Hi OB folks,
I am brand new to OpenBabel and I`m trying to learn how to use the
conformerSearch in OB. However, I am finding some odd results and
would like to hear from you about hints on how to generate multiple
conformers using OB.
Below there is a piece of my C++ code. The code compiles fine.
However, I get a message indicating that my initial conformer does not
pass the filter. I took a look in OB documentation about the filters
in ConformerSearch and could not find clues on how to handle this
situation. I am not sure if the problem is related to the molecule or
to the file format (I am using a MOL2 file downloaded from ZINC).
So, some questions: The conformerSearch API requires a mol2 file
with/without hydrogens? Can the filter parameters be changed?
Just to clarify, I also tried to use the WeightedRotorSearch and this
method could not generate any conformer as well. Any clues?
The output:
Initial conformer does not pass filter!
Initial conformer count: 0
Generation #1 0
Generation #2 NaN
Generation #3 NaN
Generation #4 NaN
Generation #5 NaN
Generation #6 NaN
Generation #7 NaN
Generation #8 NaN
Generation #9 NaN
Generation #10 NaN
..
Code piece:
#################################################################
OBconv = new OBConversion;
OBmol = new OBMol;
// Supressing OpenBabel warning messages
messageHandler = new OBMessageHandler;
messageHandler->SetOutputLevel(obError);
OpenBabel::obErrorLog = *messageHandler;
OBconv->SetInAndOutFormats("mol2", "mol2");
bool file_read = OBconv->ReadFile(OBmol, molfile);
if (!file_read){
printf("Could not open file %s for reading.\n",
molfile.c_str());
exit(1);
}
//Checking...
// printf("Number of atoms: %d.\n", OBmol->NumAtoms());
// printf("Number of rotors: %d.\n", OBmol->NumRotors());
// printf("Number of Heavy atoms: %d.\n", OBmol->NumHvyAtoms());
// printf("Total charge: %d.\n", OBmol->GetTotalCharge());
// printf("Automatic Partial Charge? %d\n",
OBmol->HasPartialChargesPerceived());
double total=0.00;
FOR_ATOMS_OF_MOL(atom, OBmol){
total+=atom->GetPartialCharge();
}
printf("Total charge: %5.2f\n", total);
OBmol->SetTotalCharge(int(total));
printf("OBMol charge: %d\n", OBmol->GetTotalCharge());
OBconf = new OBConformerSearch;
OBconf->Setup(*OBmol, 30, 5, 5, 25);
OBconf->Search();
OBconf->GetConformers(*OBmol);
printf("Number of conformers: %d.\n", OBmol->NumConformers());
OBmol->SetConformer(1);
OBconv->WriteFile(OBmol, "test.mol2");
##########################################################################
--
[ ]s
--alessandro
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