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* Expose QueryOpts::replaceAtomWithQueryAtom. * Indentation error. * Response to review. * Update docstrings in response to review. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
336 lines
15 KiB
C++
336 lines
15 KiB
C++
//
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// Copyright (C) 2003-2017 Rational Discovery LLC and Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#define NO_IMPORT_ARRAY
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#include <RDBoost/python.h>
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#include <string>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <RDGeneral/types.h>
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namespace python = boost::python;
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namespace RDKit {
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/*
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NOTE: it looks like there is a typo in the below code
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ATOM_GREATER_QUERY is intentionally being used for the LessQueryAtom
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and ATOM_LESS_QUERY for GreaterQueryAtom in the python API.
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The C++ API is internally consistent and logical, but having
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AtomNumLessQueryAtom(6) return atoms where 6 is less than their atomic
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number feels backwards in Python.
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*/
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#define QAFUNC1(_funcname_, _func_, _typ_) \
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QueryAtom *_funcname_##EqualsQueryAtom(_typ_ val, bool negate) { \
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QueryAtom *res = new QueryAtom(); \
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res->setQuery(_func_(val)); \
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if (negate) res->getQuery()->setNegation(true); \
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return res; \
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} \
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QueryAtom *_funcname_##LessQueryAtom(_typ_ val, bool negate) { \
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QueryAtom *res = new QueryAtom(); \
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res->setQuery( \
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_func_<ATOM_GREATER_QUERY>(val, std::string(#_funcname_ "Less"))); \
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if (negate) res->getQuery()->setNegation(true); \
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return res; \
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} \
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QueryAtom *_funcname_##GreaterQueryAtom(_typ_ val, bool negate) { \
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QueryAtom *res = new QueryAtom(); \
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res->setQuery( \
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_func_<ATOM_LESS_QUERY>(val, std::string(#_funcname_ "Greater"))); \
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if (negate) res->getQuery()->setNegation(true); \
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return res; \
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}
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#define QAFUNC2(_funcname_, _func_, _typ_) \
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QueryAtom *_funcname_(bool negate) { \
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QueryAtom *res = new QueryAtom(); \
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res->setQuery(_func_()); \
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if (negate) res->getQuery()->setNegation(true); \
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return res; \
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}
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QAFUNC1(AtomNum, makeAtomNumQuery, int);
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QAFUNC1(ExplicitValence, makeAtomExplicitValenceQuery, int);
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QAFUNC1(TotalValence, makeAtomTotalValenceQuery, int);
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QAFUNC1(ExplicitDegree, makeAtomExplicitDegreeQuery, int);
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QAFUNC1(TotalDegree, makeAtomTotalDegreeQuery, int);
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QAFUNC1(NonHydrogenDegree, makeAtomNonHydrogenDegreeQuery, int);
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QAFUNC1(HCount, makeAtomHCountQuery, int);
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QAFUNC1(Mass, makeAtomMassQuery, int);
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QAFUNC1(Isotope, makeAtomIsotopeQuery, int);
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QAFUNC1(FormalCharge, makeAtomFormalChargeQuery, int);
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QAFUNC1(Hybridization, makeAtomHybridizationQuery, int);
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QAFUNC1(InNRings, makeAtomInNRingsQuery, int);
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QAFUNC1(MinRingSize, makeAtomMinRingSizeQuery, int);
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QAFUNC1(RingBondCount, makeAtomRingBondCountQuery, int);
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QAFUNC1(NumRadicalElectrons, makeAtomNumRadicalElectronsQuery, int);
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QAFUNC1(NumHeteroatomNeighbors, makeAtomNumHeteroatomNbrsQuery, int);
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QAFUNC1(NumAliphaticHeteroatomNeighbors,
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makeAtomNumAliphaticHeteroatomNbrsQuery, int);
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QAFUNC2(IsUnsaturatedQueryAtom, makeAtomUnsaturatedQuery, int);
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QAFUNC2(IsAromaticQueryAtom, makeAtomAromaticQuery, int);
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QAFUNC2(IsAliphaticQueryAtom, makeAtomAliphaticQuery, int);
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QAFUNC2(IsInRingQueryAtom, makeAtomInRingQuery, int);
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QAFUNC2(HasChiralTagQueryAtom, makeAtomHasChiralTagQuery, int);
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QAFUNC2(MissingChiralTagQueryAtom, makeAtomMissingChiralTagQuery, int);
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QAFUNC2(IsBridgeheadQueryAtom, makeAtomIsBridgeheadQuery, int);
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QAFUNC2(AAtomQueryAtom, makeAAtomQuery, int);
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QAFUNC2(AHAtomQueryAtom, makeAHAtomQuery, int);
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QAFUNC2(QAtomQueryAtom, makeQAtomQuery, int);
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QAFUNC2(QHAtomQueryAtom, makeQHAtomQuery, int);
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QAFUNC2(XAtomQueryAtom, makeXAtomQuery, int);
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QAFUNC2(XHAtomQueryAtom, makeXHAtomQuery, int);
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QAFUNC2(MAtomQueryAtom, makeMAtomQuery, int);
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QAFUNC2(MHAtomQueryAtom, makeMHAtomQuery, int);
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QueryAtom *HasPropQueryAtom(const std::string &propname, bool negate) {
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auto *res = new QueryAtom();
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res->setQuery(makeHasPropQuery<Atom>(propname));
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if (negate) {
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res->getQuery()->setNegation(true);
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}
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return res;
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}
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QueryBond *HasPropQueryBond(const std::string &propname, bool negate) {
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auto *res = new QueryBond();
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res->setQuery(makeHasPropQuery<Bond>(propname));
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if (negate) {
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res->getQuery()->setNegation(true);
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}
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return res;
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}
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template <class Ob, class Ret, class T>
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Ret *PropQuery(const std::string &propname, const T &v, bool negate) {
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auto *res = new Ret();
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res->setQuery(makePropQuery<Ob, T>(propname, v));
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if (negate) {
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res->getQuery()->setNegation(true);
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}
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return res;
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}
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template <class Ob, class Ret, class T>
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Ret *PropQueryWithTol(const std::string &propname, const T &v, bool negate,
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const T &tol = T()) {
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auto *res = new Ret();
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res->setQuery(makePropQuery<Ob, T>(propname, v, tol));
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if (negate) {
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res->getQuery()->setNegation(true);
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}
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return res;
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}
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template <class Ob, class Ret>
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Ret *PropQueryWithTol(const std::string &propname, const ExplicitBitVect &v,
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bool negate, float tol = 0.0) {
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auto *res = new Ret();
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res->setQuery(makePropQuery<Ob>(propname, v, tol));
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if (negate) {
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res->getQuery()->setNegation(true);
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}
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return res;
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}
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namespace {
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Atom *replaceAtomWithQueryAtomHelper(ROMol &mol, Atom &atom) {
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return QueryOps::replaceAtomWithQueryAtom(static_cast<RWMol *>(&mol), &atom);
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}
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} // namespace
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struct queries_wrapper {
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static void wrap() {
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#define QADEF1(_funcname_) \
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python::def(#_funcname_ "EqualsQueryAtom", _funcname_##EqualsQueryAtom, \
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(python::arg("val"), python::arg("negate") = false), \
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"Returns a QueryAtom that matches atoms where " #_funcname_ \
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" is equal to the target value.", \
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python::return_value_policy<python::manage_new_object>()); \
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python::def( \
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#_funcname_ "LessQueryAtom", _funcname_##LessQueryAtom, \
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(python::arg("val"), python::arg("negate") = false), \
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"Returns a QueryAtom that matches atoms where " #_funcname_ \
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" is less than the target value.\n" \
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"NOTE: the direction of comparison is reversed relative to the C++ API", \
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python::return_value_policy<python::manage_new_object>()); \
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python::def( \
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#_funcname_ "GreaterQueryAtom", _funcname_##GreaterQueryAtom, \
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(python::arg("val"), python::arg("negate") = false), \
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"Returns a QueryAtom that matches atoms where " #_funcname_ \
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" is equal to the target value.\n" \
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"NOTE: the direction of comparison is reversed relative to the C++ API", \
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python::return_value_policy<python::manage_new_object>());
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#define QADEF2(_funcname_) \
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python::def(#_funcname_ "QueryAtom", _funcname_##QueryAtom, \
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(python::arg("negate") = false), \
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"Returns a QueryAtom that matches atoms when " #_funcname_ \
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" is True.", \
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python::return_value_policy<python::manage_new_object>());
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QADEF1(AtomNum);
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QADEF1(ExplicitValence);
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QADEF1(TotalValence);
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QADEF1(ExplicitDegree);
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QADEF1(TotalDegree);
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QADEF1(HCount);
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QADEF1(Mass);
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QADEF1(Isotope);
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QADEF1(FormalCharge);
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QADEF1(Hybridization);
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QADEF1(InNRings);
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QADEF1(MinRingSize);
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QADEF1(RingBondCount);
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QADEF1(NumRadicalElectrons)
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QADEF1(NumHeteroatomNeighbors)
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QADEF1(NumAliphaticHeteroatomNeighbors)
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QADEF1(NonHydrogenDegree)
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QADEF2(IsUnsaturated);
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QADEF2(IsAromatic);
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QADEF2(IsAliphatic);
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QADEF2(IsInRing);
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QADEF2(HasChiralTag);
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QADEF2(MissingChiralTag);
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QADEF2(IsBridgehead);
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QADEF2(AAtom);
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QADEF2(AHAtom);
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QADEF2(XAtom);
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QADEF2(XHAtom);
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QADEF2(QAtom);
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QADEF2(QHAtom);
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QADEF2(MAtom);
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QADEF2(MHAtom);
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python::def("HasPropQueryAtom", HasPropQueryAtom,
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(python::arg("propname"), python::arg("negate") = false),
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"Returns a QueryAtom that matches when the property 'propname' "
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"exists in the atom.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasPropQueryBond", HasPropQueryBond,
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(python::arg("propname"), python::arg("negate") = false),
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"Returns a QueryBond that matches when the property 'propname' "
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"exists in the bond.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasIntPropWithValueQueryAtom",
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PropQueryWithTol<Atom, QueryAtom, int>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false, python::arg("tolerance") = 0),
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"Returns a QueryAtom that matches when the property 'propname' "
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"has the specified int value.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasBoolPropWithValueQueryAtom",
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PropQuery<Atom, QueryAtom, bool>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false),
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"Returns a QueryAtom that matches when the property 'propname' "
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"has the specified boolean"
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" value.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasStringPropWithValueQueryAtom",
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PropQuery<Atom, QueryAtom, std::string>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false),
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"Returns a QueryAtom that matches when the property 'propname' "
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"has the specified string "
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"value.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasDoublePropWithValueQueryAtom",
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PropQueryWithTol<Atom, QueryAtom, double>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false, python::arg("tolerance") = 0.0),
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"Returns a QueryAtom that matches when the property 'propname' "
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"has the specified "
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"value +- tolerance",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasBitVectPropWithValueQueryAtom",
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PropQueryWithTol<Atom, QueryAtom>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false, python::arg("tolerance") = 0),
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"Returns a QueryAtom that matches when the property 'propname' "
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"has the specified explicit bit vector"
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" value. The Tolerance is the allowed Tanimoto difference",
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python::return_value_policy<python::manage_new_object>());
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/////////////////////////////////////////////////////////////////////////////////////
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// Bond Queries
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python::def("HasPropQueryBond", HasPropQueryBond,
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(python::arg("propname"), python::arg("negate") = false),
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"Returns a QueryBond that matches when the property 'propname' "
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"exists in the bond.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasPropQueryBond", HasPropQueryBond,
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(python::arg("propname"), python::arg("negate") = false),
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"Returns a QueryBond that matches when the property 'propname' "
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"exists in the bond.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasIntPropWithValueQueryBond",
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PropQueryWithTol<Bond, QueryBond, int>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false, python::arg("tolerance") = 0),
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"Returns a QueryBond that matches when the property 'propname' "
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"has the specified int value.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasBoolPropWithValueQueryBond",
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PropQuery<Bond, QueryBond, bool>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false),
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"Returns a QueryBond that matches when the property 'propname' "
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"has the specified boolean"
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" value.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasStringPropWithValueQueryBond",
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PropQuery<Bond, QueryBond, std::string>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false),
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"Returns a QueryBond that matches when the property 'propname' "
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"has the specified string "
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"value.",
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python::return_value_policy<python::manage_new_object>());
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python::def("HasDoublePropWithValueQueryBond",
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PropQueryWithTol<Bond, QueryBond, double>,
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(python::arg("propname"), python::arg("val"),
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python::arg("negate") = false, python::arg("tolerance") = 0.0),
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"Returns a QueryBond that matches when the property 'propname' "
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"has the specified "
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"value +- tolerance",
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python::return_value_policy<python::manage_new_object>());
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std::string docString = R"DOC(Changes the given atom in the molecule to
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a query atom and returns the atom which can then be modified, for example
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with additional query constraints added. The new atom is otherwise a copy
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of the old.
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If the atom already has a query, nothing will be changed.)DOC";
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python::def(
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"ReplaceAtomWithQueryAtom", replaceAtomWithQueryAtomHelper,
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(python::arg("mol"), python::arg("atom")), docString.c_str(),
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python::return_value_policy<python::reference_existing_object>());
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};
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};
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} // namespace RDKit
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void wrap_queries() { RDKit::queries_wrapper::wrap(); }
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