If you want to use C++, there is ESBTL, "a PDB parser and data
structure for the structural and geometric analysis of biological
macromolecules" (http://esbtl.sourceforge.net), MMTK
(http://dirac.cnrs-orleans.fr/MMTK/). Open Babel can read PDB files
but the last time I checked it was not possible t
On Mon, May 9, 2011 at 10:27 AM, JP wrote:
> Using RDKit 2010.10
> Some error messages need to be more helpful. For e.g. in a 10,000 molecule
> smiles file:
> [23:07:01] Can't kekulize mol
> Traceback (most recent call last):
> File "./x.py", line 314, in
> main()
> File "./x.py", line 3
On Mon, May 9, 2011 at 7:29 PM, Andrew Fant wrote:
>
> If you need to work with PDB files, you might look at biopython, which has
> support for that format available. I don't know specifically about occupancy
> and B-factors, but it would be someplace to start.
>
Along those lines, another one
On May 9, 2011, at 11:29 AM, Greg Landrum wrote:
> Hi Paul
>
> On Mon, May 9, 2011 at 1:13 PM, wrote:
>>
>> Dear folks,
>>
>> is there a way to add occupancy & B-factors (e.g. 1.00 50.0) to a PDB file?
>>
>
> At the moment the RDKit has no way of processing PDB files.
>
> -greg
If you nee
Hi Paul
On Mon, May 9, 2011 at 1:13 PM, wrote:
>
> Dear folks,
>
> is there a way to add occupancy & B-factors (e.g. 1.00 50.0) to a PDB file?
>
At the moment the RDKit has no way of processing PDB files.
-greg
--
Wha
Dear Adrian,
On Mon, May 9, 2011 at 2:24 PM, Adrian Schreyer wrote:
> Hi Greg,
>
> there is a typo on the page describing the creation of a database
> using eMolecules:
>
> sed in the form 's/\\//' to escape backslashes will only replace
> the first occurrence of the match, the 'g' at the end
Dear Paul,
On Mon, May 9, 2011 at 4:28 PM, wrote:
>
> the Wiki is a great place to start right from scratch with the RDKit ML
> capabilities!
Glad to hear it.
>
> However, I wonder how to build a 3-class model:
>
> "
> for i,m in enumerate(ms):
> if m.GetProp('ACTIVITY_CLASS')=='active':
> a
Hi JP,
They will be publicly available. I'll send a link when they are.
-greg
On Mon, May 9, 2011 at 12:20 PM, JP wrote:
>
> Dearest Greg,
> Are your slides about the RDkit DB cartridge talk in Cambridge publicly
> available?
> Cheers
>
> Jean-Paul Ebejer
> Early Stage Researcher
> InhibOx Ltd
Dear Greg,
the Wiki is a great place to start right from scratch with the RDKit ML
capabilities!
However, I wonder how to build a 3-class model:
"
for i,m in enumerate(ms):
if m.GetProp('ACTIVITY_CLASS')=='active':
act=1
else:
act=0
pts.append([m.GetProp('CompoundName')]+list(descrs[i])+[
Hi Greg,
there is a typo on the page describing the creation of a database
using eMolecules:
sed in the form 's/\\//' to escape backslashes will only replace
the first occurrence of the match, the 'g' at the end is necessary to
replace all occurrences on a line.
grep '6172136' eMolecules-20
Dear folks,
is there a way to add occupancy & B-factors (e.g. 1.00 50.0) to a PDB file?
Thanks & Cheers,
Paul
This message and any attachment are confidential and may be privileged or
otherwise protected from disclosure. If you are not the intended recipient,
you must not copy this message or
Dearest Greg,
Are your slides about the RDkit DB cartridge talk in Cambridge publicly
available?
Cheers
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
36-37 Pembroke Street
Oxford
OX1 1BP
UK
(+44 / 0) 1865 262 034
This email and any files transmitted with it are confiden
Using RDKit 2010.10
Some error messages need to be more helpful. For e.g. in a 10,000 molecule
smiles file:
[23:07:01] Can't kekulize mol
Traceback (most recent call last):
File "./x.py", line 314, in
main()
File "./x.py", line 303, in main
mols = doSomething(...)
File "./x.py",
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