Dear All,
I trying to expose in python two vector of 3D descriptors but when I compile
have got this error message
[ 96%] Built target rdMolHash
[ 96%] Building CXX object
Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o
[ 98%] Built target ChemReactions
Guillaume,
I'm not sure if this is everything, but you definitely need to put an#ifdef
RDK_BUILD_DESCRIPTORS3Dblock around the definition of MORSEs and RDFs in the
Python wrapper code.
-greg
On Thu, Oct 13, 2016 at 10:25 AM +0200, "Guillaume GODIN"
wrote:
Dear All,
Dear Greg,
Thanks for the tip, but same error after adding the if statement.
All the cpp & cpp test works fine, but I have not clue why python wrap failed.
BR,
Guillaume
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41
Hello everyone,
A new user of Rdkit and new subscriber of the mailing list reporting here.
I have a question to ask, as stated in the subject. I have googled and
consulted the documentation of rdkit, but found no answer. Basically, I want to
run a search with a smarts string on my molecule. I a
ha! that was a fun one.
The compile guards at in RDF.h:
https://github.com/thegodone/rdkit/blob/master/Code/GraphMol/Descriptors/RDF.h#L44
and MORSE.h:
https://github.com/thegodone/rdkit/blob/master/Code/GraphMol/Descriptors/MORSE.h#L44
are wrong.
By the way, the syntax:
std::vector>
like you see
?Ho yes, sorry I didn't see that!
thanks
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
Hi,? ? I spent a lot of time to explorer "How to get the property of name when
using SmilesMolSupplier"
I had a smiles file like this:===c1c1\t1\n...===where 1 means that it is
positve
So I wanted to read this smiles file via SMilesMolSupplier and I knew that the
second column is the d
Hi Hongbin,
suppl[0].GetPropNames() is an interable object, so you can use it in for
loops such as:
for i in suppl[0].GetPropNames():
print (i)
or you may convert it to a list:
l = list(suppl[0].GetPropNames())
print (l)
Cheers,
p.
On 10/13/16 11:31, 杨弘宾 wrote:
Hi,
I spent a lot of
I agree. I tend to think molecules should have GetName/SetName since this is a
common operation.
One note though:
mol.GetPropsAsDict()
Might help with introspection. There are optionally arguments that allow
looking at private and computed properties, I.e.
mol.GetPropsAsDict(True,True)
I b
Paolo, _Name might be considered a private property, you might need to use
GetPropNames(True,True) or something like that.
Brian Kelley
> On Oct 13, 2016, at 6:56 AM, Paolo Tosco wrote:
>
> Hi Hongbin,
>
> suppl[0].GetPropNames() is an interable object, so you can use it in for
> loops
Hi Paolo,?? ? Thank you for your answer. I tried and found an interesting issue:
>>> mol = suppl[1]
>>> print mol.GetProp('_Name')
>>> print list(mol.GetPropNames())---output---1[]
I guess that the _Name property is a hidden variable. ?Maybe the user cannot
find this property_name
On Thu, Oct 13, 2016 at 2:30 PM, Brian Kelley wrote:
> I agree. I tend to think molecules should have GetName/SetName since this
> is a common operation.
>
>
I used to argue about this point, but at this point I've either been
convinced or just gotten tired of the argument, so I'd be happy to ac
On 13/10/2016 05:04, Bin Song wrote:
> Hello everyone,
>
> A new user of Rdkit and new subscriber of the mailing list reporting here.
>
> I have a question to ask, as stated in the subject. I have googled and
> consulted the
> documentation of rdkit, but found no answer. Basically, I want to run
On 10/13/2016 12:12 PM, Paul Emsley wrote:
> Are you sure? I use HasSubstrMatch to match hydrogens.
Perhaps this
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05897.html
may be useful?
If OP's looking at crystal structures, they're likely dealing with pdb
data model where al
Hello Paul,
I will take a look at your code. Thank you.
Original Message
Subject: Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a
specific atom
Local Time: October 14, 2016 1:12 AM
UTC Time: October 13, 2016 5:12 PM
From: pems...@mrc-lmb.cam.ac.uk
To: r
Hello Dimitri,
Yes, I do have explicit hydrogen throughout entire process.
Thank you for the tip. I will check out the link.
Bin
Original Message
Subject: Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a
specific atom
Local Time: October 14, 2016 2:26 A
Hi Greg,
So I fix the compilation issues for python but I have a segmentation fault
error and I cannot find the error in RDF part...
Could you take a look please ?
BR,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)
Taking this off list for the moment.
On Fri, Oct 14, 2016 at 7:14 AM, Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:
> Hi Greg,
>
>
> So I fix the compilation issues for python but I have a segmentation fault
> error and I cannot find the error in RDF part...
>
>
> Could you take a look
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