Hi,
On Tue, Jul 31, 2012 at 7:22 PM, Alessandro Nascimento
<al.s.nascime...@gmail.com> wrote:
> 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.
You should minimize the molecule first.
> 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).
The file format should not matter.
> So, some questions: The conformerSearch API requires a mol2 file
> with/without hydrogens? Can the filter parameters be changed?
It requires hydrogens since the forcefields need explicit hydrogens.
> 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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