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//
// Copyright (c) 2024, Glysade Inc
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//#include "node.h"
#include "utils.h"
#include "fragment.h"
namespace RDKit {
namespace ChemDraw {
bool parseBond(RWMol &mol, unsigned int fragmentId, CDXBond &bond,
PageData &pagedata) {
int bond_id = bond.GetObjectID();
Atom *start_atom = pagedata.atomIds[bond.m_beginNodeID];
Atom *end_atom = pagedata.atomIds[bond.m_endNodeID];
if ((!start_atom || !end_atom)) {
BOOST_LOG(rdErrorLog) << "Bad bond in CDXML skipping fragment "
<< fragmentId << "..." << std::endl;
return false;
}
Bond::BondType order = Bond::UNSPECIFIED;
std::unique_ptr<QueryBond> qb;
switch (bond.m_bondOrder) {
case kCDXBondOrder_Single:
order = Bond::BondType::SINGLE;
break;
case kCDXBondOrder_Double:
order = Bond::BondType::DOUBLE;
break;
case kCDXBondOrder_Triple:
order = Bond::BondType::TRIPLE;
break;
case kCDXBondOrder_Quadruple:
order = Bond::BondType::QUADRUPLE;
break;
case kCDXBondOrder_Quintuple:
order = Bond::BondType::QUINTUPLE;
break;
case kCDXBondOrder_Sextuple:
order = Bond::BondType::HEXTUPLE;
break;
case kCDXBondOrder_OneHalf:
order = Bond::BondType::AROMATIC;
start_atom->setIsAromatic(true);
end_atom->setIsAromatic(true);
break;
case kCDXBondOrder_TwoHalf:
order = Bond::BondType::TWOANDAHALF;
break;
case kCDXBondOrder_ThreeHalf:
order = Bond::BondType::THREEANDAHALF;
break;
case kCDXBondOrder_FourHalf:
order = Bond::BondType::FOURANDAHALF;
break;
case kCDXBondOrder_FiveHalf:
order = Bond::BondType::FIVEANDAHALF;
break;
case kCDXBondOrder_Dative:
order = Bond::BondType::DATIVE;
break;
case kCDXBondOrder_Ionic:
order = Bond::BondType::IONIC;
break;
case kCDXBondOrder_SingleOrDouble: {
order = Bond::BondType::SINGLE;
qb = std::make_unique<QueryBond>();
qb->setQuery(makeSingleOrDoubleBondQuery());
break;
}
case kCDXBondOrder_SingleOrAromatic: {
order = Bond::BondType::SINGLE;
qb = std::make_unique<QueryBond>();
qb->setQuery(makeSingleOrAromaticBondQuery());
break;
}
case kCDXBondOrder_DoubleOrAromatic: {
order = Bond::BondType::DOUBLE;
qb = std::make_unique<QueryBond>();
qb->setQuery(makeDoubleOrAromaticBondQuery());
break;
}
case kCDXBondOrder_Any: {
qb = std::make_unique<QueryBond>();
qb->setQuery(makeBondNullQuery());
break;
}
case kCDXBondOrder_Hydrogen:
BOOST_LOG(rdErrorLog)
<< "Unhandled bond order Hydrogen, skipping fragment" << std::endl;
return false;
case kCDXBondOrder_ThreeCenter:
BOOST_LOG(rdErrorLog)
<< "Unhandled bond order ThreeCenter, skipping fragment" << std::endl;
return false;
case kCDXBondOrder_Half:
BOOST_LOG(rdErrorLog)
<< "Unhandled bond order Half, skipping fragment" << std::endl;
return false;
default:
BOOST_LOG(rdErrorLog) << "Bad bond, skipping fragment" << std::endl;
return false;
};
// The RDKit only supports one direction for wedges so
// normalize it
bool swap_bond_ends = false;
switch (bond.m_display) {
case kCDXBondDisplay_Solid:
break;
case kCDXBondDisplay_Dash:
break;
case kCDXBondDisplay_Hash:
break;
case kCDXBondDisplay_WedgedHashBegin:
break;
case kCDXBondDisplay_WedgedHashEnd:
swap_bond_ends = true;
break;
case kCDXBondDisplay_Bold:
break;
case kCDXBondDisplay_WedgeBegin:
break;
case kCDXBondDisplay_WedgeEnd:
swap_bond_ends = true;
break;
case kCDXBondDisplay_Wavy:
break;
case kCDXBondDisplay_HollowWedgeBegin:
break;
case kCDXBondDisplay_HollowWedgeEnd:
break;
case kCDXBondDisplay_WavyWedgeBegin:
break;
case kCDXBondDisplay_WavyWedgeEnd:
break;
case kCDXBondDisplay_Dot:
break;
case kCDXBondDisplay_DashDot:
break;
case kCDXBondDisplay_DottedHydrogen:
break;
}
unsigned int bondIdx = 0;
auto startIdx = start_atom->getIdx();
auto endIdx = end_atom->getIdx();
if (swap_bond_ends) std::swap(startIdx, endIdx);
if (qb) {
qb->setBeginAtomIdx(startIdx);
qb->setEndAtomIdx(endIdx);
bondIdx = mol.addBond(qb.release(), true) - 1;
} else {
bondIdx = mol.addBond(startIdx, endIdx, order) - 1;
}
Bond *bnd = mol.getBondWithIdx(bondIdx);
if (order == Bond::BondType::AROMATIC) {
bnd->setIsAromatic(true);
bnd->getBeginAtom()->setIsAromatic(true);
bnd->getEndAtom()->setIsAromatic(true);
}
bnd->setProp(CDX_BOND_ID, bond.GetObjectID());
switch (bond.m_display) {
case kCDXBondDisplay_WedgedHashBegin:
case kCDXBondDisplay_WedgedHashEnd: {
bnd->setBondDir(Bond::BondDir::BEGINDASH);
bnd->setProp(common_properties::_MolFileBondCfg, 3);
} break;
case kCDXBondDisplay_WedgeBegin:
case kCDXBondDisplay_WedgeEnd: {
bnd->setBondDir(Bond::BondDir::BEGINWEDGE);
bnd->setProp(common_properties::_MolFileBondCfg, 1);
} break;
case kCDXBondDisplay_Wavy: {
switch (order) {
case Bond::BondType::SINGLE:
bnd->setBondDir(Bond::BondDir::UNKNOWN);
bnd->setProp(common_properties::_MolFileBondCfg, 2);
break;
case Bond::BondType::DOUBLE:
bnd->setBondDir(Bond::BondDir::EITHERDOUBLE);
bnd->setStereo(Bond::STEREOANY);
break;
default:
BOOST_LOG(rdWarningLog)
<< "ignoring Wavy bond set on a non double bond id: " << bond_id
<< std::endl;
}
break;
default:
break;
}
}
return true;
}
}
} // namespace RDKit
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