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d5d4d194ec
* atropisomer handling added * fixed non-used variables, linking directives * BOOST LIB start/stop fixes, linking fix * Fixes for RDKIT CI errors * minimalLib fix * changed vector<enum> for java builds * check for extra chars in CIP labeling * removed wrong deprecated message * fix ostrstream output error? * restored _ChiralAtomRank to lowercase first letter * changes for merged master * Fixed catch label for new Catch package * update expected psql results * get swig wrappers building * restore MolFileStereochem to FileParsers * fix java wrapper for reapplyMolBlockWedging * some suggestions * move a couple functions out of Bond * Merge branch 'master' into pr/atropisomers2 * merged master * Renamed setStereoanyFromSquiggleBond * atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol * fix for CI build * attempt to fix java build in CI * attempt to fix java build in CI #2 * New routine to remove non-explicit 3D-geneated chirality * changed to use pair for atrop atoms and related bonds * Changes as per PR reviews * PR review respnses * PR review reponse - more * Fix merge from master * fixing java ci after merge * Updated the help doc for atripisomers * update the atropisomer docs * improve the images * add the source CXSMILES --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
745 lines
28 KiB
C++
745 lines
28 KiB
C++
// $Id: MMPA_UnitTest.cpp $
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//
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// Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#ifndef _MSC_VER
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#include <RDGeneral/test.h>
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#include <unistd.h>
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#include <fcntl.h>
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#include <sys/time.h>
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#endif
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#ifdef _WIN32
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#include <windows.h>
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#else
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#include <sys/resource.h>
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#endif
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#include <cstdio>
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#include <cstring>
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#include <ctime>
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#include <string>
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#include <iostream>
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#include <RDGeneral/RDLog.h>
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#include <RDGeneral/utils.h>
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#include <GraphMol/Chirality.h>
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#include <GraphMol/test_fixtures.h>
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#include "../RDKitBase.h"
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#include "../FileParsers/FileParsers.h" //MOL single molecule !
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#include "../FileParsers/MolSupplier.h" //SDF
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#include "../SmilesParse/SmilesParse.h"
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#include "../SmilesParse/SmilesWrite.h"
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#include "../SmilesParse/SmartsWrite.h"
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#include "../Substruct/SubstructMatch.h"
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#include "MMPA.h"
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using namespace RDKit;
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static unsigned n_failed = 0;
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static unsigned long long T0;
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static unsigned long long t0;
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#ifdef _MSC_VER
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#define DELTA_EPOCH_IN_MICROSECS 11644473600000000ULL
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struct timezone {
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int tz_minuteswest; // minutes W of Greenwich
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int tz_dsttime; // type of dst correction
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};
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static inline int gettimeofday(struct timeval* tv, struct timezone* tz) {
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FILETIME ft;
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unsigned __int64 tmpres = 0;
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static int tzflag;
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if (nullptr != tv) {
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GetSystemTimeAsFileTime(&ft);
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tmpres |= ft.dwHighDateTime;
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tmpres <<= 32;
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tmpres |= ft.dwLowDateTime;
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// converting file time to unix epoch
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tmpres -= DELTA_EPOCH_IN_MICROSECS;
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tmpres /= 10; // convert into microseconds
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tv->tv_sec = (long)(tmpres / 1000000UL);
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tv->tv_usec = (long)(tmpres % 1000000UL);
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}
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if (nullptr != tz) {
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if (!tzflag) {
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_tzset();
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tzflag++;
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}
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tz->tz_minuteswest = _timezone / 60;
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tz->tz_dsttime = _daylight;
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}
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return 0;
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}
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#endif
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static inline unsigned long long nanoClock(
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void) { // actually returns microseconds
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struct timeval t;
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gettimeofday(&t, (struct timezone*)nullptr);
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return t.tv_usec + t.tv_sec * 1000000ULL;
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}
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void printTime() {
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unsigned long long t1 = nanoClock();
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double sec = double(t1 - t0) / 1000000.;
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printf("Time elapsed %.6lf seconds\n", sec);
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t0 = nanoClock();
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}
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std::string getSmilesOnly(
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const char* smiles,
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std::string* id = nullptr) { // remove label, because RDKit parse FAILED
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const char* sp = strchr(smiles, ' ');
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unsigned n = (sp ? sp - smiles + 1 : strlen(smiles));
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if (id) {
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*id = std::string(smiles + (n--));
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}
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return std::string(smiles, n);
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}
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void debugTest1(const char* init_mol) {
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std::unique_ptr<RWMol> m(SmilesToMol(init_mol));
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std::cout << "INIT MOL: " << init_mol << "\n";
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std::cout << "CONV MOL: " << MolToSmiles(*m, true) << "\n";
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}
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/*
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* Work-around functions for RDKit canonical
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*/
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std::string createCanonicalFromSmiles(const char* smiles) {
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std::unique_ptr<RWMol> m(SmilesToMol(smiles));
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std::string res = MolToSmiles(*m, true);
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// replaceAllMap(res);
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return res;
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}
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std::string createCanonicalFromSmiles(std::string smiles) {
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return createCanonicalFromSmiles(smiles.c_str());
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}
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// UNIT Test Set:
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//=========================================================================
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void test1() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "MMPA test1()\n" << std::endl;
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// DEBUG PRINT. MolToSmiles() fails with new RDKit version
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//-----
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const char* smi[] = {
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717",
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};
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/*
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C[*:1].O=C(NCCO)c1c(n([O-])c2ccccc2[n+]1=O)[*:1]
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Cc1c([n+](=O)c2ccccc2n1[O-])[*:1].O=C(NCCO)[*:1]
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*
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*/
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const char* fs_sm[] = {
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// 15 reference result's SMILES.
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"",
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"C[*:1].O=C(NCCO)c1c(n([O-])c2ccccc2[n+]1=O)[*:1]",
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// ORIGINAL: "","[*:1]C.[*:1]c1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]",
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"[*:1]c1c([*:2])[n+](=O)c2ccccc2n1[O-]",
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"[*:1]C.[*:2]C(=O)NCCO",
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"[*:2]CNC([*:1])=O",
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"[*:2]CO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"[*:2]C[*:1]",
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"[*:2]CO.[*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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"[*:2]NC([*:1])=O",
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"[*:2]CCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"[*:2]NC(=O)c1c([*:1])n([O-])c2ccccc2[n+]1=O",
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"[*:1]C.[*:2]CCO",
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"[*:2]CNC(=O)c1c([*:1])n([O-])c2ccccc2[n+]1=O",
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"[*:1]C.[*:2]CO",
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"[*:2]CCNC(=O)c1c([*:1])n([O-])c2ccccc2[n+]1=O",
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"[*:1]C.[*:2]O",
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"",
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"Cc1c([n+](=O)c2ccccc2n1[O-])[*:1].O=C(NCCO)[*:1]",
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// ORIGINAL: "","[*:1]C(=O)NCCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"",
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"[*:1]CCO.[*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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"",
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"[*:1]CO.[*:1]CNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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"",
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"[*:1]O.[*:1]CCNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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"[*:2]CC[*:1]",
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"[*:2]O.[*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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"[*:2]CCNC([*:1])=O",
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"[*:2]O.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"[*:2]C[*:1]",
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"[*:2]O.[*:1]CNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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};
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char fs[15][256]; // 15 reference results with updated RDKit's SMARTS Writer
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const char* fs1[] = {
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// 15+1dup reordered reference results
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// Fix for updated RDKit. new SMILES for the same molecule:
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,C[*:1].O=C(NCCO)c1c("
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"n([O-])c2ccccc2[n+]1=O)[*:1]",
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// was
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// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]C.[*:1]c1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]c1c([*:2])[n+](="
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"O)c2ccccc2n1[O-],[*:1]C.[*:2]C(=O)NCCO",
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// exchanged atom mapping labels (1<->2):
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CNC([*:1])=O,[*:"
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"2]CO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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// was
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// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]CNC([*:2])=O,[*:1]CO.[*:2]c1c(C)n([O-])c2ccccc2[n+]1=O",
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// exchanged atom mapping labels (1<->2):
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]C[*:1],[*:2]CO.["
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"*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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// was
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// "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",
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// exchanged atom mapping labels (1<->2):
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]NC([*:1])=O,[*:"
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"2]CCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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// was
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// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]NC([*:2])=O,[*:1]CCO.[*:2]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]NC(=O)c1c([*:1])"
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"n([O-])c2ccccc2[n+]1=O,[*:1]C.[*:2]CCO",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CNC(=O)c1c([*:1]"
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")n([O-])c2ccccc2[n+]1=O,[*:1]C.[*:2]CO",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CCNC(=O)c1c([*:"
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"1])n([O-])c2ccccc2[n+]1=O,[*:1]C.[*:2]O",
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// Fix for updated RDKit. new SMILES for the same molecule:
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,Cc1c([n+](=O)"
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"c2ccccc2n1[O-])[*:1].O=C(NCCO)[*:1]",
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// was
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// "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]C(=O)NCCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]CCO.[*:1]NC(=O)"
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"c1c(C)n([O-])c2ccccc2[n+]1=O",
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// #10
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]CO.[*:1]CNC(=O)"
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"c1c(C)n([O-])c2ccccc2[n+]1=O",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,,[*:1]O.[*:1]CCNC(=O)"
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"c1c(C)n([O-])c2ccccc2[n+]1=O",
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// exchanged atom mapping labels (1<->2):
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///-- dup of #5:
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///"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]NC([*:1])=O,[*:2]CCO.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CC[*:1],[*:2]O.["
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"*:1]NC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]CCNC([*:1])=O,[*"
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":2]O.[*:1]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:2]C[*:1],[*:2]O.[*"
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":1]CNC(=O)c1c(C)n([O-])c2ccccc2[n+]1=O",
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/* ORIGINALS of exchanged atom mapping labels (1<->2):
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///dup of #5:
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]NC([*:2])=O,[*:1]CCO.[*:2]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"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",
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"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,[*:1]CCNC([*:2])=O,[*:1]O.[*:2]c1c(C)n([O-])c2ccccc2[n+]1=O",
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"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",
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*/
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};
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// FIX RDKit update. But MolToSmiles() fails with new RDKit version
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for (size_t r = 0; r < sizeof(fs) / sizeof(fs[0]); r++) {
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// strcpy(fs[r], fs1[r]);
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// MolToSmiles() fails with new RDKit version in DEBUG Build
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char core[256] = "", side[256];
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if (fs_sm[2 * r][0]) {
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RWMol* m = SmilesToMol(fs_sm[2 * r]);
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strcpy(core, MolToSmiles(*m, true).c_str());
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delete m;
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}
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if (fs_sm[2 * r + 1][0]) {
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RWMol* m = SmilesToMol(fs_sm[2 * r + 1]);
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strcpy(side, MolToSmiles(*m, true).c_str());
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delete m;
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}
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sprintf(fs[r], "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,%s,%s",
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core, side);
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}
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strcpy(fs[0], fs1[0]);
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strcpy(fs[8], fs1[8]);
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//-----------------------------------
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for (unsigned int i = 0; i < sizeof(smi) / sizeof(smi[0]); i++) {
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static const std::string es("NULL");
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std::string id;
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std::string smiles = getSmilesOnly(smi[i], &id);
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ROMol* mol = SmilesToMol(smiles);
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std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> res;
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t0 = nanoClock();
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RDKit::MMPA::fragmentMol(*mol, res, 3);
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printTime();
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delete mol;
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std::cout << "TEST FINISHED "
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"!!!\n*******************************************************"
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"\n"
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" --- VERIFY RESULTS ---\n";
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// === VERIFY RESULTS ===
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std::map<size_t, size_t> fs2res;
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std::cout << "\nTEST " << i + 1 << " mol: " << smi[i] << "\n";
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bool test_failed = false;
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for (size_t j = 0; j < res.size(); j++) {
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// std::cout <<" "<< j+1 << ": ";
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// std::cout << (res[j].first.get() ?
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// MolToSmiles(*res[j].first ) : es) <<", ";
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// std::cout << (res[j].second.get() ?
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// MolToSmiles(*res[j].second) : es) <<"\n";
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std::stringstream ss;
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ss << smiles << "," << id << ",";
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ss << (res[j].first.get() ? MolToSmiles(*res[j].first, true) : "") << ",";
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ss << (res[j].second.get() ? MolToSmiles(*res[j].second, true) : "");
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size_t matchedRefRes = -1;
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bool failed = true;
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for (size_t r = 0; r < sizeof(fs) / sizeof(fs[0]); r++) {
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if (0 == strcmp(std::string(ss.str()).c_str(), fs[r])) { // PASSED
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failed = false;
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matchedRefRes = r;
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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::unique_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::unique_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";
|
|
// clang-format off
|
|
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]"};
|
|
// clang-format on
|
|
doTest(smi, fs, sizeof(fs) / sizeof(fs[0]));
|
|
}
|
|
|
|
{ // Case1 SIMPLE: (PASSED)
|
|
const char* smi = "CC(N1CC1)C(=O) Case1-SIMPLE";
|
|
// clang-format off
|
|
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]",
|
|
};
|
|
// clang-format on
|
|
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;
|
|
}
|
|
*/
|
|
//====================================================================================================
|
|
//====================================================================================================
|
|
|
|
void testGithub6900() {
|
|
UseLegacyStereoPerceptionFixture useLegacy(false);
|
|
// auto mol = "CN1CCCN=C1/C=C/c1cccs1"_smiles;
|
|
auto mol = "N/C=C/C"_smiles;
|
|
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> res;
|
|
RDKit::MMPA::fragmentMol(*mol, res, 3);
|
|
}
|
|
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
|
|
testGithub6900();
|
|
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;
|
|
}
|