int main (int argc, const char** argv)
{
int i;
int done_with_options = 0;
int approximate = 0;
int scaffold = 0;
int aromatic = 1;
const char *outfile_hl = 0;
const char *outfile_rg = 0;
const char *outfile_maxscaf = 0;
const char *outfile_allscafs = 0;
const char *outfile_scaf_r = 0;
int deco = 0;
int structures = 0;
indigoSetErrorHandler(onError, 0);
printf("R-Group deconvolution utility, powered by Indigo API version %s\n", indigoVersion());
structures = indigoCreateArray();
indigoSetOptionBool("treat-x-as-pseudoatom", 1);
indigoSetOptionBool("ignore-stereochemistry-errors", 1);
for (i = 1; i < argc; i++)
{
if (!done_with_options && argv[i][0] == '-')
{
if (strcmp(argv[i], "--") == 0)
done_with_options = 1;
else if (strcmp(argv[i], "-h") == 0 ||
strcmp(argv[i], "-?") == 0 ||
strcmp(argv[i], "/?") == 0 ||
strcmp(argv[i], "-help") == 0 ||
strcmp(argv[i], "--help") == 0)
{
_printHelpMessage();
return 0;
}
else if (strcmp(argv[i], "-a") == 0)
approximate = 1;
else if (strcmp(argv[i], "-l") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting filename after -l\n");
return -1;
}
scaffold = indigoLoadMoleculeFromFile(argv[i]);
}
else if (strcmp(argv[i], "-o") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting filename after -o\n");
return -1;
}
outfile_hl = argv[i];
}
else if (strcmp(argv[i], "-r") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting filename after -r\n");
return -1;
}
outfile_rg = argv[i];
}
else if (strcmp(argv[i], "-s") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting filename after -s\n");
return -1;
}
outfile_maxscaf = argv[i];
}
else if (strcmp(argv[i], "-sr") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting filename after -sr\n");
return -1;
}
outfile_scaf_r = argv[i];
}
else if (strcmp(argv[i], "-S") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting filename after -S\n");
return -1;
}
outfile_allscafs = argv[i];
}
else if (strcmp(argv[i], "-na") == 0)
aromatic = 0;
else
{
fprintf(stderr, "Unknown option: %s", argv[i]);
_printHelpMessage();
return -1;
}
}
else
{
char dirname[1024];
char errbuf[1024];
const char *filename = 0;
int k;
for (k = (int)strlen(argv[i]) - 1; k >= 0; k--)
if (argv[i][k] == '/' || argv[i][k] == '\\')
break;
if (k == -1)
strncpy(dirname, ".", sizeof(dirname));
else if (k == 0)
{
dirname[0] = argv[i][0];
dirname[1] = 0;
}
else if (k == strlen(argv[i]) - 1)
{
fprintf(stderr, "can not handle filenames ending with a slash\n");
return -1;
}
else if (k > sizeof(dirname) - 1)
{
fprintf(stderr, "filename too long\n");
return -1;
}
else
{
memcpy(dirname, argv[i], k);
dirname[k] = 0;
}
_replaceSlashes(dirname);
filename = argv[i] + k + 1;
{
OsDirIter dir_iter;
int rc = osDirSearch(dirname, filename, &dir_iter);
if (rc == OS_DIR_OK)
{
int count = 0;
while ((rc = osDirNext(&dir_iter)) == OS_DIR_OK)
{
_replaceSlashes(dir_iter.path);
_handleInputFile(dir_iter.path, structures);
count++;
}
if (rc != OS_DIR_END)
{
fprintf(stderr, "%s\n", osDirLastError(errbuf, sizeof(errbuf)));
return -1;
}
if (count == 0)
{
fprintf(stderr, "can not find %s in directory %s\n", filename, dirname);
return -1;
}
}
else
{
fprintf(stderr, "%s\n", osDirLastError(errbuf, sizeof(errbuf)));
return -1;
}
}
}
}
if (indigoCount(structures) < 1)
{
fprintf(stderr, "no input structures\n");
_printHelpMessage();
return -1;
}
printf("got %d input structures\n", indigoCount(structures));
indigoSetOptionBool("deconvolution-aromatization", aromatic);
if (scaffold == 0)
{
printf("calculating scaffold... ");
fflush(stdout);
if (approximate)
scaffold = indigoExtractCommonScaffold(structures, "approximate");
else
scaffold = indigoExtractCommonScaffold(structures, "exact");
printf("done\n");
fflush(stdout);
}
if (outfile_maxscaf != 0)
{
printf("saving the scaffold to %s\n", outfile_maxscaf);
indigoSaveMolfileToFile(scaffold, outfile_maxscaf);
}
if (outfile_allscafs != 0)
{
int output = indigoWriteFile(outfile_allscafs);
int allscafs = indigoAllScaffolds(scaffold);
int item, iter = indigoIterateArray(allscafs);
printf("saving all obtained scaffolds (%d total) to %s\n",
indigoCount(allscafs), outfile_allscafs);
while ((item = indigoNext(iter)))
{
indigoSdfAppend(output, item);
indigoFree(item);
}
indigoFree(iter);
indigoFree(output);
}
if (outfile_hl == 0 && outfile_rg == 0 && outfile_scaf_r == 0)
{
printf("none of -o, -r, -sr specified, nothing left to do\n");
return 0;
}
printf("decomposing the structures... ");
fflush(stdout);
deco = indigoDecomposeMolecules(scaffold, structures);
printf("done\n");
fflush(stdout);
if (outfile_scaf_r != 0)
{
int sr = indigoDecomposedMoleculeScaffold(deco);
indigoLayout(sr);
printf("saving the scaffold with R-sites to %s\n", outfile_scaf_r);
indigoSaveMolfileToFile(sr, outfile_scaf_r);
}
if (outfile_hl != 0)
{
int output = indigoWriteFile(outfile_hl);
int item, iter = indigoIterateDecomposedMolecules(deco);
printf("saving the highlighted structures to %s\n", outfile_hl);
while ((item = indigoNext(iter)))
{
indigoSdfAppend(output, indigoDecomposedMoleculeHighlighted(item));
indigoFree(item);
}
indigoFree(iter);
indigoFree(output);
}
if (outfile_rg != 0)
{
int output = indigoWriteFile(outfile_rg);
int item, iter = indigoIterateDecomposedMolecules(deco);
printf("saving the structures with R-groups to %s\n", outfile_rg);
while ((item = indigoNext(iter)))
{
indigoSdfAppend(output, indigoDecomposedMoleculeWithRGroups(item));
indigoFree(item);
}
indigoFree(iter);
indigoFree(output);
}
return 0;
};
int parseParams (Params* p, int argc, char *argv[]) {
int i;
if (strcmp(argv[1], "-") == 0)
{
if (_isReaction(argv[2]))
{
p->mode = MODE_SINGLE_REACTION;
p->string_to_load = argv[2];
}
else
{
p->mode = MODE_SINGLE_MOLECULE;
p->string_to_load = argv[2];
}
if (argc <= 3)
USAGE();
i = 3;
}
else
{
p->infile_ext[0] = 0;
if (strlen(argv[1]) >= 4 && argv[1][strlen(argv[1]) - 4] == '.')
{
p->infile_ext[3] = 0;
strncpy(p->infile_ext, argv[1] + strlen(argv[1]) - 3, 3);
}
else if (strlen(argv[1]) > 7 && argv[1][strlen(argv[1]) - 7] == '.')
{
p->infile_ext[6] = 0;
strncpy(p->infile_ext, argv[1] + strlen(argv[1]) - 6, 6);
}
p->file_to_load = argv[1];
if (strcasecmp(p->infile_ext, "mol") == 0)
p->mode = MODE_SINGLE_MOLECULE;
else if (strcasecmp(p->infile_ext, "rxn") == 0)
p->mode = MODE_SINGLE_REACTION;
else if (strcasecmp(p->infile_ext, "smi") == 0)
{
int reaction;
if (_isMultiline(argv[1], &reaction))
p->mode = MODE_MULTILINE_SMILES;
else
{
if (reaction)
p->mode = MODE_SINGLE_REACTION;
else
p->mode = MODE_SINGLE_MOLECULE;
}
}
else if (strcasecmp(p->infile_ext, "cml") == 0)
{
int reaction;
if (_isMultipleCML(argv[1], &reaction))
p->mode = MODE_MULTIPLE_CML;
else
{
if (reaction)
p->mode = MODE_SINGLE_REACTION;
else
p->mode = MODE_SINGLE_MOLECULE;
}
}
else if (strcasecmp(p->infile_ext, "sdf") == 0 || strcasecmp(p->infile_ext, "sdf.gz") == 0)
p->mode = MODE_SDF;
else if (strcasecmp(p->infile_ext, "rdf") == 0 || strcasecmp(p->infile_ext, "rdf.gz") == 0)
p->mode = MODE_RDF;
else
USAGE();
i = 2;
}
p->outfile = argv[i++];
if (strlen(p->outfile) < 5 || p->outfile[strlen(p->outfile) - 4] != '.')
USAGE();
p->outfile_ext[3] = 0;
strncpy(p->outfile_ext, p->outfile + strlen(p->outfile) - 3, 3);
indigoSetOptionBool("treat-x-as-pseudoatom", 1);
indigoSetOptionBool("render-coloring", 1);
indigoSetOptionBool("render-highlight-color-enabled", 1);
for (; i < argc; i++)
{
if (strcmp(argv[i], "-w") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting number after -w\n");
return -1;
}
if (sscanf(argv[i], "%d", &p->width) != 1 || p->width <= 0)
{
fprintf(stderr, "%s is not a valid width\n", argv[i]);
return -1;
}
}
else if (strcmp(argv[i], "-h") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting number after -h\n");
return -1;
}
if (sscanf(argv[i], "%d", &p->height) != 1 || p->height <= 0)
{
fprintf(stderr, "%s is not a valid height\n", argv[i]);
return -1;
}
}
else if (strcmp(argv[i], "-margins") == 0)
{
int horz, vert;
if (i + 2 >= argc)
{
fprintf(stderr, "expecting two numbers after -margins\n");
return -1;
}
if (sscanf(argv[i + 1], "%d", &horz) != 1 || horz < 0)
{
fprintf(stderr, "%s is not a valid horizontal margin\n", argv[i]);
return -1;
}
if (sscanf(argv[i + 2], "%d", &vert) != 1 || vert < 0)
{
fprintf(stderr, "%s is not a valid vertical margin\n", argv[i + 1]);
return -1;
}
indigoSetOptionXY("render-margins", horz, vert);
i += 2;
}
else if (strcmp(argv[i], "-thickness") == 0)
{
float rt;
if (++i == argc)
{
fprintf(stderr, "expecting number after -thickness\n");
return -1;
}
if (sscanf(argv[i], "%f", &rt) != 1 || rt < 0)
{
fprintf(stderr, "%s is not a valid relative thickness\n", argv[i]);
return -1;
}
indigoSetOptionFloat("render-relative-thickness", rt);
}
else if (strcmp(argv[i], "-linewidth") == 0)
{
float rt;
if (++i == argc)
{
fprintf(stderr, "expecting number after -linewidth\n");
return -1;
}
if (sscanf(argv[i], "%f", &rt) != 1 || rt < 0)
{
fprintf(stderr, "%s is not a valid line width value\n", argv[i]);
return -1;
}
indigoSetOptionFloat("render-bond-line-width", rt);
}
else if (strcmp(argv[i], "-bond") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting number after -bond\n");
return -1;
}
if (sscanf(argv[i], "%d", &p->bond) != 1 || p->bond <= 0)
{
fprintf(stderr, "%s is not a valid bond length\n", argv[i]);
return -1;
}
}
else if (strcmp(argv[i], "-coloring") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting 'on' or 'off' after -coloring\n");
return -1;
}
if (strcasecmp(argv[i], "on") == 0)
indigoSetOptionBool("render-coloring", 1);
else if (strcasecmp(argv[i], "off") == 0)
indigoSetOptionBool("render-coloring", 0);
else
{
fprintf(stderr, "expecting 'on' or 'off' after -coloring\n");
return -1;
}
}
else if (strcmp(argv[i], "-hlthick") == 0)
{
indigoSetOptionBool("render-highlight-thickness-enabled", 1);
}
else if (strcmp(argv[i], "-hlcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -hlcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionBool("render-highlight-color-enabled", 1);
indigoSetOptionColor("render-highlight-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-bgcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -bgcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-background-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-basecolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -basecolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-base-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-aamcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -aamcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-aam-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-dsgcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -aamcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-data-sgroup-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-hydro") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -hydro\n");
return -1;
}
indigoSetOption("render-implicit-hydrogens-visible", argv[i]);
p->hydro_set = 1;
}
else if (strcmp(argv[i], "-label") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -label\n");
return -1;
}
indigoSetOption("render-label-mode", argv[i]);
}
else if (strcmp(argv[i], "-arom") == 0)
{
p->aromatization = AROM;
}
else if (strcmp(argv[i], "-dearom") == 0)
{
p->aromatization = DEAROM;
}
else if (strcmp(argv[i], "-stereo") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -stereo\n");
return -1;
}
indigoSetOption("render-stereo-style", argv[i]);
}
else if (strcmp(argv[i], "-cdbwsa") == 0)
{
indigoSetOptionBool("render-center-double-bond-when-stereo-adjacent", 1);
}
else if (strcmp(argv[i], "-query") == 0)
{
p->query_set = 1;
}
else if (strcmp(argv[i], "-smarts") == 0)
{
p->smarts_set = 1;
}
else if (strcmp(argv[i], "-id") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -id\n");
return -1;
}
p->id = argv[i];
}
else if (strcmp(argv[i], "-catalysts") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -catalysts\n");
return -1;
}
indigoSetOption("render-catalysts-placement", argv[i]);
}
else if (strcmp(argv[i], "-comment") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -comment\n");
return -1;
}
p->comment = argv[i];
}
else if (strcmp(argv[i], "-commentoffset") == 0)
{
int offset;
if (++i >= argc)
{
fprintf(stderr, "expecting an integer after -commentoffset\n");
return -1;
}
if (sscanf(argv[i], "%d", &offset) != 1 || offset < 0)
{
fprintf(stderr, "%s is not a valid comment offset\n", argv[i]);
return -1;
}
indigoSetOptionInt("render-comment-offset", offset);
}
else if (strcmp(argv[i], "-commentfield") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -commentfield\n");
return -1;
}
p->comment_field = argv[i];
}
else if (strcmp(argv[i], "-commentname") == 0)
{
p->comment_name = 1;
}
else if (strcmp(argv[i], "-commentsize") == 0)
{
int commentsize;
if (++i == argc)
{
fprintf(stderr, "expecting number after -commentsize\n");
return -1;
}
if (sscanf(argv[i], "%d", &commentsize) != 1 || commentsize <= 0)
{
fprintf(stderr, "%s is not a valid font size\n", argv[i]);
return -1;
}
indigoSetOptionFloat("render-comment-font-size", (float)commentsize);
}
else if (strcmp(argv[i], "-commentcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -commentcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-comment-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-commentalign") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -commentalign\n");
return -1;
}
indigoSetOption("render-comment-alignment", argv[i]);
}
else if (strcmp(argv[i], "-commentpos") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -commentpos\n");
return -1;
}
indigoSetOption("render-comment-position", argv[i]);
}
else if (strcmp(argv[i], "-atomnumbers") == 0)
indigoSetOptionBool("render-atom-ids-visible", 1);
else if (strcmp(argv[i], "-bondnumbers") == 0)
indigoSetOptionBool("render-bond-ids-visible", 1);
else if (strcmp(argv[i], "-onebased") == 0)
indigoSetOptionBool("render-atom-bond-ids-from-one", 1);
else if (strcmp(argv[i], "-help") == 0)
{
usage();
return 0;
}
else
{
fprintf(stderr, "unknown option: %s\n", argv[i]);
return -1;
}
}
if (p->bond > 0)
indigoSetOptionFloat("render-bond-length", (float)p->bond);
if (p->width > 0)
indigoSetOptionInt("render-image-width", p->width);
if (p->height > 0)
indigoSetOptionInt("render-image-height", p->height);
if (p->hydro_set && p->query_set)
{
fprintf(stderr, "-hydro conflicts with -query (implicit hydrogens do not exist in queries)\n");
}
return 0;
}
