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* ChemDraw Document and read/write support for the RDKit * Add missing test file * Rev chemdraw version * Rev chemdraw version * Rev chemdraw version for g++11 * Update CMakeLists.txt Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Build chemdraw from an external CMake file * Remove unused platform bigendian check * Revert changes to constants, remove unused ones * Keep the original constant names * Remove __main__ section * Use as much of the ChemDraw CMakeList as possible * Skip installing expat * Rev chemdraw version to fix windows issue * Don't install expat, set the appropriate CHEMDRAW_BUILD definition * resolve windows builds * Fix minimal lib builds * Move ChemDraw document to private header * Move utility functions to ChemDraw namespace * Move ChemDraw to v2 unique ptr api namespace * Make class enum * Switch to camelCase * Response to review * Move ChemDrawToDocument to ChemDraw namespace * Update External/ChemDraw/Wrap/rdChemDraw.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Fix typo * Update External/ChemDraw/Wrap/rdChemDraw.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Add better documentation --------- Co-authored-by: Brian Kelley <bkelley@glysade.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
111 lines
4.1 KiB
C++
111 lines
4.1 KiB
C++
//
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// Copyright (c) 2024, Glysade Inc
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#ifndef CHEMDRAW_UTILS_H
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#define CHEMDRAW_UTILS_H
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/QueryAtom.h>
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#include <GraphMol/QueryBond.h>
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#include <GraphMol/QueryOps.h>
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#include "ChemDrawStartInclude.h"
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#include "chemdraw/CDXStdObjects.h"
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#include "ChemDrawEndInclude.h"
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namespace RDKit {
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namespace ChemDraw {
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constexpr double RDKIT_DEPICT_BONDLENGTH = 1.5;
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const std::string NEEDS_FUSE("CDX_NEEDS_FUSE");
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const std::string CDX_FRAG_ID("CDX_FRAG_ID");
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const std::string CDX_GROUP_ID("CDX_GROUP_ID");
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const std::string FUSE_LABEL("CDX_NODE_ID");
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const std::string CDX_SCHEME_ID("CDX_SCHEME_ID");
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const std::string CDX_STEP_ID("CDX_STEP_ID");
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const std::string CDX_REAGENT_ID("CDX_REAGENT_ID");
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const std::string CDX_PRODUCT_ID("CDX_PRODUCT_ID");
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const std::string CDX_AGENT_ID("CDX_AGENT_ID");
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const std::string CDX_ATOM_POS("CDX_ATOM_POS");
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const std::string CDX_ATOM_ID("_CDX_ATOM_ID");
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const std::string CDX_BOND_ID("_CDX_BOND_ID");
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const std::string CDX_BOND_ORDERING("CDX_BOND_ORDERING");
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const std::string CDX_CIP("CDX_CIP");
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const std::string CDX_IMPLICIT_HYDROGEN_STEREO("CDX_ATOM_STEREO");
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// Convert a ChemDrawNode to a string
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std::string NodeType(CDXNodeType nodetype);
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// Scale the bonds to the targetBondLength. If bondLength is zero
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// use the average bond length in the molecule
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void scaleBonds(const ROMol &mol, Conformer &conf, double targetBondLength,
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double bondLength);
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// Indicate which atoms should be fused together from various
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// fragments in the ChemDraw file
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unsigned int get_fuse_label(Atom *atm);
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void set_fuse_label(Atom *atm, unsigned int idx);
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// Replace fragments that are not possible with molzip
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bool replaceFragments(RWMol &mol);
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// Add a Query to a molecule
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template <typename Q>
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Atom *addquery(Q *qry, std::string symbol, RWMol &mol, unsigned int idx) {
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PRECONDITION(qry, "bad query");
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auto *atm = mol.getAtomWithIdx(idx);
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auto qa = std::make_unique<QueryAtom>(*atm);
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qa->setQuery(qry);
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qa->setNoImplicit(true);
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mol.replaceAtom(idx, qa.get());
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Atom *res = mol.getAtomWithIdx(idx);
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if (symbol != "") {
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res->setProp(common_properties::atomLabel, symbol);
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}
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return res;
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}
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// Simple Structure for keeping track of Stereo Groups
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struct StereoGroupInfo {
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int sgroup = -1;
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bool conflictingSgroupTypes = false;
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StereoGroupType grouptype;
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std::vector<Atom *> atoms;
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};
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// check to see if we have a tetrahedral flag and ChemDraw CIP set but no
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// stereo assigned, if so check the bond ordering for CW and CCW
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void checkChemDrawTetrahedralGeometries(RWMol &mol);
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}
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} // namespace RDKit
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#endif
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