I've finally found time to start using RDKit and started with descriptor
calculation. Following the examples on the wiki (
http://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit), I get a KeyError
any time I attempt to obtain HeavyAtomCount, RingCount, PEOP_VSA, SMR_VSA,
Slogp_VSA, EState_VSA,
to send a list of
the resulting descriptors or a correlation matrix if you or anyone else is
interested.
On Wed, Sep 17, 2008 at 11:36 PM, Greg Landrum greg.land...@gmail.comwrote:
Dear Kirk,
On Thu, Sep 18, 2008 at 12:58 AM, Robert DeLisle rkdeli...@gmail.com
wrote:
I've finally found time
without text...
sorry]
On Wed, Oct 15, 2008 at 7:59 PM, Robert DeLisle rkdeli...@gmail.com
wrote:
As you know, I've been working with descriptors in RDKit, and I think
I've
found a bug in the calculation of H-bond Acceptors. Attached is an
example
structure, N-methyl-1H-indole-6
Greg,
I notice within the Python API that RDKit has the ability to communicate
with PyMol. I have not, however, been able to find an example and haven't
quite figured it out on my own. Could you provide an example of opening a
file in PyMol through RDKit, please?
-Kirk
I agree with Nik an additional 2 pence. In fact, while reading Greg's
original note, my thoughts were essentially identical to Nik's comments.
-Kirk
On Tue, Oct 28, 2008 at 2:40 AM, nikolaus.sti...@novartis.com wrote:
Hi Greg,
maybe some comments on your suggestions.
1) Should the
Greg,
After running through the process with exception handling in place I was
able to isolate 10 structures that were being problematic. All of them had
at least one bond designated as 0 order in the SD file - much as you found
for some of the other structures previously. I assume that these
at 12:45 AM, Greg Landrum greg.land...@gmail.comwrote:
Dear Kirk,
On Fri, Nov 21, 2008 at 12:38 AM, Robert DeLisle rkdeli...@gmail.com
wrote:
After running through the process with exception handling in place I was
able to isolate 10 structures that were being problematic. All of them
Can't you get a 32-bit source file and rebuild it for 64?
On Fri, Mar 27, 2009 at 2:36 PM, George Oakman oakm...@hotmail.com wrote:
Thank you all for great comments, what I need to so is starting to be
clearer.
I just can't find a X86_64 lapack RPM for RHEL4, but I'll keep looking.
If
Greg,
Yes, that did the trick - thank you. Interestingly, my previous version
didn't seem to have that dependency. Odd.
Now if I can just get my apache web server to recognize it as well. 8^)
-Kirk
On Wed, Nov 25, 2009 at 9:47 PM, Greg Landrum greg.land...@gmail.comwrote:
Dear Kirk,
Gianluca,
Interesting. My failed Fedora 12 (32-bit) did not have any issues with
PYTHON_INCLUDE_DIR but rather the CMake - Boost library issue that Greg
describes.
-Kirk
On Wed, Jan 20, 2010 at 2:48 AM, Gianluca Sforna gia...@gmail.com wrote:
On Wed, Jan 20, 2010 at 6:03 AM, Greg Landrum
Oops! I meant Q4_2009.
I was working on a Windows system with Python 2.6. I did not build PIL from
source - I simply downloaded the Windows installer. Reverting to the 1.1.6
version was the only change I made that fixed the font error.
I have another LINUX system that has the same font error
Greg,
I found the files of interest and ran a few tests. The files resulting from
the tests are in the attached archive and here are the details.
The structures in question came from the non-aggregators set of Shoichet
which were available on his web page. My original intent was to convert the
The easiest trap is simply this:
if (m is None):
#error handling code
The problem that I have had is that this will effectively skip bad
molecules, but in a large SD file, it is difficult to find out which
molecules they were.
sd = Chem.SDMolSupplier(test.sdf)
for m in sd:
if m is None:
I've been working to build RDKit on Centos 5, and I'm hitting a very common
error. Unfortunately, none of the standard fixes have helped.
Details:
The error that I'm seeing is this:
[ 82%] Building CXX object
Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o
[ 83%] Building CXX
things like
Boost_INCLUDE_DIR and Boost_LIBRARY_DIRS all point to /usr/local/include
and /usr/local/lib, etc.
Eddie
On Nov 15, 2010, at 12:45 PM, Robert DeLisle wrote:
I've been working to build RDKit on Centos 5, and I'm hitting a very
common error. Unfortunately, none of the standard
/lib64/libboost_python.so.2: undefined symbol:
PyUnicodeUCS4_FromEncodedObject
-Kirk
On Mon, Nov 15, 2010 at 3:28 PM, Robert DeLisle rkdeli...@gmail.com wrote:
Yep, I've defintely done that. I've even gone so far as to wipe out the
directory entirely and start with a fresh RDKit
PM, Robert DeLisle wrote:
It must be something in the release version of RDKit. I just grabbed the
SVN version, put it in the same location, followed the same procedures, and
it has just compiled fine without any other changes on my part.
Greg - any ideas what the difference is here
greg.land...@gmail.com wrote:
Kirk,
On Tue, Nov 16, 2010 at 12:38 AM, Robert DeLisle rkdeli...@gmail.com
wrote:
Yes, that is also true.
The error in my most recent messages stems from the default build of
Python
supporst Unicode UCS2, but apparently boost expects UCS4
-- Forwarded message --
From: Robert DeLisle rkdeli...@gmail.com
Date: Tue, Nov 16, 2010 at 3:03 PM
Subject: Re: Re: [Rdkit-discuss] Building RDKit on CentOS 5
To: Greg Landrum greg.land...@gmail.com, Robert DeLisle
rkdeli...@gmail.com
'm sorry for the slow response. Busy day
, line 18, in
module
from rdkit import rdBase
ImportError: /usr/lib64/libboost_python.so.2: undefined symbol:
Py_InitModule4
On Tue, Nov 16, 2010 at 3:04 PM, Robert DeLisle rkdeli...@gmail.com wrote:
-- Forwarded message --
From: Robert DeLisle rkdeli...@gmail.com
Date
Peter - This is great! I've only browsed through the script you have, but I
do see a few differences. I'll give it a shot now and report back. Thank
you so much for posting this.
Greg - I ran ldd on rdBase.so, and here's the output:
libRDGeneral.so.1 =
and install, it seems to work just fine
and the images produced from RDKit are much improved. The build process is:
export CFLAGS=-fpermissive
python setup.py build_ext -i
python setup.py install
On Wed, Nov 17, 2010 at 9:51 AM, Robert DeLisle rkdeli...@gmail.com
Greg,
After finalizing my build of RDKit on CentOS (as per my previous message
thread), I decided to give it a shot on Fedora 14. I'm happy to report that
this build goes incredibly smoothly without even a hiccup. The details for
Fedora 14's standard install are:
GCC 4.5.1-4
Boost 1.44.0
-01-05 at 17:41 -0500, Robert DeLisle wrote:
I have been able to reproducibly build RDKit on CentOS 5.5, but it
required a significant amount of updating of the build components.
The attached walk-through script should get you there. I do not
recall ever seeing
to /etc/yum.repos.d/ ?
On 22 February 2011 18:41, Robert DeLisle rkdeli...@gmail.com
wrote:
What are your environment settings? You should have at minimum,
these:
$RDBASE = the directory where you have installed the RDKit code
$LD_LIBRARY_PATH = /usr/local/lib:/$RDBASE
Keeping everyone on the thread..
-- Forwarded message --
From: Robert DeLisle rkdeli...@gmail.com
Date: Apr 19, 2011 3:42 PM
Subject: Re: Re: Re: [Rdkit-discuss] Bug in MolToFile?
To: Greg Landrum greg.land...@gmail.com
Greg,
Thank you again for the off-line assistance.
Just
I will defer to Greg's expertise for a more accurate answer, but I would
suspect that the problem is the difference in using the system version of
Python and a version of RDKit that is built with a newer version of GCC.
You may be getting stuck in dependency confusion between the two versions.
/wiki/WorkingBuilds).
But even this is god knows how many permutations (gcc / boost / mpfr / gmp
/ bison / flex etc) away from mine...
I'd be interested in Greg's take on supported platforms.
What a start to the weekend!
On 10 June 2011 20:04, Robert DeLisle rkdeli...@gmail.com wrote:
I
Greg and JP,
For my own education, could this be related to having upgraded GCC through
the CentOS install instructions, but using the old Python? The new version
of RDKit would have been built with the newer GCC but the old Python may not
refer to the correct libraries?
Or am I mixing concepts
It works here on CentOS 5.6. Testing with my code goes fine, but the test
step (ctest from the build directory) results in 72/76 tests failed.
Problem with the test DB?
On Fri, Jul 1, 2011 at 5:40 AM, Greg Landrum greg.land...@gmail.com wrote:
Dear all,
This morning I tagged the beta for
RDKit-sters,
I'm working with a huge SD file that by all ways I measure it contains
~5,050,000 structures. (This is an eMolecules dataset.) In processing the
file, I've run into an odd error. Even with the following very simple
code, the file seems to be bottomless. I let it run overnight and
uses a bad SDF that ends with character 24:
$ tail -1 test.sdf | hexdump
000 24 24 24 24
004
If you provide a link to the SD file, I can also help you check.
Eddie
On Nov 21, 2011, at 10:20 AM, Robert DeLisle wrote:
RDKit-sters,
I'm working with a huge SD file that by all ways I
Andrew,
Good catch! I had wondered if there might be a size problem but couldn't
make the connection that you made. I'll find another method to partition
the file.
-Kirk
On Mon, Nov 21, 2011 at 12:01 PM, Andrew Dalke da...@dalkescientific.comwrote:
On Nov 21, 2011, at 7:47 PM, Robert
On Mon, Nov 21, 2011 at 12:22 PM, Robert DeLisle rkdeli...@gmail.comwrote:
Andrew,
Good catch! I had wondered if there might be a size problem but couldn't
make the connection that you made. I'll find another method to partition
the file.
-Kirk
On Mon, Nov 21, 2011 at 12:01 PM
to process this many structures too often 8^) but I'll
certainly give the ForwardSDMolSupplier a try just in case I do.
On Mon, Nov 21, 2011 at 1:00 PM, Greg Landrum greg.land...@gmail.comwrote:
Kirk,
On Mon, Nov 21, 2011 at 8:42 PM, Robert DeLisle rkdeli...@gmail.com
wrote
Just my $0.02. You may realize and have tried all of this already, but...
I've spent a lot of time getting RDKit built on CentOS since version
5.4. The newer versions make this much easier with updated CMake,
GCC, etc. One problem that I've had is trying to build while still
having CentOS'
Long time no email.
I'm attempting to build RDKit on CentOS 5.8 and I'm getting the following
error:
In file included from
/usr/local/include/boost/fusion/include/std_pair.hpp:10:0,
from /usr/local/include/boost/math/tools/tuple.hpp:90,
from
[b.GetEndAtomIdx()],b.GetBondType() )
for nm in Chem.GetMolFrags(em.GetMol(), asMols=True):
AllChem.Compute2DCoords(nm)
sdout.write(nm)
On Fri, May 31, 2013 at 2:41 PM, Robert DeLisle rkdeli...@gmail.com wrote:
I am attempting to reduce a molecule (attached SDF) to just its ring
systems using
Hello, all. Long time, no see.
I have a project in which an application is being developed in Java and I
would like to use some of the RDKit functionality to enhance it. I can
easily write the Python code to do what I need, but I need to get that into
a form that can be accessed from Java.
The
Hi again, all!
I'm trying to install RDKit on a 64-bit Windows 7 instance (in
VirtualBox). I've done the following:
installed Python 2.7 (32-bit)
installed NumPy (for Python 2.7 32-bit)
installed PIL (for Python 2.7 32-bit)
environment variables are:
RDBASE = c:\RDKit_2014_09_1
PYTHONPATH =
OOPS!
On Sun, Nov 9, 2014 at 4:37 PM, Robert DeLisle rkdeli...@gmail.com wrote:
Hi again, all!
I'm trying to install RDKit on a 64-bit Windows 7 instance (in
VirtualBox). I've done the following:
installed Python 2.7 (32-bit)
installed NumPy (for Python 2.7 32-bit)
installed PIL
://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02381.html
On Sun, Nov 9, 2014 at 4:37 PM, Robert DeLisle rkdeli...@gmail.com wrote:
OOPS!
On Sun, Nov 9, 2014 at 4:37 PM, Robert DeLisle rkdeli...@gmail.com
wrote:
Hi again, all!
I'm trying to install RDKit on a 64-bit Windows 7
, you can get win64 python binaries for numpy and many other useful
packages here: http://www.lfd.uci.edu/~gohlke/pythonlibs/
-greg
On Mon, Nov 10, 2014 at 12:46 AM, Robert DeLisle rkdeli...@gmail.com
wrote:
Let's try this one last time. Somehow I got two early sends of that
e-mail. I
RDkit-ers,
I've been working with RDKit from Java for a while now and I'm spinning my
wheels due to being too new to Java. I'm very comfortable with RDKit from
Python, but Java is a new animal for me. I've downloaded the RDKit Java
binaries and I have this:
boost_system-vc100-mt-1_51.dll
By the way, I'm looking through the Java wrapper and I'm not seeing any
functions that would provide access to the 2D depiction code from Java.
Does that exist and I'm just not seeing it?
-Kirk
On Sun, Nov 30, 2014 at 9:37 PM, Robert DeLisle rkdeli...@gmail.com wrote:
Thanks, Greg
Thanks again, Greg!
I can imagine 2D depiction is a tricky bit of code. I'll leave that one to
the experts.
All the best!
Kirk
On Nov 30, 2014 9:47 PM, Greg Landrum greg.land...@gmail.com wrote:
On Mon, Dec 1, 2014 at 5:39 AM, Robert DeLisle rkdeli...@gmail.com
wrote:
By the way, I'm
21')
> mol = AllChem.AddHs(mol)
> AllChem.EmbedMolecule(mol)
> AllChem.MMFFOptimizeMolecule(mol)
> s.ShowMol(mol, name = 'bilastine', showOnly = False)
> s.Zoom('bilastine')
> s.SetDisplayStyle('bilastine', 'sticks')
>
> I obtained the expected display:
>
>
>
> Cheers,
> p.
>
>
&
Back again!
I apologize for resurrecting an old topic, but I'm once again trying to
work with PyMOL through RDKit. I've been following the approach in this
thread (
http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00325.html)
but it seems not to work any longer. I'm using
In working with RDKit I've been able to align 2D structures based upon a
common core of MCS using
AllChem.GenerateDepictionMatching2DStructure(m,p)
The next step for me is to generate 3D structures and align them based upon
that same common core. Obviously this leads to multiple steps, not the
y.cluster.hierarchy*.
>
> z = hc.linkage(dist_mat)dendrogram = hc.dendrogram(z, labels=dist_df.columns,
> leaf_rotation=90)plt.show()
>
>
> A helpful page for dendrograms using SciPy is this one:
> https://joernhees.de/blog/2015/08/26/scipy-hierarchical-clustering-and-d
Next up is clustering...
I've got about 350 structures to cluster and I've worked through the
example code from the RDKit Cookbook (
http://www.rdkit.org/docs/Cookbook.html#clustering-molecules). All seems
well and good there, but I would like to see the dendrogram. I see that
there is a
RDKitters,
I'm working on a project in which I want to align a collection of
structures with their most similar structures and display the results in
PyMOL. To accomplish this, I've built a Python script similar to the one
attached here in which I start with pairs of structures, find the MCS of
Even better! Thanks, Greg.
On Mon, Apr 18, 2016, 12:37 AM Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Kirk,
>
> Welcome back!
> Those were fixed for the 2015.09 release:
> https://github.com/rdkit/rdkit/pull/644
>
> Best,
> -greg
>
>
> On Mon,
Long time no message!
Anywho, I've been working today with RDKit 2015.03.01 and in the process of
generating a grid of molecule depictions (Draw.MolsToGridImage()), I
received the error message below.
>From the last line, it seems there has been an API change that changes
tostring() to
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