unsigned int> prevBondOrdering; | ||
(*begin)->getProp(RDKit::common_properties::_smilesAtomOutputOrder, prevAtomOrdering); | ||
(*begin)->getProp(RDKit::common_properties::_smilesBondOutputOrder, prevBondOrdering); | ||
for (auto i : prevAtomOrdering) { | ||
atomOrdering.push_back(i + at_count); | ||
} | ||
for (auto i : prevBondOrdering) { | ||
bondOrdering.push_back(i + bnd_count); | ||
} | ||
at_count = rwmol.getNumAtoms(); | ||
bnd_count = rwmol.getNumBonds(); | ||
} | ||
} | ||
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std::string chemicalReactionToRxnToString(const RDKit::ChemicalReaction &rxn, | ||
bool toSmiles, bool canonical) { | ||
bool toSmiles, bool canonical, bool includeCX) { | ||
std::string res = ""; | ||
res += chemicalReactionTemplatesToString(rxn, RDKit::Reactant, toSmiles, | ||
canonical); | ||
|
@@ -102,6 +129,32 @@ std::string chemicalReactionToRxnToString(const RDKit::ChemicalReaction &rxn, | |
res += ">"; | ||
res += chemicalReactionTemplatesToString(rxn, RDKit::Product, toSmiles, | ||
canonical); | ||
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if (includeCX) { | ||
// I think this will work? combine reactants, agents and products into a | ||
// single molecule and get the cxextension for that | ||
// blank rwmol | ||
RDKit::RWMol rwmol; | ||
std::vector<unsigned int> atomOrdering; | ||
std::vector<unsigned int> bondOrdering; | ||
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insertTemplates(rxn, rwmol, atomOrdering, bondOrdering, RDKit::Reactant); | ||
insertTemplates(rxn, rwmol, atomOrdering, bondOrdering, RDKit::Agent); | ||
insertTemplates(rxn, rwmol, atomOrdering, bondOrdering, RDKit::Product); | ||
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rwmol.setProp(RDKit::common_properties::_smilesAtomOutputOrder, atomOrdering, true); | ||
rwmol.setProp(RDKit::common_properties::_smilesBondOutputOrder, bondOrdering, true); | ||
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// ignore atom properties -- really this is to avoid the atom map numbers, maybe we just want to remove | ||
// those | ||
auto flags = RDKit::SmilesWrite::CXSmilesFields::CX_ATOM_PROPS ^ RDKit::SmilesWrite::CXSmilesFields::CX_ALL; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Are you doing this to remove the RGroup labels from the output? |
||
auto ext = RDKit::SmilesWrite::getCXExtensions(rwmol, flags); | ||
if (!ext.empty()) { | ||
res += " "; | ||
res += ext; | ||
} | ||
} | ||
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return res; | ||
} | ||
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|
@@ -121,14 +174,14 @@ void write_template(std::ostringstream &res, RDKit::ROMol &tpl) { | |
namespace RDKit { | ||
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//! returns the reaction SMARTS for a reaction | ||
std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn) { | ||
return chemicalReactionToRxnToString(rxn, false, false); | ||
std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn, bool includeCX) { | ||
return chemicalReactionToRxnToString(rxn, false, false, includeCX); | ||
}; | ||
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//! returns the reaction SMILES for a reaction | ||
std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn, | ||
bool canonical) { | ||
return chemicalReactionToRxnToString(rxn, true, canonical); | ||
return chemicalReactionToRxnToString(rxn, true, canonical, false); | ||
}; | ||
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//! returns an RXN block for a reaction | ||
|
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This is duplicated, it's declared again inside the loop.