Hi all,
I use rdkit through its Python API. As part of an iterative computation on
a molecule, I have to repeatedly remove different combinations of bonds
from it. I noticed that the calls to Chem.EditableMol() to create the em,
to em.GetMol() to get back the new molecule, and to
Hi Curt,
On Fri, Jul 10, 2015 at 11:40 PM, Curt Fischer curt.r.fisc...@gmail.com
wrote:
I use rdkit through its Python API. As part of an iterative computation
on a molecule, I have to repeatedly remove different combinations of bonds
from it. I noticed that the calls to
Hi Jane,
The Getting Started in Python documentation might be a good first place
to look:
http://rdkit.org/docs/GettingStartedInPython.html
particularly the section on substructure searching:
http://rdkit.org/docs/GettingStartedInPython.html#substructure-searching
Best,
-greg
On Wed, Jul 15,
A couple of followups here since I had some time on a plane yesterday.
On Wed, Jul 15, 2015 at 11:02 AM, Greg Landrum greg.land...@gmail.com
wrote:
On Tuesday, July 14, 2015, Michael Reutlinger rd...@mulchi.de wrote:
thanks for your answer. I also figured that the invariant feature of the
Hi,
It's not easy (for me) to read through the Java code and figure out what is
going on, but it looks to me like you are leaking rdmol in each iteration
of your loop.
The problem that the RDKit Java wrappers (really any Java wrapper created
with SWIG) has here is that the JVM doesn't know how
Hi Michael,
On Tuesday, July 14, 2015, Michael Reutlinger rd...@mulchi.de wrote:
Hi Greg,
thanks for your answer. I also figured that the invariant feature of the
AtomPair functions should be well suited. Initially, I thought that the
pi-electron and neighbouring atom count would always be
Hi Sergio,
On Tue, Jul 14, 2015 at 9:53 PM, Wong, Sergio E. wong...@llnl.gov
javascript:_e(%7B%7D,'cvml','wong...@llnl.gov'); wrote:
Dear Greg;
Thank you for the file and the suggestion. I tried following the
examples and your suggestion and yet, I am still getting some errors. Here
Hello,
Im very new to rdkit and have some questions. I want to find out how to convert a molecule into a reduced graph by identifying its functional
groups with the help of Smarts. Hence, I found the functions Chem.MolFromSmiles and Chem.MolFromSmarts. I would like to know how the SMARTS are
Hi Greg,
I know what you mean. :) I had tried that before, but executing an
rdmol.delete() at the end of the loop didn't help. And, I just re-tried
that to no avail.
I remember having a similar issue with the SDMolSupplier before, where just
reading the file consumed a ton of memory. This
Just to add, I can confirm that re-writing this in Python did indeed bounce
the memory issue I've been having. Total consumption never crossed 0.1% of
my system memory. :) Way less than the 89% I was seeing with the Java
version of the same application!
On Wed, Jul 15, 2015 at 2:05 PM, Matthew
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