Hi all,
Compiling the latest version and I am having an issue I can't figure out
with RDKit 2020_03. I can compile RDKit with python, without issue. But,
when I throw the flag for the Java Swig wrappers I get this after
everything is compiled:
GraphMolJavaJAVA_wrap.cxx:227069:12: error:
Hi all,
I've been fighting this again with the 2017_09_1 and the 2018_03_1 builds.
Both fail to pass all of the tests and for neither does the python wrapper
work at all (Java Wrappers work fine). Here is the 2017_09_1 test results:
99% tests passed, 1 tests failed out of 164
Total Test time
ests in verbose mode:
>
> ctest -I 5,5 -V
> ctest -I 9,9 -V
>
> I'd also suggest to check that your Boost libraries are in your
> LD_LIBRARY_PATH, as you have built your own.
>
> Cheers,
> p.
>
>
> On 06/21/17 19:17, Matthew Lardy wrote:
>
> Hi all,
>
&
Hi all,
I'm trying to get a new build for any version of RDKit from 2016_4 to the
most reccent release. Everything builds correctly, but when I perform the
tests each version fails at the same place:
Start 5: testMultiFPB
5/116 Test #5: testMultiFPB
Passed1.99 sec
>
> The following tests passed:
> JavaAromaticTests
>
> 100% tests passed, 0 tests failed out of 1
>
> Total Test time (real) = 2.00 sec
> glandrum@Otter:/scratch/RDKit_git/build$
>
>
> I do not have CLASSPATH set and I don't think it's
f.
>
> Here is what I normally use for testing ( note I usually build into an
> rdkit_build directory via: -DCMAKE_INSTALL_PREFIX=
> )
>
>
> RDBASE=`pwd`/../../rdkit LD_LIBRARY_PATH=`pwd`/rdkit_build/lib
> PYTHONPATH=`pwd`/rdkit_build/lib/python2.7/site-packages ctest
>
in thread "main" java.lang.NoClassDefFoundError:
org/hamcrest/SelfDescribing
Is my CLASSPATH wrong? Did I forget a SO in my LD_LIBRARY_PATH?
Thanks in advance!
Matt
On Mon, Apr 18, 2016 at 9:56 AM, Matthew Lardy <mla...@gmail.com> wrote:
> My thoughts exactly. I've forg
THS=ON
>>
>> When running cmake, otherwise cmake can get very confused.
>>
>>
>>
>> Brian Kelley
>>
>> On Apr 15, 2016, at 6:26 PM, Matthew Lardy <mla...@gmail.com> wrote:
>>
>> I'll add, that remembering that cmake and ccmake ca
/rdkit/blob/master/.travis.yml
>
> Note the
>
> -D Boost_NO_SYSTEM_PATHS=ON
>
> When running cmake, otherwise cmake can get very confused.
>
>
>
> Brian Kelley
>
> On Apr 15, 2016, at 6:26 PM, Matthew Lardy <mla...@gmail.com> wrote:
>
> I'll add, that remem
in ccmake) are called, I'd love to know.
Thanks in advance!
Matthew
On Fri, Apr 15, 2016 at 2:58 PM, Matthew Lardy <mla...@gmail.com> wrote:
> Hi all,
>
> If someone has an insight I would love to hear it about how best to build
> RDKit from scratch.
>
> I am using the follow
Hi all,
If someone has an insight I would love to hear it about how best to build
RDKit from scratch.
I am using the following to build the 2015.03 release:
RedHat Linux version 6.4
gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC)
swig version 3.0.8
cmake version 3.0.0
boost version 1.53.0
t you might as well use 3.x
> if you can)
> - boost 1.58 (this is what comes with ubuntu 15.10)
> - cmake 3.2.2 (what comes with ubuntu 15.10)
>
> -greg
>
>
>
>
> On Fri, Apr 15, 2016 at 1:39 AM, Matthew Lardy <mla...@gmail.com> wrote:
>
>> Hi all,
>
Hi all,
Does someone know which version of boost, cmake, and swig seems to work
best for the current release?
Thanks in advance!
Matt
--
Find and fix application performance issues faster with Applications Manager
'),))
>
> In [20]: Chem.MolToSmiles(ps[0][0])
> Out[20]: 'CCc1c1F'
>
>
> I hope that helps,
> -greg
>
>
>
> On Mon, Sep 21, 2015 at 4:41 PM, Matthew Lardy <mla...@gmail.com> wrote:
>
>> I've repeated the previously seen behavior in Python in case
r x in
ps])
print Chem.MolToSmiles(ps[0][0])
#for p in uniq:
#print Chem.MolToSmiles(p)
#for prod in uniq:
# writer.write(prod)
else:
writer.write(m)
writer.close()
gz.close()
On Mon, Sep 21, 2015 at 12:39 PM, Matthew Lardy <mla...@gmai
Hi all,
I am attempting to transform a functional group in a series of molecules.
The reaction is pretty simple (a re-aromatization):
C=C1CC=CC=C1>>Cc1c1
The code which generates this runs without error (and it was written in
Java). What I don't understand is that the products of the
think
calling rdmol.delete() at the end of each iteration (this frees the
underlying C++ object) should help.
-greg
On Tuesday, July 14, 2015, Matthew Lardy mla...@gmail.com wrote:
Hi all,
I have had a strange issue that I can't seem to find a way around. The
following code block
not aggressive enough while cleaning up memory. I think
calling rdmol.delete() at the end of each iteration (this frees the
underlying C++ object) should help.
-greg
On Tuesday, July 14, 2015, Matthew Lardy mla...@gmail.com wrote:
Hi all,
I have had a strange issue that I can't seem
Hi all,
I have had a strange issue that I can't seem to find a way around. The
following code block consumes a ton of memory, which is strange as just
using the SD File reader I have no memory issues. I think that the issue
is related to the java garbage collection not being picked up, even
Hi all,
I am trying to open and write compressed sd files with the Java wrappers. I
know, and have, been able to do this in Python but has anyone cracked how
to read and write sdf.gz files in Java?
Thanks in advance!
Matthew
PropertyMol pmol = PropertyMol(mol)
Hope the information above helps a bit.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
[image: View Christos Kannas's profile on LinkedIn]
http://cy.linkedin.com/in/christoskannas
On 12 March 2015 at 15:33, Matthew Lardy mla...@gmail.com wrote
Hi,
I've noticed some strangeness between the Java and Python wrappers that I
have spent some time battling. If I load a SD file, via the SDMolSupplier
and then write out the file with SDWriter I lose all of the tags for the
molecules. Also if I pickle an SD file, reload it and then iterate
probably something to do with the bounding boxes (they get scaled
during the map generation process). In the previous case it was enough to
set bbox_inches='tight' when saving the image to solve the problem.
I hope this helps.
Best,
Sereina
On 21 Feb 2015, at 02:28, Matthew Lardy mla
Hi,
I am having an issue with the python similaritymaps. I am only seeing a
fraction of the molecule. Anyone else have this issue?
Thanks in advance!
Matthew
--
Download BIRT iHub F-Type - The Free Enterprise-Grade
Greg!
Matthew
On Thu, Feb 19, 2015 at 10:29 PM, Greg Landrum greg.land...@gmail.com
wrote:
On Thu, Feb 19, 2015 at 11:59 PM, Matthew Lardy mla...@gmail.com wrote:
I have been able to build models via scikit-learn with the RDKit python
wrappers. That all works beautifully!
It's a nice
2015-02-20 7:29 GMT+01:00 Greg Landrum greg.land...@gmail.com:
On Thu, Feb 19, 2015 at 11:59 PM, Matthew Lardy mla...@gmail.com wrote:
I have been able to build models via scikit-learn with the RDKit python
wrappers. That all works beautifully!
It's a nice combination, isn't it?
What
Hi all,
I know that this isn't the best forum for this, but I am stuck and was
hopeful that someone else has made it through this.
I have been able to build models via scikit-learn with the RDKit python
wrappers. That all works beautifully! What I am struggling to get are the
weights, or
/chemical-reaction-notes-i.html
Best,
-greg
On Sat, Jan 31, 2015 at 7:59 AM, Greg Landrum greg.land...@gmail.com
wrote:
Hi Matthew,
On Fri, Jan 30, 2015 at 11:06 PM, Matthew Lardy mla...@gmail.com wrote:
I am having an issue using the Smarts based Reaction transformations in
RDKit
Hi all,
I am having an issue using the Smarts based Reaction transformations in
RDKit. This is a weird transformation, but I wanted to replace any or all
of the protons on an aromatic ring with an F.
The original transformation that I tried was:
c(F)c
But that didn't work. So then I tried
to find a path
through this as well.
Thanks, as always, for responding so quickly! I'll share the logs once I
locate them!
Matthew
On Tue, Nov 11, 2014 at 8:46 PM, Greg Landrum greg.land...@gmail.com
wrote:
Hi Matthew,
On Wed, Nov 12, 2014 at 12:24 AM, Matthew Lardy mla...@gmail.com wrote
Hi all,
What I hope is a quick question. I have a smiles string of a compound with
an exo-double bond that does not specify E or Z. I want to take these
geometry unspecified smiles strings and force one conformation and return a
smiles string. So I have the following SMARTS transformation:
Hi Mattie,
I would also caution you that the version of CMake appears to be very
important. Previously, I have had no issues building the wrappers using
Cmake (v. 2.8.10.2), Boost (v.1.55), and Swig (2.0.10) on CentOS 6.4-6.5.
It took me a long time to figure that out.
Hopefully that is
.
If this is the code you are using for the distance matrix:
On Thu, Jul 17, 2014 at 12:18 AM, Matthew Lardy mla...@gmail.com wrote:
dm=[]
for i,fp in enumerate(zims_fps[:26000]): # only 1000 in the demo (in
the interest of time)
dm.extend(DataStructs.BulkTanimotoSimilarity(fp,zims_fps[1+1:26000
selected to avoid the pathological case he describes.
Dave
On Thu, Jul 17, 2014 at 5:19 AM, Greg Landrum greg.land...@gmail.com
wrote:
one other short thing.
If this is the code you are using for the distance matrix:
On Thu, Jul 17, 2014 at 12:18 AM, Matthew Lardy mla...@gmail.com wrote
Hi all,
I have been playing with the diversity selection in RDKit. I am running
through a set of ~26,000 molecules to pick a set of 200 diverse molecules.
I saw some examples of how to do this in Python (my variant of their script
below), but the memory consumption is massive. I burned through
it in a simple, easy to
use GUI front-end.
Best regards,
Igor
On Wed, Jul 16, 2014 at 6:18 PM, Matthew Lardy mla...@gmail.com wrote:
Hi all,
I have been playing with the diversity selection in RDKit. I am running
through a set of ~26,000 molecules to pick a set of 200 diverse molecules.
I saw some
) for x in
Chem.ForwardSDMolSupplier(gzip.open('a.sdf.gz')) if x is not None]
because zims keeps the whole file in memory for no good reason :-)
(is that sdf.gz big?)
Markus
On Thu, Jul 17, 2014 at 12:43 AM, Matthew Lardy mla...@gmail.com wrote:
Hi Igor,
Thanks! Maybe I am a throwback
Hi Sergio,
What version of Swig, Boost and Cmake are you using? I found that
switching to Swig (v2.0.10), Boost (v1.55), and Cmake (v 2.8.10.2) resolved
those types of errors when I was having them.
At least that worked on CentOS 6.x. :)
Matt
On Thu, Jun 5, 2014 at 1:09 PM, Wong, Sergio E.
:03, Matthew Lardy mla...@gmail.com wrote:
Hi all,
I am having this issue with the Java wrapper while trying to create a
smiles string from a RWMol class object. I don't care about trying to
figure out what is going wrong, I just want to bypass this record without
my application closing. Any
, Matthew Lardy wrote:
Hi all,
Thanks all! I should have been a bit more explicit. This is the context
of the offending line:
try {
smi = rdmol.MolToSmiles();
} catch (org.RDKit.MolSanitizeException e) {
System.err.println(Bad Mol Found: + smi);
}
I thought after reading the comments
!
Matt
On Mon, Jun 2, 2014 at 1:27 PM, Matthew Lardy mla...@gmail.com wrote:
Hi Jan,
The exception should be a org.RDKit.MolSanitizeException, but the
following code fails too:
String smi = ;
try {
smi = rdmol.MolToSmiles();
} catch (Exception e) {
System.err.println(Bad Mol Found
...@gmail.com
wrote:
The code distribution on source forge hasn't been updated in over a year.
Please use github instead
On Thursday, May 29, 2014, Matthew Lardy mla...@gmail.com wrote:
Hi Greg,
So I took a development copy from sourceforge, but I am now unable to
compile the C++ code. Is anyone
, 2014 at 9:17 PM, Greg Landrum greg.land...@gmail.comwrote:
Hi Matt,
On Fri, May 23, 2014 at 6:01 PM, Matthew Lardy mla...@gmail.com wrote:
Hi all,
I am loving the Swig based wrappers for RDKit,
Great to hear!
but I keep running across one issue. Memory use. Using the
SDMolSupplier I
Hi all,
I am loving the Swig based wrappers for RDKit, but I keep running across
one issue. Memory use. Using the SDMolSupplier I typically eat 2-3GBs of
memory to process 10-20K molecules. Is anyone else having this issue and,
if so, has anyone solved it?
Thanks in advance!
Matt
Hi all,
Hopefully this is easy, but I have an ROMol object that I want to convert
into a PDB file. It seems to me that the MolToPDBFile is exactly what I
should be using, but I am missing the protons in the resulting file.
What's weird is that the input file has protons, and I have added a step
check to ensure that it is indeed seeing the protons, and get back to you.
Thanks!
Matt
On Thu, May 1, 2014 at 8:44 PM, Greg Landrum greg.land...@gmail.com wrote:
Hi Matt,
On Thu, May 1, 2014 at 11:19 PM, Matthew Lardy mla...@gmail.com wrote:
Hopefully this is easy, but I have an ROMol
Hi all,
I've noticed that I am unable to reorder SD tags in RDKit. It appears that
no matter what I try, they get reordered in alphabetical order. Is anyone
else experiencing this behaviour?
Thanks!
Matt
--
Flow-based
Thanks Oriol and Greg!
I wasn't aware of needing to do that, but I will give it a whirl. :)
Thanks so much for your help!
Matt
On Tue, Jan 14, 2014 at 2:34 AM, Greg Landrum greg.land...@gmail.comwrote:
On Tue, Jan 14, 2014 at 3:37 AM, Oriol López Massaguer olo...@imim.eswrote:
I use
Hi all,
First Swig and Java:
While I was able to build the Java wrappers (2013-09-01-beta), and the
resulting jars passed the tests (at least the Java wrappers did) I am being
frustrated by the following error:
Exception in thread main java.lang.UnsatisfiedLinkError:
Hi Yingfeng,
Forgive me if I am jumping in without knowing all that you have tried, but
did you try pulling boost with Yum? I was able to get RDKit, and the Java
wrappers, to cleanly compile on CentOS 6.4 with that flavor of boost.
Matt
On Mon, Jul 15, 2013 at 9:39 PM, Greg Landrum
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