on error: Segmentation fault
Current thread 0x7faa949d8740 (most recent call first):
File "", line 1 in
Segmentation fault
*At core, I have 2 questions:* Is RDKit able to represent stereochemistry
about this bond if the hydrogen is implicit? It's fine if not, I just want
to k
Thanks, Greg-
>
>> What is the correct treatment of bond stereochemistry at centers for
>> which a hydrogen is required in order to specify the bond stereochemistry?
>> For example, an imine with a hydrogen substituent (trivial example,
>> F/C=N/[H]).
>>
>
> In these cases the H cannot be implici
ther ignore the md5sum
for these packages for now (this is what is done for other fast moving
packages) or to get the correct tagged version of these libraries.
- dan nealschneider
(né wandschneider)
Senior Developer
Schr*ö*dinger, Inc
Portland, OR
On Mon, Jun 25, 2018 at 2:19 PM Kaushik Lakkaraj
library is stored in
/data/kaushik/src/rdkit-Release_2018_03_2/External/CoordGen/master.tar.gz
(Is it actually maeparser, or is it coordgen?).
- dan nealschneider
(né wandschneider)
Senior Developer
Schr*ö*dinger, Inc
Portland, OR
On Thu, Jun 28, 2018 at 1:13 PM Kaushik Lakkaraju
wrote
like:
bond = mol.GetBondBetweenAtoms(begin, end)
if bond.GetBeginAtomIdx() != begin:
assert bond.GetBeginAtomIdx() == end
stereoatom1, stereoatom2 = stereoatom2, stereoatom1
bond.SetStereoAtoms(stereoatom1, stereoatom2)
bond.SetStereo(stereo)
- dan nealschneider
(né wandschneider)
S
with a shared_ptr and then allow the shared_ptr
to clean it up you're asking for trouble. Maybe you were trying to copy the
atom, and control ownership with the shared_ptr?
- dan nealschneider
(né wandschneider)
Senior Developer
Schr*ö*dinger, Inc
Portland, OR
On Tue, Dec 11, 2018
r the indices or
a Python list of atoms or atom indices.
The way that I get a list of atoms is that a user lassos them in a GUI.
- dan nealschneider
(né wandschneider)
Senior Developer
Schr*ö*dinger, Inc
Portland, OR
___
Rdkit-discuss mailing li
Navid-
If there aren't any conformers, then atoms don't have coordinates. In that
case, I'm not sure that it makes sense to measure an angle between the
atoms. Maybe you want to generate the 3d coordinates using embedmol, or a
2d depiction using rddepict.
*dan nealschneider* | s
*dan nealschneider* | senior developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>
On Wed, Sep 25, 2019 at 2:35 PM Zoltan Takacs wrote:
> Dear RDkitters,
>
> I am playing around with the assignstereochemistry function and I am
> getting confused. If I change the numb
Guillaume-
You may want to add hydrogens before embedding. Not sure *specifically* why
it's required in this case - maybe the stereo center needs a hydrogen in
order to pop it into 3d?
*dan nealschneider* | senior developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>
On
Navid-
You probably need to "sanitize" the mol:
rdkit.Chem.rdmolops.SanitizeMol(mol)
*dan nealschneider* | senior developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>
On Tue, Oct 22, 2019 at 6:31 PM Navid Shervani-Tabar
wrote:
> Hello,
>
> I am trying
You've specified that the ring is aromatic in your smiles input. Did you
mean "C1CCC2C(C1)OC(N2)=O"?
*dan nealschneider* | senior developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>
On Wed, Oct 30, 2019 at 12:00 PM Hao wrote:
> Hello,
>
> It
Looks like you're missing libRDKitmaeparser.so.1,
libRDKitcoordgen.so.1, libRDKitRingDecomposerLib.so.1,
and libRDKitDataStructs.so.1. Are they in a directory pointed to by your
LD_LIBRARY_PATH?
*dan nealschneider* | senior developer
[image: Schrodinger Logo] <https://www.schrodinger.co
umentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path
)
*dan nealschneider* | lead developer
[image: Schrodinger Logo] <https://www.schrodinger.com/&g
ROMOL_SPTR mol1(RDKit::SmilesToMol("")); // this is a
boost::shared_ptr, requires #include
std::unique_ptr mol2(RDKit::SmilesToMol("CCCC")); // requires
#include
*dan nealschneider* | lead developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>
On Thu,
In addition to Andrew's suggestions, I'd also recommend that you submit a
bug report to the maker of your other tool! They probably want to know
about this issue - I know I would if it's one of ours...
*dan nealschneider* | lead developer
[image: Schrodinger Logo] <https://w
Gustavo -
That sounds like the "maximum common substructure" problem. Here's the
relevant section in RDKit's "Getting started in Python"
https://www.rdkit.org/docs/GettingStartedInPython.html#maximum-common-substructure
*dan nealschneider* | lead developer
[i
from those
other reports was that this is something fishy with whitespace characters.
Thanks!
dan nealschneider | senior staff developer
*he/him/his*
[image: Schrödinger, Inc.] <https://schrodinger.com/>
On Mon, Apr 4, 2022 at 11:02 AM Giovanni Tricarico <
giovanni.tricar...@glpg.c
oup in Python if that would be helpful.
dan nealschneider | senior staff developer
*he/him/his*
[image: Schrödinger, Inc.] <https://schrodinger.com/>
On Tue, May 24, 2022 at 1:42 PM wrote:
> Hi,
>
>
>
> how would I get the SGroups information into a ROMol so that this is
>
perties, but so do .cif and
.mae.
I'm not speaking for Schrödinger, but this *is* what I tell our internal
developers.
dan nealschneider | senior staff developer
*he/him/his*
[image: Schrödinger, Inc.] <https://schrodinger.com/>
On Thu, Jun 16, 2022 at 7:42 AM Greg Landrum wrote:
e one, including
terminal methyls, and also =C and ≡C. If you also want the neighbor:
[!#0][#6d1]
If you want terminal methyls only:
[!#0][#6H3]
Good luck!
dan nealschneider | senior staff developer
*he/him/his*
[image: Schrödinger, Inc.] <https://schrodinger.com/>
On Mon, Jan 30, 2023
I'd also be curious how the index is causing you problems. All SD reading
code that I know about ignores those suffixes. If you're not using RDKit to
read the SD file, maybe it would be best to update whatever it is you
*are *using
to parse the file.
dan nealschneider | senior staff
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