Hi James and Greg,
On Oct 25, 2013, at 4:03 AM, Greg Landrum wrote:
1. Do I remember correctly that there was a proposal (from
Roger) to add some auto bond-type perception to the PDB parser for
ligands (or is that just wishful thinking!)?
Roger will have to confirm this, but I
Hi James,
Regarding the AssignBondOrdersFromTemplate() method:
As far as I understood, the PDB reader assigns bond orders to the amino
acids in a protein, but if a ligand is present it puts all bonds of it to
SINGLE bonds as auto bond-type perception is not trivial (see Roger's
comments).
Question to rdkit pandas users (pandaskitters?):
I managed to have the mol_send(m) object in a pandas frame:
[image: Inline images 1]
if I do this: data['mol'].map(str).map(Chem.Mol)
I get the mol in base64 PNG:
[image: Inline images 2]
How do I display the column as rendered images (and keep
It worked! Many thanks!
g
On 25 October 2013 16:18, Greg Landrum greg.land...@gmail.com wrote:
Hi George,
Nikolas is really the expert here, but this just worked for me:
curs.execute('select molregno,mol_send(m) from rdk.mols where m@
%s',('c12c1nncc2',))
d = curs.fetchall()
df2 =
Hi George,
Glad that Greg already helped you getting it working. Just to add some information: The methods RenderImagesInAllDataFrames and ChangeMoleculeRendering are related in their effects but doing slightly different things.
RenderImagesInAllDataFrames is patching
Dear RDkit community:
I’ve been maintaining a fink package for RDkit (primarily as a dependency for
coot).
cf: http://tinyurl.com/rdkitfink
It compiles and on OSX 10.6, 10.7 and 10.8, but not 10.9. (This includes the
2013_9 pre-release, FWIW.)
With 10.9, the migration to clang++ is upon
Hi Sereina,
Sereina wrote:
Regarding the AssignBondOrdersFromTemplate() method:
As far as I understood, the PDB reader assigns bond orders to the amino acids
in a protein, but if a ligand is present it puts all bonds of it to SINGLE
bonds as auto bond-type perception is not trivial (see
There is no g++ for OSX 10.9 at all?
Would one of these work by any chance?
http://sourceforge.net/projects/hpc/files/hpc/gcc/
Igor
On Fri, Oct 25, 2013 at 12:43 PM, William G. Scott wgsc...@ucsc.edu wrote:
Dear RDkit community:
I’ve been maintaining a fink package for RDkit (primarily as a
On 25/10/13 08:09, James Davidson wrote:
Hi Roger,
Thanks for the response
The use of an integer file format flavor argument allows the caller to
customize the behavior of the readers and writers. The semantics is that a
reasonable default is zero (for all bits), but that new features may
Hi James,
Okay, now it's clear. I somehow (wrongly) thought the PDB reader would give
you the protein and the ligand as two molecules and then it wouldn't have
been a problem... I will discuss with Greg on how to best do this and get
back to you.
Best,
Sereina
2013/10/25 James Davidson
Not an easy one. Since I don't have a Mac with 10.9 installed, I can't try it
out either.
I have been able to build the rdkit with clang++ in the past without problems
and could certainly give that a try on a Linux box. Which version of clang are
you using?
What are you seeing for error
On Oct 25, 2013, at 10:11 AM, Roger Sayle wrote:
The use of an integer file format flavor argument allows the caller
to customize the behavior of the readers and writers. The semantics
is that a reasonable default is zero (for all bits), but that new
features may be added without changing
Hi James,
There's something very strange going on here with PyMol.
On Oct 25, 2013, at 1:09 PM, James Davidson wrote:
I can't see any double-bonds rendered in PyMOL:
CONECT344 10
Here atom 3 has two bonds to atom 4. Why isn't it displayed double?
This PDB *will* render
Hi Greg:
I’ve just placed two log files on http://fennario.ucsc.edu/~wgscott/temp/rdkit/
One was generated using the /usr/bin/g++ compiler on 10.9, i.e.,
zsh-% /usr/bin/g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
On Fri, Oct 25, 2013 at 11:06 PM, William G. Scott wgsc...@ucsc.edu wrote:
Hi Greg:
I’ve just placed two log files on
http://fennario.ucsc.edu/~wgscott/temp/rdkit/
The error messages look really familiar, but I unfortunately can't find a
reference for them. I will keep dredging around
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