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//
// Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#pragma once
#include <stdio.h>
#include <string.h>
#include <stddef.h>
#include <time.h>
#include <iostream>
#ifdef _MSC_VER
#define _CRT_SECURE_NO_WARNINGS
#include <Windows.h> // for Winmm.lib timeGetTime()
#ifdef _DEBUG // check memory leaks
#include <crtdbg.h>
#define _CRTDBG_MAP_ALLOC
#ifndef new
#define new new (_NORMAL_BLOCK, __FILE__, __LINE__)
#endif
#endif
#else
#include <unistd.h>
#include <fcntl.h>
#include <sys/time.h>
#ifndef _WIN32
#include <sys/resource.h>
#endif
#endif
// SELECT ALGORITHM OPTIONS by comment some lines to exclude additional or
// experimental optimisations:
#define SEED_GROW_DEEP // fast and works much times faster (but it can depend
// on molecules)
//#define EXCLUDE_WRONG_COMPOSITION // fast but with a little effect, because
// amount of external bonds usually is very small.
// Exclude mismatched bonds combinations during seed growing (2^N-1 stage)
#define FAST_SUBSTRUCT_CACHE // based on a hash of Morgan code
#define DUP_SUBSTRUCT_CACHE // based on list of query atoms and bonds. For
// rings where seeds growing in both directions
// throw the same ring.
#define FAST_INCREMENTAL_MATCH // fast and some time very usefull. request
// PRECOMPUTED_TABLES_MATCH
// previous match result based match checking without finding new matched
// substructure location in the target
#define VERBOSE_STATISTICS_ON
#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 *)0);
return t.tv_usec + t.tv_sec * 1000000ULL;
}
namespace RDKit {
namespace FMCS {
#ifdef VERBOSE_STATISTICS_ON
// compute statistics of really very very fast calls.
// It a bit decrease overal performance, but might be interested for
// investigation purpose (only)
//#define VERBOSE_STATISTICS_FASTCALLS_ON
struct ExecStatistics {
unsigned TotalSteps, MCSFoundStep;
unsigned long long MCSFoundTime;
unsigned InitialSeed, MismatchedInitialSeed;
unsigned Seed, RemainingSizeRejected;
unsigned SeedCheck, SingleBondExcluded;
unsigned MatchCall, MatchCallTrue;
unsigned FastMatchCall, FastMatchCallTrue, SlowMatchCallTrue;
unsigned ExactMatchCall, ExactMatchCallTrue; // hash cache
unsigned FindHashInCache, HashKeyFoundInCache;
unsigned AtomCompareCalls, BondCompareCalls; // long long
unsigned AtomFunctorCalls, BondFunctorCalls; // long long
unsigned WrongCompositionRejected, WrongCompositionDetected;
unsigned DupCacheFound, DupCacheFoundMatch;
ExecStatistics()
: TotalSteps(0),
MCSFoundStep(0),
MCSFoundTime(nanoClock()),
InitialSeed(0),
MismatchedInitialSeed(0),
Seed(0),
RemainingSizeRejected(0),
SeedCheck(0),
SingleBondExcluded(0),
MatchCall(0),
MatchCallTrue(0),
FastMatchCall(0),
FastMatchCallTrue(0),
SlowMatchCallTrue(0),
ExactMatchCall(0),
ExactMatchCallTrue(0),
FindHashInCache(0),
HashKeyFoundInCache(0),
AtomCompareCalls(0),
BondCompareCalls(0),
AtomFunctorCalls(0),
BondFunctorCalls(0),
WrongCompositionRejected(0),
WrongCompositionDetected(0),
DupCacheFound(0),
DupCacheFoundMatch(0) {}
};
#endif
}
}
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