mirror of
https://github.com/rdkit/rdkit.git
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b417465e93
* Adds MolToCDXMLBlock to FileParsers * Simplified code, removed warning * Fix C# wrapper for MolToCDX * Add C# test, fix cscode in swig * Fix typo in tests * Set default format to CDXML for MolToCDXML Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Add CDXML writer smoke tests --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
281 lines
10 KiB
OpenEdge ABL
281 lines
10 KiB
OpenEdge ABL
/*
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* $Id$
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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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%{
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#include <GraphMol/RWMol.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/CDXMLParser.h>
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#include <GraphMol/FileParsers/SequenceParsers.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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%template(RWMol_Vect) std::vector< boost::shared_ptr<RDKit::RWMol> >;
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// ignore the methods that allow the molecule to take ownership of atoms/Bonds
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// (instead of copying them). This just leads to memory problems with Java
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%ignore RDKit::RWMol::addAtom(Atom *atom,bool updateLabel,bool takeOwnership);
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%ignore RDKit::RWMol::addBond(Bond *bond,bool takeOwnership);
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%newobject RDKit::v1::SmilesToMol;
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%newobject RDKit::v1::SmartsToMol;
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%newobject RDKit::v1::MolBlockToMol;
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%newobject RDKit::v1::MolFileToMol;
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%shared_ptr(RDKit::RWMol)
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%include "enums.swg"
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#if swifjava
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%javaconst(1);
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#endif
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%ignore RDKit::v2::SmilesParse;
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%ignore RDKit::v1::CDXMLDataStreamToMols;
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%ignore RDKit::v1::CDXMLFileToMols;
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%ignore RDKit::v1::CDXMLToMols;
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%ignore RDKit::v2::CDXMLParser::MolsFromCDXMLDataStream;
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%ignore RDKit::v2::CDXMLParser::MolsFromCDXML;
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%ignore RDKit::v2::CDXMLParser::MolsFromCDXMLFile;
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%ignore *::MolsFromCDXMLDataStream;
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%include <GraphMol/FileParsers/FileParsers.h>
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%include <GraphMol/FileParsers/CDXMLParser.h>
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%include <GraphMol/SmilesParse/SmilesParse.h>
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%typemap(javacode) RDKit::RWMol %{
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// expose mols from MolsFromCDXMLByteArray
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public static RWMol_Vect MolsFromCDXMLByteArray(
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byte[] pkl, boolean sanitize, boolean removeHs) {
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UChar_Vect vec = null;
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try {
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vec = new UChar_Vect();
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vec.reserve(pkl.length);
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for (int i = 0; i < pkl.length; ++i) {
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vec.add((byte)pkl[i]);
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}
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return RWMol.MolsFromCDXML(vec, sanitize, removeHs);
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} finally {
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if (vec != null) {
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vec.delete();
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}
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}
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}
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public static RWMol_Vect MolsFromCDXMLByteArray(byte [] pkl) {
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return MolsFromCDXMLByteArray(pkl, true, true);
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}
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%}
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%typemap(cscode) RDKit::RWMol %{
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public static RWMol_Vect MolsFromCDXMLByteArray(
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byte[] text, bool sanitize=true, bool removeHs=true) {
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UChar_Vect vec = null;
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try {
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vec = new UChar_Vect();
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vec.Capacity = text.Length;
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for (int i = 0; i < text.Length; ++i) {
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vec.Add((byte)text[i]);
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}
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return RWMol.MolsFromCDXML(vec, sanitize, removeHs);
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} finally {
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if (vec != null) {
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vec.Dispose();
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}
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}
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}
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%}
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%include <GraphMol/RWMol.h>
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%extend RDKit::RWMol {
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static RDKit::RWMOL_SPTR MolFromSmiles(const std::string &smi,int debugParse=0,bool sanitize=1,
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std::map<std::string,std::string> *replacements=0){
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return RDKit::RWMOL_SPTR(RDKit::SmilesToMol(smi, debugParse, sanitize,replacements));
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}
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static RDKit::RWMOL_SPTR MolFromSmiles(const std::string &smi, const RDKit::v1::SmilesParserParams ¶ms){
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return RDKit::RWMOL_SPTR(RDKit::SmilesToMol(smi, params));
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}
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static RDKit::RWMOL_SPTR MolFromSmarts(const std::string &sma,int debugParse=0,bool mergeHs=false,
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std::map<std::string,std::string> *replacements=0){
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return RDKit::RWMOL_SPTR(RDKit::SmartsToMol(sma, debugParse, mergeHs,replacements));
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}
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static RDKit::RWMOL_SPTR MolFromMolBlock(const std::string &molB,
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bool sanitize=true,bool removeHs=true,bool strictParsing=true){
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RDKit::RWMol *mol=RDKit::MolBlockToMol(molB,sanitize,removeHs,strictParsing);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromMolFile(const std::string &filename,
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bool sanitize=true,bool removeHs=true,bool strictParsing=true){
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RDKit::RWMol *mol=RDKit::MolFileToMol(filename,sanitize,removeHs,strictParsing);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromTPLFile(const std::string &fName,bool sanitize=true,
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bool skipFirstConf=false) {
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RDKit::RWMol *mol=0;
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mol=RDKit::TPLFileToMol(fName, sanitize, skipFirstConf);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromMol2File(const std::string &fName,bool sanitize=true,bool removeHs=true,
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RDKit::Mol2Type variant=RDKit::Mol2Type::CORINA, bool cleanupSubstructures=true) {
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RDKit::RWMol *mol=0;
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mol=RDKit::Mol2FileToMol(fName, sanitize, removeHs, variant, cleanupSubstructures);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromMol2Block(const std::string &molBlock,bool sanitize=true,bool removeHs=true,
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RDKit::Mol2Type variant=RDKit::Mol2Type::CORINA, bool cleanupSubstructures=true) {
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RDKit::RWMol *mol=0;
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mol=RDKit::Mol2BlockToMol(molBlock, sanitize, removeHs, variant, cleanupSubstructures);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromPDBBlock(const std::string &molB,
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bool sanitize=true,bool removeHs=true,
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unsigned int flavor=0,bool proximityBonding=true){
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RDKit::RWMol *mol=0;
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mol=RDKit::PDBBlockToMol(molB,sanitize,removeHs,flavor,proximityBonding);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromPDBFile(const std::string &fName,
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bool sanitize=true,bool removeHs=true,
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unsigned int flavor=0,bool proximityBonding=true){
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RDKit::RWMol *mol=0;
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mol=RDKit::PDBFileToMol(fName,sanitize,removeHs,flavor,proximityBonding);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromSequence(const std::string &text,
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bool sanitize=true,int flavor=0){
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RDKit::RWMol *mol=0;
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mol=RDKit::SequenceToMol(text,sanitize,flavor);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromFASTA(const std::string &text,
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bool sanitize=true,int flavor=0){
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RDKit::RWMol *mol=0;
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mol=RDKit::FASTAToMol(text,sanitize,flavor);
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return RDKit::RWMOL_SPTR(mol);
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}
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static RDKit::RWMOL_SPTR MolFromHELM(const std::string &text,
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bool sanitize=true){
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RDKit::RWMol *mol=0;
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mol=RDKit::HELMToMol(text,sanitize);
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return RDKit::RWMOL_SPTR(mol);
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}
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static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXML(const std::string &text,
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bool sanitize=true, bool removeHs=true){
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auto res = RDKit::CDXMLToMols(text, sanitize, removeHs);
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std::vector<RDKit::RWMOL_SPTR> mols;
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for(auto &mol: res) {
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mols.emplace_back(mol.release());
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}
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return mols;
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}
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static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXML(
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const std::vector<unsigned char> &text, bool sanitize=true, bool removeHs=true) {
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std::string str(text.begin(), text.end());
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RDKit::v2::CDXMLParser::CDXMLParserParams params;
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params.sanitize=sanitize;
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params.removeHs=removeHs;
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auto res = RDKit::v2::CDXMLParser::MolsFromCDXML(str, params);
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std::vector<RDKit::RWMOL_SPTR> mols;
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for(auto &mol: res) {
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mols.emplace_back(mol.release());
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}
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return mols;
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}
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static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXML(
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const std::string &text,
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const RDKit::v2::CDXMLParser::CDXMLParserParams ¶ms=RDKit::v2::CDXMLParser::CDXMLParserParams()) {
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auto res = RDKit::v2::CDXMLParser::MolsFromCDXML(text, params);
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std::vector<RDKit::RWMOL_SPTR> mols;
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for(auto &mol: res) {
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mols.emplace_back(mol.release());
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}
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return mols;
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}
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static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXMLFile(
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const std::string &filename,
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const RDKit::v2::CDXMLParser::CDXMLParserParams ¶ms=RDKit::v2::CDXMLParser::CDXMLParserParams()) {
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auto res = RDKit::v2::CDXMLParser::MolsFromCDXMLFile(filename, params);
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std::vector<RDKit::RWMOL_SPTR> mols;
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for(auto &mol: res) {
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mols.emplace_back(mol.release());
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}
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return mols;
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}
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/* Methods from MolFileStereoChem.h */
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void DetectAtomStereoChemistry(const RDKit::Conformer *conf) {
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RDKit::DetectAtomStereoChemistry(*($self), conf);
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}
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void DetectBondStereoChemistry(const RDKit::Conformer *conf) {
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RDKit::DetectBondStereoChemistry(*($self), conf);
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}
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void ClearSingleBondDirFlags(bool onlyWedgeFlags=false) {
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RDKit::MolOps::clearSingleBondDirFlags(*($self), onlyWedgeFlags);
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};
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void reapplyMolBlockWedging() {
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RDKit::Chirality::reapplyMolBlockWedging(*($self));
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}
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void clearMolBlockWedgingInfo() {
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RDKit::Chirality::clearMolBlockWedgingInfo(*($self));
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}
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void invertMolBlockWedgingInfo() {
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RDKit::Chirality::invertMolBlockWedgingInfo(*($self));
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}
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void markUnspecifiedStereoAsUnknown(int confId) {
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RDKit::markUnspecifiedStereoAsUnknown(*($self), confId);
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}
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/* From Kekulize.cpp, MolOps.h */
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void Kekulize(bool markAtomsBonds=true, bool canonical=true, unsigned int maxBackTracks=100) {
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RDKit::MolOps::Kekulize(*($self), markAtomsBonds, canonical, maxBackTracks);
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}
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/* MolOps.h */
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void sanitizeMol() {
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RDKit::MolOps::sanitizeMol(*($self));
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}
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}
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