I'm afraid not. :-/ You could try one of the other approaches like the
genetic algorithm, and see whether it progresses faster.
On Wed, 12 Dec 2018 at 21:45, Michele Galasso
wrote:
> Hello everyone!
>
>
> I am using the weighted rotor search implemented in Open Babel in order to
> search for
Hello everyone!
I am using the weighted rotor search implemented in Open Babel in order to
search for low-energy conformers of a huge molecule.
Since the total number of rotamers is of the order 10^16, I cannot explore a
decent portion of the search space by running the code serially (I use
Ok problems solved from last post, I was missing the OBBuilder part (see
below for ethane from smiles). I think this should now be the same as what
gen3d does but with the python openbabel commands.
import openbabel
mol = openbabel.OBMol()
cv = openbabel.OBConversion()
mol = openbabel.OBMol()
cv = openbabel.OBConversion()
cv.SetInAndOutFormats('smi', outfile_type)
cv.ReadString(mol, smiles_string)
mol.AddHydrogens()
ff = openbabel.OBForceField.FindForceField(MMFF94)
# so far this has done nothing
ff.SteepestDescent(1500, 1.0e-4)
That's great, many thanks for the help. One other thing, I mentioned pybel
because I haven't got the OBMol conversion from input smiles string to
output file with 3D coordinates. Would you mind giving a quick example of
this (or directing me to online documentation, I couldn't find much here)?
Hello,
You should use:
ff.GetCoordinates(mol)
Where ff is your OBForceField class and mol is OBMol.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/7/13 scott_m js...@cam.ac.uk
That's great, many thanks for the help. One other thing, I mentioned pybel
Thanks Chris, do you have a link for that?
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Is it possible to do a weighted rotor search in pybel? I have been using
openbabel and the WeightedRotorSearch function. I couldn't find any simple
example online and wanted to find out if the approach below is ok and if
anyone would advise changes. Am I right in saying that the mol is updated to
