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rdkit/Code/GraphMol/FMCS/Test/testFMCS.cpp
Brian Kelley 54311dff9c Suppresses warnings in tests
2015-10-18 16:09:58 -04:00

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// $Id: testFMCS.cpp $
//
// Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#ifdef WIN32
#include <Windows.h>
#else
#include <unistd.h>
#include <fcntl.h>
#include <sys/time.h>
#include <sys/resource.h>
#endif
#include <stdio.h>
#include <string.h>
#include <time.h>
#include <string>
#include <iostream>
#include "../../RDKitBase.h"
#include "../../FileParsers/FileParsers.h" //MOL single molecule !
#include "../../FileParsers/MolSupplier.h" //SDF
#include "../../SmilesParse/SmilesParse.h"
#include "../../SmilesParse/SmilesWrite.h"
#include "../../SmilesParse/SmartsWrite.h"
#include "../FMCS.h"
#include "../DebugTrace.h" //#ifdef VERBOSE_STATISTICS_ON
using namespace RDKit;
unsigned long long T0;
unsigned long long t0;
void printTime() {
unsigned long long t1 = nanoClock();
double sec = double(t1-t0) / 1000000.;
printf("Time elapsed %.3lf seconds\n", sec);
t0 = nanoClock();
}
std::string getSmilesOnly(const char* smiles, std::string* id=0) { // remove label, because RDKit parse FAILED
const char* sp = strchr(smiles,' ');
unsigned n = (sp ? sp-smiles+1 : strlen(smiles));
if(id)
*id = std::string(smiles+n);
return std::string(smiles, n);
}
std::string getSmilesOnlyTxt(const char* smiles, std::string* id=0) { // remove label from string like "CHEMBL90218 NS(=O)(=O)c1ccc(NC(=O)c2cccc(C(=O)O)n2)c(Cl)c1"
const char* sp = strchr(smiles,' ');
if(sp && '\0'!=*sp) {
if(id)
*id = std::string(smiles, sp-smiles);
sp++;
size_t i=strlen(sp);
while(i>0 && sp[i-1]<' ') --i;
return std::string(sp, i);
} else
return smiles;
}
std::string getSmilesOnlyChEMBL(const char* smiles, std::string* id=0) { // remove label, because RDKit parse FAILED
const char* sp = strchr(smiles, '\t');
if(sp) {
unsigned n = (sp ? sp-smiles+1 : strlen(smiles));
if(id)
*id = std::string(smiles, n);
sp = strchr(++sp,'\t');
if(sp)
sp++;
}
return std::string(sp);
}
//====================================================================================================
MCSParameters p;
void testFileMCSB(const char* test, unsigned timeout=30, std::vector<unsigned> test_N=std::vector<unsigned>()) { // optional list of some tests for investigation
p.Verbose = false;
std::vector<ROMOL_SPTR> mols; // IT CAN OCCUPY A LOT OF MEMORY. store SMILES only to reduce memory usage.
char str [4096];
std::string molFile, id;
std::map<std::string, size_t> molIdMap;
std::vector<std::string> smilesList;
std::list< std::vector<std::string> > testCase;
std::string referenceOutFile(test);
referenceOutFile += ".REF.out";
std::string outFile(test);
if(!test_N.empty()) {
if(1==test_N.size())
sprintf(str,".%u.out", test_N[0]);
else
sprintf(str,".%u-%u.out", test_N[0], test_N.back());
outFile += str;
} else {
outFile += ".Cpp.out";
}
std::string outSmilesFile(test);
outSmilesFile += ".smiles";
unsigned n=0, passed=0, failed=0, failed_less=0, timedout=0;
double secTotal = 0.;
std::vector<MCSResult> referenceResults;
std::vector<float> referenceResultsTime;
FILE* f = fopen(referenceOutFile.c_str(), "rt");
if(!f)
perror("Could not open reference test result file");
else {
std::cout<<"Loading reference test results ... \n";
while(fgets(str, sizeof(str), f))
if('#' != str[0]) {
char c;
int frag;
float t;
char mcs [1024];
MCSResult res;
sscanf(str, "%u %c %d %d %d %f %s", &n, &c, &frag, &res.NumAtoms, &res.NumBonds, &t, mcs);
res.Canceled = ('.' != c);
res.SmartsString = mcs;
referenceResults.push_back(res);
referenceResultsTime.push_back(t);
}
}
fclose(f);
f = fopen(test, "rt");
if(!f) {
perror("Could not open test case list MCSB file");
exit(1);
}
{
std::cout<<"Loading MCSB test list ... \n";
if(fgets(str, sizeof(str), f))
if(fgets(str, sizeof(str), f)) {
char* c = strrchr(str, '\n'); // remove LineFeed
if(c)
*c = '\0';
c = strrchr(str, '\r');
if(c)
*c = '\0';
molFile = str + 6; // #File filename
}
std::cout<<"Molecules file:"<<molFile<<"\n";
n = 0;
while(fgets(str, sizeof(str), f))
if('#' != str[0]) {
//str= "1 CHEMBL526291 CHEMBL498211 ..."
char name [256];
unsigned nn, len;
n++;
testCase.push_back(std::vector<std::string>());
sscanf(str, "%u%n", &nn, &len);
while('\0'!=*(str+len) && 1==sscanf(str+len, "%s%n", name, &nn)) {
len += nn;
testCase.back().push_back(std::string(name));
}
}
std::cout<<n<<" Test cases loaded\n";
}
fclose(f);
f = fopen(molFile.c_str(), "rt");
if(!f) {
perror("Could not open molecules file");
exit(1);
}
std::cout<<"Loading SMILES ... \n";
n = 0;
while(fgets(str, sizeof(str), f)) {
std::cout<<"\rLine: "<< ++n <<" ";
if('#' != str[0] && ' ' != str[0] && '/' != str[0]) { // commented to skip
char* c = strrchr(str, '\n'); // remove LineFeed
if(c)
*c = '\0';
c = strrchr(str, '\r');
if(c)
*c = '\0';
std::string sm = getSmilesOnly(str, &id);
smilesList.push_back(sm); // without Id and LineFeed
mols.push_back(ROMOL_SPTR(SmilesToMol(sm))); // SmartsToMol ???
molIdMap[id] = mols.size()-1;// index in mols
}
}
fclose(f);
printTime();
f = fopen(outFile.c_str(), "wt");
if(!f) {
perror("Could not create output file");
exit(1);
}
setvbuf(f , 0, _IOFBF, 4*1024);
FILE* fs = 0; //fopen(outSmilesFile.c_str(), "wt");
if(fs)
setvbuf(fs, 0, _IOFBF, 4*1024);
#ifdef xxVERBOSE_STATISTICS_ON
FILE* ft = fopen((outFile+".stat.csv").c_str(), "wt");
setvbuf(ft, 0, _IOFBF, 4*1024); // small file
if(ft)
fprintf(ft, "N; Status; dAtoms; dBonds; t(sec); ref.t; Seed; MatchCall; AtomCmp; BondCmp\n"); //CSV Header
#endif
n = 0;
p.Timeout = timeout;
p.Threshold = 1.0;
fprintf(f, "#software RDKit C++ FMCS \n#options timeout=%u threshold=%g\n", p.Timeout, p.Threshold);
std::cout<<"Perform test cases ... \n";
for(std::list< std::vector<std::string> >::const_iterator tc = testCase.begin(); tc != testCase.end(); tc++, n++) {
if(!test_N.empty() && test_N.end() == std::find(test_N.begin(), test_N.end(), n+1))
continue;
std::cout<<"\rTest: "<< n+1 <<" ";
if(!test_N.empty()) // test case is listed
std::cout<<"\n";
std::vector<ROMOL_SPTR> tcmols;
fprintf(f, "# %u Using ", n+1);
if(fs)
fprintf(fs, "\n//TEST %u\n", n+1);
for(std::vector<std::string>::const_iterator mid = tc->begin(); mid != tc->end(); mid++) {
std::map<std::string, size_t>::const_iterator id = molIdMap.find(*mid);
if(molIdMap.end() == id)
continue;
size_t i = id->second;
tcmols.push_back(mols[i]);
fprintf(f, "%s ", mid->c_str());
if(fs)
fprintf(fs, "\"%s%s\",\n", smilesList[i].c_str(), mid->c_str());
}
fprintf(f, "\n");
// ExecStatistics curStat = stat; //to compute the difference for this test only
unsigned long long tc0 = nanoClock();
MCSResult res = findMCS(tcmols, &p); // *** T E S T ***
unsigned long long tc1 = nanoClock();
double sec = double(tc1-tc0) / 1000000.; // without time of SMILES to ROMol conversion
secTotal += sec;
if(!test_N.empty())
std::cout<<"\n" << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
else if(!referenceResults[n].Canceled && !res.Canceled && (/*referenceResults[n].NumAtoms > res.NumAtoms ||*/ referenceResults[n].NumBonds > res.NumBonds))
std::cout<<" - failed. LESS: "<<res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds ("<<referenceResults[n].NumAtoms - res.NumAtoms<<", "<<referenceResults[n].NumBonds-res.NumBonds<<")\n";
if(!referenceResults.empty()) {
fprintf(f, "# %u REFCMP: time %s %.2f sec.\n", n+1, fabs(referenceResultsTime[n] - sec)<sec/25.?"EQUAL"
:(referenceResultsTime[n] < sec ? (sec<.7?"slow":"SLOW")
:(sec<.7 && referenceResultsTime[n]<0.7 ? "fast":"FAST")), referenceResultsTime[n]);
if(!referenceResults[n].Canceled) { // && !res.Canceled)
if(referenceResults[n].NumAtoms == res.NumAtoms && referenceResults[n].NumBonds == res.NumBonds)
fprintf(f, "# %u REFCMP: res %s %s %u %u %s.\n", n+1, "PASSED"
, "-------"
, referenceResults[n].NumAtoms, referenceResults[n].NumBonds, referenceResults[n].SmartsString.c_str());
else
fprintf(f, "# %u REFCMP: res %s %s %u %u %s.\n", n+1, "FAILED"
, /*referenceResults[n].NumAtoms > res.NumAtoms ||*/ referenceResults[n].NumBonds > res.NumBonds ? "MISSING":"GREATER"
, referenceResults[n].NumAtoms, referenceResults[n].NumBonds, referenceResults[n].SmartsString.c_str());
if(referenceResults[n].Canceled
||(referenceResults[n].NumAtoms == res.NumAtoms && referenceResults[n].NumBonds == res.NumBonds))
passed++;
else if(res.Canceled)
timedout++;
else {
if(referenceResults[n].NumBonds > res.NumBonds)
failed_less++;
failed++;
}
} else
fprintf(f, "# %u REFCMP: res ABSENT - timeout\n", n+1);
}
// 1 . 1 25 28 1.69 F-c1:c:c:
fprintf(f, "%u %c %d %u %u %.2f %s\n", n+1, (res.Canceled ? 'F':'.'), 1 //number of fragments in the MCS
, res.NumAtoms, res.NumBonds, sec, res.SmartsString.c_str());
if(fs)
fprintf(fs, "//# %u %c %u %u %.2f sec MCS: %s\n", n+1, (res.Canceled ? 'F':'.'), res.NumAtoms, res.NumBonds, sec, res.SmartsString.c_str());
#ifdef xxVERBOSE_STATISTICS_ON
if(ft) // statistic details
fprintf(ft, "%u; %s; %d; %d; %.2f; %.2f; %u; %u; %u; %u\n",n+1
, !res.Canceled ? "ok" : referenceResults[n].Canceled ? "bad" : "TIMEOUT"
, referenceResults[n].Canceled ? 0 : res.NumAtoms - referenceResults[n].NumAtoms
, referenceResults[n].Canceled ? 0 : res.NumBonds - referenceResults[n].NumBonds
, sec, referenceResultsTime[n]
, stat.Seed - curStat.Seed
, stat.MatchCall - curStat.MatchCall
, stat.AtomCompareCalls - curStat.AtomCompareCalls
, stat.BondCompareCalls - curStat.BondCompareCalls
);
stat.AtomCompareCalls = 0; // 32 bit counter with very big value -> possible overflow
stat.BondCompareCalls = 0;
#endif
}
fprintf(f, "#\n#\n# %u passed, %u failed, %u failed_less, %u timed out.\n# Total %.2f seconds, Average %.2f seconds, Average exclude timeouts about %.2f seconds.\n"
, passed, failed, failed_less, timedout, secTotal, secTotal/n, (secTotal-30.6*timedout)/n);
#ifdef xxVERBOSE_STATISTICS_ON
fprintf(f, "#\n# --- STATISTICS:---\n# Total value | Average\n"
"# Seeds Num %15u | %8u (amount of generated seeds)\n"
"# BestSizeR %15u | %8u = %d%% (rejected by RemainingSize against BestSize seed)\n"
"# MatchCall %15u | %8u (SubstructMatch function calls)\n"
"# MatchTRUE %15u | %8u = %d%%\n"
#ifdef FAST_SUBSTRUCT_CACHE
// "#HashCache %15u | %8u keys\n"
// "#HashCache %15u | %8u entries\n"
"# HashCacheFind %15u | %8u \n"
"# HashKeysFound %15u | %8u = %d%% hash keys found \n"
"# ExactMatchCall %15u | %8u (SubstructMatch function calls)\n"
"# ExactMatchTRUE %15u | %8u \n"
#endif
, stat.Seed, stat.Seed/n
, stat.RemainingSizeRejected, stat.RemainingSizeRejected/n
, 0==stat.Seed ? 0 : int((double)stat.RemainingSizeRejected / (double)stat.Seed *100.)
, stat.MatchCall , stat.MatchCall/n
, stat.MatchCallTrue , stat.MatchCallTrue/n
, int((double)stat.MatchCallTrue / (double)stat.MatchCall *100.)
#ifdef FAST_SUBSTRUCT_CACHE
// , stat.HashCacheKeysSize, stat.HashCacheKeysSize/n
// , stat.HashCacheEntries , stat.HashCacheEntries/n
, stat.FindHashInCache, stat.FindHashInCache/n
, stat.HashKeyFoundInCache,stat.HashKeyFoundInCache/n
, 0==stat.FindHashInCache ? 0 : int((double)stat.HashKeyFoundInCache / (double)stat.FindHashInCache *100.)
, stat.ExactMatchCall , stat.ExactMatchCall/n
, stat.ExactMatchCallTrue, stat.ExactMatchCallTrue/n
#endif
);
#endif
if(f)
fclose(f);
if(fs)
fclose(fs);
#ifdef xxVERBOSE_STATISTICS_ON
if(ft)
fclose(ft);
#endif
printTime();
}
//=========================================================================
void test504() {
std::cout << "\ntest504()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
//TEST 504
"C(CCNC(C1CC1[c:1]1[c:2]c(Cl)c(Cl)c[c:3]1)=O)CCN1CCC(NC(Nc2ccc(Cl)cc2)=O)C1 CHEMBL545864", // - QUERY
//"C(CCNC(C1CC1[c:1]1[c:2]c(Cl)c(Cl)c[c:3]1)=O)CCN1CCC(NC(Nc2ccccc2)=O)C1 CHEMBL545864", // - QUERY - Cl:30
"FC(F)(F)c1cc(NC(N2CCCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)ccc1Cl CHEMBL528228",
"FC(F)(F)c1cc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)C2)=O)ccc1Cl CHEMBL525875",
"Fc1ccc(NC(N2CCCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)cc1C(F)(F)F CHEMBL527277",
"FC(F)(F)c1cc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)ccc1Cl CHEMBL537333",
"Fc1ccc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)C2)=O)cc1C(F)(F)F CHEMBL588077",
"FC(F)(F)c1ccc(NC(NC2CCN(CCCCCNC(C3CC3c3cc(Cl)c(Cl)cc3)=O)C2)=O)cc1 CHEMBL525307",
"Fc1ccc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)cc1C(F)(F)F CHEMBL581847",
"FC(F)(F)c1ccc(NC(NC2CCN(CCCCCNC(C3CC3c3cc(Cl)c(Cl)cc3)=O)CC2)=O)cc1 CHEMBL579547",
"N#Cc1cccc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)c1 CHEMBL529994",
};
RWMol* qm = SmilesToMol( getSmilesOnly(smi[0]) );
unsigned nq = qm->getNumAtoms();
for(size_t ai = 0; ai < nq; ai++) {
Atom* atom = qm->getAtomWithIdx(ai);
atom->setProp(common_properties::molAtomMapNumber, (int)ai);
}
std::cout<<"Query +MAP "<< MolToSmiles(*qm) <<"\n";
mols.push_back(ROMOL_SPTR(qm)); // with RING INFO
for(size_t i=1; i<sizeof(smi)/sizeof(smi[0]); i++)
mols.push_back(ROMOL_SPTR(SmilesToMol( getSmilesOnly(smi[i]) ))); // with RING INFO
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
std::string testChEMBL_Txt(const char* test, double th=1.0, const char* csv="chembl_II_sets.C++.res.csv") {
std::cout << "\ntestChEMBL_Txt() "<<test<<"\n";
std::vector<ROMOL_SPTR> mols;
char smiles[4096];
//unsigned n=0;
FILE* f = fopen(test, "rt");
if(!f) {
perror("fopen testChEMBL_Txt()");
return "";
}
char testsmi[512];
strcpy(testsmi, test);
strcpy(testsmi + strlen(test)-3, "smi");
FILE* fsmi = fopen(testsmi, "wt");
FILE* fres = fopen(csv, "at");
while(fgets(smiles, sizeof(smiles), f)) {
if('#' != smiles[0] && ' ' != smiles[0] && '/' != smiles[0]) { // commented to skip
std::string id;
std::string smi = getSmilesOnlyTxt(smiles, &id);
fprintf(fsmi, "%s\n", (smi+" "+ id).c_str());
mols.push_back(ROMOL_SPTR(SmilesToMol(smi)));
}
}
fclose(f);
fclose(fsmi);
p.Threshold = th;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
unsigned long long tc1 = nanoClock();
double sec = double(tc1-t0) / 1000000.;
std::cout << "MCS : "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
fprintf(fres, "%s;%lu;%.1f;%.4f;%u;%u;%s;", test, mols.size(), th, sec, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
p.BondTyper = MCSBondCompareOrderExact;
t0 = nanoClock();
res = findMCS(mols, &p);
tc1 = nanoClock();
sec = double(tc1-t0) / 1000000.;
p.BondTyper = MCSBondCompareOrder;
std::cout << "MCS : "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
fprintf(fres, "%.1f;%u;%u;%s\n", sec, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
fclose(fres);
return testsmi;
}
void testChEMBL_TxtALL_chembl_II_sets(double th=1.0) {
FILE* fres = fopen("chembl_II_sets.C.res.csv", "wt");
fprintf(fres,"test;Nmols;threshold;t,sec;atoms;bonds;mcs;E t,sec;E atoms;E bonds;E mcs\n");
fclose(fres);
const char* test[] = {
"Target_no_100_15113.txt",
"Target_no_100_16613.txt",
"Target_no_100_30745.txt",
"Target_no_100_30861.txt",
"Target_no_100_31495.txt",
"Target_no_100_34869.txt",
"Target_no_100_36158.txt",
"Target_no_100_36559.txt",
"Target_no_100_37434.txt",
"Target_no_100_39147.txt",
"Target_no_100_43754.txt",
"Target_no_100_44011.txt",
"Target_no_100_44158.txt",
"Target_no_100_48076.txt",
"Target_no_100_48961.txt",
"Target_no_100_49648.txt",
"Target_no_100_49703.txt",
"Target_no_100_51128.txt",
"Target_no_100_51343.txt",
"Target_no_100_51842.txt",
"Target_no_100_54554.txt",
"Target_no_100_55749.txt",
"Target_no_10188_17256.txt",
"Target_no_10188_20244.txt",
"Target_no_10188_20245.txt",
"Target_no_10188_30149.txt",
"Target_no_10188_30499.txt",
"Target_no_10188_36186.txt",
"Target_no_10188_39262.txt",
"Target_no_10188_43966.txt",
"Target_no_10188_45279.txt",
"Target_no_10188_48029.txt",
"Target_no_10188_49064.txt",
"Target_no_10188_49801.txt",
"Target_no_10188_50681.txt",
"Target_no_10188_54039.txt",
"Target_no_10188_58265.txt",
"Target_no_10188_58358.txt",
"Target_no_10188_58866.txt",
"Target_no_10188_60810.txt",
"Target_no_10193_21358.txt",
"Target_no_10193_21597.txt",
"Target_no_10193_30111.txt",
"Target_no_10193_30349.txt",
"Target_no_10193_31746.txt",
"Target_no_10193_31822.txt",
"Target_no_10193_35220.txt",
"Target_no_10193_37603.txt",
"Target_no_10193_37964.txt",
"Target_no_10193_39508.txt",
"Target_no_10193_42164.txt",
"Target_no_10193_42577.txt",
"Target_no_10193_44072.txt",
"Target_no_10193_45522.txt",
"Target_no_10193_46700.txt",
"Target_no_10193_46719.txt",
"Target_no_10193_46744.txt",
"Target_no_10193_48517.txt",
"Target_no_10193_49087.txt",
"Target_no_10193_50034.txt",
"Target_no_10193_51475.txt",
"Target_no_10193_53483.txt",
"Target_no_10193_53506.txt",
"Target_no_10193_54598.txt",
"Target_no_10193_55614.txt",
"Target_no_10193_55737.txt",
"Target_no_10193_57090.txt",
"Target_no_10193_57705.txt",
"Target_no_10193_57785.txt",
"Target_no_10193_58463.txt",
"Target_no_10193_58700.txt",
"Target_no_10193_61003.txt",
"Target_no_10193_61349.txt",
"Target_no_10260_38526.txt",
"Target_no_10260_50778.txt",
"Target_no_10260_52179.txt",
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"Target_no_93_1308.txt",
"Target_no_93_34759.txt",
"Target_no_93_35447.txt",
"Target_no_93_42214.txt",
"Target_no_93_45877.txt",
"Target_no_93_47082.txt",
"Target_no_93_57082.txt",
};
FILE *fcmd = fopen("chembl_II_sets.bat", "wt");
// commands for prepare Python test:
fprintf(fcmd, "DEL %s\n", "chembl_II_sets.P.res.csv"); //clear before append results
fprintf(fcmd, "SET PATH=%%PATH%%;C:/LIB\n");
fprintf(fcmd, "SET PYTHONPATH=C:/Projects/RDKit/RDKit_2013_09_1\n");
fprintf(fcmd, "ECHO P test;P Nmols;P status;P time,sec;P nAtoms;P nBonds;P MCS >%s\n", "chembl_II_sets.P.res.csv");
p.Timeout = 60;
p.Verbose = false;
for(size_t i=0; i<sizeof(test)/sizeof(test[0]); i++) {
std::string smiName = std::string("chembl_II_sets/") + test[i];
std::string testsmi = testChEMBL_Txt(smiName.c_str(), th, "chembl_II_sets.C.res.csv");
fprintf(fcmd, "fmcs_bench.py --timeout %u %s >>%s\n", p.Timeout, testsmi.c_str(), "chembl_II_sets.P.res.csv"); // command for the same Python test
}
}
void testChEMBL_TxtSLOW_chembl_II_sets(double th=1.0) {
FILE* fres = fopen("chembl_II_sets.SLOW.C++.res.csv", "wt");
fprintf(fres,"test;threshold;t,sec;atoms;bonds;mcs\n");
fclose(fres);
const char* test[] = {
"Target_no_10980_51302.txt",
"Target_no_114_31443.txt",
"Target_no_10260_54285.txt",
"Target_no_11489_37339.txt",
"Target_no_10980_52937.txt",
"Target_no_114_48395.txt",
"Target_no_10280_45765.txt",
"Target_no_10188_50681.txt",
"Target_no_114_46087.txt",
"Target_no_10188_58358.txt",
"Target_no_11140_54121.txt",
"Target_no_114_37208.txt",
"Target_no_10193_53483.txt",
"Target_no_10980_31623.txt",
"Target_no_10280_60672.txt",
"Target_no_10188_45279.txt",
"Target_no_11140_49860.txt",
"Target_no_10280_53081.txt",
"Target_no_11489_46089.txt",
"Target_no_10188_54039.txt",
"Target_no_114_34747.txt",
"Target_no_11365_30331.txt",
"Target_no_10188_48029.txt",
"Target_no_114_16827.txt",
"Target_no_100_30745.txt",
"Target_no_108_49591.txt",
"Target_no_107_49591.txt",
"Target_no_10980_35957.txt",
"Target_no_11489_37318.txt",
"Target_no_10188_58265.txt",
"Target_no_107_58879.txt",
"Target_no_11140_37272.txt",
"Target_no_10188_39262.txt",
"Target_no_10280_47928.txt",
"Target_no_107_49345.txt",
"Target_no_10188_20244.txt",
"Target_no_10980_20853.txt",
"Target_no_11365_58566.txt",
"Target_no_114_44562.txt",
"Target_no_100_16613.txt",
"Target_no_11489_39561.txt",
"Target_no_10434_35926.txt",
"Target_no_10980_31508.txt",
"Target_no_11489_34818.txt",
"Target_no_10188_58866.txt",
"Target_no_11489_58958.txt",
"Target_no_11140_39472.txt",
"Target_no_10980_5739.txt",
"Target_no_11489_54754.txt",
"Target_no_10260_38526.txt",
"Target_no_11489_58262.txt",
"Target_no_107_34921.txt",
"Target_no_107_30866.txt",
"Target_no_108_30866.txt",
"Target_no_10980_36641.txt",
"Target_no_10980_30840.txt",
"Target_no_107_31249.txt",
"Target_no_11140_53395.txt",
"Target_no_10193_46700.txt",
"Target_no_10980_30994.txt",
"Target_no_11140_37038.txt",
};
for(size_t i=0; i<sizeof(test)/sizeof(test[0]); i++)
testChEMBL_Txt((std::string("chembl_II_sets/") + test[i]).c_str(), th,"chembl_II_sets.SLOW.C++.res.csv");
}
void testChEMBLdat(const char* test, double th=1.0) {
std::cout << "\ntestChEMBLdat() "<<test<<"\n";
std::vector<ROMOL_SPTR> mols;
char smiles[4096];
unsigned n=0;
FILE* f = fopen(test, "rt");
if(!f) {
perror("fopen testChEMBLdat()");
return;
}
FILE* fs = fopen((std::string(test)+".smi").c_str(), "wt");
std::cout<<"Loading SMILES ... \n";
t0 = nanoClock();
while(fgets(smiles, sizeof(smiles), f)) {
std::cout<<"\rLine: "<< ++n <<" ";
if('#' != smiles[0] && ' ' != smiles[0] && '/' != smiles[0]) { // commented to skip
mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnlyChEMBL(smiles))));
fputs(getSmilesOnlyChEMBL(smiles).c_str(), fs);
}
}
fclose(f);
fclose(fs);
printTime();
std::cout<<"FIND MCS in "<<mols.size()<<" molecules.\n\n";
t0 = nanoClock();
p.Threshold = th;
MCSResult res = findMCS(mols, &p);
std::cout << "MCS : "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
void testChEMBLdatALL(double th=1.0) {
const char* test[] = {
"cmp_list_ChEMBL_100126_actives.dat",
"cmp_list_ChEMBL_100579_actives.dat",
"cmp_list_ChEMBL_100_actives.dat",
"cmp_list_ChEMBL_10188_actives.dat",
"cmp_list_ChEMBL_10193_actives.dat",
"cmp_list_ChEMBL_10198_actives.dat",
"cmp_list_ChEMBL_10260_actives.dat",
"cmp_list_ChEMBL_10280_actives.dat",
"cmp_list_ChEMBL_10378_actives.dat",
"cmp_list_ChEMBL_10417_actives.dat",
"cmp_list_ChEMBL_10434_actives.dat",
"cmp_list_ChEMBL_10475_actives.dat",
"cmp_list_ChEMBL_10498_actives.dat",
"cmp_list_ChEMBL_104_actives.dat",
"cmp_list_ChEMBL_10579_actives.dat",
"cmp_list_ChEMBL_105_actives.dat",
"cmp_list_ChEMBL_10752_actives.dat",
"cmp_list_ChEMBL_10773_actives.dat",
"cmp_list_ChEMBL_107_actives.dat",
"cmp_list_ChEMBL_108_actives.dat",
"cmp_list_ChEMBL_10927_actives.dat",
"cmp_list_ChEMBL_10980_actives.dat",
"cmp_list_ChEMBL_11085_actives.dat",
"cmp_list_ChEMBL_11140_actives.dat",
"cmp_list_ChEMBL_11225_actives.dat",
"cmp_list_ChEMBL_11279_actives.dat",
"cmp_list_ChEMBL_11336_actives.dat",
"cmp_list_ChEMBL_11359_actives.dat",
"cmp_list_ChEMBL_11365_actives.dat",
"cmp_list_ChEMBL_11442_actives.dat",
"cmp_list_ChEMBL_11488_actives.dat",
"cmp_list_ChEMBL_11489_actives.dat",
"cmp_list_ChEMBL_114_actives.dat",
"cmp_list_ChEMBL_11534_actives.dat",
"cmp_list_ChEMBL_11536_actives.dat",
"cmp_list_ChEMBL_11575_actives.dat",
"cmp_list_ChEMBL_11631_actives.dat",
"cmp_list_ChEMBL_11682_actives.dat",
"cmp_list_ChEMBL_116_actives.dat",
"cmp_list_ChEMBL_121_actives.dat",
"cmp_list_ChEMBL_12209_actives.dat",
"cmp_list_ChEMBL_12252_actives.dat",
"cmp_list_ChEMBL_12261_actives.dat",
"cmp_list_ChEMBL_12670_actives.dat",
"cmp_list_ChEMBL_12679_actives.dat",
"cmp_list_ChEMBL_126_actives.dat",
"cmp_list_ChEMBL_12840_actives.dat",
"cmp_list_ChEMBL_12911_actives.dat",
"cmp_list_ChEMBL_12952_actives.dat",
"cmp_list_ChEMBL_12968_actives.dat",
"cmp_list_ChEMBL_13001_actives.dat",
"cmp_list_ChEMBL_130_actives.dat",
"cmp_list_ChEMBL_134_actives.dat",
"cmp_list_ChEMBL_15_actives.dat",
"cmp_list_ChEMBL_165_actives.dat",
"cmp_list_ChEMBL_17045_actives.dat",
"cmp_list_ChEMBL_18061_actives.dat",
"cmp_list_ChEMBL_19905_actives.dat",
"cmp_list_ChEMBL_20014_actives.dat",
"cmp_list_ChEMBL_20174_actives.dat",
"cmp_list_ChEMBL_219_actives.dat",
"cmp_list_ChEMBL_234_actives.dat",
"cmp_list_ChEMBL_237_actives.dat",
"cmp_list_ChEMBL_259_actives.dat",
"cmp_list_ChEMBL_25_actives.dat",
"cmp_list_ChEMBL_276_actives.dat",
"cmp_list_ChEMBL_28_actives.dat",
"cmp_list_ChEMBL_36_actives.dat",
"cmp_list_ChEMBL_43_actives.dat",
"cmp_list_ChEMBL_51_actives.dat",
"cmp_list_ChEMBL_52_actives.dat",
"cmp_list_ChEMBL_61_actives.dat",
"cmp_list_ChEMBL_65_actives.dat",
"cmp_list_ChEMBL_72_actives.dat",
"cmp_list_ChEMBL_87_actives.dat",
"cmp_list_ChEMBL_8_actives.dat",
"cmp_list_ChEMBL_90_actives.dat",
"cmp_list_ChEMBL_93_actives.dat",
"cmp_list_ChEMBL_zinc_decoys.dat",
};
for(size_t i=0; i<sizeof(test)/sizeof(test[0]); i++)
testChEMBLdat((std::string("benchmarking_platform-master/compounds/ChEMBL/") + test[i]).c_str(), th);
}
void testTarget_no_10188_30149() {
std::cout << "\ntestTarget_no_10188_30149()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
//Target_no_10188_30149.txt // VERY SLOWER than Python
"CN(C)CCNC(=O)c1ccc(-c2n[nH]c3cc(Nc4ccccc4Cl)ccc32)cc1 CHEMBL399167",
"O=C(O)c1cccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL197613",
"c1ccc(Nc2ccc3c(c2)[nH]nc3-c2ccccc2)cc1 CHEMBL383177", /// == QUERY
"NC(=O)c1cccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL199136",
"Clc1ccccc1Nc1ccc2c(c1)n[nH]c2-c1ccccc1 CHEMBL440566",
"O=C(NCCCN1CCOCC1)c1cccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL198687",
"O=C(O)c1ccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)cc1 CHEMBL197698",
"O=C(NC1CCNCC1)c1cccc(-c2n[nH]c3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL194806",
"COc1ccccc1Nc1ccc2c(c1)[nH]nc2-c1ccccc1 CHEMBL254443",
"CN(C)CCNC(=O)c1cccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL198821",
};
for(size_t i=0; i<sizeof(smi)/sizeof(smi[0]); i++)
mols.push_back(ROMOL_SPTR(SmilesToMol( getSmilesOnly(smi[i]) )));
t0 = nanoClock();
#ifdef _DEBUG // check memory leaks
_CrtMemState _ms;
_CrtMemCheckpoint(&_ms);
#endif
{
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
}
#ifdef _DEBUG // check memory leaks
_CrtMemDumpAllObjectsSince(&_ms);
#endif
printTime();
}
void testTarget_no_10188_49064() {
std::cout << "\ntestTarget_no_10188_49064()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3cccc(O)c3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(F)cc3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(OC4OC(CO)C(O)C(O)C4O)cc3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(NC(=O)CCl)cc3)nc21",
"Cn1c2nc(Nc3ccc(NC(=O)CCN)cc3)ncc2cc(-c2c(Cl)cccc2Cl)c1=O",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3cccc(COCC(O)CO)c3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(O)cc3)nc21",
"CC(=O)Nc1ccc(Nc2ncc3cc(-c4c(Cl)cccc4Cl)c(=O)n(C)c3n2)cc1",
"Cn1c2nc(Nc3ccc(N)cc3)ncc2cc(-c2c(Cl)cccc2Cl)c1=O",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(NC(=O)CCNC(=O)OC(C)(C)C)cc3)nc21",
"Cc1ccc(Nc2ncc3cc(-c4c(Cl)cccc4Cl)c(=O)n(C)c3n2)cc1",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3cccc(CO)c3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(NCC(O)CO)cc3)nc21",
"CCc1cccc(Nc2ncc3cc(-c4c(Cl)cccc4Cl)c(=O)n(C)c3n2)c1",
"Cn1c2nc(Nc3cccc(N)c3)ncc2cc(-c2c(Cl)cccc2Cl)c1=O",
"CC(=O)Nc1cccc(Nc2ncc3cc(-c4c(Cl)cccc4Cl)c(=O)n(C)c3n2)c1",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(CCO)cc3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(I)cc3)nc21",
"CN1CCN(C(=O)c2ccc(Nc3ncc4cc(-c5c(Cl)cccc5Cl)c(=O)n(C)c4n3)cc2)CC1",
};
for(size_t i=0; i<sizeof(smi)/sizeof(smi[0]); i++)
mols.push_back(ROMOL_SPTR(SmilesToMol( getSmilesOnly(smi[i]) )));
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
void testCmndLineSMILES(int argc, const char* argv[]) {
std::vector<ROMOL_SPTR> mols;
for(int i=1; i<argc; i++)
mols.push_back(ROMOL_SPTR(SmilesToMol(argv[i])));
MCSResult res = findMCS(mols);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
double testFileSDF(const char* test) {
std::cout << "\ntestFileSDF(): " << test << "\n";
std::vector<ROMOL_SPTR> mols;
std::string fn(test);
RDKit::SDMolSupplier suppl(fn);
while(!suppl.atEnd()) {
ROMol *m=suppl.next();
if(m)
mols.push_back(ROMOL_SPTR(m));
}
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
return t;
}
void testFileSDF_RandomSet_SMI(const char* path="benchmark", const char* test="chembl13-10000-random-pairs.sdf") {
p.Timeout = 60;
p.Verbose = false;
//unsigned long long To = nanoClock();
std::cout << "\ntestFileSDF_RandomSet(): " << path<<"/"<<test << "\n";
std::vector<ROMOL_SPTR> mols;
FILE* fcsv = fopen((std::string(path)+"_"+test+".SMI.C.csv").c_str(), "wt");
fprintf(fcsv, "test;Nmols;status;t,sec;nAtoms;nBonds;C++ MCS; E status;E t,sec;E nAtoms;E nBonds;E C++ MCS\n");
bool fileExist = true;
unsigned n = 1;
for( ; fileExist ; n++) {
char smiName[256];
sprintf(smiName,"%s/smiles/%s.%u.smi", path, test, n);
FILE* fsmi = fopen(smiName, "rt");
if(!fsmi) {
fileExist = false;
break;
}
char smiles[4096];
while(fgets(smiles, sizeof(smiles), fsmi)) {
mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(smiles))));
}
fclose(fsmi);
if(mols.size()>1) {
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
printTime();
std::cout << n <<" MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), res.isCompleted()?" ":"TIMEOUT", t, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
}
if(mols.size()>1) {
p.BondTyper = MCSBondCompareOrderExact;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
printTime();
std::cout << n <<" MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), res.isCompleted()?" ":"TIMEOUT", t, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
p.BondTyper = MCSBondCompareOrder;
}
mols.clear();
}
fclose(fcsv);
}
void testFileSDF_RandomSet(const char* test="chembl13-10000-random-pairs.sdf", const char* path="benchmark") {
p.Timeout = 60;
p.Verbose = false;
//unsigned long long To = nanoClock();
std::cout << "\ntestFileSDF_RandomSet(): " << path<<"/"<<test << "\n";
std::vector<ROMOL_SPTR> mols;
std::vector<ROMOL_SPTR> all_mols;
FILE* fall = fopen((std::string(path)+"_ALL.P.bat").c_str(), "at");
fprintf(fall, "CALL %s\n", (std::string(path)+"_"+test+".P.bat").c_str());
fclose(fall);
FILE* fcmd = fopen((std::string(path)+"_"+test+".P.bat").c_str(), "wt");
FILE* fcsv = fopen((std::string(path)+"_"+test+".C.csv").c_str(), "wt");
fprintf(fcsv, "test;Nmols;status;t,sec;nAtoms;nBonds;C++ MCS; E status;E t,sec;E nAtoms;E nBonds;E C++ MCS\n");
std::string fn(std::string(path)+"/"+test);
RDKit::MolSupplier* suppl = 0;
try {
if('f' == test[strlen(test)-1]) // sdf file
suppl = new RDKit::SDMolSupplier(fn);
else if('i' == test[strlen(test)-1]) // smi file
suppl = new RDKit::SmilesMolSupplier(fn);
} catch(...) {
std::cout << "ERROR: RDKit could not load input file" << "\n";
return;
}
if(!suppl) {
std::cout << "ERROR: unsupported input file format" << "\n";
return;
}
// commands for prepare Python test:
fprintf(fcmd, "DEL %s\n", (std::string(path)+"_"+test+".P.csv").c_str()); //clear before append results
fprintf(fcmd, "SET PATH=%%PATH%%;C:/LIB\n");
fprintf(fcmd, "SET PYTHONPATH=C:/Projects/RDKit/RDKit_2013_09_1\n");
fprintf(fcmd, "ECHO P test;P Nmols;P status;P time,sec;P nAtoms;P nBonds;P MCS >%s\n", (std::string(path)+"_"+test+".P.csv").c_str());
unsigned n = 1;
std::cout << "\n****** Load all molecules from SFD and PAIR SET test *********\n\n";
for( ; !suppl->atEnd() ; n++) {
char smiName[256];
sprintf(smiName,"%s/smiles/%s.%u.smi", path, test, n);
FILE* fsmi = fopen(smiName, "wt");
if(!fsmi) {
std::cout << "ERROR: could not create SMI file " << smiName <<"\n";
return;
}
ROMol *m=0;
for(int i=0; i<2 && !suppl->atEnd(); i++) { // load sequential pair
m = suppl->next();
if(m) {
mols.push_back(ROMOL_SPTR(m));
all_mols.push_back(mols.back());
fprintf(fsmi,"%s Mol%u\n", MolToSmiles(*m).c_str(), n+i);
}
}
fclose(fsmi);
if(mols.size()<2) {
unlink(smiName);
n--;
} else {
fprintf(fcmd, "fmcs_bench.py --id %u --timeout %u --threshold %.2f %s >>%s\n", n, p.Timeout, p.Threshold, smiName, (std::string(path)+"_"+test+".P.csv").c_str()); // command for the same Python test
if(mols.size()>1) {
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
if(t < 0.00001)
t = 0.00001; // avoid division by zero
printTime();
std::cout << n <<" MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), res.isCompleted()?" ":"TIMEOUT", t, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
}
if(mols.size()>1) {
p.BondTyper = MCSBondCompareOrderExact;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
if(t < 0.00001)
t = 0.00001; // avoid division by zero
printTime();
std::cout << n <<" MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
fprintf(fcsv, "%s;%.5f;%u;%u;%s\n", res.isCompleted()?" ":"TIMEOUT", t, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
p.BondTyper = MCSBondCompareOrder;
}
}
mols.clear();
}
delete(suppl);
std::cout << "\n****** RANDOM SET test *********\n\n";
const unsigned N_RandomTests = all_mols.size() * 7;
srand(1); // make stable pseudorandom sequence
for(unsigned jn=0; n <= N_RandomTests; jn++, n++) {
char smiName[256];
sprintf(smiName,"%s/smilesRAND/%s.%u.smi", path, test, n);
FILE* fsmi = fopen(smiName, "wt");
fprintf(fcmd, "fmcs_bench.py --id %u --timeout %u --threshold %.2f %s >>%s\n", n, p.Timeout, p.Threshold, smiName, (std::string(path)+"_"+test+".P.csv").c_str()); // command for the same Python test
//ROMol *m=0;
unsigned iN = 3+rand()%32;
for(unsigned i=0; i < iN; i++) { // load random set
mols.push_back(all_mols[rand()%(all_mols.size()-1)]);
fprintf(fsmi,"%s Mol%u\n", MolToSmiles(*mols.back()).c_str(), n+i);
}
fclose(fsmi);
if(mols.size()>1) {
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
if(t < 0.00001)
t = 0.00001; // avoid division by zero
printTime();
std::cout << n <<" MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), res.isCompleted()?" ":"TIMEOUT", t, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
}
if(mols.size()>1) {
p.BondTyper = MCSBondCompareOrderExact;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
if(t < 0.00001)
t = 0.00001; // avoid division by zero
printTime();
std::cout << n <<" MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
fprintf(fcsv, "%s;%.5f;%u;%u;%s\n", res.isCompleted()?" ":"TIMEOUT", t, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
p.BondTyper = MCSBondCompareOrder;
}
mols.clear();
}
fclose(fcsv);
fclose(fcmd);
std::cout << "\n****** BIG MCS RANDOM SET test *********\n\n";
unsigned maxMol = 0;
for(unsigned i=0; i < all_mols.size(); i++) {
if(maxMol < all_mols[i]->getNumBonds())
maxMol = all_mols[i]->getNumBonds();
}
const unsigned N_BigRandomTests = all_mols.size() > 2000 ? all_mols.size()/2 : all_mols.size()*2;
const unsigned N_BigRandomTestsAttempts = all_mols.size()*130;
const unsigned SizeOfBigMCS_ForBigRandomTests = maxMol < 24 ? maxMol*2/3 : 21;
fall = fopen((std::string(path)+"_ALL_BIG.P.bat").c_str(), "at");
fprintf(fall, "CALL %s\n", (std::string(path)+"_"+test+".BIG_MCS.P.bat").c_str());
fclose(fall);
fcmd = fopen((std::string(path)+"_"+test+".BIG_MCS.P.bat").c_str(), "wt");
fcsv = fopen((std::string(path)+"_"+test+".BIG_MCS.C.csv").c_str(), "wt");
fprintf(fcsv, "test;Nmols;status;t,sec;nAtoms;nBonds;C++ MCS; E status;E t,sec;E nAtoms;E nBonds;E C++ MCS\n");
const unsigned n1 = n;
fprintf(fcmd, "DEL %s\n", (std::string(path)+"_"+test+".BIG_MCS.P.csv").c_str()); //clear before append results
fprintf(fcmd, "SET PATH=%%PATH%%;C:/LIB\n");
fprintf(fcmd, "SET PYTHONPATH=C:/Projects/RDKit/RDKit_2013_09_1\n");
fprintf(fcmd, "ECHO P test;P Nmols;P status;P time,sec;P nAtoms;P nBonds;P MCS >%s\n", (std::string(path)+"_"+test+".BIG_MCS.P.csv").c_str());
for(size_t jn=0; jn < N_BigRandomTestsAttempts && n-n1 <= N_BigRandomTests; jn++) {
char smiName[512];
sprintf(smiName,"%s/smilesBIG/%s.%u.smi", path, test, n);
//ROMol *m=0;
unsigned iN = 2+rand()%24;
mols.clear();
for(size_t i=0; i < iN; i++) // load random set
for(size_t ij=0; ij < all_mols.size()/2; ij++) {
unsigned mi = rand()%(all_mols.size()-1);
if(all_mols[mi]->getNumBonds() < SizeOfBigMCS_ForBigRandomTests)
continue;
mols.push_back(all_mols[mi]);
break;
}
MCSResult res;
if(mols.size()>1) {
t0 = nanoClock();
res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
if(t < 0.00001)
t = 0.00001; // avoid division by zero
printTime();
std::cout << n <<" MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
if(res.NumBonds >= SizeOfBigMCS_ForBigRandomTests && res.isCompleted()) {
fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), res.isCompleted()?" ":"TIMEOUT", t, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
fprintf(fcmd, "fmcs_bench.py --id %u --timeout %u --threshold %.2f %s >>%s\n", n, p.Timeout, p.Threshold, smiName, (std::string(path)+"_"+test+".BIG_MCS.P.csv").c_str()); // command for the same Python test
n++;
}
}
if(res.NumBonds >= SizeOfBigMCS_ForBigRandomTests && res.isCompleted()) {
FILE* fsmi = fopen(smiName, "wt");
for(size_t i=0; i < mols.size(); i++) { // load random set
fprintf(fsmi,"%s Mol%u\n", MolToSmiles(*mols[i]).c_str(), rdcast<unsigned int>(n+i));
}
fclose(fsmi);
}
if(res.NumBonds >= SizeOfBigMCS_ForBigRandomTests && res.isCompleted()) {
p.BondTyper = MCSBondCompareOrderExact;
t0 = nanoClock();
res = findMCS(mols, &p);
double t = (nanoClock() - t0) / 1000000.;
if(t < 0.00001)
t = 0.00001; // avoid division by zero
printTime();
std::cout << n <<" MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
fprintf(fcsv, "%s;%.5f;%u;%u;%s\n", res.isCompleted()?" ":"TIMEOUT", t, res.NumAtoms, res.NumBonds, res.SmartsString.c_str());
p.BondTyper = MCSBondCompareOrder;
}
mols.clear();
}
fclose(fcsv);
fclose(fcmd);
t0 = T0;
std::cout << n << " tests processed\n";
printTime();
}
void testFileSMILES(const char* test) {
std::vector<ROMOL_SPTR> mols;
char smiles[4096];
unsigned n=0;
FILE* f = fopen(test, "rt");
std::cout<<"Loading SMILES ... \n";
while(fgets(smiles, sizeof(smiles), f)) {
std::cout<<"\rLine: "<< ++n <<" ";
if('#' != smiles[0] && ' ' != smiles[0] && '/' != smiles[0]) // commented to skip
// if(strlen(smiles) > 92) // minimal query size !!!
mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(smiles))));
}
fclose(f);
printTime();
std::cout<<"FIND MCS in "<<mols.size()<<" molecules.\n\n";
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS : "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
//====================================================================================================
//====================================================================================================
void testGregSDFFileSetFiltered() {
const std::string sdf_dir("Greg'sComparision/data/filtered/");
const char* sdf[] = {
//fmcs: 0.11 27 29 beta2_adrenergic_aid465635.filtered.sdf O=C(O)C1:C:C:C(C2:C:C:C(CCNCC(O)C3:C:C:C:C:C:3):C:C:2):C:C:1
"beta2_adrenergic_aid465635.filtered.sdf",
//fmcs: 1.90 22 23 beta2_adrenergic_aid578239.filtered.sdf CNC1:C:C:C(CCNCC(O)COC2:C:C:C:C:C:2):C:C:1
"beta2_adrenergic_aid578239.filtered.sdf",
//fmcs: 1.88 22 23 beta2_adrenergic_aid578240.filtered.sdf CNC1:C:C:C(CCNCC(O)COC2:C:C:C:C:C:2):C:C:1
"beta2_adrenergic_aid578240.filtered.sdf",
//fmcs: 0.07 17 18 beta2_adrenergic_aid759384.filtered.sdf CCNCC(O)C1:C:C:C(O):C2:N:C(=O):[SH]:C:2:1
"beta2_adrenergic_aid759384.filtered.sdf",
//fmcs: 1.01 25 25 d3_aid329485.filtered.sdf C:C:C:C:C:CC(=O)NCCCCN1CCN(C:C:C:C:C:C)CC1
"d3_aid329485.filtered.sdf",
//fmcs: 0.13 20 21 d3_aid367038.filtered.sdf C:C:C:C:N:C:CCN1CCN(C2:C:C:C:C:C:2)CC1
"d3_aid367038.filtered.sdf",
//fmcs: 0.78 27 29 d3_aid563533.filtered.sdf O=C(C:C:C1:C:C:C:C:C:1)NCCCCN1CCN(C2:C:C:C:C:C:2)CC1
"d3_aid563533.filtered.sdf",
//fmcs: 0.09 14 14 d3_aid563770.filtered.sdf CCCN(CC)C(=O)C1:C:C:C:C:C:1
"d3_aid563770.filtered.sdf",
//fmcs: 0.14 22 24 d3_aid578980.filtered.sdf C(:C:N:C1:C:C:N:C:N:1)CN1CCN(C2:C:C:C:C:C:2)CC1
"d3_aid578980.filtered.sdf",
//fmcs: 0.20 15 17 d3_aid58783.filtered.sdf CCN1CC2COC3:C:C:C:C:C:3C2C1
"d3_aid58783.filtered.sdf",
//fmcs: 0.08 14 14 d3_aid62278.filtered.sdf C:C(CNCC):N:CC1:C:C:C:C:C:1
"d3_aid62278.filtered.sdf",
//fmcs: 0.05 7 7 d3_aid62281.filtered.sdf CC1:C:C:C:C:C:1
"d3_aid62281.filtered.sdf",
//fmcs: 33.13 26 27 d3_aid62457.filtered.sdf CC(=O)NCCCCN1CCC2:C:C:C(OS(=O)(=O)C(F)(F)F):C:C:2C1
"d3_aid62457.filtered.sdf",
//fmcs: 0.08 14 15 d3_aid62774.filtered.sdf CCN1CCCC(C2:C:C:C:C:C:2)C1
"d3_aid62774.filtered.sdf",
//fmcs: 0.33 14 14 d3_aid642590.filtered.sdf C:C:C:C:C:C:CCN1CCCCC1
"d3_aid642590.filtered.sdf",
};
double totalT=0.;
for(size_t i=0; i<sizeof(sdf)/sizeof(sdf[0]); i++)
totalT += testFileSDF((sdf_dir+sdf[i]).c_str());
printf("\nTOTAL Time elapsed %.2lf seconds\n================================================\n", totalT);
}
//====================================================================================================
//====================================================================================================
int main(int argc, const char* argv[]) {
p.Verbose = true;
// use maximum CPU resoures to increase time measuring accuracy and stability in multi process environment
#ifdef WIN32
// SetPriorityClass (GetCurrentProcess(), REALTIME_PRIORITY_CLASS );
SetThreadPriority(GetCurrentThread (), THREAD_PRIORITY_HIGHEST );
#else
setpriority(PRIO_PROCESS, getpid(), -20);
#endif
T0 = nanoClock();
t0 = nanoClock();
//testFileSDF_RandomSet("cmp_list_ChEMBL_12209_actives.dat.smi"); //FAST Test
//a lot of benchmark tests
testChEMBL_TxtALL_chembl_II_sets();
testFileSDF_RandomSet("chembl13-10000-random-pairs.sdf");
testFileSDF_RandomSet("chembl13_pairs.smi");
testFileSDF_RandomSet("chembl13_knearest_2.smi");
testFileSDF_RandomSet("chembl13_knearest_10.smi");
testFileSDF_RandomSet("chembl13_knearest_100.smi");
p.Threshold = 0.8;
testFileSDF_RandomSet("chembl13_threshold_80.smi");
p.Threshold = 0.9;
testFileSDF_RandomSet("chembl13_threshold_90.smi");
//// testFileSDF_RandomSet("");
return 0;
//------------------------
/*
// p.BondTyper = MCSBondCompareOrderExact;
testChEMBL_Txt("chembl_II_sets/Target_no_10980_51302.txt"); // 271 sec SLOW !!!
// return 0;
// testChEMBL_TxtALL_chembl_II_sets();
// testTarget_no_10188_30149();
// return 0;
// SLOW tests
test330();
testChEMBL_Txt("chembl_II_sets/Target_no_10980_52937.txt");
testChEMBL_Txt("chembl_II_sets/Target_no_11489_37339.txt");
testChEMBL_Txt("chembl_II_sets/Target_no_10260_54285.txt");
testChEMBL_Txt("chembl_II_sets/Target_no_10980_51302.txt"); // 271 sec SLOW !!!
*/
#ifdef xxWIN32 // brief test set for testing and issue investigation
#ifdef _DEBUG // check memory leaks
_CrtMemState _ms;
_CrtMemCheckpoint(&_ms);
#endif
//while(1) // check memory leaks in TaskManager or 'top -p ...'
{
}
#ifdef _DEBUG // check memory leaks
_CrtMemDumpAllObjectsSince(&_ms);
#endif
//testChEMBL_TxtALL_chembl_II_sets();
//testChEMBL_Txt("chembl_II_sets/Target_no_10980_51302.txt"); // 271 sec SLOW !!!
return 0;
{
RWMol* m = SmilesToMol("[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#7]-[#6]2:[#6]:[#6]:[#6]3:[#6](:[#6]:2):[#7]:[#7]:[#6]:3-[#6]4:[#6]:[#6]:[#6]:[#6]:[#6]:4");
#ifdef _DEBUG // check memory leaks
_CrtMemState _ms;
_CrtMemCheckpoint(&_ms);
#endif
std::cout << MolToSmarts(*m, true) <<"\n";
// while(1) // check memory leaks
testTarget_no_10188_30149();
testTarget_no_10188_49064();
#ifdef _DEBUG // check memory leaks
_CrtMemDumpAllObjectsSince(&_ms);
#endif
delete m;
return 0;
// while(true) // MT test
// test330();
testChEMBLdatALL();
testGregSDFFileSetFiltered();
/*
testChEMBLdat("cmp_list_ChEMBL_100126_actives.dat");
testChEMBLdat("cmp_list_ChEMBL_100126_actives.dat", 0.8);
testChEMBLdat("cmp_list_ChEMBL_12209_actives.dat");
*/
return 0;
// testFileSDF("Greg'sComparision/data/filtered/d3_aid58783.filtered.sdf");
// testGregSDFFileSetFiltered();
//return 0;
return 0;
// testGregSDFFileSetFiltered();
//return 0;
std::vector<unsigned> tc;
tc.push_back(90);
tc.push_back(326);
tc.push_back(330);
//992 PYTHON 20 21 N1(-C-C=C(-c2:c(:c:c:c):c:n:c:2)-C-C-1)-C-C-C-C-C-C
//992 . 1 27 28 1.10 CNcc(CCCCCN1CCC(=CC1)c1cncc1ccc)cccc
//now 25 26
/*
tc.push_back(33);
tc.push_back(59);
tc.push_back(124);
tc.push_back(345);
tc.push_back(605);
tc.push_back(619);
*/
testFileMCSB(argv[1], 300, tc);
return 0;
}
#endif
if(3 == argc && '-' == argv[1][0])
switch(argv[1][1]) { // ./test -s|m|b <filename with test files list>
case 's': { // smiles files list
char test[256];
FILE* f = fopen(argv[2], "rt");
while(fgets(test, sizeof(test), f))
testFileSMILES(test);
fclose(f);
}
break;
case 'm': { // SDF mol files list
char test[256];
FILE* f = fopen(argv[2], "rt");
while(fgets(test, sizeof(test), f))
testFileSDF(test);
fclose(f);
}
break;
case 'b': {
std::vector<unsigned> tc; // empty -> all
testFileMCSB(argv[2], 30, tc); // .mcsb
}
break;
default:
break;
}
else if(2 == argc) { // .sdf /.smi file
if(0==strcmp(argv[1]+strlen(argv[1])-4, ".smi"))
testFileSMILES(argv[1]);// .smi
else if(0==strcmp(argv[1]+strlen(argv[1])-4, ".sdf"))
testFileSDF(argv[1]); // .sdf
else if(0==strcmp(argv[1]+strlen(argv[1])-4, "mcsb"))
testFileMCSB(argv[1], 30); // .mcsb
else if(0==strcmp(argv[1]+strlen(argv[1])-4, ".dat"))
testChEMBLdat(argv[1]); // .sdf
else
printf("UNKNOWN File Extention.\n");
} else if(argc > 1+2)
testCmndLineSMILES(argc, argv);
else {
testGregSDFFileSetFiltered();
}
// BOOST_LOG(rdInfoLog) << "*******************************************************\n";
unsigned long long t1 = nanoClock();
double sec = double(t1-T0) / 1000000.;
printf("TOTAL Time elapsed %.2lf seconds\n", sec);
return 0;
}
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