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https://github.com/rdkit/rdkit.git
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95a92282d1
o rdkit gains a RDKit::common_properties namespace that contains common string value properties o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns true/false on success or failure. This is used to optimize access. o rdkit learns how to pass property keys by reference, not value. A new namespace has been added to RDKit, common_properties that contains the std::string values for commonly used properties. This helps to avoid typos in string values but also avoids a creation of std::strings from character values. All accessors (has/get/clear and getPropIfPresent) now pass the key by reference. Additionally, getPropIfPresent removes the double lookup of hasProp/getProp which can be a significant speedup in the smiles and smarts parsers (10-20%)
134 lines
3.8 KiB
C++
134 lines
3.8 KiB
C++
// $Id$
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//
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// Copyright (C) 2007 Greg Landrum
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include "FileParsers.h"
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <string>
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using namespace RDKit;
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void test1(){
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BOOST_LOG(rdInfoLog) << "testing basic tpl parsing" << std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/cmpd2.tpl";
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RWMol *m;
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Conformer conf;
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std::string propVal;
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m = TPLFileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms()==12);
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TEST_ASSERT(m->getNumBonds()==12);
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TEST_ASSERT(m->getNumConformers()==2);
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TEST_ASSERT(m->hasProp(common_properties::_Name));
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m->getProp(common_properties::_Name,propVal);
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TEST_ASSERT(propVal=="compound 2");
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TEST_ASSERT(m->hasProp("Conf_1_Name"));
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m->getProp("Conf_1_Name",propVal);
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TEST_ASSERT(propVal=="conf 1");
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conf = m->getConformer(0);
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TEST_ASSERT(feq(conf.getAtomPos(0).x,-1.02))
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TEST_ASSERT(feq(conf.getAtomPos(0).y,0.96))
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TEST_ASSERT(feq(conf.getAtomPos(0).z,-0.04))
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conf = m->getConformer(1);
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TEST_ASSERT(feq(conf.getAtomPos(0).x,-2.02))
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TEST_ASSERT(feq(conf.getAtomPos(0).y,0.96))
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TEST_ASSERT(feq(conf.getAtomPos(0).z,-0.04))
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delete m;
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m = TPLFileToMol(fName,true,true);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms()==12);
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TEST_ASSERT(m->getNumBonds()==12);
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TEST_ASSERT(m->getNumConformers()==1);
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conf = m->getConformer(0);
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TEST_ASSERT(feq(conf.getAtomPos(0).x,-1.02))
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TEST_ASSERT(feq(conf.getAtomPos(0).y,0.96))
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TEST_ASSERT(feq(conf.getAtomPos(0).z,-0.04))
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delete m;
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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void test2(){
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BOOST_LOG(rdInfoLog) << "testing tpl writing" << std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/cmpd1.tpl";
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RWMol *m,*m2;
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Conformer conf;
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std::string propVal;
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m = TPLFileToMol(fName,true,true);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms()==18);
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TEST_ASSERT(m->getNumBonds()==18);
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TEST_ASSERT(m->getNumConformers()==9);
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TEST_ASSERT(m->hasProp(common_properties::_Name));
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m->getProp(common_properties::_Name,propVal);
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TEST_ASSERT(propVal=="compound 1");
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TEST_ASSERT(m->hasProp("Conf_1_Name"));
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m->getProp("Conf_1_Name",propVal);
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TEST_ASSERT(propVal=="conf9");
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std::stringstream strm;
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strm << MolToTPLText(*m,"TPLCharge");
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unsigned int line;
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m2 = TPLDataStreamToMol(&strm,line);
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TEST_ASSERT(m2);
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TEST_ASSERT(m2->getNumAtoms()==18);
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TEST_ASSERT(m2->getNumBonds()==18);
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TEST_ASSERT(m2->getNumConformers()==9);
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TEST_ASSERT(m2->hasProp(common_properties::_Name));
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m2->getProp(common_properties::_Name,propVal);
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TEST_ASSERT(propVal=="compound 1");
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TEST_ASSERT(m2->hasProp("Conf_1_Name"));
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m2->getProp("Conf_1_Name",propVal);
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TEST_ASSERT(propVal=="conformer_1");
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std::stringstream strm2;
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strm2 << MolToTPLText(*m,"TPLCharge",true);
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delete m2;
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m2 = TPLDataStreamToMol(&strm2,line,true,true);
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TEST_ASSERT(m2);
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TEST_ASSERT(m2->getNumAtoms()==18);
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TEST_ASSERT(m2->getNumBonds()==18);
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TEST_ASSERT(m2->getNumConformers()==8);
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TEST_ASSERT(m2->hasProp(common_properties::_Name));
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m2->getProp(common_properties::_Name,propVal);
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TEST_ASSERT(propVal=="compound 1");
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TEST_ASSERT(m2->hasProp("Conf_1_Name"));
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m2->getProp("Conf_1_Name",propVal);
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TEST_ASSERT(propVal=="conformer_1");
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delete m;
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delete m2;
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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int main(int argc,char *argv[]){
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RDLog::InitLogs();
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test1();
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test2();
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return 0;
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}
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