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/* MaxMinPicker.cpp */
#include <cstring>
#include <cstdio>
#include <sys/time.h>
#include <vector>
#include <string>
#include <GraphMol/GraphMol.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/Fingerprints/MorganFingerprints.h>
#include <DataStructs/BitOps.h>
#include "MaxMinPicker.h"
#include "LeaderPicker.h"
std::vector<RDKit::ROMol *> mols;
std::vector<ExplicitBitVect *> fps;
// ExplicitBitVect **fps;
const char *poolname;
const char *pickname;
unsigned int origsize;
unsigned int picksize;
unsigned int poolsize;
unsigned int newpicks;
int seed;
unsigned long ticks = 0;
static unsigned int LoadDatabase(FILE *fp) {
char buffer[32768];
unsigned int result = 0;
while (fgets(buffer, sizeof(buffer), fp)) {
if (buffer[0] == '#' || buffer[0] == ' ' || buffer[0] == '\t') continue;
char *ptr = buffer;
while (*ptr && *ptr != ' ' && *ptr != '\t') ptr++;
if (*ptr) {
*ptr++ = '\0';
char *end = ptr;
while (*end && *end != '\n' && *end != '\r') end++;
*end = '\0';
}
RDKit::RWMol *mol;
try {
mol = RDKit::SmilesToMol(buffer);
} catch (...) {
mol = (RDKit::RWMol *)0;
}
if (mol) {
ExplicitBitVect *fp;
fp = RDKit::MorganFingerprints::getFingerprintAsBitVect(*mol, 2, 2048);
fps.push_back(fp);
delete mol;
result++;
}
}
fprintf(stderr, "%u molecules\n", result);
return result;
}
static unsigned int LoadDatabase(const char *fname) {
if (fname && strcmp(fname, "-")) {
FILE *fp = fopen(fname, "rb");
if (!fp) return 0;
unsigned int result = LoadDatabase(fp);
fclose(fp);
return result;
} else
return LoadDatabase(stdin);
}
#ifdef UNUSED
static void GenerateFingerprints() {
unsigned int count = (unsigned int)mols.size();
unsigned int size = (unsigned int)(count * sizeof(void *));
fps = (ExplicitBitVect **)malloc(size);
for (unsigned int i = 0; i < count; i++)
fps[i] =
RDKit::MorganFingerprints::getFingerprintAsBitVect(*mols[i], 2, 2048);
fprintf(stderr, "%u Fingerprints\n", count);
}
static void DestroyFingerprints() {
unsigned int count = (unsigned int)mols.size();
for (unsigned int i = 0; i < count; i++) delete fps[i];
free(fps);
}
#endif
static void DisplayUsage() {
fputs("usage: MaxMinPicker [options] <poolfile> [<pickfile>]\n", stderr);
exit(1);
}
static void ProcessCommandLine(int argc, char *argv[]) {
poolname = (const char *)0;
pickname = (const char *)0;
newpicks = 1000;
for (int i = 1; i < argc; i++) {
const char *ptr = argv[i];
if (ptr[0] == '-' && ptr[1]) {
if (ptr[1] >= '0' && ptr[1] <= '9') {
newpicks = atoi(ptr + 1);
} else
DisplayUsage();
} else if (!poolname) {
poolname = ptr;
} else if (!pickname) {
pickname = ptr;
} else
DisplayUsage();
}
if (!poolname) DisplayUsage();
}
double MyDist(int i, int j) {
ticks++;
return 1.0 - TanimotoSimilarity(*fps[i], *fps[j]);
}
int main(int argc, char *argv[]) {
struct timeval beg, end;
double elapsed;
ProcessCommandLine(argc, argv);
gettimeofday(&beg, (struct timezone *)0);
origsize = LoadDatabase(poolname);
gettimeofday(&end, (struct timezone *)0);
elapsed = (end.tv_sec + 0.000001 * end.tv_usec) -
(beg.tv_sec + 0.000001 * beg.tv_usec);
fprintf(stderr, "Elapsed time: %g secs\n", elapsed);
if (pickname) {
gettimeofday(&beg, (struct timezone *)0);
picksize = LoadDatabase(pickname);
gettimeofday(&end, (struct timezone *)0);
elapsed = (end.tv_sec + 0.000001 * end.tv_usec) -
(beg.tv_sec + 0.000001 * beg.tv_usec);
fprintf(stderr, "Elapsed time: %g secs\n", elapsed);
} else
picksize = 0;
poolsize = origsize + picksize;
if (newpicks == 0) newpicks = origsize;
#ifdef UNUSED
gettimeofday(&beg, (struct timezone *)0);
GenerateFingerprints();
gettimeofday(&end, (struct timezone *)0);
elapsed = (end.tv_sec + 0.000001 * end.tv_usec) -
(beg.tv_sec + 0.000001 * beg.tv_usec);
fprintf(stderr, "Elapsed time: %g secs\n", elapsed);
#endif
RDKit::INT_VECT firstPicks;
if (picksize) {
firstPicks.reserve(picksize);
for (unsigned int i = 0; i < picksize; i++)
firstPicks.push_back((int)(i + origsize));
}
// RDPickers::MaxMinPicker mmpicker;
double threshold = 0.9; // 0.675;
RDPickers::LeaderPicker ldpicker(threshold, 4);
gettimeofday(&beg, (struct timezone *)0);
RDKit::INT_VECT iv = ldpicker.lazyPick(MyDist, poolsize, picksize + newpicks,
firstPicks, threshold, 16);
gettimeofday(&end, (struct timezone *)0);
elapsed = (end.tv_sec + 0.000001 * end.tv_usec) -
(beg.tv_sec + 0.000001 * beg.tv_usec);
fprintf(stderr, "Elapsed time: %g secs\n", elapsed);
unsigned int count = (unsigned int)iv.size();
for (unsigned int i = 0; i < std::min(iv.size(), (size_t)10); ++i) {
for (unsigned int j = 0; j < i; ++j) {
std::cerr << iv[i] << " " << iv[j] << ": " << MyDist(iv[i], iv[j])
<< std::endl;
}
}
fprintf(stderr, "%u picks\n", count);
fprintf(stderr, "%g threshold\n", threshold);
fprintf(stderr, "%lu comparisons\n", ticks);
// DestroyFingerprints();
return 0;
}
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