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580 lines
16 KiB
C++
580 lines
16 KiB
C++
// $Id$
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//
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// Copyright (C) 2002-2009 Greg Landrum and 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 <string>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include "MolSupplier.h"
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#include "MolWriters.h"
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#include "FileParsers.h"
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#include <RDGeneral/FileParseException.h>
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#include <RDGeneral/StreamOps.h>
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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using namespace RDKit;
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void testSmilesWriter() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
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SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
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std::string oname = rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
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STR_VECT propNames;
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propNames.push_back(std::string("Column_2"));
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SmilesWriter *writer = new SmilesWriter(oname, " ");
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writer->setProps(propNames);
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STR_VECT names;
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STR_VECT props;
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ROMol *mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp("_Name", mname);
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mol->getProp("Column_2", pval);
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names.push_back(mname);
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props.push_back(pval);
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writer->write(*mol);
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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writer->flush();
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delete writer;
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delete nSup;
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// now read the molecules back in a check if we have the same properties etc
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nSup = new SmilesMolSupplier(oname);
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int i = 0;
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mol = nSup->next();
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while (mol){
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std::string mname, pval;
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mol->getProp("_Name", mname);
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mol->getProp("Column_2", pval);
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CHECK_INVARIANT(mname == names[i], "");
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CHECK_INVARIANT(pval == props[i], "");
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i++;
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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}
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void testSmilesWriter2() {
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{
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std::stringstream ss;
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SmilesWriter *writer = new SmilesWriter(&ss, " ","Name",false);
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RWMol *mol;
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mol = SmilesToMol("c1ccccc1");
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//MolOps::Kekulize(*mol);
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writer->write(*mol);
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delete mol;
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mol = SmilesToMol("F[C@H](Cl)Br");
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writer->write(*mol);
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delete mol;
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writer->flush();
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TEST_ASSERT(ss.str()=="c1ccccc1 0\nFC(Cl)Br 1\n");
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delete writer;
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}
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{
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std::stringstream ss;
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SmilesWriter *writer = new SmilesWriter(&ss, " ","Name",false,false,true);
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RWMol *mol;
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mol = SmilesToMol("c1ccccc1");
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MolOps::Kekulize(*mol);
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writer->write(*mol);
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delete mol;
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mol = SmilesToMol("F[C@H](Cl)Br");
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writer->write(*mol);
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delete mol;
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writer->flush();
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TEST_ASSERT(ss.str()=="C1=CC=CC=C1 0\nF[C@H](Cl)Br 1\n");
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delete writer;
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}
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}
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void testSmilesWriterNoNames() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
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SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
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std::string oname = rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
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STR_VECT propNames;
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propNames.push_back(std::string("Column_2"));
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SmilesWriter *writer = new SmilesWriter(oname," ","");
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writer->setProps(propNames);
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STR_VECT props;
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ROMol *mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp("Column_2", pval);
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mol->setProp("_Name","bogus");
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props.push_back(pval);
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writer->write(*mol);
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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writer->flush();
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delete writer;
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delete nSup;
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// now read the molecules back in a check if we have the same properties etc
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nSup = new SmilesMolSupplier(oname,",",0,-1);
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int i = 0;
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mol = nSup->next();
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while (mol){
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std::string mname, pval;
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mol->getProp("_Name", mname);
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TEST_ASSERT(mname!="bogus");
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mol->getProp("Column_2", pval);
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TEST_ASSERT(pval == props[i]);
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i++;
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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}
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void testSmilesWriterClose() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
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SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
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std::string oname = rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
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STR_VECT propNames;
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propNames.push_back(std::string("Column_2"));
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SmilesWriter *writer = new SmilesWriter(oname," ","");
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writer->setProps(propNames);
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STR_VECT props;
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ROMol *mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp("Column_2", pval);
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mol->setProp("_Name","bogus");
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props.push_back(pval);
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writer->write(*mol);
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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writer->close();
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delete nSup;
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// now read the molecules back in a check if we have the same properties etc
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nSup = new SmilesMolSupplier(oname,",",0,-1);
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int i = 0;
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mol = nSup->next();
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while (mol){
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std::string mname, pval;
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mol->getProp("_Name", mname);
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TEST_ASSERT(mname!="bogus");
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mol->getProp("Column_2", pval);
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TEST_ASSERT(pval == props[i]);
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i++;
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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}
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void testSDWriter() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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SDMolSupplier sdsup(fname);
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std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.sdf";
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SDWriter *writer = new SDWriter(ofile);
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STR_VECT names;
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while (!sdsup.atEnd()) {
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ROMol *mol = sdsup.next();
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std::string mname;
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mol->getProp("_Name", mname);
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names.push_back(mname);
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writer->write(*mol);
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delete mol;
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}
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writer->flush();
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CHECK_INVARIANT(writer->numMols() == 16, "");
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// make sure we can close() the writer and delete it:
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writer->close();
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delete writer;
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// now read in the file we just finished writing
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SDMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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std::string mname;
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mol->getProp("_Name", mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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i++;
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}
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// now read in a file with aromatic information on the bonds
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std::string infile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_arom.sdf";
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SDMolSupplier nreader(infile);
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i = 0;
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while (!nreader.atEnd()) {
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ROMol *mol = nreader.next();
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std::string mname;
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mol->getProp("_Name", mname);
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CHECK_INVARIANT(mname == names[i], "");
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i++;
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delete mol;
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}
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}
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void testTDTWriter() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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SDMolSupplier sdsup(fname);
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std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.tdt";
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TDTWriter *writer = new TDTWriter(ofile);
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STR_VECT names;
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while (!sdsup.atEnd()) {
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ROMol *mol = sdsup.next();
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std::string mname;
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mol->getProp("CAS_RN", mname);
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names.push_back(mname);
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writer->write(*mol);
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delete mol;
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}
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writer->flush();
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TEST_ASSERT(writer->numMols() == 16);
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delete writer;
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// now read in the file we just finished writing
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TDTMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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if(mol){
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std::string mname;
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mol->getProp("CAS_RN", mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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}
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i++;
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}
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TEST_ASSERT(i==16);
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}
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void testSmilesWriterStrm() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
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SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
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std::string oname = rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
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std::ofstream *oStream=new std::ofstream(oname.c_str());
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STR_VECT propNames;
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propNames.push_back(std::string("Column_2"));
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SmilesWriter *writer = new SmilesWriter(oStream, " ");
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writer->setProps(propNames);
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STR_VECT names;
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STR_VECT props;
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ROMol *mol = nSup->next();
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while (mol) {
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std::string mname, pval;
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mol->getProp("_Name", mname);
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mol->getProp("Column_2", pval);
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names.push_back(mname);
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props.push_back(pval);
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writer->write(*mol);
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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writer->flush();
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delete writer;
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delete nSup;
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// now read the molecules back in a check if we have the same properties etc
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nSup = new SmilesMolSupplier(oname);
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int i = 0;
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mol = nSup->next();
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while (mol){
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std::string mname, pval;
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mol->getProp("_Name", mname);
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mol->getProp("Column_2", pval);
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CHECK_INVARIANT(mname == names[i], "");
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CHECK_INVARIANT(pval == props[i], "");
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i++;
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delete mol;
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try {
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mol = nSup->next();
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} catch (FileParseException &) {
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break;
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}
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}
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}
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void testSDWriterStrm() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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SDMolSupplier sdsup(fname);
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std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.sdf";
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std::ofstream *oStream=new std::ofstream(ofile.c_str());
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SDWriter *writer = new SDWriter(oStream);
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STR_VECT names;
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while (!sdsup.atEnd()) {
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ROMol *mol = sdsup.next();
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std::string mname;
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mol->getProp("_Name", mname);
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names.push_back(mname);
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writer->write(*mol);
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delete mol;
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}
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writer->flush();
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CHECK_INVARIANT(writer->numMols() == 16, "");
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delete writer;
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// now read in the file we just finished writing
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SDMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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std::string mname;
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mol->getProp("_Name", mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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i++;
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}
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// now read in a file with aromatic information on the bonds
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std::string infile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_arom.sdf";
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SDMolSupplier nreader(infile);
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i = 0;
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while (!nreader.atEnd()) {
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ROMol *mol = nreader.next();
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std::string mname;
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mol->getProp("_Name", mname);
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CHECK_INVARIANT(mname == names[i], "");
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i++;
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delete mol;
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}
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}
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void testTDTWriterStrm() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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SDMolSupplier sdsup(fname);
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std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.tdt";
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std::ofstream *oStream=new std::ofstream(ofile.c_str());
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TDTWriter *writer = new TDTWriter(oStream);
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STR_VECT names;
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while (!sdsup.atEnd()) {
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ROMol *mol = sdsup.next();
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std::string mname;
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mol->getProp("CAS_RN", mname);
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names.push_back(mname);
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writer->write(*mol);
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delete mol;
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}
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writer->flush();
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TEST_ASSERT(writer->numMols() == 16);
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delete writer;
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// now read in the file we just finished writing
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TDTMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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if(mol){
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std::string mname;
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mol->getProp("CAS_RN", mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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}
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i++;
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}
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TEST_ASSERT(i==16);
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}
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void testSDMemoryCorruption() {
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Data/NCI/first_200.props.sdf";
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SDMolSupplier sdsup(fname,true);
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std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf";
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std::ostream *os=new std::ofstream(ofile.c_str());
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//std::ostream *os=new std::stringstream();
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SDWriter *writer = new SDWriter(os,false);
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STR_VECT names;
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#if 1
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ROMol *m1=sdsup.next();
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MolOps::sanitizeMol(*(RWMol *)m1);
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#else
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ROMol *m1=SmilesToMol("C1CC1");
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TEST_ASSERT(m1);
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#endif
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sdsup.reset();
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int nDone=0;
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while (!sdsup.atEnd()) {
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//std::cerr<<nDone<<std::endl;
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ROMol *mol = sdsup.next();
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//std::cerr<<"m:"<<mol<<std::endl;
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TEST_ASSERT(mol);
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std::string mname;
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mol->getProp("_Name", mname);
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names.push_back(mname);
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//std::cerr<<" w"<<std::endl;
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writer->write(*mol);
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//std::cerr<<" ok"<<std::endl;
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delete mol;
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nDone++;
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}
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CHECK_INVARIANT(nDone == 200, "");
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writer->flush();
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CHECK_INVARIANT(writer->numMols() == 200, "");
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delete writer;
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#if 1
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// now read in the file we just finished writing
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SDMolSupplier reader(ofile);
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int i = 0;
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while (!reader.atEnd()) {
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ROMol *mol = reader.next();
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std::string mname;
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mol->getProp("_Name", mname);
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CHECK_INVARIANT(mname == names[i], "");
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delete mol;
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i++;
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}
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#endif
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}
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int main() {
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RDLog::InitLogs();
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#if 1
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BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
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BOOST_LOG(rdInfoLog) << "Running testSmilesWriter()\n";
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|
testSmilesWriter();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriter2()\n";
|
|
testSmilesWriter2();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriterNoNames()\n";
|
|
testSmilesWriterNoNames();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriterClose()\n";
|
|
testSmilesWriterNoNames();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSDWriter()\n";
|
|
testSDWriter();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testTDTWriter()\n";
|
|
testTDTWriter();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSmilesWriterStrm()\n";
|
|
testSmilesWriterStrm();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSDWriterStrm()\n";
|
|
testSDWriterStrm();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testTDTWriterStrm()\n";
|
|
testTDTWriterStrm();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
#endif
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Running testSDMemoryCorruption()\n";
|
|
testSDMemoryCorruption();
|
|
BOOST_LOG(rdInfoLog) << "Finished\n";
|
|
BOOST_LOG(rdInfoLog) << "-----------------------------------------\n\n";
|
|
}
|