pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-03 21:44:30 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
75f03412ef151a4dc14dfee986e29c3690a4c071
rdkit/Code/GraphMol/MMPA/MMPA_UnitTest.cpp
Eisuke Kawashima 75f03412ef Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00

732 lines
28 KiB
C++
Raw Blame History

// $Id: MMPA_UnitTest.cpp $
//
// Copyright (c) 2015, 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.
//
#ifndef _MSC_VER
#include <RDGeneral/test.h>
#include <unistd.h>
#include <fcntl.h>
#include <sys/time.h>
#endif
#ifdef _WIN32
#include <Windows.h>
#else
#include <sys/resource.h>
#endif
#include <cstdio>
#include <cstring>
#include <ctime>
#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 "../SmilesParse/SmartsWrite.h"
#include "../Substruct/SubstructMatch.h"
#include "MMPA.h"
using namespace RDKit;
static unsigned n_failed = 0;
static unsigned long long T0;
static unsigned long long t0;
#ifdef _MSC_VER
#define DELTA_EPOCH_IN_MICROSECS 11644473600000000ULL
struct timezone {
int tz_minuteswest; // minutes W of Greenwich
int tz_dsttime; // type of dst correction
};
static inline 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
static inline unsigned long long nanoClock(
void) { // actually returns microseconds
struct timeval t;
gettimeofday(&t, (struct timezone*)nullptr);
return t.tv_usec + t.tv_sec * 1000000ULL;
}
void printTime() {
unsigned long long t1 = nanoClock();
double sec = double(t1 - t0) / 1000000.;
printf("Time elapsed %.6lf 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 n = (sp ? sp - smiles + 1 : strlen(smiles));
if (id) {
*id = std::string(smiles + (n--));
}
return std::string(smiles, n);
}
void debugTest1(const char* init_mol) {
std::auto_ptr<RWMol> m(SmilesToMol(init_mol));
std::cout << "INIT MOL: " << init_mol << "\n";
std::cout << "CONV MOL: " << MolToSmiles(*m, true) << "\n";
}
/*
* Work-around functions for RDKit canonical
*/
std::string createCanonicalFromSmiles(const char* smiles) {
std::auto_ptr<RWMol> m(SmilesToMol(smiles));
std::string res = MolToSmiles(*m, true);
// replaceAllMap(res);
return res;
}
std::string createCanonicalFromSmiles(std::string smiles) {
return createCanonicalFromSmiles(smiles.c_str());
}
// UNIT Test Set:
//=========================================================================
void test1() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "MMPA test1()\n" << std::endl;
// DEBUG PRINT. MolToSmiles() fails with new RDKit version
//-----
const char* smi[] = {
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717",
};
/*
C[*:1].O=C(NCCO)c1c(n([O-])c2ccccc2[n+]1=O)[*:1]
Cc1c([n+](=O)c2ccccc2n1[O-])[*:1].O=C(NCCO)[*:1]
*
*/
const char* fs_sm[] = {
// 15 reference result's SMILES.
"", "C[*:1].O=C(NCCO)c1c(n([O-])c2ccccc2[n+]1=O)[*:1]",
// ORIGINAL: "","[*:1]C.[*:1]c1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]",
"[*:1]c1c([*:2])[n+](=O)c2ccccc2n1[O-]", "[*:1]C.[*:2]C(=O)NCCO",
"[*:2]CNC([*:1])=O", "[*:2]CO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
"[*:2]C[*:1]", "[*:2]CO.[*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
"[*:2]NC([*:1])=O", "[*:2]CCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
"[*:2]NC(=O)c1c([*:1])n([O-])c2ccccc2[n+]1=O", "[*:1]C.[*:2]CCO",
"[*:2]CNC(=O)c1c([*:1])n([O-])c2ccccc2[n+]1=O", "[*:1]C.[*:2]CO",
"[*:2]CCNC(=O)c1c([*:1])n([O-])c2ccccc2[n+]1=O", "[*:1]C.[*:2]O",
"", "Cc1c([n+](=O)c2ccccc2n1[O-])[*:1].O=C(NCCO)[*:1]",
// ORIGINAL: "","[*:1]C(=O)NCCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
"", "[*:1]CCO.[*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O", "",
"[*:1]CO.[*:1]CNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O", "",
"[*:1]O.[*:1]CCNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O", "[*:2]CC[*:1]",
"[*:2]O.[*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O", "[*:2]CCNC([*:1])=O",
"[*:2]O.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O", "[*:2]C[*:1]",
"[*:2]O.[*:1]CNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
};
char fs[15][256]; // 15 reference results with updated RDKit's SMARTS Writer
const char* fs1[] = {
// 15+1dup reordered reference results
// Fix for updated RDKit. new SMILES for the same molecule:
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,C[*:1].O=C(NCCO)c1c("
"n([O-])c2ccccc2[n+]1=O)[*:1]",
// was
// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]C.[*:1]c1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]c1c([*:2])[n+](="
"O)c2ccccc2n1[O-],[*:1]C.[*:2]C(=O)NCCO",
// exchanged atom mapping labels (1<->2):
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CNC([*:1])=O,[*:"
"2]CO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
// was
// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]CNC([*:2])=O,[*:1]CO.[*:2]c1c(C)n([O-])c2ccccc2[n+]1=O",
// exchanged atom mapping labels (1<->2):
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]C[*:1],[*:2]CO.["
"*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
// was
// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]C[*:2],[*:1]CO.[*:2]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
// exchanged atom mapping labels (1<->2):
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]NC([*:1])=O,[*:"
"2]CCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
// was
// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]NC([*:2])=O,[*:1]CCO.[*:2]c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]NC(=O)c1c([*:1])"
"n([O-])c2ccccc2[n+]1=O,[*:1]C.[*:2]CCO",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CNC(=O)c1c([*:1]"
")n([O-])c2ccccc2[n+]1=O,[*:1]C.[*:2]CO",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CCNC(=O)c1c([*:"
"1])n([O-])c2ccccc2[n+]1=O,[*:1]C.[*:2]O",
// Fix for updated RDKit. new SMILES for the same molecule:
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,Cc1c([n+](=O)"
"c2ccccc2n1[O-])[*:1].O=C(NCCO)[*:1]",
// was
// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]C(=O)NCCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]CCO.[*:1]NC(=O)"
"c1c(C)n([O-])c2ccccc2[n+]1=O",
//#10
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]CO.[*:1]CNC(=O)"
"c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]O.[*:1]CCNC(=O)"
"c1c(C)n([O-])c2ccccc2[n+]1=O",
// exchanged atom mapping labels (1<->2):
///-- dup of #5:
///"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]NC([*:1])=O,[*:2]CCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CC[*:1],[*:2]O.["
"*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CCNC([*:1])=O,[*"
":2]O.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]C[*:1],[*:2]O.[*"
":1]CNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
/* ORIGINALS of exchanged atom mapping labels (1<->2):
///dup of #5:
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]NC([*:2])=O,[*:1]CCO.[*:2]c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]CC[*:2],[*:1]O.[*:2]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]CCNC([*:2])=O,[*:1]O.[*:2]c1c(C)n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]C[*:2],[*:1]O.[*:2]CNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
*/
};
// FIX RDKit update. But MolToSmiles() fails with new RDKit version
for (size_t r = 0; r < sizeof(fs) / sizeof(fs[0]); r++) {
// strcpy(fs[r], fs1[r]);
// MolToSmiles() fails with new RDKit version in DEBUG Build
char core[256] = "", side[256];
if (fs_sm[2 * r][0]) {
RWMol* m = SmilesToMol(fs_sm[2 * r]);
strcpy(core, MolToSmiles(*m, true).c_str());
delete m;
}
if (fs_sm[2 * r + 1][0]) {
RWMol* m = SmilesToMol(fs_sm[2 * r + 1]);
strcpy(side, MolToSmiles(*m, true).c_str());
delete m;
}
sprintf(fs[r], "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,%s,%s",
core, side);
}
strcpy(fs[0], fs1[0]);
strcpy(fs[8], fs1[8]);
//-----------------------------------
for (unsigned int i = 0; i < sizeof(smi) / sizeof(smi[0]); i++) {
static const std::string es("NULL");
std::string id;
std::string smiles = getSmilesOnly(smi[i], &id);
ROMol* mol = SmilesToMol(smiles);
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> > res;
t0 = nanoClock();
RDKit::MMPA::fragmentMol(*mol, res, 3);
printTime();
delete mol;
std::cout << "TEST FINISHED "
"!!!\n*******************************************************"
"\n"
" --- VERIFY RESULTS ---\n";
// === VERIFY RESULTS ===
std::map<size_t, size_t> fs2res;
std::cout << "\nTEST " << i + 1 << " mol: " << smi[i] << "\n";
bool test_failed = false;
for (size_t j = 0; j < res.size(); j++) {
// std::cout <<" "<< j+1 << ": ";
// std::cout << (res[j].first.get() ?
// MolToSmiles(*res[j].first ) : es) <<", ";
// std::cout << (res[j].second.get() ?
// MolToSmiles(*res[j].second) : es) <<"\n";
std::stringstream ss;
ss << smiles << "," << id << ",";
ss << (res[j].first.get() ? MolToSmiles(*res[j].first, true) : "") << ",";
ss << (res[j].second.get() ? MolToSmiles(*res[j].second, true) : "");
size_t matchedRefRes = -1;
bool failed = true;
for (size_t r = 0; r < sizeof(fs) / sizeof(fs[0]); r++) {
if (0 == strcmp(std::string(ss.str()).c_str(), fs[r])) { // PASSED
failed = false;
matchedRefRes = r;
fs2res[r] = j;
break;
}
}
if (j < 9) {
std::cout << " ";
}
if (failed) {
test_failed = true;
std::cout << j + 1 << ": NOREF. Reference data NOT LISTED in test case."
<< ss.str() << "\n"; // << "FS: " << fs[j] <<"\n";
} else {
std::cout << j + 1 << ": PASSED. matchedRefRes = " << matchedRefRes + 1
<< "\n"; // ok: << "ss: " << ss.str() <<"\n";
}
std::cout.flush();
}
std::cout << "\n --- UNMATCHED Reference RESULTS: --- \n";
for (size_t r = 0; r < sizeof(fs) / sizeof(fs[0]); r++) {
if (fs2res.end() == fs2res.find(r)) {
test_failed = true;
std::cout << (r < 9 ? " " : "") << r + 1 << ": " << fs[r] << "\n";
}
}
std::cout << " -----------------------------------\n"
<< "DO TEST_ASSERT():\n";
if (test_failed) {
n_failed++;
}
TEST_ASSERT(!test_failed);
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test2() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "MMPA test2()\n" << std::endl;
const char* smi[] = {
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717",
};
const char* fs[] = {
// 15 reordered reference results
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=[n+]1c([*:2])c([*:"
"1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,Cc1c(C(=O)NCC[*:1])["
"n+](=O)c2ccccc2n1[O-].O[*:1]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,OCC[*:1].Cc1c(C(=O)"
"N[*:1])[n+](=O)c2ccccc2n1[O-]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,C[*:1].O=C(NCCO)c1c("
"[*:1])n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C("
"=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])c1c([*:1])"
"n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],"
"Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C(C[*:2])[*:1],Cc1c("
"C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,Cc1c(C(=O)NC[*:1])["
"n+](=O)c2ccccc2n1[O-].OC[*:1]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,O=C(NCCO)[*:1].Cc1c("
"[*:1])[n+](=O)c2ccccc2n1[O-]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C("
"=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])c1c([*:"
"1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])c1c([*:1]"
")n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],"
"Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],"
"Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]"};
for (unsigned int i = 0; i < sizeof(smi) / sizeof(smi[0]); i++) {
static const std::string es("NULL");
std::string id;
std::string smiles = getSmilesOnly(smi[i], &id);
std::auto_ptr<ROMol> mol(SmilesToMol(smiles));
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> > res;
t0 = nanoClock();
/*
* General test fragment
*/
RDKit::MMPA::fragmentMol(*mol, res);
printTime();
std::map<size_t, size_t> fs2res;
std::map<std::string, size_t> ref_map;
std::stringstream ref_str;
std::string s_token;
/*
* Create reference map
*/
for (size_t r = 0; r < sizeof(fs) / sizeof(fs[0]); r++) {
std::stringstream ss_token(fs[r]);
int token_num = 0;
ref_str.str("");
while (getline(ss_token, s_token, ',')) {
if (token_num == 2) {
ref_str << createCanonicalFromSmiles(s_token.c_str()) << ",";
}
if (token_num == 3) {
ref_str << createCanonicalFromSmiles(s_token.c_str());
}
token_num++;
}
ref_map[ref_str.str()] = r;
}
std::cout << "\nTEST " << i + 1 << " mol: " << smi[i] << "\n";
bool has_failed = false;
for (size_t res_idx = 0; res_idx < res.size(); res_idx++) {
std::cout << " " << res_idx + 1 << ": ";
/*
* Somehow canonical smiles does not return the same result after just
* saving.
* Workaround is: save -> load -> save
*/
std::string first_res =
(res[res_idx].first.get() ? createCanonicalFromSmiles(MolToSmiles(
*res[res_idx].first, true))
: "");
std::string second_res =
(res[res_idx].second.get() ? createCanonicalFromSmiles(MolToSmiles(
*res[res_idx].second, true))
: "");
std::cout << (res[res_idx].first.get() ? first_res : es) << ", ";
std::cout << (res[res_idx].second.get() ? second_res : es) << "\n";
std::stringstream res_str;
res_str << first_res << "," << second_res;
if (res_idx < 9) {
std::cout << " ";
}
if (ref_map.find(res_str.str()) != ref_map.end()) {
size_t matchedRefRes = ref_map[res_str.str()];
fs2res[matchedRefRes] = res_idx;
std::cout << res_idx + 1
<< ": PASSED. matchedRefRes = " << matchedRefRes + 1
<< "\n"; // ok: << "ss: " << ss.str() <<"\n";
} else {
std::cout << res_idx + 1
<< ": NOREF. Reference data NOT LISTED in test case."
<< res_str.str() << "\n"; //<< "FS: " << fs[j] <<"\n";
has_failed = true;
}
std::cout.flush();
}
if (has_failed && fs2res.size() < sizeof(fs) / sizeof(fs[0])) {
n_failed++;
std::cout << "\n --- UNMATCHED Reference RESULTS: --- \n";
for (size_t r = 0; r < sizeof(fs) / sizeof(fs[0]); r++) {
if (fs2res.end() == fs2res.find(r)) {
std::cout << (r < 9 ? " " : "") << r + 1 << ": " << fs[r] << "\n";
}
}
} else {
std::cout << "\n --- ALL PASSED --- \n";
}
}
std::cout << " -----------------------------------\n";
BOOST_LOG(rdInfoLog) << "\tDone" << std::endl;
}
//====================================================================================================
void doTest(const char* smi, const char* fs[], unsigned fs_size) {
static const std::string es("NULL");
std::string id;
std::string smiles = getSmilesOnly(smi, &id);
std::auto_ptr<ROMol> mol(SmilesToMol(smiles));
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> > res;
std::cout << "\nTEST mol: " << id << " " << smi << "\n";
t0 = nanoClock();
RDKit::MMPA::fragmentMol(*mol, res);
printTime();
// Create reference map
std::map<size_t, size_t> fs2res;
std::map<std::string, size_t> ref_map;
std::stringstream ref_str;
std::string s_token;
for (size_t r = 0; r < fs_size; r++) {
std::stringstream ss_token(fs[r]);
int token_num = 0;
ref_str.str("");
while (getline(ss_token, s_token, ',')) {
if (token_num == 2) {
ref_str << createCanonicalFromSmiles(s_token.c_str()) << ",";
}
if (token_num == 3) {
ref_str << createCanonicalFromSmiles(s_token.c_str());
}
token_num++;
}
ref_map[ref_str.str()] = r;
}
bool has_failed = false;
for (size_t res_idx = 0; res_idx < res.size(); res_idx++) {
if (res_idx < 9) {
std::cout << " ";
}
std::cout << res_idx + 1 << ": res= ";
/*
* Somehow canonical smiles does not return the same result after just
* saving.
* Workaround is: save -> load -> save
*/
std::string first_res =
(res[res_idx].first.get()
? createCanonicalFromSmiles(MolToSmiles(*res[res_idx].first, true))
: "");
std::string second_res =
(res[res_idx].second.get() ? createCanonicalFromSmiles(MolToSmiles(
*res[res_idx].second, true))
: "");
std::cout << (res[res_idx].first.get() ? first_res : es) << ",";
std::cout << (res[res_idx].second.get() ? second_res : es) << "\n";
std::stringstream res_str;
res_str << first_res << "," << second_res;
if (res_idx < 9) {
std::cout << " ";
}
if (ref_map.find(res_str.str()) != ref_map.end()) {
size_t matchedRefRes = ref_map[res_str.str()];
fs2res[matchedRefRes] = res_idx;
std::cout << res_idx + 1
<< ": PASSED. matchedRefRes = " << matchedRefRes + 1
<< "\n"; // ok: << "ss: " << ss.str() <<"\n";
} else {
std::cout << res_idx + 1
<< ": NOREF. Reference data NOT LISTED in test case."
<< "\n"; // res_str.str() << "\n"; //<< "FS: " << fs[j] <<"\n";
has_failed = true;
}
std::cout.flush();
}
if (has_failed && fs2res.size() < fs_size) {
n_failed++;
std::cout << "\n --- UNMATCHED Reference RESULTS: --- \n";
for (size_t r = 0; r < fs_size; r++) {
if (fs2res.end() == fs2res.find(r)) {
std::cout << (r < 9 ? " " : "") << r + 1 << ": " << fs[r] << "\n";
}
}
} else {
std::cout << "\n --- ALL PASSED --- \n";
}
std::cout << " -----------------------------------\n";
}
void test3() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "MMPA test3()\n" << std::endl;
{ // test2:
const char* smi = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717";
const char* fs[] = {
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=[n+]1c([*:2])c([*"
":1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,Cc1c(C(=O)NCC[*:1]"
")[n+](=O)c2ccccc2n1[O-].O[*:1]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,OCC[*:1].Cc1c(C(="
"O)N[*:1])[n+](=O)c2ccccc2n1[O-]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,C[*:1].O=C(NCCO)"
"c1c([*:1])n([O-])c2ccccc2[n+]1=O",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c("
"C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])c1c([*:"
"1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],"
"Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C(C[*:2])[*:1],"
"Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,Cc1c(C(=O)NC[*:1])"
"[n+](=O)c2ccccc2n1[O-].OC[*:1]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,O=C(NCCO)[*:1]."
"Cc1c([*:1])[n+](=O)c2ccccc2n1[O-]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c("
"C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])c1c([*"
":1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])c1c([*:"
"1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],"
"Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]",
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],"
"Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]"};
doTest(smi, fs, sizeof(fs) / sizeof(fs[0]));
}
{ // Case1 SIMPLE: (PASSED)
const char* smi = "CC(N1CC1)C(=O) Case1-SIMPLE";
const char* fs[] = {
// from Greg's message
"CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O="
"C[*:3]",
// from the results:
"CC(N1CC1)C(=O),Case1-SIMPLE,,C[*:1].O=CC(N1CC1)[*:1]",
"CC(N1CC1)C(=O),Case1-SIMPLE,O=CC([*:1])[*:2],C1CN1[*:2].C[*:1]",
"CC(N1CC1)C(=O),Case1-SIMPLE,C1CN1C([*:1])[*:2],C[*:1].O=C[*:2]",
"CC(N1CC1)C(=O),Case1-SIMPLE,,C1CN1[*:1].CC(C=O)[*:1]",
"CC(N1CC1)C(=O),Case1-SIMPLE,CC([*:1])[*:2],C1CN1[*:1].O=C[*:2]",
"CC(N1CC1)C(=O),Case1-SIMPLE,,CC(N1CC1)[*:1].O=C[*:1]",
};
doTest(smi, fs, sizeof(fs) / sizeof(fs[0]));
}
{ // Case1 (with additionally labeled central carbon [C:7]):
const char* smi = "Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1";
const char* fs[] = {
"Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC["
"NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1]"
// "Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[C:7]([*:1])([*:2])[*:3],C1CC[NH+]([*:1])C1.C[*:2].Cc1ccccc1NC(=O)[*:3]",
};
doTest(smi, fs, sizeof(fs) / sizeof(fs[0]));
}
{ // Case2:
const char* smi = "O=C(OCc1ccccc1)C(O)c1ccccc1 Case2";
const char* fs[] = {
"O=C(OCc1ccccc1)C(O)c1ccccc1,Case2,C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)"
"[*:1].O[*:2].c1ccc([*:3])cc1",
};
doTest(smi, fs, sizeof(fs) / sizeof(fs[0]));
}
BOOST_LOG(rdInfoLog) << "\tDone" << std::endl;
}
void testCase_1() {
// Case1 (with additionally labeled central carbon [C:7]):
const char* smi = "Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1";
const char* fs[] = {
"Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+"
"]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1]"};
doTest(smi, fs, sizeof(fs) / sizeof(fs[0]));
}
/*
void test4() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" <<
std::endl;
BOOST_LOG(rdInfoLog) << "MMPA test4()\n" << std::endl;
{
const char* smi = "Cc1ccccc1NC(=O)[C:9](C)[NH+]1CCCC1 CASE-4-1";
const char* fs[] = { ""
};
doTest(smi, fs, sizeof(fs)/sizeof(fs[0]));
}
{
const char* smi = "c1ccccc1NC(=O)[C:9](C)[NH+]1CCCC1 CASE-4-2";
const char* fs[] = { ""
};
doTest(smi, fs, sizeof(fs)/sizeof(fs[0]));
}
BOOST_LOG(rdInfoLog) << "\tDone" << std::endl;
}
*/
//====================================================================================================
//====================================================================================================
int main() {
BOOST_LOG(rdInfoLog)
<< "*******************************************************\n";
BOOST_LOG(rdInfoLog) << "MMPA Unit Test \n";
// 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();
testCase_1();
// /*
test2();
test3();
// test4();
// */
// debugTest1("C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O");
// debugTest1("C[*:1].O=C(NCCO)c1c(n([O-])c2ccccc2[n+]1=O)[*:1]");
/*
unsigned long long t1 = nanoClock();
double sec = double(t1-T0) / 1000000.;
printf("TOTAL Time elapsed %.4lf seconds\n", sec);
*/
BOOST_LOG(rdInfoLog)
<< "*******************************************************\n";
if (0 != n_failed) {
std::cout << n_failed << " TEST CASES FAILED \n";
TEST_ASSERT(0 != n_failed);
} else {
std::cout << " --- ALL TEST CASES PASSED --- \n";
}
BOOST_LOG(rdInfoLog)
<< "*******************************************************\n";
return 0;
}
Reference in New Issue View Git Blame Copy Permalink