mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
1039 lines
28 KiB
C++
1039 lines
28 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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#include "fragment.h"
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#include "bond.h"
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#include "node.h"
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namespace RDKit {
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namespace ChemDraw {
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namespace {
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const char *sequenceTypeToName(CDXSeqType seqtype) {
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switch (seqtype) {
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case kCDXSeqType_Unknown:
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return "Unknown";
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case kCDXSeqType_Peptide:
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return "Peptide (Helm)"; // HELM peptides
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case kCDXSeqType_Peptide1:
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return "Peptide1 (Single Letter Amino Acid)"; // Single letter amino
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// acids (Legacy biopolymer
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// support)
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case kCDXSeqType_Peptide3:
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return "Peptide3 (Three letter amino acid)"; // Three letter amino acids
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// (Legacy biopolymer
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// support)
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case kCDXSeqType_DNA:
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return "DNA";
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case kCDXSeqType_RNA:
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return "RNA";
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case kCDXSeqType_Biopolymer:
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return "Biopolymer";
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default:
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return "";
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}
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}
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} // namespace
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bool parseFragment(RWMol &mol, CDXFragment &fragment, PageData &pagedata,
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int &missingFragId, int externalAttachment) {
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int frag_id = fragment.GetObjectID();
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if (fragment.m_sequenceType != kCDXSeqType_Unknown) {
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BOOST_LOG(rdWarningLog)
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<< "Unhandled chemdraw sequence type "
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<< sequenceTypeToName(fragment.m_sequenceType) << std::endl;
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return false;
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}
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if (frag_id == -1) {
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// ChemDraw simply assigns a new one
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BOOST_LOG(rdWarningLog)
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<< "Invalid or missing fragment id from CDXML fragment, assigning new one..."
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<< std::endl;
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frag_id = missingFragId;
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missingFragId--;
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}
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mol.setProp(CDX_FRAG_ID, frag_id);
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// for atom in frag
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std::map<std::pair<int, StereoGroupType>, StereoGroupInfo> sgroups;
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// nodetypes =
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// https://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/properties/Node_Type.htm
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bool skip_fragment =
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false; // is there an irrecoverable error for this fragment
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for (auto child : fragment.ContainedObjects()) {
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auto id = (CDXDatumID)child.second->GetTag();
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#ifdef DEBUG
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std::cerr << "Data Type: " << id << std::endl;
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#endif
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switch (id) {
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case kCDXObj_Node: {
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auto &node = (CDXNode &)(*child.second);
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if (!parseNode(mol, frag_id, node, pagedata, sgroups, missingFragId,
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externalAttachment)) {
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skip_fragment = true;
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}
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break;
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}
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case kCDXObj_Bond: {
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auto &bond = (CDXBond &)(*child.second);
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if (!parseBond(mol, frag_id, bond, pagedata)) {
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skip_fragment = true;
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break;
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}
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}
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case kCDXProp_EndObject:
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break;
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case kCDXProp_CreationUserName:
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break;
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case kCDXProp_CreationDate:
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break;
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case kCDXProp_CreationProgram:
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break;
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case kCDXProp_ModificationUserName:
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break;
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case kCDXProp_ModificationDate:
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break;
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case kCDXProp_ModificationProgram:
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break;
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case kCDXProp_Unused1:
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break;
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case kCDXProp_Name:
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break;
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case kCDXProp_Comment:
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break;
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case kCDXProp_ZOrder:
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break;
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case kCDXProp_RegistryNumber:
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break;
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case kCDXProp_RegistryAuthority:
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break;
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case kCDXProp_Unused2:
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break;
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case kCDXProp_RepresentsProperty:
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break;
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case kCDXProp_IgnoreWarnings:
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break;
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case kCDXProp_ChemicalWarning:
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break;
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case kCDXProp_Visible:
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break;
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case kCDXProp_Transparent:
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break;
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case kCDXProp_SupersededBy:
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break;
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case kCDXProp_StructurePerspective:
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break;
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case kCDXProp_FontTable:
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break;
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case kCDXProp_2DPosition:
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break;
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case kCDXProp_3DPosition:
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break;
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case kCDXProp_2DExtent:
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break;
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case kCDXProp_3DExtent:
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break;
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case kCDXProp_BoundingBox:
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break;
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case kCDXProp_RotationAngle:
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break;
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case kCDXProp_BoundsInParent:
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break;
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case kCDXProp_3DHead:
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break;
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case kCDXProp_3DTail:
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break;
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case kCDXProp_TopLeft:
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break;
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case kCDXProp_TopRight:
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break;
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case kCDXProp_BottomRight:
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break;
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case kCDXProp_BottomLeft:
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break;
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case kCDXProp_3DCenter:
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break;
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case kCDXProp_3DMajorAxisEnd:
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break;
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case kCDXProp_3DMinorAxisEnd:
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break;
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case kCDXProp_ColorTable:
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break;
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case kCDXProp_ForegroundColor:
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break;
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case kCDXProp_BackgroundColor:
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break;
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case kCDXProp_FadePercent:
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break;
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case kCDXProp_Unused8:
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break;
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case kCDXProp_Unused9:
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break;
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case kCDXProp_ForegroundAlpha:
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break;
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case kCDXProp_BackgroundAlpha:
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break;
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case kCDXProp_HighlightColor:
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break;
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case kCDXProp_Node_Type:
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break;
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case kCDXProp_Node_LabelDisplay:
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break;
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case kCDXProp_Node_Element:
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break;
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case kCDXProp_Atom_ElementList:
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break;
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case kCDXProp_Atom_Formula:
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break;
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case kCDXProp_Atom_Isotope:
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break;
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case kCDXProp_Atom_Charge:
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break;
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case kCDXProp_Atom_Radical:
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break;
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case kCDXProp_Atom_RestrictFreeSites:
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break;
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case kCDXProp_Atom_RestrictImplicitHydrogens:
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break;
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case kCDXProp_Atom_RestrictRingBondCount:
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break;
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case kCDXProp_Atom_RestrictUnsaturatedBonds:
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break;
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case kCDXProp_Atom_RestrictRxnChange:
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break;
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case kCDXProp_Atom_RestrictRxnStereo:
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break;
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case kCDXProp_Atom_AbnormalValence:
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break;
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case kCDXProp_Unused3:
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break;
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case kCDXProp_Atom_NumHydrogens:
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break;
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case kCDXProp_Unused4:
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break;
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case kCDXProp_Unused5:
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break;
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case kCDXProp_Atom_HDot:
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break;
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case kCDXProp_Atom_HDash:
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break;
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case kCDXProp_Atom_Geometry:
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break;
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case kCDXProp_Atom_BondOrdering:
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break;
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case kCDXProp_Node_Attachments:
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break;
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case kCDXProp_Atom_GenericNickname:
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break;
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case kCDXProp_Atom_AltGroupID:
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break;
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case kCDXProp_Atom_RestrictSubstituentsUpTo:
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break;
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case kCDXProp_Atom_RestrictSubstituentsExactly:
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break;
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case kCDXProp_Atom_CIPStereochemistry:
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break;
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case kCDXProp_Atom_Translation:
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break;
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case kCDXProp_Atom_AtomNumber:
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break;
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case kCDXProp_Atom_ShowQuery:
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break;
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case kCDXProp_Atom_ShowStereo:
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break;
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case kCDXProp_Atom_ShowAtomNumber:
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break;
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case kCDXProp_Atom_LinkCountLow:
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break;
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case kCDXProp_Atom_LinkCountHigh:
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break;
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case kCDXProp_Atom_IsotopicAbundance:
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break;
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case kCDXProp_Atom_ExternalConnectionType:
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break;
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case kCDXProp_Atom_GenericList:
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break;
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case kCDXProp_Atom_ShowTerminalCarbonLabels:
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break;
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case kCDXProp_Atom_ShowNonTerminalCarbonLabels:
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break;
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case kCDXProp_Atom_HideImplicitHydrogens:
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break;
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case kCDXProp_Atom_ShowEnhancedStereo:
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break;
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case kCDXProp_Atom_EnhancedStereoType:
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break;
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case kCDXProp_Atom_EnhancedStereoGroupNum:
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break;
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case kCDXProp_Node_NeedsClean:
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break;
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case kCDXProp_Atom_ResidueID:
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break;
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case kCDXProp_Atom_ShowResidueID:
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break;
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case kCDXProp_Atom_ExternalConnectionNum:
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break;
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case kCDXProp_Atom_ShowAtomID:
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break;
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case kCDXProp_Atom_AtomID:
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break;
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case kCDXProp_Node_HydrogenBondAttachmentAtoms:
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break;
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case kCDXProp_Node_HydrogenBonds:
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break;
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case kCDXProp_Mole_Racemic:
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break;
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case kCDXProp_Mole_Absolute:
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break;
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case kCDXProp_Mole_Relative:
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break;
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case kCDXProp_Mole_Formula:
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break;
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case kCDXProp_Mole_Weight:
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break;
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case kCDXProp_Frag_ConnectionOrder:
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break;
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case kCDXProp_Frag_SequenceType:
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break;
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case kCDXProp_Frag_IsFromGuidedStereo:
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break;
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case kCDXProp_Frag_IsComplement:
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break;
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case kCDXProp_Bond_Order:
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break;
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case kCDXProp_Bond_Display:
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break;
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case kCDXProp_Bond_Display2:
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break;
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case kCDXProp_Bond_DoublePosition:
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break;
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case kCDXProp_Bond_Begin:
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break;
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case kCDXProp_Bond_End:
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break;
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case kCDXProp_Bond_RestrictTopology:
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break;
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case kCDXProp_Bond_RestrictRxnParticipation:
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break;
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case kCDXProp_Bond_BeginAttach:
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break;
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case kCDXProp_Bond_EndAttach:
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break;
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case kCDXProp_Bond_CIPStereochemistry:
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break;
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case kCDXProp_Bond_BondOrdering:
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break;
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case kCDXProp_Bond_ShowQuery:
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break;
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case kCDXProp_Bond_ShowStereo:
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break;
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case kCDXProp_Bond_CrossingBonds:
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break;
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case kCDXProp_Bond_ShowRxn:
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break;
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case kCDXProp_Bond_Connectivity:
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break;
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case kCDXProp_Bond_BeginExternalNum:
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break;
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case kCDXProp_Bond_EndExternalNum:
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break;
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case kCDXProp_Bond_Connectivity_Routed:
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break;
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case kCDXProp_Text:
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break;
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case kCDXProp_Justification:
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break;
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case kCDXProp_LineHeight:
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break;
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case kCDXProp_WordWrapWidth:
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break;
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case kCDXProp_LineStarts:
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break;
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case kCDXProp_LabelAlignment:
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break;
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case kCDXProp_LabelLineHeight:
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break;
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case kCDXProp_CaptionLineHeight:
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break;
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case kCDXProp_InterpretChemically:
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break;
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case kCDXProp_UTF8Text:
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break;
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case kCDXProp_MacPrintInfo:
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break;
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case kCDXProp_WinPrintInfo:
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break;
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case kCDXProp_PrintMargins:
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break;
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case kCDXProp_ChainAngle:
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break;
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case kCDXProp_BondSpacing:
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break;
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case kCDXProp_BondLength:
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break;
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case kCDXProp_BoldWidth:
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break;
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case kCDXProp_LineWidth:
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break;
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case kCDXProp_MarginWidth:
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break;
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case kCDXProp_HashSpacing:
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break;
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case kCDXProp_LabelStyle:
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break;
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case kCDXProp_CaptionStyle:
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break;
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case kCDXProp_CaptionJustification:
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break;
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case kCDXProp_FractionalWidths:
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break;
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case kCDXProp_Magnification:
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break;
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case kCDXProp_WidthPages:
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break;
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case kCDXProp_HeightPages:
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break;
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case kCDXProp_DrawingSpaceType:
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|
break;
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case kCDXProp_Width:
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break;
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case kCDXProp_Height:
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break;
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case kCDXProp_PageOverlap:
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|
break;
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case kCDXProp_Header:
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|
break;
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|
case kCDXProp_HeaderPosition:
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break;
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|
case kCDXProp_Footer:
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|
break;
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|
case kCDXProp_FooterPosition:
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|
break;
|
|
case kCDXProp_PrintTrimMarks:
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|
break;
|
|
case kCDXProp_LabelStyleFont:
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|
break;
|
|
case kCDXProp_CaptionStyleFont:
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|
break;
|
|
case kCDXProp_LabelStyleSize:
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|
break;
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|
case kCDXProp_CaptionStyleSize:
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|
break;
|
|
case kCDXProp_LabelStyleFace:
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|
break;
|
|
case kCDXProp_CaptionStyleFace:
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|
break;
|
|
case kCDXProp_LabelStyleColor:
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|
break;
|
|
case kCDXProp_CaptionStyleColor:
|
|
break;
|
|
case kCDXProp_BondSpacingAbs:
|
|
break;
|
|
case kCDXProp_LabelJustification:
|
|
break;
|
|
case kCDXProp_FixInplaceExtent:
|
|
break;
|
|
case kCDXProp_Side:
|
|
break;
|
|
case kCDXProp_FixInplaceGap:
|
|
break;
|
|
case kCDXProp_CartridgeData:
|
|
break;
|
|
case kCDXProp_AminoAcidTermini:
|
|
break;
|
|
case kCDXProp_ShowSequenceTermini:
|
|
break;
|
|
case kCDXProp_ShowSequenceBonds:
|
|
break;
|
|
case kCDXProp_ResidueWrapCount:
|
|
break;
|
|
case kCDXProp_ResidueBlockCount:
|
|
break;
|
|
case kCDXProp_Unused10:
|
|
break;
|
|
case kCDXProp_Unused11:
|
|
break;
|
|
case kCDXProp_BondSpacingType:
|
|
break;
|
|
case kCDXProp_LabelStyleFontName:
|
|
break;
|
|
case kCDXProp_CaptionStyleFontName:
|
|
break;
|
|
case kCDXProp_ShowSequenceUnlinkedBranches:
|
|
break;
|
|
case kCDXProp_MonomerRenderingStyle:
|
|
break;
|
|
case kCDXProp_Window_IsZoomed:
|
|
break;
|
|
case kCDXProp_Window_Position:
|
|
break;
|
|
case kCDXProp_Window_Size:
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|
break;
|
|
case kCDXProp_Graphic_Type:
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|
break;
|
|
case kCDXProp_Line_Type:
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|
break;
|
|
case kCDXProp_Arrow_Type:
|
|
break;
|
|
case kCDXProp_Rectangle_Type:
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|
break;
|
|
case kCDXProp_Oval_Type:
|
|
break;
|
|
case kCDXProp_Orbital_Type:
|
|
break;
|
|
case kCDXProp_Bracket_Type:
|
|
break;
|
|
case kCDXProp_Symbol_Type:
|
|
break;
|
|
case kCDXProp_Curve_Type:
|
|
break;
|
|
case kCDXProp_Arrowhead_Size:
|
|
break;
|
|
case kCDXProp_Arc_AngularSize:
|
|
break;
|
|
case kCDXProp_Bracket_LipSize:
|
|
break;
|
|
case kCDXProp_Curve_Points:
|
|
break;
|
|
case kCDXProp_Bracket_Usage:
|
|
break;
|
|
case kCDXProp_Polymer_RepeatPattern:
|
|
break;
|
|
case kCDXProp_Polymer_FlipType:
|
|
break;
|
|
case kCDXProp_BracketedObjects:
|
|
break;
|
|
case kCDXProp_Bracket_RepeatCount:
|
|
break;
|
|
case kCDXProp_Bracket_ComponentOrder:
|
|
break;
|
|
case kCDXProp_Bracket_SRULabel:
|
|
break;
|
|
case kCDXProp_Bracket_GraphicID:
|
|
break;
|
|
case kCDXProp_Bracket_BondID:
|
|
break;
|
|
case kCDXProp_Bracket_InnerAtomID:
|
|
break;
|
|
case kCDXProp_Curve_Points3D:
|
|
break;
|
|
case kCDXProp_Arrowhead_Type:
|
|
break;
|
|
case kCDXProp_Arrowhead_CenterSize:
|
|
break;
|
|
case kCDXProp_Arrowhead_Width:
|
|
break;
|
|
case kCDXProp_ShadowSize:
|
|
break;
|
|
case kCDXProp_Arrow_ShaftSpacing:
|
|
break;
|
|
case kCDXProp_Arrow_EquilibriumRatio:
|
|
break;
|
|
case kCDXProp_Arrowhead_Head:
|
|
break;
|
|
case kCDXProp_Arrowhead_Tail:
|
|
break;
|
|
case kCDXProp_Fill_Type:
|
|
break;
|
|
case kCDXProp_Curve_Spacing:
|
|
break;
|
|
case kCDXProp_Closed:
|
|
break;
|
|
case kCDXProp_Arrow_Dipole:
|
|
break;
|
|
case kCDXProp_Arrow_NoGo:
|
|
break;
|
|
case kCDXProp_CornerRadius:
|
|
break;
|
|
case kCDXProp_Frame_Type:
|
|
break;
|
|
case kCDXProp_Arrow_SourceID:
|
|
break;
|
|
case kCDXProp_Arrow_TargetID:
|
|
break;
|
|
case kCDXProp_Arrow_IsSmart_Deleted:
|
|
break;
|
|
case kCDXProp_Picture_Edition:
|
|
break;
|
|
case kCDXProp_Picture_EditionAlias:
|
|
break;
|
|
case kCDXProp_MacPICT:
|
|
break;
|
|
case kCDXProp_WindowsMetafile:
|
|
break;
|
|
case kCDXProp_OLEObject:
|
|
break;
|
|
case kCDXProp_EnhancedMetafile:
|
|
break;
|
|
case kCDXProp_Compressed_MacPICT:
|
|
break;
|
|
case kCDXProp_Compressed_WindowsMetafile:
|
|
break;
|
|
case kCDXProp_Compressed_OLEObject:
|
|
break;
|
|
case kCDXProp_Compressed_EnhancedMetafile:
|
|
break;
|
|
case kCDXProp_Uncompressed_MacPICT_Size:
|
|
break;
|
|
case kCDXProp_Uncompressed_WindowsMetafile_Size:
|
|
break;
|
|
case kCDXProp_Uncompressed_OLEObject_Size:
|
|
break;
|
|
case kCDXProp_Uncompressed_EnhancedMetafile_Size:
|
|
break;
|
|
case kCDXProp_GIF:
|
|
break;
|
|
case kCDXProp_TIFF:
|
|
break;
|
|
case kCDXProp_PNG:
|
|
break;
|
|
case kCDXProp_JPEG:
|
|
break;
|
|
case kCDXProp_BMP:
|
|
break;
|
|
case kCDXProp_PDF:
|
|
break;
|
|
case kCDXProp_Spectrum_XSpacing:
|
|
break;
|
|
case kCDXProp_Spectrum_XLow:
|
|
break;
|
|
case kCDXProp_Spectrum_XType:
|
|
break;
|
|
case kCDXProp_Spectrum_YType:
|
|
break;
|
|
case kCDXProp_Spectrum_XAxisLabel:
|
|
break;
|
|
case kCDXProp_Spectrum_YAxisLabel:
|
|
break;
|
|
case kCDXProp_Spectrum_DataPoint:
|
|
break;
|
|
case kCDXProp_Spectrum_Class:
|
|
break;
|
|
case kCDXProp_Spectrum_YLow:
|
|
break;
|
|
case kCDXProp_Spectrum_YScale:
|
|
break;
|
|
case kCDXProp_TLC_OriginFraction:
|
|
break;
|
|
case kCDXProp_TLC_SolventFrontFraction:
|
|
break;
|
|
case kCDXProp_TLC_ShowOrigin:
|
|
break;
|
|
case kCDXProp_TLC_ShowSolventFront:
|
|
break;
|
|
case kCDXProp_ShowBorders:
|
|
break;
|
|
case kCDXProp_TLC_ShowSideTicks:
|
|
break;
|
|
case kCDXProp_TLC_Rf:
|
|
break;
|
|
case kCDXProp_TLC_Tail:
|
|
break;
|
|
case kCDXProp_TLC_ShowRf:
|
|
break;
|
|
case kCDXProp_GEP_ShowScale:
|
|
break;
|
|
case kCDXProp_GEP_ScaleUnit:
|
|
break;
|
|
case kCDXProp_GEP_StartRange:
|
|
break;
|
|
case kCDXProp_GEP_EndRange:
|
|
break;
|
|
case kCDXProp_GEP_ShowValue:
|
|
break;
|
|
case kCDXProp_GEP_Value:
|
|
break;
|
|
case kCDXProp_GEP_LaneLabelsAngle:
|
|
break;
|
|
case kCDXProp_GEP_AxisWidth:
|
|
break;
|
|
case kCDXProp_BioShape_Type:
|
|
break;
|
|
case kCDXProp_1SubstrateEnzyme_ReceptorSize:
|
|
break;
|
|
case kCDXProp_Receptor_NeckWidth:
|
|
break;
|
|
case kCDXProp_HelixProtein_CylinderWidth:
|
|
break;
|
|
case kCDXProp_HelixProtein_CylinderHeight:
|
|
break;
|
|
case kCDXProp_HelixProtein_CylinderDistance:
|
|
break;
|
|
case kCDXProp_HelixProtein_PipeWidth:
|
|
break;
|
|
case kCDXProp_HelixProtein_Extra:
|
|
break;
|
|
case kCDXProp_Membrane_ElementSize:
|
|
break;
|
|
case kCDXProp_Membrane_StartAngle:
|
|
break;
|
|
case kCDXProp_Membrane_EndAngle:
|
|
break;
|
|
case kCDXProp_DNA_WaveLength:
|
|
break;
|
|
case kCDXProp_DNA_WaveWidth:
|
|
break;
|
|
case kCDXProp_DNA_Offset:
|
|
break;
|
|
case kCDXProp_DNA_WaveHeight:
|
|
break;
|
|
case kCDXProp_Gprotein_UpperHeight:
|
|
break;
|
|
case kCDXProp_NamedAlternativeGroup_TextFrame:
|
|
break;
|
|
case kCDXProp_NamedAlternativeGroup_GroupFrame:
|
|
break;
|
|
case kCDXProp_NamedAlternativeGroup_Valence:
|
|
break;
|
|
case kCDXProp_GeometricFeature:
|
|
break;
|
|
case kCDXProp_RelationValue:
|
|
break;
|
|
case kCDXProp_BasisObjects:
|
|
break;
|
|
case kCDXProp_ConstraintType:
|
|
break;
|
|
case kCDXProp_ConstraintMin:
|
|
break;
|
|
case kCDXProp_ConstraintMax:
|
|
break;
|
|
case kCDXProp_IgnoreUnconnectedAtoms:
|
|
break;
|
|
case kCDXProp_DihedralIsChiral:
|
|
break;
|
|
case kCDXProp_PointIsDirected:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyType:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyDisplayID:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyIsActive:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyUnknown:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyName:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyFormula:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyExactMass:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyMolWeight:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyMOverZ:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyAnalysis:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyBoilingPoint:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyMeltingPoint:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyCriticalTemp:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyCriticalPressure:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyCriticalVolume:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyGibbsEnergy:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyLogP:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyMR:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyHenrysLaw:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyHeatOfForm:
|
|
break;
|
|
case kCDXProp_ChemicalPropertytPSA:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyCLogP:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyCMR:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyLogS:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyPKa:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyID:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyFragmentLabel:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyTypeIUPACAtomNumber:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyIsChemicallySignificant:
|
|
break;
|
|
case kCDXProp_ChemicalPropertyExternalBonds:
|
|
break;
|
|
case kCDXProp_ReactionStep_Atom_Map:
|
|
break;
|
|
case kCDXProp_ReactionStep_Reactants:
|
|
break;
|
|
case kCDXProp_ReactionStep_Products:
|
|
break;
|
|
case kCDXProp_ReactionStep_Plusses:
|
|
break;
|
|
case kCDXProp_ReactionStep_Arrows:
|
|
break;
|
|
case kCDXProp_ReactionStep_ObjectsAboveArrow:
|
|
break;
|
|
case kCDXProp_ReactionStep_ObjectsBelowArrow:
|
|
break;
|
|
case kCDXProp_ReactionStep_Atom_Map_Manual:
|
|
break;
|
|
case kCDXProp_ReactionStep_Atom_Map_Auto:
|
|
break;
|
|
case kCDXProp_RxnAutonumber_Style:
|
|
break;
|
|
case kCDXProp_RxnAutonumber_Conditions:
|
|
break;
|
|
case kCDXProp_RxnAutonumber_Start:
|
|
break;
|
|
case kCDXProp_RxnAutonumber_Format:
|
|
break;
|
|
case kCDXProp_ObjectTag_Type:
|
|
break;
|
|
case kCDXProp_Unused6:
|
|
break;
|
|
case kCDXProp_Unused7:
|
|
break;
|
|
case kCDXProp_ObjectTag_Tracking:
|
|
break;
|
|
case kCDXProp_ObjectTag_Persistent:
|
|
break;
|
|
case kCDXProp_ObjectTag_Value:
|
|
break;
|
|
case kCDXProp_Positioning:
|
|
break;
|
|
case kCDXProp_PositioningAngle:
|
|
break;
|
|
case kCDXProp_PositioningOffset:
|
|
break;
|
|
case kCDXProp_Sequence_Identifier:
|
|
break;
|
|
case kCDXProp_CrossReference_Container:
|
|
break;
|
|
case kCDXProp_CrossReference_Document:
|
|
break;
|
|
case kCDXProp_CrossReference_Identifier:
|
|
break;
|
|
case kCDXProp_CrossReference_Sequence:
|
|
break;
|
|
case kCDXProp_Template_PaneHeight:
|
|
break;
|
|
case kCDXProp_Template_NumRows:
|
|
break;
|
|
case kCDXProp_Template_NumColumns:
|
|
break;
|
|
case kCDXProp_Group_Integral:
|
|
break;
|
|
case kCDXProp_SG_DataType:
|
|
break;
|
|
case kCDXProp_SG_PropertyType:
|
|
break;
|
|
case kCDXProp_SG_DataValue:
|
|
break;
|
|
case kCDXProp_SG_ComponentIsReactant:
|
|
break;
|
|
case kCDXProp_SG_ComponentIsHeader:
|
|
break;
|
|
case kCDXProp_IsHidden:
|
|
break;
|
|
case kCDXProp_IsReadOnly:
|
|
break;
|
|
case kCDXProp_IsEdited:
|
|
break;
|
|
case kCDXProp_SG_ComponentReferenceID:
|
|
break;
|
|
case kCDXProp_PlasmidMap_NumberBasePairs:
|
|
break;
|
|
case kCDXProp_PlasmidMap_MarkerStart:
|
|
break;
|
|
case kCDXProp_PlasmidMap_MarkerOffset:
|
|
break;
|
|
case kCDXProp_PlasmidMap_MarkerAngle:
|
|
break;
|
|
case kCDXProp_PlasmidMap_RegionStart:
|
|
break;
|
|
case kCDXProp_PlasmidMap_RegionEnd:
|
|
break;
|
|
case kCDXProp_PlasmidMap_RegionOffset:
|
|
break;
|
|
case kCDXProp_PlasmidMap_RingRadius:
|
|
break;
|
|
case kCDXProp_RLogic_Group:
|
|
break;
|
|
case kCDXProp_RLogic_Occurrence:
|
|
break;
|
|
case kCDXProp_RLogic_RestH:
|
|
break;
|
|
case kCDXProp_RLogic_IfThenGroup:
|
|
break;
|
|
case kCDXProp_Annotation_Keyword:
|
|
break;
|
|
case kCDXProp_Annotation_Content:
|
|
break;
|
|
case kCDXProp_SplitterPositions:
|
|
break;
|
|
case kCDXProp_PageDefinition:
|
|
break;
|
|
case kCDXProp_Property_Rule:
|
|
break;
|
|
case kCDXProp_Property_DataType:
|
|
break;
|
|
case kCDXProp_Property_Value:
|
|
break;
|
|
case kCDXUser_TemporaryBegin:
|
|
break;
|
|
case kCDXUser_TemporaryEnd:
|
|
break;
|
|
case kCDXObj_Document:
|
|
break;
|
|
case kCDXObj_Page:
|
|
break;
|
|
case kCDXObj_Group:
|
|
break;
|
|
case kCDXObj_Fragment:
|
|
break;
|
|
case kCDXObj_Text:
|
|
break;
|
|
case kCDXObj_Graphic:
|
|
break;
|
|
case kCDXObj_Curve:
|
|
break;
|
|
case kCDXObj_EmbeddedObject:
|
|
break;
|
|
case kCDXObj_NamedAlternativeGroup:
|
|
break;
|
|
case kCDXObj_TemplateGrid:
|
|
break;
|
|
case kCDXObj_RegistryNumber:
|
|
break;
|
|
case kCDXObj_ReactionScheme:
|
|
break;
|
|
case kCDXObj_ReactionStep:
|
|
break;
|
|
case kCDXObj_ObjectDefinition:
|
|
break;
|
|
case kCDXObj_Spectrum:
|
|
break;
|
|
case kCDXObj_ObjectTag:
|
|
break;
|
|
case kCDXObj_OleClientItem:
|
|
break;
|
|
case kCDXObj_Sequence:
|
|
break;
|
|
case kCDXObj_CrossReference:
|
|
break;
|
|
case kCDXObj_Splitter:
|
|
break;
|
|
case kCDXObj_Table:
|
|
break;
|
|
case kCDXObj_BracketedGroup:
|
|
break;
|
|
case kCDXObj_BracketAttachment:
|
|
break;
|
|
case kCDXObj_CrossingBond:
|
|
break;
|
|
case kCDXObj_Border:
|
|
break;
|
|
case kCDXObj_Geometry:
|
|
break;
|
|
case kCDXObj_Constraint:
|
|
break;
|
|
case kCDXObj_TLCPlate:
|
|
break;
|
|
case kCDXObj_TLCLane:
|
|
break;
|
|
case kCDXObj_TLCSpot:
|
|
break;
|
|
case kCDXObj_ChemicalProperty:
|
|
break;
|
|
case kCDXObj_Arrow:
|
|
break;
|
|
case kCDXObj_StoichiometryGrid:
|
|
break;
|
|
case kCDXObj_SGComponent:
|
|
break;
|
|
case kCDXObj_SGDatum:
|
|
break;
|
|
case kCDXObj_BioShape:
|
|
break;
|
|
case kCDXObj_PlasmidMap:
|
|
break;
|
|
case kCDXObj_PlasmidMarker:
|
|
break;
|
|
case kCDXObj_PlasmidRegion:
|
|
break;
|
|
case kCDXObj_RLogic:
|
|
break;
|
|
case kCDXObj_RLogicItem:
|
|
break;
|
|
case kCDXObj_Annotation:
|
|
break;
|
|
case kCDXObj_GEPPlate:
|
|
break;
|
|
case kCDXObj_GEPBand:
|
|
break;
|
|
case kCDXObj_Marker:
|
|
break;
|
|
case kCDXObj_GEPLane:
|
|
break;
|
|
case kCDXObj_DocumentProperties:
|
|
break;
|
|
case kCDXObj_Property:
|
|
break;
|
|
case kCDXObj_ColoredMolecularArea:
|
|
break;
|
|
case kCDXObj_UnknownObject:
|
|
break;
|
|
}
|
|
}
|
|
|
|
// Add the stereo groups
|
|
if (!sgroups.empty()) {
|
|
std::vector<StereoGroup> stereo_groups;
|
|
for (auto &sgroup : sgroups) {
|
|
unsigned gId = 0;
|
|
if (sgroup.second.grouptype != StereoGroupType::STEREO_ABSOLUTE &&
|
|
sgroup.second.sgroup > 0) {
|
|
gId = sgroup.second.sgroup;
|
|
}
|
|
std::vector<Bond *> newBonds;
|
|
stereo_groups.emplace_back(sgroup.second.grouptype, sgroup.second.atoms,
|
|
newBonds, gId);
|
|
}
|
|
mol.setStereoGroups(std::move(stereo_groups));
|
|
}
|
|
|
|
return !skip_fragment;
|
|
}
|
|
} // namespace ChemDraw
|
|
} // namespace RDKit
|