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133 lines
3.9 KiB
C++
133 lines
3.9 KiB
C++
//
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// Copyright (C) 2014 Novartis Institutes for BioMedical Research
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#pragma once
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#include <cstdio>
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#include <cstring>
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#include <cstddef>
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#include <ctime>
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#ifdef _MSC_VER
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#define _CRT_SECURE_NO_WARNINGS
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#define NOMINMAX
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#include <Winsock2.h> // for timeval
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#ifdef _DEBUG // check memory leaks
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#include <crtdbg.h>
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#define _CRTDBG_MAP_ALLOC
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#ifndef new
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#define new new (_NORMAL_BLOCK, __FILE__, __LINE__)
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#endif
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#endif
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#else
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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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#ifndef _WIN32
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#include <sys/resource.h>
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#endif
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#endif
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// SELECT ALGORITHM OPTIONS by comment some lines to exclude additional or
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// experimental optimisations:
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#define SEED_GROW_DEEP // fast and works much times faster (but it can depend
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// on molecules)
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// #define EXCLUDE_WRONG_COMPOSITION // fast but with a little effect, because
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// amount of external bonds usually is very small.
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// Exclude mismatched bonds combinations during seed growing (2^N-1 stage)
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#define FAST_SUBSTRUCT_CACHE // based on a hash of Morgan code
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#define DUP_SUBSTRUCT_CACHE // based on list of query atoms and bonds. For
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// rings where seeds growing in both directions
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// throw the same ring.
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#define FAST_INCREMENTAL_MATCH // fast and some time very useful. request
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// PRECOMPUTED_TABLES_MATCH
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// previous match result based match checking without finding new matched
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// substructure location in the target
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#define VERBOSE_STATISTICS_ON
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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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namespace RDKit {
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namespace FMCS {
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#ifdef VERBOSE_STATISTICS_ON
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// compute statistics of really very very fast calls.
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// It a bit decrease overal performance, but might be interested for
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// investigation purpose (only)
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// #define VERBOSE_STATISTICS_FASTCALLS_ON
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struct ExecStatistics {
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unsigned int TotalSteps{0}, MCSFoundStep{0};
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unsigned long long MCSFoundTime;
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unsigned int InitialSeed{0}, MismatchedInitialSeed{0};
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unsigned int Seed{0}, RemainingSizeRejected{0};
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unsigned int SeedCheck{0}, IndividualBondExcluded{0};
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unsigned int MatchCall{0}, MatchCallTrue{0};
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unsigned int FastMatchCall{0}, FastMatchCallTrue{0}, SlowMatchCallTrue{0};
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unsigned int ExactMatchCall{0}, ExactMatchCallTrue{0}; // hash cache
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unsigned int FindHashInCache{0}, HashKeyFoundInCache{0};
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unsigned int AtomCompareCalls{0}, BondCompareCalls{0};
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unsigned int AtomFunctorCalls{0}, BondFunctorCalls{0};
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unsigned int WrongCompositionRejected{0}, WrongCompositionDetected{0};
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unsigned int DupCacheFound{0}, DupCacheFoundMatch{0};
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ExecStatistics() : MCSFoundTime(nanoClock()) {}
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};
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#endif
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} // namespace FMCS
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} // namespace RDKit
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