Hi,
in principle there should be no restriction on the under limit for the number
of atoms, so I can’t recall exactly why we did put this 'atoms < 3’ restriction
in the code in first instance. So I guess you can safely remove this check and
replace it with a lower limit like 1 or so.
Hans
On
Hi,
I have the following Python code to rename the first residue in a PDB
file. The renaming works except that OpenBabel appends a '1',
obviously the residue number, to the new name in the mol2 output. How
can I force OpenBabel to stop altering my residue name?
import pybel
mol = pybel.readfi
Hi all,
When I use gen3d with P#P I get a molecule with two hydrogens. Should it not
be the diphosphorus molecule with chemical formula P2? Using [P]#[P]
produces the desired result but I wanted to find out why gen3d does this.
Best wishes,
Scott
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Hi,
Currently I'm working on GOLD docking results, and try to process them
through OB. Unfortunately OB doesn't understand GOLD's explicit lone pair
pseudo atoms (atom type: Lp). For mol2 -> mol2 conversion it changes it to
Xx type atoms, for sdf (sdf defines them as * type) -> mol2 they are
chang
On Fri, Nov 8, 2013 at 3:52 AM, scott_m wrote:
> Hi all,
>
> When I use gen3d with P#P I get a molecule with two hydrogens. Should it
> not
> be the diphosphorus molecule with chemical formula P2? Using [P]#[P]
> produces the desired result but I wanted to find out why gen3d does this.
>
Differe
Hi Craig,
Thanks for the reply. I used sdf:
obabel -:'P#P' -osdf > P2.sdf --gen3d
Best wishes,
Scott
On 8 November 2013 15:17, Craig James wrote:
> On Fri, Nov 8, 2013 at 3:52 AM, scott_m wrote:
>
>> Hi all,
>>
>> When I use gen3d with P#P I get a molecule with two hydrogens. Should it
>>
On Fri, Nov 8, 2013 at 8:57 AM, Scott McKechnie wrote:
> Thanks for the reply. I used sdf:
>
> obabel -:'P#P' -osdf > P2.sdf --gen3d
>
When I do this, I get a molecule with four hydrogens, not two. However, I
still think it's wrong. The SMILES specification says that the "normal
valence" for p
On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
> However even for good geometries OB has problems with bond orders
> sometimes as I pointed out the other day. Is there anything that can be
> done about that? Changing smiles?
Bond order perception is never going to be bullet-proof, part
On 2013-11-08 18:54, Geoffrey Hutchison wrote:
>
> On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
>
>> However even for good geometries OB has problems with bond orders
>> sometimes as I pointed out the other day. Is there anything that can be
>> done about that? Changing smiles?
>
> Bond o
You should probably copy *all* other files from the Open Babel GUI installation.
The overall problem is that the plugin formats are not being found. I
think that in future versions of Open Babel we will try to compile
these directly into the main Open Babel .dll as it causes problems for
people (l
I don't have the exact code to hand, but it's something like the
following in Python:
myop = OBOp.FindType("gen3d")
success = myop.Do(myOBMol)
- Noel
On 7 November 2013 18:13, Wallace Chan wrote:
> Dear All,
>
> I am having some frustration trying to generate a 3D SDF file from an InChI
> ID.
Thank you, Noel.
I already copied all the files from the Open Babel GUI installation folder, the
web page can display without error, but the part calling OpenBabel functions
just return zero or empty. However it worked fine under Visual studio
environment. I also tried to change some IIS applic
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