Hi,
Does the input file contain 3D-coordinates? As far as I have seen, neither
confab nor conformer will generate an initial 3D structure if it’s not already
present.
Kind regards,
Fredrik
6 maj 2014 kl. 19:39 skrev Douglas Houston dhous...@staffmail.ed.ac.uk:
Anyone have any comment on
/usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L
outputs:
charges
descriptors
fingerprints
forcefields
formats
loaders
ops
How do I tell?
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itiwks- /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L ops
0xoutfile.xxx Additional file output
addfilenameAppend input filename to title
AddInIndexAppend input index to title
AddPolarHAdds hydrogen to polar atoms only
canonicalCanonicalize the atom order
Hi,
Is the input molecule flexible? It would be much easier to test if you
could sent it to the list.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-05-07 11:19 GMT+02:00 Fredrik Wallner fred...@wallner.nu:
Continue by running
obabel -L formats
and
obabel
OK will do.
Just out of curiosity, what is my install of Babel doing when I specify
those options? Just ignoring them, without informing the user?
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obconformer when run outputs:
Usage: obconformer NSteps GeomSteps file
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obconformer with arguments: /usr/local/bin/obconformer 10 10
crystal_ligand.sdf
outputs:
The conformers appear to be generated - how do I get them written out? The
input structure is in 3D by the way.
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Dear all,
I am working with a program (in C++) which has its own way of dealing
with atoms and molecules. I would like to use the OpenBabel library to
assign types to atoms. For now, when I need to do it I write a .xyz
file and then read it in an OBMol object and assign the types.
This works,
Never written something like this, but briefly looking at some code in
openbabel for reading molecules, you should do
atom = obMol.NewAtom();
At the beginning of each loop. Your code looks like it is just due referencing
an unset pointer, so no surprise it segfaults.
You maybe also have to do
