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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.
//
#ifndef CHEMDRAW_UTILS_H
#define CHEMDRAW_UTILS_H
#include <GraphMol/RDKitBase.h>
#include <GraphMol/QueryAtom.h>
#include <GraphMol/QueryBond.h>
#include <GraphMol/QueryOps.h>
#include "ChemDrawStartInclude.h"
#include "chemdraw/CDXStdObjects.h"
#include "ChemDrawEndInclude.h"
namespace RDKit {
namespace ChemDraw {
constexpr double RDKIT_DEPICT_BONDLENGTH = 1.5;
const std::string NEEDS_FUSE("CDX_NEEDS_FUSE");
const std::string CDX_FRAG_ID("CDX_FRAG_ID");
const std::string CDX_GROUP_ID("CDX_GROUP_ID");
const std::string FUSE_LABEL("CDX_NODE_ID");
const std::string CDX_SCHEME_ID("CDX_SCHEME_ID");
const std::string CDX_STEP_ID("CDX_STEP_ID");
const std::string CDX_REAGENT_ID("CDX_REAGENT_ID");
const std::string CDX_PRODUCT_ID("CDX_PRODUCT_ID");
const std::string CDX_AGENT_ID("CDX_AGENT_ID");
const std::string CDX_ATOM_POS("CDX_ATOM_POS");
const std::string CDX_ATOM_ID("_CDX_ATOM_ID");
const std::string CDX_BOND_ID("_CDX_BOND_ID");
const std::string CDX_BOND_ORDERING("CDX_BOND_ORDERING");
const std::string CDX_CIP("CDX_CIP");
const std::string CDX_IMPLICIT_HYDROGEN_STEREO("CDX_ATOM_STEREO");
// Convert a ChemDrawNode to a string
std::string NodeType(CDXNodeType nodetype);
// Scale the bonds to the targetBondLength. If bondLength is zero
// use the average bond length in the molecule
void scaleBonds(const ROMol &mol, Conformer &conf, double targetBondLength,
double bondLength);
// Indicate which atoms should be fused together from various
// fragments in the ChemDraw file
unsigned int get_fuse_label(Atom *atm);
void set_fuse_label(Atom *atm, unsigned int idx);
// Replace fragments that are not possible with molzip
bool replaceFragments(RWMol &mol);
// Add a Query to a molecule
template <typename Q>
Atom *addquery(Q *qry, std::string symbol, RWMol &mol, unsigned int idx) {
PRECONDITION(qry, "bad query");
auto *atm = mol.getAtomWithIdx(idx);
auto qa = std::make_unique<QueryAtom>(*atm);
qa->setQuery(qry);
qa->setNoImplicit(true);
mol.replaceAtom(idx, qa.get());
Atom *res = mol.getAtomWithIdx(idx);
if (symbol != "") {
res->setProp(common_properties::atomLabel, symbol);
}
return res;
}
// Simple Structure for keeping track of Stereo Groups
struct StereoGroupInfo {
int sgroup = -1;
bool conflictingSgroupTypes = false;
StereoGroupType grouptype;
std::vector<Atom *> atoms;
};
// check to see if we have a tetrahedral flag and ChemDraw CIP set but no
// stereo assigned, if so check the bond ordering for CW and CCW
void checkChemDrawTetrahedralGeometries(RWMol &mol);
}
} // namespace RDKit
#endif
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