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// $Id: Bond.cpp 2007 2012-03-28 07:06:44Z glandrum $
//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#define NO_IMPORT_ARRAY
#include <boost/python.hpp>
#include <string>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/QueryBond.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <RDGeneral/types.h>
namespace python = boost::python;
namespace RDKit{
int BondHasProp(const Bond *bond, const char *key) {
int res = bond->hasProp(key);
return res;
}
std::string BondGetProp(const Bond *bond, const char *key) {
if (!bond->hasProp(key)) {
PyErr_SetString(PyExc_KeyError,key);
throw python::error_already_set();
}
std::string res;
bond->getProp(key, res);
return res;
}
bool BondIsInRing(const Bond *bond){
if(!bond->getOwningMol().getRingInfo()->isInitialized()){
MolOps::findSSSR(bond->getOwningMol());
}
return bond->getOwningMol().getRingInfo()->numBondRings(bond->getIdx())!=0;
}
bool BondIsInRingSize(const Bond *bond,int size){
if(!bond->getOwningMol().getRingInfo()->isInitialized()){
MolOps::findSSSR(bond->getOwningMol());
}
return bond->getOwningMol().getRingInfo()->isBondInRingOfSize(bond->getIdx(),size);
return false;
}
INT_VECT getBondStereoAtoms(const Bond *bond){
return bond->getStereoAtoms();
}
std::string BondGetSmarts(const Bond *bond,bool allBondsExplicit){
std::string res;
if(bond->hasQuery()){
res=SmartsWrite::GetBondSmarts(static_cast<const QueryBond *>(bond));
} else {
res=SmilesWrite::GetBondSmiles(bond,-1,false,allBondsExplicit);
}
return res;
}
std::string bondClassDoc="The class to store Bonds.\n\
Note: unlike Atoms, is it currently impossible to construct Bonds from\n\
Python.\n";
struct bond_wrapper {
static void wrap(){
python::class_<Bond>("Bond",bondClassDoc.c_str(),python::no_init)
.def("GetOwningMol",&Bond::getOwningMol,
"Returns the Mol that owns this bond.\n",
python::return_value_policy<python::reference_existing_object>())
.def("GetBondType",&Bond::getBondType,
"Returns the type of the bond as a BondType\n")
.def("SetBondType",&Bond::setBondType,
"Set the type of the bond as a BondType\n")
.def("GetBondDir",&Bond::getBondDir,
"Returns the type of the bond as a BondDir\n")
.def("SetBondDir",&Bond::setBondDir,
"Set the type of the bond as a BondDir\n")
.def("GetStereo",&Bond::getStereo,
"Returns the CIP-classification of the bond as a BondStereo\n")
// this is no longer exposed because it requires that stereo atoms
// be set. This is a task that is tricky and "dangerous".
//.def("SetStereo",&Bond::setStereo,
// "Set the CIP-classification of the bond as a BondStereo\n")
.def("GetStereoAtoms",getBondStereoAtoms,
"Returns the indices of the atoms setting this bond's stereochemistry.")
.def("GetValenceContrib",
(double (Bond::*)(const Atom *) const)&Bond::getValenceContrib,
"Returns the contribution of the bond to the valence of an Atom.\n\n"
" ARGUMENTS:\n\n"
" - atom: the Atom to consider.\n")
.def("GetIsAromatic",&Bond::getIsAromatic)
.def("SetIsAromatic",&Bond::setIsAromatic)
.def("GetIsConjugated",&Bond::getIsConjugated,
"Returns whether or not the bond is considered to be conjugated.")
.def("SetIsConjugated",&Bond::setIsConjugated)
.def("GetIdx",&Bond::getIdx,
"Returns the bond's index (ordering in the molecule)\n")
.def("GetBeginAtomIdx",&Bond::getBeginAtomIdx,
"Returns the index of the bond's first atom.\n")
.def("GetEndAtomIdx",&Bond::getEndAtomIdx,
"Returns the index of the bond's first atom.\n")
.def("GetOtherAtomIdx",&Bond::getOtherAtomIdx,
"Given the index of one of the bond's atoms, returns the\n"
"index of the other.\n")
.def("GetBeginAtom",&Bond::getBeginAtom,
python::return_value_policy<python::reference_existing_object>(),
"Returns the bond's first atom.\n")
.def("GetEndAtom",&Bond::getEndAtom,
python::return_value_policy<python::reference_existing_object>(),
"Returns the bond's second atom.\n")
.def("GetOtherAtom",&Bond::getOtherAtom,
python::return_value_policy<python::reference_existing_object>(),
"Given one of the bond's atoms, returns the other one.\n")
// FIX: query stuff
.def("Match",(bool (Bond::*)(const Bond *) const)&Bond::Match,
"Returns whether or not this bond matches another Bond.\n\n"
" Each Bond (or query Bond) has a query function which is\n"
" used for this type of matching.\n\n"
" ARGUMENTS:\n"
" - other: the other Bond to which to compare\n")
.def("IsInRingSize",BondIsInRingSize,
"Returns whether or not the bond is in a ring of a particular size.\n\n"
" ARGUMENTS:\n"
" - size: the ring size to look for\n")
.def("IsInRing",BondIsInRing,
"Returns whether or not the bond is in a ring of any size.\n\n")
.def("HasQuery",&Bond::hasQuery,
"Returns whether or not the bond has an associated query\n\n")
.def("GetSmarts",BondGetSmarts,
(python::arg("bond"),
python::arg("allBondsExplicit")=false),
"returns the SMARTS (or SMILES) string for a Bond")
.def("GetProp", BondGetProp,
"Returns the value of the property.\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to return (a string).\n\n"
" RETURNS: a string\n\n"
" NOTE:\n"
" - If the property has not been set, a KeyError exception will be raised.\n")
.def("HasProp", BondHasProp,
"Queries a Bond to see if a particular property has been assigned.\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to check for (a string).\n")
.def("GetPropNames",&Bond::getPropList,
(python::arg("self")),
"Returns a list of the properties set on the Bond.\n\n"
)
;
python::enum_<Bond::BondType>("BondType")
.value("UNSPECIFIED",Bond::UNSPECIFIED)
.value("SINGLE",Bond::SINGLE)
.value("DOUBLE",Bond::DOUBLE)
.value("TRIPLE",Bond::TRIPLE)
.value("QUADRUPLE",Bond::QUADRUPLE)
.value("QUINTUPLE",Bond::QUINTUPLE)
.value("HEXTUPLE",Bond::HEXTUPLE)
.value("ONEANDAHALF",Bond::ONEANDAHALF)
.value("TWOANDAHALF",Bond::TWOANDAHALF)
.value("THREEANDAHALF",Bond::THREEANDAHALF)
.value("FOURANDAHALF",Bond::FOURANDAHALF)
.value("FIVEANDAHALF",Bond::FIVEANDAHALF)
.value("AROMATIC",Bond::AROMATIC)
.value("IONIC",Bond::IONIC)
.value("HYDROGEN",Bond::HYDROGEN)
.value("THREECENTER",Bond::THREECENTER)
.value("DATIVEONE",Bond::DATIVEONE)
.value("DATIVE",Bond::DATIVE)
.value("DATIVEL",Bond::DATIVEL)
.value("DATIVER",Bond::DATIVER)
.value("OTHER",Bond::OTHER)
;
python::enum_<Bond::BondDir>("BondDir")
.value("NONE",Bond::NONE)
.value("BEGINWEDGE",Bond::BEGINWEDGE)
.value("BEGINDASH",Bond::BEGINDASH)
.value("ENDDOWNRIGHT",Bond::ENDDOWNRIGHT)
.value("ENDUPRIGHT",Bond::ENDUPRIGHT)
.value("UNKNOWN",Bond::UNKNOWN)
;
python::enum_<Bond::BondStereo>("BondStereo")
.value("STEREONONE",Bond::STEREONONE)
.value("STEREOANY",Bond::STEREOANY)
.value("STEREOZ",Bond::STEREOZ)
.value("STEREOE",Bond::STEREOE)
;
};
};
}// end of namespace
void wrap_bond() {
RDKit::bond_wrapper::wrap();
}
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