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//
// Copyright (C) 2001-2017 Greg Landrum and 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.
//
#include "Bond.h"
#include "Atom.h"
#include "ROMol.h"
#include <RDGeneral/Invariant.h>
namespace RDKit {
Bond::Bond() : RDProps() { initBond(); };
Bond::Bond(BondType bT) : RDProps() {
initBond();
d_bondType = bT;
};
Bond::Bond(const Bond &other) : RDProps(other) {
// NOTE: we do *not* copy ownership!
dp_mol = nullptr;
d_bondType = other.d_bondType;
d_beginAtomIdx = other.d_beginAtomIdx;
d_endAtomIdx = other.d_endAtomIdx;
d_dirTag = other.d_dirTag;
d_stereo = other.d_stereo;
if (other.dp_stereoAtoms) {
dp_stereoAtoms = new INT_VECT(*other.dp_stereoAtoms);
} else {
dp_stereoAtoms = nullptr;
}
df_isAromatic = other.df_isAromatic;
df_isConjugated = other.df_isConjugated;
d_index = other.d_index;
}
Bond::~Bond() { delete dp_stereoAtoms; }
Bond &Bond::operator=(const Bond &other) {
dp_mol = other.dp_mol;
d_bondType = other.d_bondType;
d_beginAtomIdx = other.d_beginAtomIdx;
d_endAtomIdx = other.d_endAtomIdx;
d_dirTag = other.d_dirTag;
if (other.dp_stereoAtoms) {
dp_stereoAtoms = new INT_VECT(*other.dp_stereoAtoms);
} else {
dp_stereoAtoms = nullptr;
}
df_isAromatic = other.df_isAromatic;
df_isConjugated = other.df_isConjugated;
d_index = other.d_index;
dp_props = other.dp_props;
return *this;
}
Bond *Bond::copy() const {
auto *res = new Bond(*this);
return res;
}
void Bond::setOwningMol(ROMol *other) {
// FIX: doesn't update topology
dp_mol = other;
}
unsigned int Bond::getOtherAtomIdx(const unsigned int thisIdx) const {
PRECONDITION(d_beginAtomIdx == thisIdx || d_endAtomIdx == thisIdx,
"bad index");
if (d_beginAtomIdx == thisIdx)
return d_endAtomIdx;
else if (d_endAtomIdx == thisIdx)
return d_beginAtomIdx;
// we cannot actually get down here
return 0;
}
void Bond::setBeginAtomIdx(unsigned int what) {
if (dp_mol) URANGE_CHECK(what, getOwningMol().getNumAtoms());
d_beginAtomIdx = what;
};
void Bond::setEndAtomIdx(unsigned int what) {
if (dp_mol) URANGE_CHECK(what, getOwningMol().getNumAtoms());
d_endAtomIdx = what;
};
void Bond::setBeginAtom(Atom *at) {
PRECONDITION(dp_mol != nullptr, "no owning molecule for bond");
setBeginAtomIdx(at->getIdx());
}
void Bond::setEndAtom(Atom *at) {
PRECONDITION(dp_mol != nullptr, "no owning molecule for bond");
setEndAtomIdx(at->getIdx());
}
Atom *Bond::getBeginAtom() const {
PRECONDITION(dp_mol != nullptr, "no owning molecule for bond");
return dp_mol->getAtomWithIdx(d_beginAtomIdx);
};
Atom *Bond::getEndAtom() const {
PRECONDITION(dp_mol != nullptr, "no owning molecule for bond");
return dp_mol->getAtomWithIdx(d_endAtomIdx);
};
Atom *Bond::getOtherAtom(Atom const *what) const {
PRECONDITION(dp_mol != nullptr, "no owning molecule for bond");
return dp_mol->getAtomWithIdx(getOtherAtomIdx(what->getIdx()));
};
double Bond::getBondTypeAsDouble() const {
switch (getBondType()) {
case UNSPECIFIED:
return 0;
break;
case IONIC:
return 0;
break;
case SINGLE:
return 1;
break;
case DOUBLE:
return 2;
break;
case TRIPLE:
return 3;
break;
case QUADRUPLE:
return 4;
break;
case QUINTUPLE:
return 5;
break;
case HEXTUPLE:
return 6;
break;
case ONEANDAHALF:
return 1.5;
break;
case TWOANDAHALF:
return 2.5;
break;
case THREEANDAHALF:
return 3.5;
break;
case FOURANDAHALF:
return 4.5;
break;
case FIVEANDAHALF:
return 5.5;
break;
case AROMATIC:
return 1.5;
break;
case DATIVEONE:
return 1.0;
break; // FIX: this should probably be different
case DATIVE:
return 1.0;
break; // FIX: again probably wrong
case ZERO:
return 0;
break;
default:
UNDER_CONSTRUCTION("Bad bond type");
}
}
double Bond::getValenceContrib(const Atom *atom) const {
switch (getBondType()) {
case UNSPECIFIED:
return 0;
break;
case IONIC:
return 0;
break;
case SINGLE:
return 1;
break;
case DOUBLE:
return 2;
break;
case TRIPLE:
return 3;
break;
case QUADRUPLE:
return 4;
break;
case QUINTUPLE:
return 5;
break;
case HEXTUPLE:
return 6;
break;
case ONEANDAHALF:
return 1.5;
break;
case TWOANDAHALF:
return 2.5;
break;
case THREEANDAHALF:
return 3.5;
break;
case FOURANDAHALF:
return 4.5;
break;
case FIVEANDAHALF:
return 5.5;
break;
case AROMATIC:
return 1.5;
break;
case DATIVEONE:
if (atom->getIdx() == getEndAtomIdx())
return 1.0;
else
return 0.0;
break;
case DATIVE:
if (atom->getIdx() == getEndAtomIdx())
return 1.0;
else
return 0.0;
break;
case ZERO:
return 0;
break;
default:
UNDER_CONSTRUCTION("Bad bond type");
}
}
void Bond::setQuery(QUERYBOND_QUERY *what) {
// Bonds don't have queries at the moment because I have not
// yet figured out what a good base query should be.
// It would be nice to be able to do substructure searches
// using molecules alone, so it'd be nice if we got this
// issue resolved ASAP.
RDUNUSED_PARAM(what);
PRECONDITION(0, "plain bonds have no Query");
}
Bond::QUERYBOND_QUERY *Bond::getQuery() const {
PRECONDITION(0, "plain bonds have no Query");
return nullptr;
};
bool Bond::Match(Bond const *what) const {
bool res;
if (getBondType() == Bond::UNSPECIFIED ||
what->getBondType() == Bond::UNSPECIFIED) {
res = true;
} else {
res = getBondType() == what->getBondType();
}
return res;
};
void Bond::expandQuery(Bond::QUERYBOND_QUERY *what,
Queries::CompositeQueryType how, bool maintainOrder) {
RDUNUSED_PARAM(what);
RDUNUSED_PARAM(how);
RDUNUSED_PARAM(maintainOrder);
PRECONDITION(0, "plain bonds have no query");
};
void Bond::initBond() {
d_bondType = UNSPECIFIED;
d_dirTag = NONE;
d_stereo = STEREONONE;
dp_mol = nullptr;
d_beginAtomIdx = 0;
d_endAtomIdx = 0;
df_isAromatic = 0;
d_index = 0;
df_isConjugated = 0;
dp_stereoAtoms = nullptr;
};
void Bond::setStereoAtoms(unsigned int bgnIdx, unsigned int endIdx) {
PRECONDITION(
getOwningMol().getBondBetweenAtoms(getBeginAtomIdx(), bgnIdx) != nullptr,
"bgnIdx not connected to begin atom of bond");
PRECONDITION(
getOwningMol().getBondBetweenAtoms(getEndAtomIdx(), endIdx) != nullptr,
"endIdx not connected to end atom of bond");
INT_VECT &atoms = getStereoAtoms();
atoms.clear();
atoms.push_back(bgnIdx);
atoms.push_back(endIdx);
};
}; // end o' namespace
std::ostream &operator<<(std::ostream &target, const RDKit::Bond &bond) {
target << bond.getIdx() << " ";
target << bond.getBeginAtomIdx() << "->" << bond.getEndAtomIdx();
target << " order: " << bond.getBondType();
if (bond.getBondDir()) target << " dir: " << bond.getBondDir();
if (bond.getStereo()) target << " stereo: " << bond.getStereo();
target << " conj?: " << bond.getIsConjugated();
target << " aromatic?: " << bond.getIsAromatic();
return target;
}
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