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rdkit/Code/GraphMol/FMCS/Test/testFMCS.cpp
Ricardo Rodriguez e3f2e4651e Refactor iostreams includes (#8846) 
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
2025-10-31 13:42:16 +01:00

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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 <RDGeneral/test.h>
#else
#include <unistd.h>
#include <fcntl.h>
#include <sys/time.h>
#include <sys/resource.h>
#endif
#include <cstdio>
#include <cstring>
#include <ctime>
#include <string>
#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
#ifdef _WIN32
#include <windows.h>
#endif
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 = nullptr) { // remove label, because RDKit parse FAILED
const char *sp = strchr(smiles, ' ');
unsigned int 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 = nullptr) { // 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 = nullptr) { // remove label, because RDKit parse FAILED
const char *sp = strchr(smiles, '\t');
if (sp) {
unsigned int 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 int timeout = 30,
std::vector<unsigned int> test_N =
std::vector<unsigned int>()) { // 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 int 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 int nn, len;
n++;
testCase.emplace_back();
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.emplace_back(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, nullptr, _IOFBF, 4 * 1024);
FILE *fs = nullptr; // fopen(outSmilesFile.c_str(), "wt");
if (fs) {
setvbuf(fs, nullptr, _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 (const auto &mid : *tc) {
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 int 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.emplace_back(qm); // with RING INFO
for (size_t i = 1; i < sizeof(smi) / sizeof(smi[0]); i++) {
mols.emplace_back(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 int 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.emplace_back(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",
"Target_no_10260_54285.txt", "Target_no_10280_30224.txt",
"Target_no_10280_31222.txt", "Target_no_10280_37349.txt",
"Target_no_10280_37369.txt", "Target_no_10280_37465.txt",
"Target_no_10280_37541.txt", "Target_no_10280_38371.txt",
"Target_no_10280_44314.txt", "Target_no_10280_44578.txt",
"Target_no_10280_45765.txt", "Target_no_10280_46281.txt",
"Target_no_10280_47928.txt", "Target_no_10280_50624.txt",
"Target_no_10280_51341.txt", "Target_no_10280_51662.txt",
"Target_no_10280_51767.txt", "Target_no_10280_53081.txt",
"Target_no_10280_53396.txt", "Target_no_10280_53407.txt",
"Target_no_10280_58823.txt", "Target_no_10280_59190.txt",
"Target_no_10280_60672.txt", "Target_no_10280_61176.txt",
"Target_no_10434_20905.txt", "Target_no_10434_30074.txt",
"Target_no_10434_30175.txt", "Target_no_10434_30423.txt",
"Target_no_10434_31555.txt", "Target_no_10434_34878.txt",
"Target_no_10434_35926.txt", "Target_no_10434_42168.txt",
"Target_no_107_20859.txt", "Target_no_107_30060.txt",
"Target_no_107_30061.txt", "Target_no_107_30606.txt",
"Target_no_107_30866.txt", "Target_no_107_31249.txt",
"Target_no_107_34921.txt", "Target_no_107_35188.txt",
"Target_no_107_36636.txt", "Target_no_107_37466.txt",
"Target_no_107_39202.txt", "Target_no_107_43952.txt",
"Target_no_107_49345.txt", "Target_no_107_49591.txt",
"Target_no_107_49854.txt", "Target_no_107_51416.txt",
"Target_no_107_53537.txt", "Target_no_107_58879.txt",
"Target_no_107_60679.txt", "Target_no_107_61269.txt",
"Target_no_108_20600.txt", "Target_no_108_20859.txt",
"Target_no_108_30060.txt", "Target_no_108_30606.txt",
"Target_no_108_30866.txt", "Target_no_108_31558.txt",
"Target_no_108_35188.txt", "Target_no_108_37466.txt",
"Target_no_108_43875.txt", "Target_no_108_48911.txt",
"Target_no_108_49591.txt", "Target_no_108_49854.txt",
"Target_no_108_57887.txt", "Target_no_108_60679.txt",
"Target_no_108_6857.txt", "Target_no_10980_15478.txt",
"Target_no_10980_20853.txt", "Target_no_10980_30840.txt",
"Target_no_10980_30862.txt", "Target_no_10980_30918.txt",
"Target_no_10980_30994.txt", "Target_no_10980_31014.txt",
"Target_no_10980_31508.txt", "Target_no_10980_31623.txt",
"Target_no_10980_35003.txt", "Target_no_10980_35004.txt",
"Target_no_10980_35281.txt", "Target_no_10980_35957.txt",
"Target_no_10980_36520.txt", "Target_no_10980_36641.txt",
"Target_no_10980_38586.txt", "Target_no_10980_44431.txt",
"Target_no_10980_45093.txt", "Target_no_10980_51302.txt",
"Target_no_10980_5247.txt", "Target_no_10980_52937.txt",
"Target_no_10980_57198.txt", "Target_no_10980_5739.txt",
"Target_no_10980_6535.txt", "Target_no_11140_20205.txt",
"Target_no_11140_20986.txt", "Target_no_11140_30091.txt",
"Target_no_11140_34698.txt", "Target_no_11140_34705.txt",
"Target_no_11140_37038.txt", "Target_no_11140_37272.txt",
"Target_no_11140_37447.txt", "Target_no_11140_38909.txt",
"Target_no_11140_38953.txt", "Target_no_11140_39472.txt",
"Target_no_11140_45825.txt", "Target_no_11140_47179.txt",
"Target_no_11140_49028.txt", "Target_no_11140_49860.txt",
"Target_no_11140_51984.txt", "Target_no_11140_53395.txt",
"Target_no_11140_53826.txt", "Target_no_11140_54121.txt",
"Target_no_11140_54530.txt", "Target_no_11140_55738.txt",
"Target_no_11140_57725.txt", "Target_no_11140_58590.txt",
"Target_no_11365_20432.txt", "Target_no_11365_30331.txt",
"Target_no_11365_37956.txt", "Target_no_11365_48114.txt",
"Target_no_11365_58566.txt", "Target_no_11489_34731.txt",
"Target_no_11489_34818.txt", "Target_no_11489_37318.txt",
"Target_no_11489_37339.txt", "Target_no_11489_37564.txt",
"Target_no_11489_39504.txt", "Target_no_11489_39561.txt",
"Target_no_11489_46082.txt", "Target_no_11489_46089.txt",
"Target_no_11489_47349.txt", "Target_no_11489_47757.txt",
"Target_no_11489_51593.txt", "Target_no_11489_54754.txt",
"Target_no_11489_58262.txt", "Target_no_11489_58958.txt",
"Target_no_114_16827.txt", "Target_no_114_20503.txt",
"Target_no_114_20724.txt", "Target_no_114_30254.txt",
"Target_no_114_30321.txt", "Target_no_114_30572.txt",
"Target_no_114_31116.txt", "Target_no_114_31281.txt",
"Target_no_114_31443.txt", "Target_no_114_34747.txt",
"Target_no_114_34920.txt", "Target_no_114_35040.txt",
"Target_no_114_36623.txt", "Target_no_114_37136.txt",
"Target_no_114_37208.txt", "Target_no_114_38298.txt",
"Target_no_114_38554.txt", "Target_no_114_39088.txt",
"Target_no_114_39543.txt", "Target_no_114_44049.txt",
"Target_no_114_44562.txt", "Target_no_114_45180.txt",
"Target_no_114_45867.txt", "Target_no_114_46087.txt",
"Target_no_114_46829.txt", "Target_no_114_47546.txt",
"Target_no_114_48395.txt", "Target_no_114_50461.txt",
"Target_no_114_50765.txt", "Target_no_114_51669.txt",
"Target_no_114_52381.txt", "Target_no_114_57231.txt",
"Target_no_114_58246.txt", "Target_no_11534_30999.txt",
"Target_no_11534_31021.txt", "Target_no_11534_31650.txt",
"Target_no_11534_35011.txt", "Target_no_11534_37014.txt",
"Target_no_11534_44598.txt", "Target_no_11534_48446.txt",
"Target_no_11534_50614.txt", "Target_no_11534_50615.txt",
"Target_no_11534_50618.txt", "Target_no_11534_51950.txt",
"Target_no_11575_31616.txt", "Target_no_11575_38381.txt",
"Target_no_11575_45757.txt", "Target_no_11575_46816.txt",
"Target_no_11575_50701.txt", "Target_no_11575_54049.txt",
"Target_no_11575_57890.txt", "Target_no_11575_61045.txt",
"Target_no_11631_30194.txt", "Target_no_11631_31421.txt",
"Target_no_11631_35538.txt", "Target_no_11631_55727.txt",
"Target_no_11631_60676.txt", "Target_no_11631_61130.txt",
"Target_no_11631_6444.txt", "Target_no_121_15623.txt",
"Target_no_121_20096.txt", "Target_no_121_21591.txt",
"Target_no_121_30184.txt", "Target_no_121_30380.txt",
"Target_no_121_30745.txt", "Target_no_121_30861.txt",
"Target_no_121_31619.txt", "Target_no_121_34869.txt",
"Target_no_121_35284.txt", "Target_no_121_36158.txt",
"Target_no_121_36915.txt", "Target_no_121_37434.txt",
"Target_no_121_37541.txt", "Target_no_121_37677.txt",
"Target_no_121_38837.txt", "Target_no_121_39530.txt",
"Target_no_121_43793.txt", "Target_no_121_44158.txt",
"Target_no_121_44164.txt", "Target_no_121_44579.txt",
"Target_no_121_44593.txt", "Target_no_121_44692.txt",
"Target_no_121_44914.txt", "Target_no_121_45878.txt",
"Target_no_121_48050.txt", "Target_no_121_48706.txt",
"Target_no_121_48944.txt", "Target_no_121_48961.txt",
"Target_no_121_49880.txt", "Target_no_121_50055.txt",
"Target_no_121_50512.txt", "Target_no_121_51064.txt",
"Target_no_121_53537.txt", "Target_no_121_55749.txt",
"Target_no_121_58879.txt", "Target_no_121_6876.txt",
"Target_no_12209_44664.txt", "Target_no_12209_46451.txt",
"Target_no_12209_50640.txt", "Target_no_12209_56102.txt",
"Target_no_12209_58015.txt", "Target_no_12209_59089.txt",
"Target_no_12209_59092.txt", "Target_no_12209_61340.txt",
"Target_no_12252_31458.txt", "Target_no_12252_38481.txt",
"Target_no_12252_42104.txt", "Target_no_12252_49475.txt",
"Target_no_12252_49933.txt", "Target_no_12252_50558.txt",
"Target_no_126_37249.txt", "Target_no_126_39117.txt",
"Target_no_126_48227.txt", "Target_no_126_48229.txt",
"Target_no_126_53969.txt", "Target_no_126_54262.txt",
"Target_no_126_55353.txt", "Target_no_126_61212.txt",
"Target_no_12952_20250.txt", "Target_no_12952_20506.txt",
"Target_no_12952_20626.txt", "Target_no_12952_20689.txt",
"Target_no_12952_21358.txt", "Target_no_12952_30158.txt",
"Target_no_12952_30349.txt", "Target_no_12952_34843.txt",
"Target_no_12952_35220.txt", "Target_no_12952_36318.txt",
"Target_no_12952_36800.txt", "Target_no_12952_39349.txt",
"Target_no_12952_45385.txt", "Target_no_12952_45676.txt",
"Target_no_12952_46700.txt", "Target_no_12952_46719.txt",
"Target_no_12952_48517.txt", "Target_no_12952_52690.txt",
"Target_no_12952_53483.txt", "Target_no_12952_55435.txt",
"Target_no_12952_56102.txt", "Target_no_12952_58015.txt",
"Target_no_12952_58375.txt", "Target_no_12952_58700.txt",
"Target_no_13001_16724.txt", "Target_no_13001_2710.txt",
"Target_no_13001_30128.txt", "Target_no_13001_31250.txt",
"Target_no_13001_35519.txt", "Target_no_13001_36905.txt",
"Target_no_13001_46788.txt", "Target_no_13001_4737.txt",
"Target_no_13001_55736.txt", "Target_no_13001_57473.txt",
"Target_no_130_16146.txt", "Target_no_130_30313.txt",
"Target_no_130_30539.txt", "Target_no_130_30653.txt",
"Target_no_130_30988.txt", "Target_no_130_31179.txt",
"Target_no_130_31339.txt", "Target_no_130_3525.txt",
"Target_no_130_36886.txt", "Target_no_130_37020.txt",
"Target_no_130_38128.txt", "Target_no_130_43952.txt",
"Target_no_130_45210.txt", "Target_no_130_45899.txt",
"Target_no_130_47889.txt", "Target_no_130_51800.txt",
"Target_no_130_53158.txt", "Target_no_130_5330.txt",
"Target_no_130_55648.txt", "Target_no_130_56096.txt",
"Target_no_130_57287.txt", "Target_no_130_57399.txt",
"Target_no_130_57606.txt", "Target_no_130_58470.txt",
"Target_no_130_60894.txt", "Target_no_15_15010.txt",
"Target_no_15_20304.txt", "Target_no_15_20542.txt",
"Target_no_15_20788.txt", "Target_no_15_21358.txt",
"Target_no_15_30349.txt", "Target_no_15_31103.txt",
"Target_no_15_31764.txt", "Target_no_15_31822.txt",
"Target_no_15_35220.txt", "Target_no_15_37964.txt",
"Target_no_15_42164.txt", "Target_no_15_44072.txt",
"Target_no_15_45522.txt", "Target_no_15_46719.txt",
"Target_no_15_46744.txt", "Target_no_15_48416.txt",
"Target_no_15_49740.txt", "Target_no_15_50034.txt",
"Target_no_15_50640.txt", "Target_no_15_53483.txt",
"Target_no_15_53506.txt", "Target_no_15_53814.txt",
"Target_no_15_55435.txt", "Target_no_15_56074.txt",
"Target_no_15_56107.txt", "Target_no_15_57090.txt",
"Target_no_15_57705.txt", "Target_no_15_57785.txt",
"Target_no_15_57861.txt", "Target_no_15_58583.txt",
"Target_no_15_59089.txt", "Target_no_15_59092.txt",
"Target_no_165_20600.txt", "Target_no_165_30764.txt",
"Target_no_165_34876.txt", "Target_no_165_37427.txt",
"Target_no_165_38266.txt", "Target_no_165_45283.txt",
"Target_no_165_46990.txt", "Target_no_165_47123.txt",
"Target_no_165_47900.txt", "Target_no_165_48050.txt",
"Target_no_165_48062.txt", "Target_no_165_48076.txt",
"Target_no_165_50718.txt", "Target_no_165_50972.txt",
"Target_no_165_51372.txt", "Target_no_165_51830.txt",
"Target_no_165_53049.txt", "Target_no_165_53505.txt",
"Target_no_165_54021.txt", "Target_no_165_54565.txt",
"Target_no_165_54570.txt", "Target_no_165_57666.txt",
"Target_no_165_57890.txt", "Target_no_165_58072.txt",
"Target_no_165_58634.txt", "Target_no_165_58643.txt",
"Target_no_165_59080.txt", "Target_no_165_59202.txt",
"Target_no_165_59346.txt", "Target_no_165_60379.txt",
"Target_no_165_60385.txt", "Target_no_165_61098.txt",
"Target_no_17045_31154.txt", "Target_no_17045_35648.txt",
"Target_no_17045_48914.txt", "Target_no_17045_51975.txt",
"Target_no_17045_52435.txt", "Target_no_17045_55790.txt",
"Target_no_17045_58958.txt", "Target_no_17045_61146.txt",
"Target_no_19905_20191.txt", "Target_no_19905_20562.txt",
"Target_no_19905_20606.txt", "Target_no_19905_20607.txt",
"Target_no_19905_30003.txt", "Target_no_19905_30402.txt",
"Target_no_19905_30726.txt", "Target_no_19905_30924.txt",
"Target_no_19905_31457.txt", "Target_no_19905_31460.txt",
"Target_no_19905_31600.txt", "Target_no_19905_31620.txt",
"Target_no_19905_31640.txt", "Target_no_19905_31782.txt",
"Target_no_19905_31797.txt", "Target_no_19905_31829.txt",
"Target_no_19905_31856.txt", "Target_no_19905_34690.txt",
"Target_no_19905_34691.txt", "Target_no_19905_34694.txt",
"Target_no_19905_35712.txt", "Target_no_19905_37497.txt",
"Target_no_19905_37539.txt", "Target_no_19905_48070.txt",
"Target_no_19905_48219.txt", "Target_no_19905_48824.txt",
"Target_no_19905_48902.txt", "Target_no_19905_52867.txt",
"Target_no_19905_53534.txt", "Target_no_19905_54570.txt",
"Target_no_19905_58727.txt", "Target_no_19905_60159.txt",
"Target_no_19905_60661.txt", "Target_no_259_30037.txt",
"Target_no_259_34734.txt", "Target_no_259_35365.txt",
"Target_no_259_35787.txt", "Target_no_259_36793.txt",
"Target_no_259_37845.txt", "Target_no_259_38328.txt",
"Target_no_259_39374.txt", "Target_no_259_43936.txt",
"Target_no_259_44059.txt", "Target_no_259_44405.txt",
"Target_no_259_44424.txt", "Target_no_259_45166.txt",
"Target_no_259_46158.txt", "Target_no_259_46425.txt",
"Target_no_259_47187.txt", "Target_no_259_48435.txt",
"Target_no_259_48817.txt", "Target_no_259_48849.txt",
"Target_no_259_48957.txt", "Target_no_259_48965.txt",
"Target_no_259_49519.txt", "Target_no_259_49921.txt",
"Target_no_259_50392.txt", "Target_no_259_50972.txt",
"Target_no_259_52405.txt", "Target_no_259_52442.txt",
"Target_no_259_53169.txt", "Target_no_259_54640.txt",
"Target_no_259_57207.txt", "Target_no_259_58537.txt",
"Target_no_259_58920.txt", "Target_no_259_60358.txt",
"Target_no_25_16077.txt", "Target_no_25_34943.txt",
"Target_no_25_36391.txt", "Target_no_25_36574.txt",
"Target_no_25_52906.txt", "Target_no_25_54642.txt",
"Target_no_43_16385.txt", "Target_no_43_20333.txt",
"Target_no_43_20774.txt", "Target_no_43_35825.txt",
"Target_no_43_37637.txt", "Target_no_43_47741.txt",
"Target_no_43_48567.txt", "Target_no_43_48841.txt",
"Target_no_43_49589.txt", "Target_no_43_50564.txt",
"Target_no_43_51201.txt", "Target_no_43_53150.txt",
"Target_no_43_55747.txt", "Target_no_43_58276.txt",
"Target_no_51_20813.txt", "Target_no_51_2331.txt",
"Target_no_51_2391.txt", "Target_no_51_30374.txt",
"Target_no_51_30512.txt", "Target_no_51_30796.txt",
"Target_no_51_31058.txt", "Target_no_51_31450.txt",
"Target_no_51_36609.txt", "Target_no_51_36636.txt",
"Target_no_51_38266.txt", "Target_no_51_43800.txt",
"Target_no_51_47621.txt", "Target_no_51_49433.txt",
"Target_no_51_49550.txt", "Target_no_51_49865.txt",
"Target_no_51_51005.txt", "Target_no_51_52373.txt",
"Target_no_51_53878.txt", "Target_no_51_54554.txt",
"Target_no_51_57508.txt", "Target_no_51_57618.txt",
"Target_no_51_59484.txt", "Target_no_51_6563.txt",
"Target_no_61_16845.txt", "Target_no_61_37106.txt",
"Target_no_61_37272.txt", "Target_no_61_47947.txt",
"Target_no_61_50754.txt", "Target_no_61_55800.txt",
"Target_no_61_57380.txt", "Target_no_65_35328.txt",
"Target_no_65_36137.txt", "Target_no_65_38826.txt",
"Target_no_65_44596.txt", "Target_no_65_51275.txt",
"Target_no_65_55671.txt", "Target_no_72_20155.txt",
"Target_no_72_30616.txt", "Target_no_72_30653.txt",
"Target_no_72_30988.txt", "Target_no_72_31339.txt",
"Target_no_72_31527.txt", "Target_no_72_31631.txt",
"Target_no_72_36047.txt", "Target_no_72_36568.txt",
"Target_no_72_36636.txt", "Target_no_72_37020.txt",
"Target_no_72_38128.txt", "Target_no_72_43952.txt",
"Target_no_72_45210.txt", "Target_no_72_47889.txt",
"Target_no_72_51064.txt", "Target_no_72_51800.txt",
"Target_no_72_5330.txt", "Target_no_72_57508.txt",
"Target_no_72_58470.txt", "Target_no_72_60894.txt",
"Target_no_87_20730.txt", "Target_no_87_20753.txt",
"Target_no_87_30097.txt", "Target_no_87_30663.txt",
"Target_no_87_35365.txt", "Target_no_87_35375.txt",
"Target_no_87_35918.txt", "Target_no_87_36010.txt",
"Target_no_87_36780.txt", "Target_no_87_36793.txt",
"Target_no_87_37845.txt", "Target_no_87_39110.txt",
"Target_no_87_39546.txt", "Target_no_87_43936.txt",
"Target_no_87_44405.txt", "Target_no_87_44424.txt",
"Target_no_87_44683.txt", "Target_no_87_45166.txt",
"Target_no_87_46648.txt", "Target_no_87_46986.txt",
"Target_no_87_47070.txt", "Target_no_87_47187.txt",
"Target_no_87_48435.txt", "Target_no_87_48817.txt",
"Target_no_87_49138.txt", "Target_no_87_49460.txt",
"Target_no_87_49519.txt", "Target_no_87_49532.txt",
"Target_no_87_49829.txt", "Target_no_87_50608.txt",
"Target_no_87_54640.txt", "Target_no_87_61082.txt",
"Target_no_90_15727.txt", "Target_no_90_20155.txt",
"Target_no_90_30407.txt", "Target_no_90_3525.txt",
"Target_no_93_12377.txt", "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 (auto &i : test) {
std::string smiName = std::string("chembl_II_sets/") + 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
}
fclose(fcmd);
}
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 (auto &i : test) {
testChEMBL_Txt((std::string("chembl_II_sets/") + 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 int 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.emplace_back(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 (auto &i : test) {
testChEMBLdat(
(std::string("benchmarking_platform-master/compounds/ChEMBL/") + 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 (auto &i : smi) {
mols.emplace_back(SmilesToMol(getSmilesOnly(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;
// clang-format off
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",
};
// clang-format on
for (auto &i : smi) {
mols.emplace_back(SmilesToMol(getSmilesOnly(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.emplace_back(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.emplace_back(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 int 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.emplace_back(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 = nullptr;
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";
fclose(fcsv);
fclose(fcmd);
return;
}
if (!suppl) {
std::cout << "ERROR: unsupported input file format"
<< "\n";
fclose(fcsv);
fclose(fcmd);
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 int 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";
delete suppl;
fclose(fcsv);
fclose(fcmd);
return;
}
ROMol *m = nullptr;
for (int i = 0; i < 2 && !suppl->atEnd(); i++) { // load sequential pair
m = suppl->next();
if (m) {
mols.emplace_back(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 int N_RandomTests = all_mols.size() * 7;
srand(1); // make stable pseudorandom sequence
for (; n <= N_RandomTests; 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 int iN = 3 + rand() % 32;
for (unsigned int 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 int maxMol = 0;
for (auto &all_mol : all_mols) {
if (maxMol < all_mol->getNumBonds()) {
maxMol = all_mol->getNumBonds();
}
}
const unsigned int N_BigRandomTests =
all_mols.size() > 2000 ? all_mols.size() / 2 : all_mols.size() * 2;
const unsigned int N_BigRandomTestsAttempts = all_mols.size() * 130;
const unsigned int 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 int 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 int 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 int 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 int 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.emplace_back(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 (auto &i : sdf) {
totalT += testFileSDF((sdf_dir + 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 resources 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 int> 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 int> 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 Extension.\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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