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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%)
103 lines
2.3 KiB
C++
103 lines
2.3 KiB
C++
// $Id$
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//
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// Copyright (C) 2002-2006 Rational Discovery LLC
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//
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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 <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <stdlib.h>
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#include <iostream>
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#include <fstream>
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#include <RDGeneral/types.h>
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/SanitException.h>
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using namespace RDKit;
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int testArom(RWMol m) {
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//BOOST_LOG(rdErrorLog) << "********************************************\n";
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//BOOST_LOG(rdErrorLog) << "Testing aromaticity :\n";
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int res = MolOps::setAromaticity(m);
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//BOOST_LOG(rdErrorLog) << "\nDone testing aromaticity \n";
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//BOOST_LOG(rdErrorLog) << "********************************************\n";
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return res;
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}
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void testKekule(RWMol &m) {
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MolOps::Kekulize(m);
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}
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void getSmiles(std::string line, std::string &smi) {
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int x = line.find("\t");
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if (x == -1) {
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x = line.find(" ");
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}
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smi = line.substr(0,x);
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std::string rem = line.substr(x+1, line.length() - x);
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x = rem.find(" ");
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std::string name;
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name = rem.substr(0, x);
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BOOST_LOG(rdInfoLog) << smi << " " << name << " " ;
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}
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int main(int argc, char *argv[]) {
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RDLog::InitLogs();
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std::string fname;
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if (argc > 1) {
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fname = argv[1];
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}
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else {
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BOOST_LOG(rdErrorLog) << "Pass in the list of smiles\n";
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}
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std::ifstream inStream(fname.c_str());
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const int MAX_LINE_LEN = 256;
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char inLine[MAX_LINE_LEN];
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std::string tmpstr;
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std::string smi;
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inStream.getline(inLine, MAX_LINE_LEN,'\n');
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tmpstr = inLine;
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//MolOps molop;
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while (tmpstr.size() > 0) {
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getSmiles(tmpstr, smi);
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RWMol *m = SmilesToMol(smi, 0, 0);
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try {
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//testKekule(*m);
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MolOps::sanitizeMol(*m);
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int nar;
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m->getProp(common_properties::numArom, nar);
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BOOST_LOG(rdInfoLog)<< nar << "\n";
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//MolOps::setHybridization(*m);
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delete m;
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}
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catch (MolSanitizeException){
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BOOST_LOG(rdErrorLog) << smi << "\n";
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delete m;
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}
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inStream.getline(inLine, MAX_LINE_LEN,'\n');
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tmpstr = inLine;
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}
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return 1;
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}
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