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Release_2017_03
rdkit/Code/GraphMol/Wrap/Bond.cpp
Greg Landrum e625c58bab Add cis/trans tags to double bonds (#1316) 
* add cis and trans to bond stereo

* compiles, does not work

* tests all pass

* Whitespace cleanup to recent changes.

* C++ test case for Bond::setStereo using Bond::STEREOCIS and Bond::STEREOTRANS

* Adding a PRECONDITION to Bond::setStereo to make sure the stereo atoms
are already specified if CIS or TRANS is being specified.

E/Z is technically defined by the topology of the molecule so the
stereo atoms are redundant (easier to understand and use!), but
ultimately redundant with the graph. However, CIS and TRANS is _only_
defined in this usage as the orientation of the atoms in the
getStereoAtoms vector.

* Exposing Bond::setStereo to Python and adding test cases to make sure
it can be used to set CIS/TRANS stereochemistry.

* verify substructure matching works

* Adding Bond::setStereoAtoms to C++ Bond class.

This allows setting the atoms to be considered for CIS or TRANS
directly without a much more costly determination of ranking that E/Z
requires.

* Wrap Bond::SetStereoAtoms into python with a new type of test case.

* docs
2017-02-26 08:15:44 -05:00

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// $Id$
//
// Copyright (C) 2003-2014 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 <RDBoost/python.h>
#include <string>
#include "props.hpp"
#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 {
namespace {
std::string qhelper(Bond::QUERYBOND_QUERY *q, unsigned int depth) {
std::ostringstream res;
if (q) {
for (unsigned int i = 0; i < depth; ++i) res << " ";
res << q->getFullDescription();
if (q->getNegation()) res << " ! ";
res << "\n";
for (Bond::QUERYBOND_QUERY::CHILD_VECT_CI ci = q->beginChildren();
ci != q->endChildren(); ++ci) {
res << qhelper((*ci).get(), depth + 1);
}
}
return res.str();
}
} // end of local namespace
std::string describeQuery(const Bond *bond) {
std::string res = "";
if (bond->hasQuery()) {
res = qhelper(bond->getQuery(), 0);
}
return res;
}
void expandQuery(QueryBond *self, const QueryBond *other,
Queries::CompositeQueryType how, bool maintainOrder) {
if (other->hasQuery()) {
const QueryBond::QUERYBOND_QUERY *qry = other->getQuery();
self->expandQuery(qry->copy(), how, maintainOrder);
}
}
int BondHasProp(const Bond *bond, const char *key) {
int res = bond->hasProp(key);
return res;
}
template <class T>
void BondSetProp(const Bond *bond, const char *key, const T &val) {
bond->setProp<T>(key, val);
}
void BondClearProp(const Bond *bond, const char *key) {
if (!bond->hasProp(key)) {
return;
}
bond->clearProp(key);
}
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("GetBondTypeAsDouble", &Bond::getBondTypeAsDouble,
"Returns the type of the bond as a double (i.e. 1.0 for SINGLE, "
"1.5 for AROMATIC, 2.0 for DOUBLE)\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 stereo configuration of the bond as a BondStereo\n")
.def("SetStereo", &Bond::setStereo,
"Set the stereo configuration of the bond as a BondStereo\n")
.def("GetStereoAtoms", getBondStereoAtoms,
"Returns the indices of the atoms setting this bond's "
"stereochemistry.\n")
.def("SetStereoAtoms", &Bond::setStereoAtoms,
"Set the indices of the atoms setting this bond's "
"stereochemistry.\n")
.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("DescribeQuery", describeQuery,
"returns a text description of the query. Primarily intended for "
"debugging purposes.\n\n")
.def("GetSmarts", BondGetSmarts,
(python::arg("bond"), python::arg("allBondsExplicit") = false),
"returns the SMARTS (or SMILES) string for a Bond")
// properties
.def("SetProp", BondSetProp<std::string>,
(python::arg("self"), python::arg("key"), python::arg("val")),
"Sets a bond property\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to be set (a string).\n"
" - value: the property value (a string).\n\n")
.def("GetProp", GetProp<Bond, std::string>,
"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("SetIntProp", BondSetProp<int>,
(python::arg("self"), python::arg("key"), python::arg("val")),
"Sets a bond property\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to be set (a string).\n"
" - value: the property value (an int).\n\n")
.def("SetUnsignedProp", BondSetProp<unsigned int>,
(python::arg("self"), python::arg("key"), python::arg("val")),
"Sets a bond property\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to be set (a string).\n"
" - value: the property value (an int >= 0).\n\n")
.def("GetIntProp", GetProp<Bond, int>,
"Returns the value of the property.\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to return (an int).\n\n"
" RETURNS: an int\n\n"
" NOTE:\n"
" - If the property has not been set, a KeyError exception "
"will be raised.\n")
.def("GetUnsignedProp", GetProp<Bond, unsigned int>,
"Returns the value of the property.\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to return (an unsigned "
"integer).\n\n"
" RETURNS: an int (Python has no unsigned type)\n\n"
" NOTE:\n"
" - If the property has not been set, a KeyError exception "
"will be raised.\n")
.def("SetDoubleProp", BondSetProp<double>,
(python::arg("self"), python::arg("key"), python::arg("val")),
"Sets a bond property\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to be set (a string).\n"
" - value: the property value (a double).\n\n")
.def("GetDoubleProp", GetProp<Bond, double>,
"Returns the value of the property.\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to return (a double).\n\n"
" RETURNS: a double\n\n"
" NOTE:\n"
" - If the property has not been set, a KeyError exception "
"will be raised.\n")
.def("SetBoolProp", BondSetProp<bool>,
(python::arg("self"), python::arg("key"), python::arg("val")),
"Sets a bond property\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to be set (a string).\n"
" - value: the property value (a boolean).\n\n")
.def("GetBoolProp", GetProp<Bond, bool>,
"Returns the value of the property.\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to return (a boolean).\n\n"
" RETURNS: a boolean\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("ClearProp", BondClearProp,
"Removes a particular property from an Bond (does nothing if not "
"already set).\n\n"
" ARGUMENTS:\n"
" - key: the name of the property to be removed.\n")
.def("GetPropNames", &Bond::getPropList,
(python::arg("self"), python::arg("includePrivate") = false,
python::arg("includeComputed") = false),
"Returns a list of the properties set on the Bond.\n\n")
.def("GetPropsAsDict", GetPropsAsDict<Bond>,
(python::arg("self"), python::arg("includePrivate") = true,
python::arg("includeComputed") = true),
"Returns a dictionary of the properties set on the Bond.\n"
" n.b. some properties cannot be converted to python types.\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)
.value("ZERO", Bond::ZERO);
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("EITHERDOUBLE", Bond::EITHERDOUBLE)
.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)
.value("STEREOCIS", Bond::STEREOCIS)
.value("STEREOTRANS", Bond::STEREOTRANS);
bondClassDoc =
"The class to store QueryBonds.\n\
These cannot currently be constructed directly from Python\n";
python::class_<QueryBond, python::bases<Bond> >(
"QueryBond", bondClassDoc.c_str(), python::no_init);
};
};
} // end of namespace
void wrap_bond() { RDKit::bond_wrapper::wrap(); }
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