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https://github.com/rdkit/rdkit.git
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d5d4d194ec
* atropisomer handling added * fixed non-used variables, linking directives * BOOST LIB start/stop fixes, linking fix * Fixes for RDKIT CI errors * minimalLib fix * changed vector<enum> for java builds * check for extra chars in CIP labeling * removed wrong deprecated message * fix ostrstream output error? * restored _ChiralAtomRank to lowercase first letter * changes for merged master * Fixed catch label for new Catch package * update expected psql results * get swig wrappers building * restore MolFileStereochem to FileParsers * fix java wrapper for reapplyMolBlockWedging * some suggestions * move a couple functions out of Bond * Merge branch 'master' into pr/atropisomers2 * merged master * Renamed setStereoanyFromSquiggleBond * atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol * fix for CI build * attempt to fix java build in CI * attempt to fix java build in CI #2 * New routine to remove non-explicit 3D-geneated chirality * changed to use pair for atrop atoms and related bonds * Changes as per PR reviews * PR review respnses * PR review reponse - more * Fix merge from master * fixing java ci after merge * Updated the help doc for atripisomers * update the atropisomer docs * improve the images * add the source CXSMILES --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
83 lines
3.1 KiB
OpenEdge ABL
83 lines
3.1 KiB
OpenEdge ABL
/*
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* $Id: Bond.i 2519 2013-05-17 03:01:18Z glandrum $
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*
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* Copyright (c) 2010, Novartis Institutes for BioMedical Research 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 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 "std_string.i"
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%include "std_vector.i"
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%include "std_map.i"
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%include "std_pair.i"
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%{
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#include <RDGeneral/types.h>
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#include <GraphMol/Bond.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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%}
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%ignore RDKit::Bond::getValenceContrib(const Atom *) const;
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%ignore RDKit::Bond::Match(const Bond *) const;
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%ignore RDKit::Bond::setBeginAtom(Atom *at);
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%ignore RDKit::Bond::setEndAtom(Atom *at);
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%ignore RDKit::getTwiceBondType(const RDKit::Bond &b);
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%include <GraphMol/Bond.h>
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%extend RDKit::Bond {
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std::string getProp(const std::string key){
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std::string res;
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($self)->getProp(key, res);
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return res;
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}
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/* Methods from MolFileStereoChem.h */
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Bond::BondDir DetermineBondWedgeState(const std::map<int, std::unique_ptr<RDKit::Chirality::WedgeInfoBase>> &wedgeBonds,
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const RDKit::Conformer *conf) {
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RDKit::DetermineBondWedgeState(($self), wedgeBonds, conf);
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}
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/* Based on corresponding methods in Atom.i */
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bool IsInRing(){
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if(!($self)->getOwningMol().getRingInfo()->isInitialized()){
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RDKit::MolOps::findSSSR(($self)->getOwningMol());
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}
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return ($self)->getOwningMol().getRingInfo()->numBondRings(($self)->getIdx())!=0;
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}
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bool IsInRingSize(int size){
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if(!($self)->getOwningMol().getRingInfo()->isInitialized()){
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RDKit::MolOps::findSSSR(($self)->getOwningMol());
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}
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return ($self)->getOwningMol().getRingInfo()->isBondInRingOfSize(($self)->getIdx(),size);
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}
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}
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