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);
}
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;
}
