std::string expandSuperatoms(const Settings& vars, const Molecule &molecule )
{
logEnterFunction();
std::string molString;
ArrayOutput so(molString);
MolfileSaver ma(so);
ma.saveMolecule(vars, molecule);
if (!vars.general.ExpandAbbreviations)
return molString;
indigoSetOption("treat-x-as-pseudoatom", "true");
indigoSetOption("ignore-stereochemistry-errors", "true");
int mol = indigoLoadMoleculeFromString(molString.c_str());
if (mol == -1)
{
fprintf(stderr, "%s\n", indigoGetLastError());
return molString;
}
int expCount = indigoExpandAbbreviations(mol);
if (expCount == -1)
{
fprintf(stderr, "%s\n", indigoGetLastError());
return molString;
}
std::string newMolfile = indigoMolfile(mol);
indigoFree(mol);
return newMolfile;
}
void renderMolecule(int structure, const char* folder, const char* file, int number, const char* title) {
// render the molecule to file
indigoLayout(structure);
indigoSetOption("render-output-format", "png");
indigoSetOption("render-comment", title);
indigoSetOption("render-comment-position", "top");
indigoSetOptionXY("render-image-size", 400, 500);
indigoSetOptionColor("render-background-color", 1.0, 1.0, 1.0);
char str[256];
if(number != -1) {
sprintf(str, "%s/%d%s%s", folder, number, "_", file);
}
else if(strcmp(folder,"")!=0)
{
sprintf(str, "%s/%s", folder, file);
}
else {
sprintf(str, "%s", file);
}
indigoRenderToFile(structure, str);
}
void renderPair(int s1, int s2, const char* folder, const char* file, int number, const char* title) {
int collection = indigoCreateArray();
indigoArrayAdd(collection, s1);
indigoArrayAdd(collection, s2);
indigoSetOption("render-output-format", "png");
indigoSetOption("render-comment", title);
indigoSetOption("render-comment-position", "top");
indigoSetOptionXY("render-image-size", 800, 1000);
indigoSetOptionColor("render-background-color", 1.0, 1.0, 1.0);
char str[256];
if(number != -1) {
sprintf(str, "./%s/%d%s%s%s", folder, number, "_", file, ".png");
}
else
{
sprintf(str, "%s%s", file, ".png");
}
indigoRenderGridToFile(collection, NULL, 2, str);
indigoFree(collection);
}
void _setComment (int obj, Params *p) {
if (p->comment_name) {
const char *name = indigoName(obj);
if (name != NULL && *name != 0) {
indigoSetOption("render-comment", name);
return;
}
}
if (p->comment_field != NULL) {
if (indigoHasProperty(obj, p->comment_field)) {
const char *prop = indigoGetProperty(obj, p->comment_field);
if (prop != NULL && *prop != 0) {
indigoSetOption("render-comment", prop);
return;
}
}
}
if (p->comment != NULL && *p->comment != 0) {
indigoSetOption("render-comment", p->comment);
return;
}
}
int performFileAction(bool verbose, imago::Settings& vars, const std::string& imageName, const std::string& configName,
const std::string& outputName)
{
logEnterFunction();
int result = 0; // ok mark
imago::VirtualFS vfs;
vars.general.StartTime = 0; // reset timelimit
if (vars.general.ExtractCharactersOnly)
{
if (verbose)
printf("Characters extraction from image '%s'\n", imageName.c_str());
}
else
{
if (verbose)
printf("Recognition of image '%s'\n", imageName.c_str());
}
try
{
imago::Image image;
if (vars.general.LogVFSEnabled)
{
imago::getLogExt().SetVirtualFS(vfs);
}
imago::ImageUtils::loadImageFromFile(image, imageName.c_str());
if (vars.general.ExtractCharactersOnly)
{
imago::Image out;
imago::prefilterEntrypoint(vars, out, image);
applyConfig(verbose, vars, configName);
imago::ChemicalStructureRecognizer _csr;
_csr.extractCharacters(vars, out);
}
else
{
RecognitionResult result = recognizeImage(verbose, vars, image, configName);
imago::FileOutput fout(outputName.c_str());
fout.writeString(result.molecule.c_str());
if (imago::getLogExt().loggingEnabled())
{
int molObj = indigoLoadMoleculeFromString(result.molecule.c_str());
if (molObj != -1)
{
indigoSetOption("render-output-format", "png");
indigoSetOption("render-background-color", "255, 255, 255");
std::string outputImg = imago::getLogExt().generateImageName();
indigoRenderToFile(molObj, outputImg.c_str());
imago::getLogExt().appendImageFile("Result image:", outputImg);
indigoFree(molObj);
}
}
}
}
catch (std::exception &e)
{
result = 2; // error mark
puts(e.what());
}
dumpVFS(vfs, "log_vfs.txt");
return result;
}
int main (int argc, char *argv[])
{
Params p;
int obj = -1, reader = -1, writer = -1;
int i = 0;
char number[100];
char outfilename[4096];
const char *id;
p.width =
p.height =
p.bond =
p.mode = -1;
p.id =
p.string_to_load =
p.file_to_load = NULL;
p.hydro_set =
p.query_set =
p.smarts_set = 0;
p.aromatization = NONE;
p.comment_field = NULL;
p.comment = NULL;
p.comment_name = 0;
if (argc <= 2)
USAGE();
indigoSetErrorHandler(onError, 0);
indigoSetOption("ignore-stereochemistry-errors", "on");
if (parseParams(&p, argc, argv) < 0)
return -1;
p.out_ext = OEXT_OTHER;
if (strcmp(p.outfile_ext, "mol") == 0)
p.out_ext = OEXT_MOL;
else if (strcmp(p.outfile_ext, "sdf") == 0)
p.out_ext = OEXT_SDF;
else if (strcmp(p.outfile_ext, "rxn") == 0)
p.out_ext = OEXT_RXN;
else if (strcmp(p.outfile_ext, "rdf") == 0)
p.out_ext = OEXT_RDF;
else if (strcmp(p.outfile_ext, "cml") == 0)
p.out_ext = OEXT_CML;
// guess whether to layout or render by extension
p.action = ACTION_LAYOUT;
if (p.out_ext == OEXT_OTHER) {
indigoSetOption("render-output-format", p.outfile_ext);
p.action = ACTION_RENDER;
}
// read in the input
reader = (p.file_to_load != NULL) ? indigoReadFile(p.file_to_load) : indigoReadString(p.string_to_load);
if (p.mode == MODE_SINGLE_MOLECULE) {
if (p.id != NULL)
ERROR("on single input, setting '-id' is not allowed\n");
if (p.out_ext == OEXT_RXN)
ERROR("reaction output specified for molecule input\n");
if (p.smarts_set)
obj = indigoLoadSmarts(reader);
else if (p.query_set)
obj = indigoLoadQueryMolecule(reader);
else
obj = indigoLoadMolecule(reader);
_prepare(obj, p.aromatization);
if (p.action == ACTION_LAYOUT) {
indigoLayout(obj);
if (p.out_ext == OEXT_MOL)
indigoSaveMolfileToFile(obj, p.outfile);
else
indigoSaveCmlToFile(obj, p.outfile);
} else {
_setComment(obj, &p);
renderToFile(obj, p.outfile);
}
} else if (p.mode == MODE_SINGLE_REACTION) {
if (p.id != NULL)
ERROR("on single input, setting '-id' is not allowed\n");
if (p.out_ext == OEXT_MOL)
ERROR("molecule output specified for reaction input\n");
if (p.smarts_set)
obj = indigoLoadReactionSmarts(reader);
else if (p.query_set)
obj = indigoLoadQueryReaction(reader);
else
obj = indigoLoadReaction(reader);
_prepare(obj, p.aromatization);
if (p.action == ACTION_LAYOUT) {
indigoLayout(obj);
if (p.out_ext == OEXT_CML)
indigoSaveCmlToFile(obj, p.outfile);
else
indigoSaveRxnfileToFile(obj, p.outfile);
} else {
_setComment(obj, &p);
renderToFile(obj, p.outfile);
}
} else {
int item;
int have_percent_s = (strstr(p.outfile, "%s") != NULL);
if (p.mode == MODE_MULTILINE_SMILES)
obj = indigoIterateSmiles(reader);
else if (p.mode == MODE_SDF)
obj = indigoIterateSDF(reader);
else if (p.mode == MODE_MULTIPLE_CML)
obj = indigoIterateCML(reader);
else if (p.mode == MODE_RDF)
obj = indigoIterateRDF(reader);
else {
fprintf(stderr, "internal error: wrong branch\n");
return -1;
}
if ((p.out_ext == OEXT_MOL || p.out_ext == OEXT_RXN || p.out_ext == OEXT_OTHER) && !have_percent_s)
ERROR("on multiple output, output file name must have '%%s'\n");
if (p.out_ext == OEXT_SDF || p.out_ext == OEXT_RDF ||
(p.out_ext == OEXT_CML && !have_percent_s))
{
writer = indigoWriteFile(p.outfile);
if (p.out_ext == OEXT_RDF)
indigoRdfHeader(writer);
if (p.out_ext == OEXT_CML)
indigoCmlHeader(writer);
}
i = -1;
while ((item = indigoNext(obj))) {
int rc;
++i;
if (writer > 0)
printf("saving item #%d... ", i);
else
{
if (p.id) {
if (!indigoHasProperty(item, p.id)) {
fprintf(stderr, "item #%d does not have %s, skipping\n", i, p.id);
continue;
}
id = indigoGetProperty(item, p.id);
snprintf(outfilename, sizeof(outfilename), p.outfile, id);
} else {
snprintf(number, sizeof(number), "%d", i);
snprintf(outfilename, sizeof(outfilename), p.outfile, number);
}
printf("saving %s... ", outfilename);
}
indigoSetErrorHandler(0, 0);
if (_prepare(item, p.aromatization) < 0)
{
printf("%s\n", indigoGetLastError());
indigoSetErrorHandler(onError, 0);
continue;
}
if (p.action == ACTION_LAYOUT)
{
if (indigoLayout(item) < 0)
{
printf("%s\n", indigoGetLastError());
indigoSetErrorHandler(onError, 0);
continue;
}
}
if (writer > 0) {
if (p.out_ext == OEXT_SDF)
rc = indigoSdfAppend(writer, item);
else if (p.out_ext == OEXT_RDF)
rc = indigoRdfAppend(writer, item);
else
rc = indigoCmlAppend(writer, item);
} else {
if (p.action == ACTION_LAYOUT) {
if (p.out_ext == OEXT_MOL)
rc = indigoSaveMolfileToFile(item, outfilename);
else if (p.out_ext == OEXT_RXN)
rc = indigoSaveRxnfileToFile(item, outfilename);
else
ERROR("extension unexpected");
} else {
_setComment(item, &p);
rc = indigoRenderToFile(item, outfilename);
}
}
if (rc < 0)
{
printf("%s\n", indigoGetLastError());
indigoSetErrorHandler(onError, 0);
continue;
}
indigoFree(item);
indigoSetErrorHandler(onError, 0);
printf("\n");
}
if (writer > 0)
{
if (p.out_ext == OEXT_CML)
indigoCmlFooter(writer);
indigoFree(writer);
}
}
indigoFree(reader);
indigoFree(obj);
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;
}
