void MolconvWindow::add_molecule(molconv::moleculePtr temp_mol)
{
d->m_system->addMolecule(temp_mol);
d->m_GraphicsItemVector.push_back(new chemkit::GraphicsMoleculeItem(d->m_system->getMolecule(d->m_system->nMolecules() - 1).get()));
ui->molconv_graphicsview->addItem(d->m_GraphicsItemVector.back());
d->m_GraphicsAxisVector.push_back(new GraphicsAxisItem(temp_mol->internalOriginPosition(), temp_mol->internalBasisVectors()));
ui->molconv_graphicsview->addItem(d->m_GraphicsAxisVector.back());
ui->molconv_graphicsview->update();
d->m_ListOfMolecules->insertMolecule(temp_mol);
d->activeMolecule = temp_mol;
ui->actionSet_internal_basis->setEnabled(true);
ui->actionDuplicate->setEnabled(true);
ui->actionRemove->setEnabled(true);
ui->actionZero_Coordinates->setEnabled(true);
ui->actionReset_Coordinates->setEnabled(true);
ui->actionProperties->setEnabled(true);
ui->actionAdd_To_Group->setEnabled(true);
ui->actionAlign->setEnabled(true);
emit new_molecule(temp_mol);
}
Datum
pgchem_remove_hydrogens (PG_FUNCTION_ARGS)
{
char *molfile = NULL;
char *smiles = NULL;
//unsigned int *efa_array = NULL;
MOLECULE *retval;
MOLECULE *arg_molecule = PG_GETARG_MOLECULE_P (0);
bool nonpolaronly = PG_GETARG_BOOL (1);
smiles =
ob_delete_hydrogens (SMIPTR (arg_molecule),
nonpolaronly ? 1 : 0);
molfile = ob_smiles_to_mol (smiles);
if(molfile == NULL || !strlen(molfile)) {
elog (ERROR, "Molfile generation failed! Offender was :\n %s",smiles);
}
//efa_array = ob_efa_array(smiles);
retval = new_molecule (smiles, molfile);
free (molfile);
free (smiles);
//free (efa_array);
PG_RETURN_MOLECULE_P (retval);
}
static MOLECULE *make_molecule(char *raw_input, int size) {
MOLECULE *result;
char *input = NULL;
char *molfile = NULL;
char *smiles = NULL;
char *endptr;
unsigned int new_len;
if(strstr (raw_input, "M END") != NULL) {
input = palloc (size+sizeof(char));
memcpy (input, raw_input, size);
endptr = strstr (input, "M END") + strlen("M END")*sizeof(char);
*endptr = 0x0;
new_len = strlen(input);
pfree (input);
input=NULL;
input = palloc (new_len + 1);
strncpy(input,raw_input,new_len);
input[new_len] = 0x0;
} else {
input = palloc (size+1);
memcpy (input, raw_input, size);
input[size]=0x0;
}
if (strstr (input, "V2000") == NULL || strstr (input, "M END") == NULL)
{ //TODO: Bad Hack. If more fmts are needed, we need a dedicated converter function
if (strstr (input, "V3000") != NULL && strstr (input, "M END") != NULL) //V3000?
{
molfile = ob_V3000_to_mol (input);
if(molfile == NULL || !strlen(molfile) || strstr(molfile,"V3000")==NULL) {
if(molfile!=NULL) {
free (molfile);
molfile=NULL;
}
elog (ERROR, "Molfile generation failed! V3000:\n %s",input);
}
smiles = ob_mol_to_smiles (input,0);
if(smiles == NULL || !strlen(smiles)) {
elog (ERROR, "SMILES generation failed! Offender was :\n %s",input);
} else if (!strlen(smiles)) {
elog (WARNING, "SMILES generation failed! Trying fallback...");
free (smiles);
smiles=NULL;
smiles = ob_mol_to_canonical_smiles (input,0);
if(smiles == NULL) {
elog (ERROR, "Canonical SMILES generation finally failed! Offender was :\n %s",input);
} else if (!strlen(smiles)) {
free(smiles);
smiles=NULL;
elog (ERROR, "SMILES generation finally failed! Offender was :\n %s",input);
}
elog (WARNING, "Fallback OK");
}
} else if (strstr (input, "InChI=") != NULL) { //InChI?
molfile = ob_inchi_to_mol (input);
if(molfile == NULL || !strlen(molfile) || strstr(molfile,"V2000")==NULL) {
if(molfile!=NULL) free (molfile);
elog (ERROR, "Molfile generation failed! InChI:\n %s",input);
}
smiles = ob_mol_to_smiles (molfile,0);
if(smiles == NULL || !strlen(smiles)) {
elog (ERROR, "SMILES generation failed! Offender was :\n %s",input);
} else if (!strlen(smiles)) {
elog (WARNING, "SMILES generation failed! Trying fallback...");
free (smiles);
smiles=NULL;
smiles = ob_mol_to_canonical_smiles (input,0);
if(smiles == NULL) {
elog (ERROR, "Canonical SMILES generation finally failed! InChI:\n %s",input);
} else if (!strlen(smiles)) {
free(smiles);
smiles=NULL;
elog (ERROR, "SMILES generation finally failed! InChi:\n %s",input);
}
elog (NOTICE, "Fallback OK");
}
} else { //SMILES?
molfile = ob_smiles_to_mol (input);
if(molfile == NULL || !strlen(molfile)) {
if(molfile!=NULL) free (molfile);
elog (ERROR, "Molfile generation failed! SMILES:\n %s",input);
}
// smiles will be free()d below, but input was palloc()ed.
smiles = strdup(input);
}
}
else //V2000
{
smiles = ob_mol_to_smiles (input,0);
if(smiles == NULL || !strlen(smiles)) {
elog (ERROR, "SMILES generation failed! Offender was :\n %s",input);
} else if (!strlen(smiles)) {
elog (WARNING, "SMILES generation failed! Trying fallback...");
free (smiles);
smiles=NULL;
smiles = ob_mol_to_canonical_smiles (input,0);
if(smiles == NULL) {
elog (ERROR, "Cacnonical SMILES generation finally failed! Offender was :\n %s",input);
} else if (!strlen(smiles)) {
free(smiles);
smiles=NULL;
elog (ERROR, "SMILES generation finally failed! Offender was :\n %s",input);
}
elog (NOTICE, "Fallback OK");
}
molfile = strdup(input);
}
if (smiles==NULL || molfile==NULL) {
elog (ERROR,
"Input is not a V2000/V3000 molfile or InChI or SMILES: %s",
input);
}
result = new_molecule (smiles, molfile);
if (smiles != NULL) {
free (smiles);
smiles=NULL;
}
if (molfile != NULL) {
free (molfile);
molfile=NULL;
}
if (input != NULL) {
pfree(input);
input=NULL;
}
return result;
}
