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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 * Rev chemdraw version --------- Co-authored-by: Brian Kelley <bkelley@glysade.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
97 lines
3.6 KiB
C++
97 lines
3.6 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_FRAGMENT_H
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#define CHEMDRAW_FRAGMENT_H
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/QueryAtom.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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#include "reaction.h"
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#include "utils.h"
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namespace RDKit {
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namespace ChemDraw {
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struct PageData {
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PageData()
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: atomIds(),
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bondIds(),
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mols(),
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fragmentLookup(),
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groupedFragments(),
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schemes() {}
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PageData(const PageData &) = delete;
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std::map<unsigned int, Atom *> atomIds;
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std::map<unsigned int, Bond *> bondIds;
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std::vector<std::unique_ptr<RWMol>> mols; // All molecules found in the doc
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std::map<unsigned int, size_t>
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fragmentLookup; // fragment.id->molecule index
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std::map<unsigned int, std::vector<int>>
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groupedFragments; // grouped.id -> [fragment.id]
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std::vector<ReactionInfo> schemes; // reaction schemes found
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void clearCDXProps() {
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for (auto &mol : mols) {
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for (auto atom : mol->atoms()) {
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atom->clearProp(CDX_ATOM_ID);
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atom->clearProp(CDX_BOND_ORDERING);
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atom->clearProp(CDX_CIP);
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}
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for (auto bond : mol->bonds()) {
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bond->clearProp(CDX_BOND_ID);
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}
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}
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}
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};
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//! Parse a CDX fragment record
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//! params
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//! RWMol mol : molecule to parse the fragment into
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//! CDXFragment fragment : fragment to read
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//! std::map<unsigned int, Atom*> ids: atom lookup, used for bonding and fusing
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//! fragments int missing_frag_id: if the fragment id is missing, this is what
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//! to use. n.b. may be obsolete, everything needs an id to be valid int
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//! external_attachment:: if this fragment has a external node, this it it's id,
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//! otherwise -1
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//! external node's are normally NickNames or new Fragments
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bool parseFragment(RWMol &mol, CDXFragment &fragment, PageData &pagedata,
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int &missingFragId, int externalAttachment = -1);
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}
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} // namespace RDKit
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#endif
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