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rdkit/External/ChemDraw/fragment.cpp
Brian Kelley 58c21baeba ChemDraw Document and read/write support for the RDKit (#8620) 
* 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>
2025-07-04 06:36:10 +02:00

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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.
//
#include "fragment.h"
#include "bond.h"
#include "node.h"
namespace RDKit {
namespace ChemDraw {
namespace {
const char *sequenceTypeToName(CDXSeqType seqtype) {
switch (seqtype) {
case kCDXSeqType_Unknown:
return "Unknown";
case kCDXSeqType_Peptide:
return "Peptide (Helm)"; // HELM peptides
case kCDXSeqType_Peptide1:
return "Peptide1 (Single Letter Amino Acid)"; // Single letter amino
// acids (Legacy biopolymer
// support)
case kCDXSeqType_Peptide3:
return "Peptide3 (Three letter amino acid)"; // Three letter amino acids
// (Legacy biopolymer
// support)
case kCDXSeqType_DNA:
return "DNA";
case kCDXSeqType_RNA:
return "RNA";
case kCDXSeqType_Biopolymer:
return "Biopolymer";
default:
return "";
}
}
} // namespace
bool parseFragment(RWMol &mol, CDXFragment &fragment, PageData &pagedata,
int &missingFragId, int externalAttachment) {
int frag_id = fragment.GetObjectID();
if (fragment.m_sequenceType != kCDXSeqType_Unknown) {
BOOST_LOG(rdWarningLog)
<< "Unhandled chemdraw sequence type "
<< sequenceTypeToName(fragment.m_sequenceType) << std::endl;
return false;
}
if (frag_id == -1) {
// ChemDraw simply assigns a new one
BOOST_LOG(rdWarningLog)
<< "Invalid or missing fragment id from CDXML fragment, assigning new one..."
<< std::endl;
frag_id = missingFragId;
missingFragId--;
}
mol.setProp(CDX_FRAG_ID, frag_id);
// for atom in frag
std::map<std::pair<int, StereoGroupType>, StereoGroupInfo> sgroups;
// nodetypes =
// https://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/properties/Node_Type.htm
bool skip_fragment =
false; // is there an irrecoverable error for this fragment
for (auto child : fragment.ContainedObjects()) {
CDXDatumID id = (CDXDatumID)child.second->GetTag();
#ifdef DEBUG
std::cerr << "Data Type: " << id << std::endl;
#endif
switch (id) {
case kCDXObj_Node: {
CDXNode &node = (CDXNode &)(*child.second);
if (!parseNode(mol, frag_id, node, pagedata, sgroups, missingFragId,
externalAttachment)) {
skip_fragment = true;
}
break;
}
case kCDXObj_Bond: {
CDXBond &bond = (CDXBond &)(*child.second);
if (!parseBond(mol, frag_id, bond, pagedata)) {
skip_fragment = true;
break;
}
}
case kCDXProp_EndObject: break;
case kCDXProp_CreationUserName: break;
case kCDXProp_CreationDate: break;
case kCDXProp_CreationProgram: break;
case kCDXProp_ModificationUserName: break;
case kCDXProp_ModificationDate: break;
case kCDXProp_ModificationProgram: break;
case kCDXProp_Unused1: break;
case kCDXProp_Name: break;
case kCDXProp_Comment: break;
case kCDXProp_ZOrder: break;
case kCDXProp_RegistryNumber: break;
case kCDXProp_RegistryAuthority: break;
case kCDXProp_Unused2: break;
case kCDXProp_RepresentsProperty: break;
case kCDXProp_IgnoreWarnings: break;
case kCDXProp_ChemicalWarning: break;
case kCDXProp_Visible: break;
case kCDXProp_Transparent: break;
case kCDXProp_SupersededBy: break;
case kCDXProp_StructurePerspective: break;
case kCDXProp_FontTable: break;
case kCDXProp_2DPosition: break;
case kCDXProp_3DPosition: break;
case kCDXProp_2DExtent: break;
case kCDXProp_3DExtent: break;
case kCDXProp_BoundingBox: break;
case kCDXProp_RotationAngle: break;
case kCDXProp_BoundsInParent: break;
case kCDXProp_3DHead: break;
case kCDXProp_3DTail: break;
case kCDXProp_TopLeft: break;
case kCDXProp_TopRight: break;
case kCDXProp_BottomRight: break;
case kCDXProp_BottomLeft: break;
case kCDXProp_3DCenter: break;
case kCDXProp_3DMajorAxisEnd: break;
case kCDXProp_3DMinorAxisEnd: break;
case kCDXProp_ColorTable: break;
case kCDXProp_ForegroundColor: break;
case kCDXProp_BackgroundColor: break;
case kCDXProp_FadePercent: break;
case kCDXProp_Unused8: break;
case kCDXProp_Unused9: break;
case kCDXProp_ForegroundAlpha: break;
case kCDXProp_BackgroundAlpha: break;
case kCDXProp_HighlightColor: break;
case kCDXProp_Node_Type: break;
case kCDXProp_Node_LabelDisplay: break;
case kCDXProp_Node_Element: break;
case kCDXProp_Atom_ElementList: break;
case kCDXProp_Atom_Formula: break;
case kCDXProp_Atom_Isotope: break;
case kCDXProp_Atom_Charge: break;
case kCDXProp_Atom_Radical: break;
case kCDXProp_Atom_RestrictFreeSites: break;
case kCDXProp_Atom_RestrictImplicitHydrogens: break;
case kCDXProp_Atom_RestrictRingBondCount: break;
case kCDXProp_Atom_RestrictUnsaturatedBonds: break;
case kCDXProp_Atom_RestrictRxnChange: break;
case kCDXProp_Atom_RestrictRxnStereo: break;
case kCDXProp_Atom_AbnormalValence: break;
case kCDXProp_Unused3: break;
case kCDXProp_Atom_NumHydrogens: break;
case kCDXProp_Unused4: break;
case kCDXProp_Unused5: break;
case kCDXProp_Atom_HDot: break;
case kCDXProp_Atom_HDash: break;
case kCDXProp_Atom_Geometry: break;
case kCDXProp_Atom_BondOrdering: break;
case kCDXProp_Node_Attachments: break;
case kCDXProp_Atom_GenericNickname: break;
case kCDXProp_Atom_AltGroupID: break;
case kCDXProp_Atom_RestrictSubstituentsUpTo: break;
case kCDXProp_Atom_RestrictSubstituentsExactly: break;
case kCDXProp_Atom_CIPStereochemistry: break;
case kCDXProp_Atom_Translation: break;
case kCDXProp_Atom_AtomNumber: break;
case kCDXProp_Atom_ShowQuery: break;
case kCDXProp_Atom_ShowStereo: break;
case kCDXProp_Atom_ShowAtomNumber: break;
case kCDXProp_Atom_LinkCountLow: break;
case kCDXProp_Atom_LinkCountHigh: break;
case kCDXProp_Atom_IsotopicAbundance: break;
case kCDXProp_Atom_ExternalConnectionType: break;
case kCDXProp_Atom_GenericList: break;
case kCDXProp_Atom_ShowTerminalCarbonLabels: break;
case kCDXProp_Atom_ShowNonTerminalCarbonLabels: break;
case kCDXProp_Atom_HideImplicitHydrogens: break;
case kCDXProp_Atom_ShowEnhancedStereo: break;
case kCDXProp_Atom_EnhancedStereoType: break;
case kCDXProp_Atom_EnhancedStereoGroupNum: break;
case kCDXProp_Node_NeedsClean: break;
case kCDXProp_Atom_ResidueID: break;
case kCDXProp_Atom_ShowResidueID: break;
case kCDXProp_Atom_ExternalConnectionNum: break;
case kCDXProp_Atom_ShowAtomID: break;
case kCDXProp_Atom_AtomID: break;
case kCDXProp_Node_HydrogenBondAttachmentAtoms: break;
case kCDXProp_Node_HydrogenBonds: break;
case kCDXProp_Mole_Racemic: break;
case kCDXProp_Mole_Absolute: break;
case kCDXProp_Mole_Relative: break;
case kCDXProp_Mole_Formula: break;
case kCDXProp_Mole_Weight: break;
case kCDXProp_Frag_ConnectionOrder: break;
case kCDXProp_Frag_SequenceType: break;
case kCDXProp_Frag_IsFromGuidedStereo: break;
case kCDXProp_Frag_IsComplement: break;
case kCDXProp_Bond_Order: break;
case kCDXProp_Bond_Display: break;
case kCDXProp_Bond_Display2: break;
case kCDXProp_Bond_DoublePosition: break;
case kCDXProp_Bond_Begin: break;
case kCDXProp_Bond_End: break;
case kCDXProp_Bond_RestrictTopology: break;
case kCDXProp_Bond_RestrictRxnParticipation: break;
case kCDXProp_Bond_BeginAttach: break;
case kCDXProp_Bond_EndAttach: break;
case kCDXProp_Bond_CIPStereochemistry: break;
case kCDXProp_Bond_BondOrdering: break;
case kCDXProp_Bond_ShowQuery: break;
case kCDXProp_Bond_ShowStereo: break;
case kCDXProp_Bond_CrossingBonds: break;
case kCDXProp_Bond_ShowRxn: break;
case kCDXProp_Bond_Connectivity: break;
case kCDXProp_Bond_BeginExternalNum: break;
case kCDXProp_Bond_EndExternalNum: break;
case kCDXProp_Bond_Connectivity_Routed: break;
case kCDXProp_Text: break;
case kCDXProp_Justification: break;
case kCDXProp_LineHeight: break;
case kCDXProp_WordWrapWidth: break;
case kCDXProp_LineStarts: break;
case kCDXProp_LabelAlignment: break;
case kCDXProp_LabelLineHeight: break;
case kCDXProp_CaptionLineHeight: break;
case kCDXProp_InterpretChemically: break;
case kCDXProp_UTF8Text: break;
case kCDXProp_MacPrintInfo: break;
case kCDXProp_WinPrintInfo: break;
case kCDXProp_PrintMargins: break;
case kCDXProp_ChainAngle: break;
case kCDXProp_BondSpacing: break;
case kCDXProp_BondLength: break;
case kCDXProp_BoldWidth: break;
case kCDXProp_LineWidth: break;
case kCDXProp_MarginWidth: break;
case kCDXProp_HashSpacing: break;
case kCDXProp_LabelStyle: break;
case kCDXProp_CaptionStyle: break;
case kCDXProp_CaptionJustification: break;
case kCDXProp_FractionalWidths: break;
case kCDXProp_Magnification: break;
case kCDXProp_WidthPages: break;
case kCDXProp_HeightPages: break;
case kCDXProp_DrawingSpaceType: break;
case kCDXProp_Width: break;
case kCDXProp_Height: break;
case kCDXProp_PageOverlap: break;
case kCDXProp_Header: break;
case kCDXProp_HeaderPosition: break;
case kCDXProp_Footer: break;
case kCDXProp_FooterPosition: break;
case kCDXProp_PrintTrimMarks: break;
case kCDXProp_LabelStyleFont: break;
case kCDXProp_CaptionStyleFont: break;
case kCDXProp_LabelStyleSize: break;
case kCDXProp_CaptionStyleSize: break;
case kCDXProp_LabelStyleFace: break;
case kCDXProp_CaptionStyleFace: break;
case kCDXProp_LabelStyleColor: 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: break;
case kCDXProp_Graphic_Type: break;
case kCDXProp_Line_Type: break;
case kCDXProp_Arrow_Type: break;
case kCDXProp_Rectangle_Type: 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 RDKit
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