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rdkit/Code/GraphMol/FMCS/testFMCS.cpp
Greg Landrum eb3b99b947 merge next changes from Alex
2014-04-05 06:41:23 +02:00

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// $Id: testFMCS.cpp $
//
// Copyright (c) 2007, 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 <RDGeneral/RDLog.h>
//#include <RDGeneral/utils.h>
#include "../RDKitBase.h"
#include "../FileParsers/FileParsers.h" //MOL single molecule !
#include "../FileParsers/MolSupplier.h" //SDF
#include "../SmilesParse/SmilesParse.h"
#include "../SmilesParse/SmilesWrite.h"
#include "FMCS.h"
#include "DebugTrace.h" //#ifdef VERBOSE_STATISTICS_ON
using namespace RDKit;
unsigned long long T0;
unsigned long long t0;
#ifdef WIN32
//#if defined(_MSC_VER) || defined(_MSC_EXTENSIONS)
// #define DELTA_EPOCH_IN_MICROSECS 11644473600000000Ui64
//#else
#define DELTA_EPOCH_IN_MICROSECS 11644473600000000ULL
//#endif
struct timezone
{
int tz_minuteswest; /* minutes W of Greenwich */
int tz_dsttime; /* type of dst correction */
};
int gettimeofday(struct timeval *tv, struct timezone *tz)
{
FILETIME ft;
unsigned __int64 tmpres = 0;
static int tzflag;
if (NULL != tv)
{
GetSystemTimeAsFileTime(&ft);
tmpres |= ft.dwHighDateTime;
tmpres <<= 32;
tmpres |= ft.dwLowDateTime;
/*converting file time to unix epoch*/
tmpres -= DELTA_EPOCH_IN_MICROSECS;
tmpres /= 10; /*convert into microseconds*/
tv->tv_sec = (long)(tmpres / 1000000UL);
tv->tv_usec = (long)(tmpres % 1000000UL);
}
if (NULL != tz)
{
if (!tzflag)
{
_tzset();
tzflag++;
}
tz->tz_minuteswest = _timezone / 60;
tz->tz_dsttime = _daylight;
}
return 0;
}
#endif
unsigned long long nanoClock (void) // actually returns microseconds
{
struct timeval t;
//struct timezone tz;
gettimeofday(&t, (struct timezone*)0);
return t.tv_usec + t.tv_sec * 1000000ULL;
}
void printTime()
{
stat = ExecStatistics();
unsigned long long t1 = nanoClock();
double sec = double(t1-t0) / 1000000.;
printf("\nTime elapsed %.2f 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);
}
//====================================================================================================
void testFileMCSB(const char* test, unsigned timeout=30, std::vector<unsigned> test_N=std::vector<unsigned>()) // optional list of some tests for investigation
{
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
{
RDKit::FMCS::ConsoleOutputEnabled = false;
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);
}
FILE* fs = fopen(outSmilesFile.c_str(), "wt");
FILE* ft = fopen((outFile+".stat.csv").c_str(), "wt");
setvbuf(f , 0, _IOFBF, 4*1024);
setvbuf(fs, 0, _IOFBF, 4*1024);
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
n = 0;
MCSParameters p;
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 != 0 && test_N != n+1)
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());
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;
}
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 VERBOSE_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"
#ifdef SMILES_CACHE
"# CacheFind %15u | %8u (SMILES generated)\n"
"# CacheTRUE %15u | %8u = %d%% (found in cache)\n"
#endif
"# 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.)
#ifdef SMILES_CACHE
, stat.FindInMatchedCache , stat.FindInMatchedCache/n
, stat.FoundInMatchedCache , stat.FoundInMatchedCache/n
, 0==stat.FindInMatchedCache ? 0 : int((double)stat.FoundInMatchedCache / (double)stat.FindInMatchedCache *100.)
#endif
, 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
fclose(f);
if(fs)
fclose(fs);
if(ft)
fclose(ft);
printTime();
}
//=========================================================================
//=========================================================================
void test1Basics()
{
// BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
// BOOST_LOG(rdInfoLog) << "FMCS test1Basics()" << std::endl;
std::vector<ROMOL_SPTR> mols;
const char* smi[] =
{
// "CC1CCC(N)CC1", "CC1CC(C)CC(C)C1" // OK test.sdf
// "OC1CCC1", "OC1CCC1" // OK ==
// "CC1CC(C=O=S)CC(C=N)C1", "CC1CC(C=O=S)CC(C=N)C1" // OK test.sdf ++
// "CC1CC(C=O=S)CC(N=C)C1", "CC1CC(C)CC(N)C1" // OK test.sdf ++
// "CC1CC(C=O=S3)C2C(N=C-O23)C1", "C7C1CC(C8)C7C(NO8)C1" // OK test.sdf ++
// "O1CCN(OSC)CO1-CC1CC(N=C-O23)C2C(C=O=S3)C1", "C7C1CC(C8)C7C(NO8)C1" // OK MCS:{0 9 8 5 7 4 2 3 11}: Smarts=CCCC(N)CC(C)CO
// "[O:8][C:1]1[C:2][C:3]([N:9])[C:4][C:5][C:6]1", "NC1(S-O-C)C[C:9](O-S-C)[C:7]CC1" // OK MCS:{0 1 7 2 6 3 4 5}: Smarts=NC1CCCC(O)C1 == N[CH:3]1[CH2:4][CH2:5][CH2:6][CH:1](O)[CH2:2]1
//MCS: N[CH:3]1[CH2:4][CH2:5][CH2:6][CH:1][(OH:8)][CH2:2]1
// PASSED ///FAILED (missing one bond to close ring):
// Python MCS = 26 bonds : COCc1cncc(c1):n:c1cccc(Oc2ccc(Cl)cc2)c1 WITH AROMATIZATION
// MCS 26: COCc1c-ncc(c1)nc1cccc(c1)Oc1ccc(Cl)cc1 24 atoms, 26 bonds Time elapsed 0.12 seconds
// MCS 25: cc(cc(cn)nc1cccc(Oc2ccc(Cl)cc2)c1)COC 24 atoms, 25 bonds. WITH AROMATIZATION !!!!
// MCS 16: COCC=CN=CC1=CC(=CC=C)C(=C)N1, 16 atoms, 16 bonds. WITHOUT AROMATIZATION !!!!
/// "COCC1=C(N=CC2=C1C1=C(OC3=CC=C(Cl)C=C3)C=CC=C1N2)C(=O)OC(C)C",
/// "COCC1=CN=C(C(=O)OC(C)C)C2=C1C1=CC=C(OC3=CC=C(Cl)C=C3)C=C1N2",
// The SAME, but pre AROMATIZATED (else PRECONDITION Exception with Implicit Hs / 16 bonds only)
// "COCc1c(ncc2[nH]c3cccc(Oc4ccc(Cl)cc4)c3c12)C(=O)OC(C)C",
// "COCc1cnc(C(=O)OC(C)C)c2[nH]c3cc(Oc4ccc(Cl)cc4)ccc3c12",
//
/* /TEST 4
"CN(C)c1ccc(CC(=O)NCCCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL153934",
"CN(C)c1ccc(CC(=O)NCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL152361",
"CN(C)c1ccc(CC(=O)NCCCCCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL157336",
"CN(C)c1ccc(CC(=O)NCCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL157429",
"CN(C)c1ccc(CC(=O)NCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL357551",
"CN(C)c1ccc(CC(=O)NCCCCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL421974",
"CN(C)c1ccc(CC(NCCCCCC(NO)=O)=O)cc1 CHEMBL484488",
"CC(C)Cc1ccc(C(C)C(=O)NC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL564780",
"c1cc([N+]([O-])=O)ccc1CC(=O)NC1CCCCCC1 CHEMBL1553142",
"CC1(C)NC(C)(C)CC(NC(=O)Cc2ccccc2)C1 CHEMBL1703640",
//# 3 . 1 14 14 0.08 sec MCS: CCCCNC(=O)Cc1ccccc1
*/
/*
//TEST 5 FAILED
//.5 . 1 20 22 0.23 N(-c1:c:c:c:c:c:1)-C-c1:n(-C-c2:c:c:c:c:c:2):c:n:c:1
//MCS: ccccc-ccc(c)NCc1cncn1Cc1ccccc1 23 atoms, 24 bonds Time elapsed 6.39 seconds
"c1ccc(Cn2c(CNc3cc(-c4ccccc4)ccc3)cnc2)cc1 CHEMBL485450", // QUERY
"Cc1ccc(Cn2c(CNc3cc(-c4ccccc4)ccc3)cnc2)cc1 CHEMBL498061",
"c1ccc(-c2ccc(Cn3c(CNc4cc(-c5ccccc5)ccc4)cnc3)cc2)cc1 CHEMBL485449",
"Clc1ccc(Cn2c(CNc3cc(-c4ccccc4)ccc3)cnc2)cc1 CHEMBL525178",
"Cc1cccc(-c2cc(NCc3cncn3Cc3ccccc3)ccc2)c1 CHEMBL482856",
"c1ccc(Cn2c(CNc3cc(-c4ccncc4)ccc3)cnc2)cc1 CHEMBL497405",
"Cc1c(-c2cc(NCc3cncn3Cc3ccccc3)ccc2)cccc1 CHEMBL520679",
"c1ccc(Cn2c(CNc3cc(-c4cnccc4)ccc3)cnc2)cc1 CHEMBL496834",
"O=[N+]([O-])c1ccc(Cn2c(CNc3cc(-c4ccccc4)ccc3)cnc2)cc1 CHEMBL497885",
"c1ccc(-c2ccc(Cn3c(CNc4ccc(-c5ccccc5)cc4)cnc3)cc2)cc1 CHEMBL497407",
*/
//"CCCCCCC1C23C4=c5c6c7c8c5c5c9c%10c%11c%12c(c%108)c8c7c7c%10c%13c%14c%15c%16c%17c%18c%19c%20c(c%21c%22c%23c(c9C(C25C[N+]1(C)C)C1c2c3c3c5c9c2-c(c%231)c(c%22%19)C%18C9C1(C5=C%13C(C43)c6%10)C%14%17C[N+](C)(C)C1CCCCCC)c%21%11)c%12c(c%16%20)c8c%157 CHEMBL439119"
/*
//WAS 8 sec test
//NOW:
//Inspected Seeds = 54250 Rejected by BestSize = 21360 Rejected by WrongComposition = 191( 134 generated)
//MatchCalls = 44607 MatchFound = 30334
//AtomCompareCalls = 103017020 BondCompareCalls = 25286076
//MCS : CCCC(NC(=O)CNC(=O)C(Cc(c)c)NC(=O)CNC(=O)CNC(=O)CNC(=O)C(C)NC=O)C(=O)NC(CCC)C(=O)NC(C)C 49 atoms, 48 bonds
//Time elapsed 20.19 seconds
//Time elapsed 35.65 seconds + FIX
//Time elapsed 123 seconds + FIX + can SMILES
"CC(C)CC(NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(C(CO)NC(C(NC(c1ccncc1)=O)NC(=O)C(Cc1ccc(Cl)cc1)NC=O)=O)=O)C(NC(CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O CHEMBL439258 modified QUERY",// CHEMBL439258
"CC(C)CC(NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(=O)C(Cc1ccccc1)NC(C(CO)NC(C(NC(c1ccncc1)=O)NC(=O)C(Cc1ccc(Cl)cc1)NC(C(NC(C)=O)Cc1cc2ccccc2cc1)=O)=O)=O)C(NC(CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O CHEMBL439258",// CHEMBL439258
"CC(C)CC(NC(=O)CNC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(C(CO)NC(C(NC(c1ccncc1)=O)NC(=O)C(Cc1ccc(Cl)cc1)NC(C(NC(C)=O)Cc1cc2ccccc2cc1)=O)=O)=O)C(NC(CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O CHEMBL439258 modified",// CHEMBL439258
"CCCCC(NC(C(CCC(O)=O)NC(C(CC(C)C)NC(C(C(C)C)NC(=O)C(CCC(O)=O)NC(C(CCCN=C(N)N)NC(C(NC(=O)C(NC(C(NC(C1CCCNC(=O)CCC(N)C(=O)NC(CC(C)C)C(=O)NC(C(C)O)C(=O)N1)=O)Cc1c[nH]cn1)=O)CC(C)C)CC(C)C)=O)=O)=O)=O)=O)C(NC(C)C(NC(CCCN=C(N)N)C(NC(C)C(NC(CCC(O)=O)C(NC(CCC(N)=O)C(NC(CC(C)C)C(NC(C)C(NC(CCC(N)=O)C(NC(CCC(N)=O)C(NC(C)C(NC(Cc1c[nH]cn1)C(NC(CO)C(NC(CC(N)=O)C(NC(CCCN=C(N)N)C(NC(CCCCN)C(NC(CC(C)C)C(NC(CCCC)C(NC(C(NC(C(C)CC)C(NC(C(N)=O)C(C)CC)=O)=O)CCC(O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O CHEMBL438567",
"CCC(C)C(NC(CNC(=O)C(C)NC(=O)C(C)NC(C(Cc1nc[nH]c1)NC(C(CC(N)=O)NC(CNC(C(CO)NC(=O)C(C)NC(=O)C(CCC(N)=O)NC(C(NC(=O)C(NC(C(CCCN=C(N)N)NC(C(CCC(N)=O)NC(C(NC(C(CCCN=C(N)N)NC(CNC(C(CCC(N)=O)NC(C(CC(C)C)NC(C(C)N)=O)=O)=O)=O)=O)CC(C)C)=O)=O)=O)CC(C)C)CC(C)C)=O)=O)=O)=O)=O)=O)C(NC(CC(C)C)C(NC(C(O)C)C(NC(CCSC)C(O)=O)=O)=O)=O CHEMBL429374",
"CC(C)CC1NC(=O)C(CCCCN)NC(=O)C(Cc2ccc(O)cc2)NC(=O)CNC(=O)C2NC(=O)C(NC(C(C(C)C)NC(CNC(C3NC(=O)CC3)=O)=O)=O)CSSCC(C(O)=O)NC(=O)C3N(CCC3O)C(=O)C(Cc3ccccc3)NC(=O)C(CSSC2)NC1=O CHEMBL1076370",
*/
// SLOW
//test 45 # Using CHEMBL551656 CHEMBL563796 CHEMBL561978 CHEMBL559467 CHEMBL550503 CHEMBL562866 CHEMBL552190 CHEMBL181547 CHEMBL359567 CHEMBL373316
// 45 . 1 30 32 27.01 n12-C-c:c(-c:2:c:c2-C(-O)(-C-C)-C(-O-C-c:2:c:1=O)=O):n:c(:c:c:c-O):c(:c):c-C-C-C
//MCS: CCCCc(cc)c1Cn2-cc3COC(=O)[C](O)(CC):c3cc2-c1nccccO 30 atoms, 32 bonds
//Time elapsed 40.41 seconds
//MCS : CCCCc(cc)cCn1c(-cncccc)cc2c(COC(=O)[C]:2(O)CC)c-1=O 30 atoms, 31 bonds
//Time elapsed 9.70 seconds
"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(OC)cc2c1C1CCCCC1 CHEMBL551656",
"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(OC)cc2c1C1CCCC1 CHEMBL563796", //Q
"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(OC)cc1c2C1CCCCCC1 CHEMBL561978",
"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(OC)cc1c2C1CCC1 CHEMBL559467",
"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(O)cc1c2C1CCCC1 CHEMBL550503",
"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(O)cc2c1C1CCCCCC1 CHEMBL562866",
"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(O)cc1c2C1CCCCC1 CHEMBL552190",
"CCC1(O)c2c(c(=O)n3c(c2)-c2nc4cc5c(cc4c(C4CCCC4)c2C3)OCO5)COC1=O CHEMBL181547",
"CCC1(O)c2c(c(=O)n3c(c2)-c2nc4c(c(C5CCCCC5)c2C3)cc2c(c4)OCO2)COC1=O CHEMBL359567",
"CCCc1c(OC)ccc2nc3c(c(CC)c21)Cn1c-3cc2c(c1=O)COC(=O)C2(O)CC CHEMBL373316",
/*
// # 190 TEST must < 0.27 sec
"COc1cc2nc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)ccc3)oc2cc1 CHEMBL1479679",
"COc1cc2nc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)c(C)cc3)oc2cc1 CHEMBL1333382",
"Cc1cc2oc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)ccc3)nc2cc1 CHEMBL1437584",
"COc1c(NC(=O)CSc2ccc(Cl)cc2)cc(-c2nc3ccccc3o2)cc1 CHEMBL1601350",
"Cc1cc2nc(-c3cccc(NC(=O)CSc4ccc(Cl)cc4)c3)oc2cc1C CHEMBL1398008",
"Cc1cc2oc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)c(C)cc3)nc2cc1 CHEMBL1612903",
"COc1cc2nc(-c3cc(NC(=O)Cc4ccc(Cl)cc4)c(C)cc3)oc2cc1 CHEMBL1316483",
"Cc1c(NC(=O)CSc2ccc(Cl)cc2)cccc1-c1nc2cc(Cl)ccc2o1 CHEMBL1568754",
"COc1ccc2oc(-c3ccc(C)c(NC(=O)COc4cc(C)cc(C)c4)c3)nc2c1 CHEMBL1436972",
"Cc1ccc(SCC(=O)Nc2cc(-c3nc4cc(C)ccc4o3)c(O)cc2)cc1 CHEMBL1611932",
//# 19 21 1.37 sec MCS: CC(=O)Nc1cccc(c1)-c1nc2ccccc2o1
// 19 21 2.36 sec MCS: CC(=O)Nc1cccc(c1)-c1nc2ccccc2o1 19 atoms, 21 bonds
*/
/*
//FIXED with //C1 - decrease excludeBonds /// FAILED !!!!!!!!
//# Using CHEMBL1515359 CHEMBL1590658 CHEMBL1447567 CHEMBL1384017 CHEMBL1456416 CHEMBL1308819 CHEMBL1703007 CHEMBL1707819 CHEMBL1500793 CHEMBL1334715
//32 . 1 31 33 0.82 S(-N1-C-C-O-C-C-1)(-c1:c:c:c(-N(-C-C)-C-C):c(-N-C(-C=C-c2:c:c:c:c:c:2)=O):c:1)(=O)=O
"O=C(Nc1cc(S(N2CCOCC2)(=O)=O)ccc1N1CCOCC1)C=Cc1ccc(Cl)cc1 CHEMBL1515359",
"c1ccc(C=CC(Nc2cc(S(N3CCOCC3)(=O)=O)ccc2N2CCOCC2)=O)cc1 CHEMBL1590658",
"Cc1ccc(C=CC(=O)Nc2cc(S(N3CCOCC3)(=O)=O)ccc2N2CCOCC2)cc1 CHEMBL1447567",
"c1ccc(C=CC(Nc2cc(S(N3CCOCC3)(=O)=O)ccc2N2CCCC2)=O)cc1 CHEMBL1384017",
"O=C(C=Cc1ccc(F)cc1)Nc1cc(S(N2CCOCC2)(=O)=O)ccc1N1CCCC1 CHEMBL1456416",
"c1cc(F)cc(C=CC(=O)Nc2c(N3CCCC3)ccc(S(N3CCOCC3)(=O)=O)c2)c1 CHEMBL1308819",
"CCN1CCN(c2ccc(S(N3CCOCC3)(=O)=O)cc2NC(=O)C=Cc2ccc(C)cc2)CC1 CHEMBL1703007",
"c1cc(C=CC(=O)Nc2cc(S(N3CCOCC3)(=O)=O)ccc2N2CCOCC2)c([N+]([O-])=O)cc1 CHEMBL1707819",
"N#CC(=Cc1ccccc1)C(=O)Nc1cc(S(N2CCOCC2)(=O)=O)ccc1N1CCCC1 CHEMBL1500793",
"C(=Cc1ccc2c(c1)OCO2)C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)=O CHEMBL1334715",
// 31 31 0.05 sec MCS: CCOCCNS(=O)(=O)c1ccc(c(c1)NC(=O)C=Cc(c)cccc)N(CC)CC
// 31 32 0.15 sec MCS: CCOCCNS(=O)(=O)c1ccc(c(c1)NC(=O)C=Cc1ccccc1)N(CC)CC 31 atoms, 32 bonds
// 31 33 0.35 sec MCS: CCN(CC)c1ccc(cc1NC(=O)C=Cc1ccccc1)S(=O)(=O)N1CCOCC1
*/
};
for(int i=0; i<sizeof(smi)/sizeof(smi[0]); i++)
{
// mols.push_back(ROMOL_SPTR(SmartsToMol(smi[i]))); //it skips aromaticity
#if 0
// optional temporary AROMATIZATION - for this test ONLY
//(to avoid PRECONDITION Exception with Implicit Hs)
std::auto_ptr<RWMol> mol(SmartsToMol(smi[i]));
unsigned dummy;
RDKit::MolOps::sanitizeMol(*mol, dummy, RDKit::MolOps::SANITIZE_ADJUSTHS|RDKit::MolOps::SANITIZE_SETAROMATICITY);
std::string s = MolToSmiles(*mol);
RWMol* m = SmartsToMol(s);
RDKit::MolOps::sanitizeMol(*m, dummy, RDKit::MolOps::SANITIZE_ADJUSTHS|RDKit::MolOps::SANITIZE_SETAROMATICITY);
mols.push_back(ROMOL_SPTR( m ));
std::cout << "MOL : " << s <<"\n";
//------
#else
std::string id;
mols.push_back(ROMOL_SPTR(SmartsToMol( getSmilesOnly(smi[i], &id) )));
std::cout << id << "\n";
#endif
}
t0 = nanoClock();
MCSParameters p;
//p.Threshold = 0.7;
//p.Timeout = 9;
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
void testRing1()
{
std::cout << "\ntestRing1()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] =
{
"COCc1c(ncc2[nH]c3cccc(Oc4ccc(Cl)cc4)c3c12)C(=O)OC(C)C",
// "COCc1cnc(C(=O)OC(C)C)c2[nH]c3cc(Oc4ccc(Cl)cc4)ccc3c12", // original molecule
"COCc1cnc(C(=O)OC(C)C)c2[nH]ccc(Oc4ccc(Cl)cc4)cccc12", // ring 3 removed
};
for(int i=0; i<sizeof(smi)/sizeof(smi[0]); i++)
mols.push_back(ROMOL_SPTR(SmilesToMol( getSmilesOnly(smi[i]) ))); // with RING INFO
// mols.push_back(ROMOL_SPTR(SmartsToMol( getSmilesOnly(smi[i]) ))); // NO RING INFO generated!!!
MCSParameters p;
p.BondCompareParameters.RingMatchesRingOnly = true;
p.BondCompareParameters.CompleteRingsOnly = true;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
void test504()
{
std::cout << "\ntest504()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] =
{
//"O=C(-N-c1:c:c:c:c:c:1)-N-C-C-C-N(-C)-C-C-C-C-C-N-C(-C1-C-C-1-c1:c:c:c(-Cl):c(-Cl):c:1)=O", // python MCS == SMARTS !!!
//"Clc1ccc(NC(=O)NC2CCN(CCCCCNC(=O)C3CC3[c:3]3[cH:2]cc(Cl)c(Cl)[cH:1]3)C2)cc1",
//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",
// "C(CCNC(C1CC1c1cc(Cl)c(Cl)cc1)=O)CCN1CCC(NC(Nc2ccc(Cl)cc2)=O)C1 CHEMBL545864", // - QUERY
// "Clc1ccc(NC(=O)NC2CCN(CCCCCNC(=O)C3CC3c3ccc(Cl)c(Cl)c3)C2)cc1", // - the same QUERY with RIGHT MCS !!!
// "Clc1ccc(NC(=O)NC2CCN(CCCCCNC(=O)C3CC3[c:1]3[cH:2]cc(Cl)c(Cl)[cH:3]3)C2)cc1", // - the same QUERY with Atom MAP and RIGHT MCS !!!
"N#Cc1cccc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)c1 CHEMBL529994",
};
RWMol* qm = SmartsToMol( getSmilesOnly(smi[0]) );
unsigned nq = qm->getNumAtoms();
for(size_t ai = 0; ai < nq; ai++)
{
Atom* atom = qm->getAtomWithIdx(ai);
atom->setProp("molAtomMapNumber", (int)ai);
}
std::cout<<"Query +MAP "<< MolToSmiles(*qm) <<"\n";
// for(int i=qm->getNumBonds()-1; i>=17; i--)
// qm->removeBond(qm->getBondWithIdx(i)->getBeginAtomIdx(), qm->getBondWithIdx(i)->getEndAtomIdx());
mols.push_back(ROMOL_SPTR(qm)); // with RING INFO
for(int i=1; i<sizeof(smi)/sizeof(smi[0]); i++)
mols.push_back(ROMOL_SPTR(SmartsToMol( getSmilesOnly(smi[i]) ))); // with RING INFO
MCSParameters p;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
void test18()
{
std::cout << "\ntest18()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] =
{
//TEST 18
"Cc1nc(CN(C(C)c2ncccc2)CCCCN)ccc1 CHEMBL1682991", //-- QUERY
"Cc1ccc(CN(C(C)c2ccccn2)CCCCN)nc1 CHEMBL1682990",
"Cc1cccnc1CN(C(C)c1ccccn1)CCCCN CHEMBL1682998",
"CC(N(CCCCN)Cc1c(N)cccn1)c1ccccn1 CHEMBL1682987",
"Cc1cc(C)c(CN(C(C)c2ccccn2)CCCCN)nc1 CHEMBL1682992",
"Cc1cc(C(C)N(CCCCN)Cc2c(C)cccn2)ncc1 CHEMBL1682993",
"Cc1nc(C(C)N(CCCCN)Cc2nc3c([nH]2)cccc3)ccc1 CHEMBL1682878",
"CC(c1ncccc1)N(CCCCN)Cc1nc2c([nH]1)cccc2 CHEMBL1682867",
"CC(N(CCCCN)Cc1c(C(C)(C)C)cccn1)c1ccccn1 CHEMBL1682989",
"CC(N(CCCCN)Cc1c(C(F)(F)F)cccn1)c1ccccn1 CHEMBL1682988",
//# 18 . 20 20 0.04 sec MCS: CC(c1ccccn1)N(CCCCN)Ccnccc
};
RWMol* qm = SmartsToMol( getSmilesOnly(smi[0]) );
unsigned nq = qm->getNumAtoms();
for(size_t ai = 0; ai < nq; ai++)
{
Atom* atom = qm->getAtomWithIdx(ai);
atom->setProp("molAtomMapNumber", (int)ai);
}
std::cout<<"Query +MAP "<< MolToSmiles(*qm) <<"\n";
mols.push_back(ROMOL_SPTR(qm)); // with RING INFO
for(int i=1; i<sizeof(smi)/sizeof(smi[0]); i++)
mols.push_back(ROMOL_SPTR(SmartsToMol( getSmilesOnly(smi[i]) ))); // with RING INFO
MCSParameters p;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
void testSimpleFast()
{
std::cout << "\ntestSimpleFast()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] =
{
// SHORT TEST for 26 bonds.
// Python MCS = 26 bonds : COCc1cncc(c1):n:c1cccc(Oc2ccc(Cl)cc2)c1
// MCS 26: COCc1c-ncc(c1)nc1cccc(c1)Oc1ccc(Cl)cc1 24 atoms, 26 bonds
/// "COCC1=C(N=CC2=C1C1=C(OC3=CC=C(Cl)C=C3)C=CC=C1N2)C(=O)OC(C)C",
/// "COCC1=CN=C(C(=O)OC(C)C)C2=C1C1=CC=C(OC3=CC=C(Cl)C=C3)C=C1N2",
// The SAME, but pre AROMATIZATED (else PRECONDITION Exception with Implicit Hs / 16 bonds only)
"COCc1c(ncc2[nH]c3cccc(Oc4ccc(Cl)cc4)c3c12)C(=O)OC(C)C",
"COCc1cnc(C(=O)OC(C)C)c2[nH]c3cc(Oc4ccc(Cl)cc4)ccc3c12",
};
for(int i=0; i<sizeof(smi)/sizeof(smi[0]); i++)
mols.push_back(ROMOL_SPTR(SmilesToMol( getSmilesOnly(smi[i]) )));
MCSParameters p;
p.BondCompareParameters.RingMatchesRingOnly = true;
p.BondCompareParameters.CompleteRingsOnly = true;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: "<<res.SmartsString<<" "<< res.NumAtoms<<" atoms, "<<res.NumBonds<<" bonds\n";
printTime();
}
void testSimple()
{
std::cout << "\ntestSimple()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] =
{
// LONG TIME TEST for performance analisis
//WAS 8 sec test (now about 30 sec)
"CC(C)CC(NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(C(CO)NC(C(NC(c1ccncc1)=O)NC(=O)C(Cc1ccc(Cl)cc1)NC=O)=O)=O)C(NC(CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O CHEMBL439258 modified QUERY",// CHEMBL439258
"CC(C)CC(NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(=O)C(Cc1ccccc1)NC(C(CO)NC(C(NC(c1ccncc1)=O)NC(=O)C(Cc1ccc(Cl)cc1)NC(C(NC(C)=O)Cc1cc2ccccc2cc1)=O)=O)=O)C(NC(CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O CHEMBL439258",// CHEMBL439258
"CC(C)CC(NC(=O)CNC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(C(CO)NC(C(NC(c1ccncc1)=O)NC(=O)C(Cc1ccc(Cl)cc1)NC(C(NC(C)=O)Cc1cc2ccccc2cc1)=O)=O)=O)C(NC(CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O CHEMBL439258 modified",// CHEMBL439258
"CCCCC(NC(C(CCC(O)=O)NC(C(CC(C)C)NC(C(C(C)C)NC(=O)C(CCC(O)=O)NC(C(CCCN=C(N)N)NC(C(NC(=O)C(NC(C(NC(C1CCCNC(=O)CCC(N)C(=O)NC(CC(C)C)C(=O)NC(C(C)O)C(=O)N1)=O)Cc1c[nH]cn1)=O)CC(C)C)CC(C)C)=O)=O)=O)=O)=O)C(NC(C)C(NC(CCCN=C(N)N)C(NC(C)C(NC(CCC(O)=O)C(NC(CCC(N)=O)C(NC(CC(C)C)C(NC(C)C(NC(CCC(N)=O)C(NC(CCC(N)=O)C(NC(C)C(NC(Cc1c[nH]cn1)C(NC(CO)C(NC(CC(N)=O)C(NC(CCCN=C(N)N)C(NC(CCCCN)C(NC(CC(C)C)C(NC(CCCC)C(NC(C(NC(C(C)CC)C(NC(C(N)=O)C(C)CC)=O)=O)CCC(O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O CHEMBL438567",
"CCC(C)C(NC(CNC(=O)C(C)NC(=O)C(C)NC(C(Cc1nc[nH]c1)NC(C(CC(N)=O)NC(CNC(C(CO)NC(=O)C(C)NC(=O)C(CCC(N)=O)NC(C(NC(=O)C(NC(C(CCCN=C(N)N)NC(C(CCC(N)=O)NC(C(NC(C(CCCN=C(N)N)NC(CNC(C(CCC(N)=O)NC(C(CC(C)C)NC(C(C)N)=O)=O)=O)=O)=O)CC(C)C)=O)=O)=O)CC(C)C)CC(C)C)=O)=O)=O)=O)=O)=O)C(NC(CC(C)C)C(NC(C(O)C)C(NC(CCSC)C(O)=O)=O)=O)=O CHEMBL429374",
"CC(C)CC1NC(=O)C(CCCCN)NC(=O)C(Cc2ccc(O)cc2)NC(=O)CNC(=O)C2NC(=O)C(NC(C(C(C)C)NC(CNC(C3NC(=O)CC3)=O)=O)=O)CSSCC(C(O)=O)NC(=O)C3N(CCC3O)C(=O)C(Cc3ccccc3)NC(=O)C(CSSC2)NC1=O CHEMBL1076370",
};
for(int i=0; i<sizeof(smi)/sizeof(smi[0]); i++)
mols.push_back(ROMOL_SPTR(SmilesToMol( getSmilesOnly(smi[i]) )));
MCSParameters p;
p.BondCompareParameters.RingMatchesRingOnly = true;
p.BondCompareParameters.CompleteRingsOnly = true;
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(SmartsToMol(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));
}
MCSParameters p;
// p.MaximizeBonds = true;
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 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(SmartsToMol(getSmilesOnly(smiles))));
}
fclose(f);
printTime();
std::cout<<"FIND MCS in "<<mols.size()<<" molecules.\n\n";
t0 = nanoClock();
MCSParameters p;
//p.Threshold = 0.7;
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(int i=0; i<sizeof(sdf)/sizeof(sdf[0]); i++)
totalT += testFileSDF((sdf_dir+sdf[i]).c_str());
printf("\nTOTAL Time elapsed %.2f seconds\n================================================\n", totalT);
}
//====================================================================================================
//====================================================================================================
int main(int argc, const char* argv[])
{
RDKit::FMCS::ConsoleOutputEnabled = 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();
#ifdef WIN32 // brief test set for testing and issue investigation
{
testGregSDFFileSetFiltered();
test18();
return 0;
testRing1();
// return 0;
testSimpleFast();
testSimple();
// return 0;
/*
testFileSDF("Greg'sComparision/data/filtered/d3_aid329485.filtered.sdf"); // 25 25 1s
testFileSDF("Greg'sComparision/data/filtered/d3_aid642590.filtered.sdf"); // 14 14 0.3s
return 0;
testFileSDF("Greg'sComparision/data/filtered/beta2_adrenergic_aid38311.filtered.sdf"); // fast. with time > python time to 18 times
testFileSDF("Greg'sComparision/data/filtered/d3_aid62457.filtered.sdf"); // slow 1 min
testFileSDF("Greg'sComparision/data/filtered/beta2_adrenergic_aid759384.filtered.sdf"); // fast
//return 0;
testGregSDFFileSetFiltered();
//return 0;
*/
std::vector<unsigned> tc;
// tc.push_back(10);
// tc.push_back(992);
//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
printf("UNKNOWN File Extention.\n");
}
else if(argc > 1+2)
testCmndLineSMILES(argc, argv);
else
{
testSimpleFast();
testSimple();
// test1Basics();
// testGregSDFFileSetFiltered();
}
// BOOST_LOG(rdInfoLog) << "*******************************************************\n";
unsigned long long t1 = nanoClock();
double sec = double(t1-T0) / 1000000.;
printf("TOTAL Time elapsed %.2f seconds\n", sec);
return 0;
}
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