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 low
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 a
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()
cv.SetInAndOutFormats('smi
Thanks Geoffrey, that helps alright but I am still stuck with zero
coordinates when I write to an output file (say mol2 or com). What am I
still missing?
mol = openbabel.OBMol()
cv = openbabel.OBConversion()
cv.SetInAndOutFormats('smi', outfile_type)
cv.ReadString(mol, smiles_string)
mol.AddHydrog
> 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)
ff.WeightedRot
Thanks Chris, do you have a link for that?
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On 13/07/2012 14:46, scott_m wrote:
> Thanks for the reply but that doesn't seem to be working for me (code below).
> If I just want to get a rough set of coordinates, what should I do? I see
> that gen3d (see link below) does a weighted rotor search as part of the
> process of making 3d coords but
Thanks for the reply but that doesn't seem to be working for me (code below).
If I just want to get a rough set of coordinates, what should I do? I see
that gen3d (see link below) does a weighted rotor search as part of the
process of making 3d coords but I wanted to just get the 3d coords and
spec
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
> That's great, many thanks for the help. One other thing, I mentioned pybel
> because I haven't g
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)?
Wha
> anyone would advise changes. Am I right in saying that the mol is updated to
> the best conformer and this is what will be written to the output file?
Yup. This is very similar to my version of this -- I usually usually something
like:
ff.SteepestDescent(1500, 1.0e-4)
ff.WeightedRo
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
t
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