On Fri, Oct 25, 2013 at 11:06 PM, William G. Scott 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 though.
One was
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
--with-gxx-include-dir=/usr/include/c++
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 dou
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 chang
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 messag
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
> Hi S
It also comes with /usr/bin/llvm-g++
but I didn’t get very far with that either.
In addition, fink has a gcc-4.8, and I get further with that, but it fails at
the linking step, I think with the boost libraries, probably as a result of
mixing compilers. So I tried re-compiling those boost libr
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 fe
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 wrote:
> Dear RDkit community:
>
> I’ve been maintaining a fink package for RDkit (primarily as a dependency
>
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
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 u
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 t
It worked! Many thanks!
g
On 25 October 2013 16:18, Greg Landrum 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 = pd.DataFram
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 = pd.DataFrame(d,columns=('molregno','pkl'))
df2['romol']=df2.apply(lambda x:Chem.Mol(str(x['pkl'])),axi
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 th
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). However,
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 be added
> without changing the API/ABI
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
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