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//
//
// Copyright (C) 2020 Schrödinger, 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 <GraphMol/Chirality.h>
#include "Sp2Bond.h"
#include "../Sort.h"
#include "../rules/Rules.h"
namespace RDKit {
namespace CIPLabeler {
Sp2Bond::Sp2Bond(const CIPMol &mol, Bond *bond, Atom *startAtom, Atom *endAtom,
Bond::BondStereo cfg)
: Configuration(mol, {startAtom, endAtom}), dp_bond{bond}, d_cfg{cfg} {
CHECK_INVARIANT(startAtom && endAtom, "bad foci")
CHECK_INVARIANT(d_cfg == Bond::STEREOTRANS || d_cfg == Bond::STEREOCIS,
"bad config")
auto stereo_atoms = Chirality::findStereoAtoms(bond);
CHECK_INVARIANT(stereo_atoms.size() == 2, "incorrect number of stereo atoms")
std::vector<Atom *> anchors{
{mol.getAtom(stereo_atoms[0]), mol.getAtom(stereo_atoms[1])}};
setCarriers(std::move(anchors));
}
void Sp2Bond::setPrimaryLabel(Descriptor desc) {
switch (desc) {
case Descriptor::seqTrans:
case Descriptor::E:
case Descriptor::seqCis:
case Descriptor::Z: {
auto carriers = getCarriers();
dp_bond->setStereoAtoms(carriers[0]->getIdx(), carriers[1]->getIdx());
dp_bond->setStereo(d_cfg);
dp_bond->setProp(common_properties::_CIPCode, to_string(desc));
return;
}
case Descriptor::R:
case Descriptor::S:
case Descriptor::r:
case Descriptor::s:
case Descriptor::M:
case Descriptor::P:
case Descriptor::m:
case Descriptor::p:
case Descriptor::SP_4:
case Descriptor::TBPY_5:
case Descriptor::OC_6:
throw std::runtime_error(
"Received a Descriptor that is not supported for double bonds");
default:
throw std::runtime_error("Received an invalid Bond Descriptor");
}
}
Descriptor Sp2Bond::label(const Rules &comp) {
auto &digraph = getDigraph();
auto root1 = digraph.getOriginalRoot();
if (digraph.getCurrentRoot() != root1) {
digraph.changeRoot(root1);
}
return label(root1, digraph, comp);
}
Descriptor Sp2Bond::label(Node *root1, Digraph &digraph, const Rules &comp) {
const auto &focus1 = getFoci()[0];
const auto &focus2 = getFoci()[1];
const auto &internal = findInternalEdge(root1->getEdges(), focus1, focus2);
if (internal == nullptr) {
return Descriptor::UNKNOWN;
}
const auto &root2 = internal->getOther(root1);
auto edges1 = root1->getEdges();
auto edges2 = root2->getEdges();
removeInternalEdges(edges1, focus1, focus2);
removeInternalEdges(edges2, focus1, focus2);
auto carriers = std::vector<Atom *>(getCarriers());
auto config = d_cfg;
if (root1->getAtom() == focus2) {
std::swap(carriers[0], carriers[1]);
}
digraph.changeRoot(root1);
const auto &priority1 = comp.sort(root1, edges1);
if (!priority1.isUnique()) {
return Descriptor::UNKNOWN;
}
// swap
if (edges1.size() > 1 && carriers[0] == edges1[1]->getEnd()->getAtom()) {
if (config == Bond::STEREOCIS) {
config = Bond::STEREOTRANS;
} else {
config = Bond::STEREOCIS;
}
}
digraph.changeRoot(root2);
const auto &priority2 = comp.sort(root2, edges2);
if (!priority2.isUnique()) {
return Descriptor::UNKNOWN;
}
// swap
if (edges2.size() > 1 && carriers[1] == edges2[1]->getEnd()->getAtom()) {
if (config == Bond::STEREOCIS) {
config = Bond::STEREOTRANS;
} else {
config = Bond::STEREOCIS;
}
}
if (config == Bond::STEREOCIS) {
if (priority1.isPseudoAsymetric() != priority2.isPseudoAsymetric()) {
return Descriptor::seqCis;
} else {
return Descriptor::Z;
}
} else if (config == Bond::STEREOTRANS) {
if (priority1.isPseudoAsymetric() != priority2.isPseudoAsymetric()) {
return Descriptor::seqTrans;
} else {
return Descriptor::E;
}
}
return Descriptor::UNKNOWN;
}
} // namespace CIPLabeler
} // namespace RDKit
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