Hi,
I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64
...
[ 82%] Building CXX object
Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o
[ 83%] Building CXX object
Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o
[ 83%] Building CXX object
On 25/08/10 16:14, Greg Landrum wrote:
Hi Paul,
On Wed, Aug 25, 2010 at 7:26 AM, Paul Emsleypaul.ems...@bioch.ox.ac.uk
wrote:
Hi,
I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64
...
unsigned long)::s_data' can not be used when making a shared object;
Hi All,
I've been tinkering a bit more with RDKit and having fun.
I have hit a problem though. I am trying to reproduce Greg's Generating
3D coordinates in RDKit-overview.pdf in C++:
This is what I have (mostly via cut 'n paste):
int
main(int argc, char **argv) {
std::string
It's kind of interesting (and encouraging) that the optimizer doesn't
completely freak out when you hand it a 2D conformer. :-)
Ah... :)
What makes 3D coordinates? (I'm guessing it's a one-liner somewhere...)
It is indeed a one-liner (two lines with a bit of error checking).
Hi,
If I try to compile using RDKit's Invariant.h using g++ with -Wundef:
/home/paul/rdkit/svn/rdkit/trunk/Code/RDGeneral/Invariant.h:142:7:
warning: INVARIANT_ASSERT_METHOD is not defined
/home/paul/rdkit/svn/rdkit/trunk/Code/RDGeneral/Invariant.h:151:7:
warning: INVARIANT_SILENT_METHOD is
On 15/09/10 05:38, Greg Landrum wrote:
Dear all,
Thanks to some really great help from Gianluca Sforna and Riccardo
Vianello, the RDKit build system has been updated to make installing
the software in standard locations (like /usr/local on linux machines)
easier. The changes should also make
On 18/09/10 05:19, Greg Landrum wrote:
On Sat, Sep 18, 2010 at 12:05 AM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
So now with the replace function in python I can easily remove
sterochem information from the molecule.
smiles_corrected = smiles_broken.replace(@,)
Once I
Hi,
It seems to me that the declaration void assignRadicals(RWMol mol)
needs to be added to MolOps.h
Cheers,
Paul.
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As a hack, I suppose that you could add
transform=scale(0.2) (or some such) to the attributes of the paths for
the glyph symbols.
i.e.
replace
path style=stroke:none; d=M 0.5 1.765625 L 0.5 -7.046875 L 5.5
-7.046875 L 5.5 1.765625 L 0.5 1.765625 Z M 1.0625 1.21875 L 4.9375
1.21875 L 4.9375
Hi,
I'm running into problems when I try to kekulize carbazole.
The description I start with is that all the bonds are marked as
Bond::AROMATIC and I do setIsAromatic(true) on all the atoms (which are
all non-hydrogens). The explicitValence() for the N is 3.
MolOps::Kekulize() fails in that
On 31/10/10 14:18, Greg Landrum wrote:
Hi Paul,
On Sun, Oct 31, 2010 at 12:09 PM, Paul Emsley
paul.ems...@bioch.ox.ac.uk wrote:
I'm running into problems when I try to kekulize carbazole.
The description I start with is that all the bonds are marked as
Bond::AROMATIC and I do
Hi,
Is there a web presence for the C++ documentation that I am missing?
The easy-to-find link:
http://rdkit.org/C++_Docs
seems empty.
Thanks,
Paul.
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Greg,
Just a small FYI:
According to ctfile.pdf, the mass difference on the atom line in the
atom block should be clamped between -3 to 4 (inclusive).
I discovered this because MolToMolFile() had written out a mol file with
mass diffs of -11, -13, -15 :)
(I had presumed that when I used
Hi Greg,
Maybe I'm missing something...
Is it possible for you to add an rdkit_headers for MolChemicalFeature.h
and friends in Code/GraphMol/MolChemicalFeatures/CMakeLists.txt?
Thanks,
Paul.
--
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On 10/04/12 12:01, Greg Landrum wrote:
On Tue, Apr 10, 2012 at 11:07 AM, Paul Emsley
paul.ems...@bioch.ox.ac.uk wrote:
(Just making sure I have not missed anything...)
Is there a function that generates unique atom names (using
at-setProp(name, name) presumably) for a given molecule? (I
Hi all,
(Sorry for another noob question)
When creating a 2d depiction, or otherwise, is there a way to turn a
carboxylate (with ONEANDAHALF bonds between the carbon and oxygens) into
something with a carbonyl oxygen (DOUBLE) and a hydroxyl oxygen (SINGLE)?
Cheers,
Paul.
On 15/04/12 16:36, Paul Emsley wrote:
On 14/04/12 06:14, Greg Landrum wrote:
On Thu, Apr 12, 2012 at 1:05 PM, Paul
Emsleypaul.ems...@bioch.ox.ac.uk wrote:
When creating a 2d depiction, or otherwise, is there a way to turn a
carboxylate (with ONEANDAHALF bonds between the carbon and oxygens
On 13/04/12 05:37, Greg Landrum wrote:
I'm very happy to announce that the next version of the RDKit --
2012.03 (a.k.a Q1 2012) -- is released.
Cool - thanks. Compiling now.
In the pages:
http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2012/
http://sourceforge.net/projects/rdkit/files/
Hi all,
I am trying to write a C++ function to examine an RDKit::ROMol... but
running it from a python script:
m = Chem.MolFromSmilesString('Oc1c1')
do_cool_stuff(m)
my C++ (which gets swigged) is:
PyObject *do_cool_stuff(PyObject *pyo) {
RDKit::ROMol *mol = magic(pyo);
On 30/04/12 08:39, Uwe Hoffmann wrote:
Hi,
Am 29.04.2012 16:19, schrieb Paul Emsley:
I am trying to write a C++ function to examine an RDKit::ROMol... but
running it from a python script:
m = Chem.MolFromSmilesString('Oc1c1')
do_cool_stuff(m)
my C++ (which gets swigged
On 07/05/12 12:49, paul.czodrow...@merckgroup.com wrote:
Dear RDKitters,
when typing in
from rdkit.sping import PIL
I end up in this error message
Traceback (most recent call last):
File stdin, line 1, inmodule
File
On 07/05/12 15:13, Uwe Hoffmann wrote:
hi,
Am 07.05.2012 14:40, schrieb Gonzalo Colmenarejo-Sanchez:
Hi,
I'm using these compilation options:
g++ -o tanird tanird.cpp -I$RDBASE/Code -I$RDBASE/Extern -L$RDBASE/lib
-lChemReactions -lFileParsers -lSmilesParse -lDepictor -lSubstructMatch
On 23/05/12 13:24, JP wrote:
The generator is going to give me an empty (third) molecule? So I
have to always dirty my code with m.GetNumAtoms() 0 in that loop.
What is the empty molecule is at the end of the file (ouch)?
I'm curious about this point in particular. I don't know the
Hi,
I've been trying to read boost python docs and I am lost...
I'd like to return a PyObject *. I have a RDKit::RWMol, say - or a
pointer to a new one if need be...
// return a regularized molecule (copy of input with coordinates replaced)
PyObject *
coot::regularize(PyObject *mol_in_py) {
On 02/06/12 04:44, Greg Landrum wrote:
On Fri, Jun 1, 2012 at 1:41 PM, Paul Emsleypaul.ems...@bioch.ox.ac.uk
wrote:
I'd like to return a PyObject *. I have a RDKit::RWMol, say - or a
pointer to a new one if need be...
If you are using a boost.python interface, and your function is
seems to have got stuck - trying again...
Original Message
Subject: Re: [Rdkit-discuss] RDKit-based implementation of QED
(quantitative estimation of drug-likeness)
Date: Mon, 11 Jun 2012 06:57:28 +0100
From: Paul Emsley paul.ems...@bioch.ox.ac.uk
To: rdkit-discuss
On 23/06/12 14:05, Paul Emsley wrote:
if you do encounter such, your solution may be somewhat simpler.
Ooops, I meant:
if you do *not* encounter such ...
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On 06/07/12 10:06, JP wrote:
I just noticed that this is a user meeting and not a dev one - so
perhaps such a topic is out of scope...
What's the difference?
A user uses python and a dev uses python, boost.python and c++?
Anyway, I too (AFAICS ATM) would be interested in your suggestion
On 06/07/12 10:27, JP wrote:
Steifl -- that is a really crafty and less painful way how to go about
it.
The SMILES is in fact, a wget call away - since I am processing PDB
deposited structures.
http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG
It is not clear to me how the SMILES
On 19/07/12 13:28, Fabian Dey wrote:
Dear all,
I am having difficulties installing RDKIT on a Centos 5.6 (with python
bindings).
I compiled and installed the latest numpy, boost and cmake version
from their sources (I had also tried using
the versions available through yum - which are
homebrew is using the old svn repo?
On 09/10/12 22:33, James Swetnam wrote:
George-
My templating fix was submitted as 2155, and HEAD in SVN is at 2234.
I'm not terribly familiar with homebrew, or why it thinks 2148 is HEAD
James
On Tue, Oct 9, 2012 at 2:27 PM, George Papadatos
On 22/01/13 05:40, Greg Landrum wrote:
Hi Paul,
On Mon, Jan 21, 2013 at 4:13 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk
wrote:
I am making heavy weather of the following problem - and am wondering if I
am missing something (such as a useful RDKit function).
I am working on this beasty
On 25/04/13 23:43, hari jayaram wrote:
Hi
I did a
export RDBASE=/home/hari/RDKit_2012_09_1
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib
Then cd into the build directory
Run cmake ..
Then run make
At around 24% I get the following error ( see below)
I installed the Ubuntu blessed
On 03/09/13 20:21, Jan Domanski wrote:
Hi,
I'm trying to trivially modify the coordinates of the 0th atom of the
0th conformer in a (3D) ROMol called m. To do that I need to get the
conformer:
RDKit::ROMol m = ...;
RDKit::Conformer conf = m.getConformer(-1);
guessing somewhat, that
https://www.dropbox.com/sh/a3s55kmxa37yx7e/vLC5uea1xP
Paul.
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On 25/10/13 08:09, James Davidson wrote:
Hi Roger,
Thanks for the response
The use of an integer file format flavor argument allows the caller to
customize the behavior of the readers and writers. The semantics is that a
reasonable default is zero (for all bits), but that new features may
On 13/01/14 17:54, JP wrote:
RDKitters!
Finally back on the mailing list!
I am sure we've been through this at the UGM (my mind must have
wandered off!), but a quick question about the PDB reader and bond
perception. Is this supported with the current PDB reader? I
remember that
On 05/04/14 19:04, Michal Krompiec wrote:
For example, it does not work well
for long conjugated oligomers - sometimes it produces molecular knots
instead of straight strands, and is quite slow for large systems.
Can you expand on that? What sort of long conjugated oligomers were you
Hi Greg,
I don't know if you care about this sort of thing, but if you do, then
you should escape - i.e. \@ - (at least) one of the @s here (in Atom.h)
//! tetrahedral: clockwise rotation (SMILES @@)
So that the output html makes more sense. Currently see
Hi,
Why are the structure images in the RDKit documentation nice and smooth
but mine have the jaggies?
What do I have to do to my PIL (or something?) for such smoothness?
Thanks,
Paul.
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On 21/07/14 17:22, Greg Landrum wrote:
Hi Paul,
On Mon, Jul 21, 2014 at 3:36 PM, Paul Emsley
pems...@mrc-lmb.cam.ac.uk mailto:pems...@mrc-lmb.cam.ac.uk wrote:
Why are the structure images in the RDKit documentation nice and
smooth but mine have the jaggies?
The jagged lines
On 26/08/14 10:42, acanada wrote:
What is the best approach to write mol/sdf files for a compound which I
already have chebi, inChi?
m=Chem.MolFromInchi('InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3')
print file('foo.mol','w+'),Chem.MolToMolBlock(m)
On 25/09/14 18:06, paul.czodrow...@merckgroup.com wrote:
Dear RDKitter,
on my new Windows laptop, I run into this issue:
import pandas as pd
import rdkit.Chem as Chem
from rdkit.Chem import PandasTools
=
ValueError Traceback (most recent call last)
ipython-input-6-52de9e808c94in
Dear Paolo (I presume :-),
I'd like to get the ro values for the bonds in an MMFF. I have the
following so far:
void mmff_bonds(RDKit::ROMol mol_in) {
RDKit::MMFF::MMFFMolProperties *mmffMolProperties = new
RDKit::MMFF::MMFFMolProperties(mol_in);
ForceFields::ForceField *field = new
On 30/09/14 00:15, Paolo Tosco wrote:
I'm afraid currently there is no public method to get r0 and kb from
ForceField contribs. I have attached a C++ sample program which shows
how to get the information you need from a ROMol.
Ah! - His eyes opened!
Thanks very much.
P.
Hi RDKitters,
I'm a bit lost with boost::python/RDKit/MacOSX.
I have a boost::python function:
RDKit::ROMol *hydrogen_transformations(const RDKit::ROMol r);
which is exposed like this:
BOOST_PYTHON_MODULE(pyrogen) {
def(hydrogen_transformations, hydrogen_transformations,
On 21/03/15 04:48, Greg Landrum wrote:
Does anyone see a problem with me doing a commit there that removes
all the code and just leaves a look in github readme?
I would have found this useful :-)
Paul.
--
Dive
Dear RDKitters,
Is is clear what the case of the second character of an atom symbol in
the atom block of a MolFile should be? i.e. "CL", "Cl" or either?
Thanks,
Paul.
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Moving on...
Now I get the message (see below). What's the difference?
In the Release-based link.txt we have:
-install_name
/Users/pemsley/autobuild/b-e-l/rdkit-Release_2015_03_1/build/lib/libSLNParse.1.dylib
In the git-based link.txt we have:
-install_name
@rpath/libSLNParse.1.dylib
Is
On 23/02/2016 15:52, Greg Landrum wrote:
On Tue, Feb 23, 2016 at 3:50 PM, Paul Emsley
<pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
This seems to be the relevant difference in the cmake output:
[ 3%] Linking CXX shared libra
Using:
Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.5.0
and boost_1_54_0:
Scanning dependencies of target testMatCalc
[ 29%] Building CXX object
Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o
[ 30%] Building CXX
Yes, but not for boost.
On 23/02/2016 13:19, Giuseppe Marco Randazzo wrote:
> Are you using homebrew?
>
>> On 23 Feb 2016, at 14:17, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:
>>
>>
>> Using:
>> Apple LLVM version 6.1.0 (clang-602.0.49) (based
says: "entry in periodic table"
I interpret this to mean "Cl", since that's what one finds in the
typical periodic table.
The RDKit, curiously, agrees with me. ;-)
:-)
-greg
On Mon, Jan 18, 2016 at 8:45 AM, Paul Emsley
<pems...@mrc-lmb.cam.ac.uk <mailto:pems...
Dear RDKitters,
I have the following test code:
std::string smiles="Clc1c1";
RDKit::ROMol *m_local = RDKit::SmilesToMol(smiles);
RDDepict::compute2DCoords(*m_local);
RDKit::Conformer conf = m_local->getConformer();
WedgeMolBonds(*m_local, );
bool includeStereo = true;
Hi Greg,
I tried to investigate this further with github rdkit but I am as yet
unable to configure/cmake it yet on this Mac (something related to boost
python has changed) :-/ :-) - will keep poking at it and/or abstracting
it...
Thanks,
Paul.
On 19/02/2016 09:19, Greg Landrum wrote:
>
>
>
On 18/03/2016 19:23, Mendez Giraldez, Raul wrote:
> Yes, I think so Paul. my $LD_LIBRARY_PATH points towards the installed boost
> (by conda) is :
>
>
On 17/03/2016 18:00, Mendez Giraldez, Raul wrote:
> Hi everybody,
>
> I'm trying to build RDKit on Red Hat Enterprise Linux Server release
> 5.11 and I get the following problem after trying to import rdkit libraries:
>
>
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
> Type "help",
Greg,
RDKit is becoming increasingly popular and is getting picked up by third
parties, including
the Linux distros. It seems to me that several RDKit library names are too
generic (and
hence confusing) for such an environment: I have in mind libs such as
Alignment, Catalog,
FileParsers
On 19/08/2016 12:52, Greg Landrum wrote:
>
> It seems logical to me, though I would probably go with RDKit instead of RD
> as the prefix.
OK, that's clearer yet.
--
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I'd like to pick apart this comment:
On 19/08/2016 15:45, Igor Filippov wrote:
> It is sometimes a bit of a pain to collect the list of the dependencies.
Do you mean that (for example) if you wanted to link with
libMolChemicalFeatures, you also
have to add libSubstructureMatch and
On 05/09/16 17:27, ??? wrote:
Hi, Menaka,
An easy way I suggest is to install boost via package manager, for
example:
$ sudo apt-get install
libboost-devlibboost-system-devlibboost-thread-devlibboost-serialization-devlibboost-python-devlibboost-regex-dev
and if you're on fedora you can
Hi RDKiters,
Is it possible to store (PDB) atom names in sdf files? If so, how is this
done? (It was not
clear to me after reading CTFile.pdf.)
(I hope that this question is allowed.)
Thanks,
Paul.
--
On 29/09/16 15:12, Marco Stenta wrote:
> Dear Colleagues,
> I am working on intramolecular hydrogen bonds, formed between
> donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper:
> Kuhn, B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601.
>
> I will use SMARTS and RDKIT to
Files 1.pdb and 2.pdb do not contain CONECT records (so missing bond
orders?).
File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't
parse that (seems valid to me, FWTW).
Paul
On 22/09/16 11:15, Amit singh wrote:
Hi
Files a.pdb and b.pdb are from RDKit test data (working
On 07/11/2016 12:37, Axel Pahl wrote:
>
> amongst other options, I can generate an RDKit mol object by one of
> these two ways:
>
> mol1 = Chem.MolFromSmiles()
> mol2 = Chem.MolFromSmarts()
>
> Is there a possibility to detect for a given mol object whether it was
> generated from Smiles or
On 18/11/2016 18:35, Gianluca Sforna wrote:
> I just wanted to mention that coot (crystallographic macromolecular
> building toolkit)[1] is the first package (at least, that I know of)
> requiring rdkit as a dependency under review [2] to enter Fedora
> repositories.
I've been cheering you on
On 18/11/2016 23:47, Greg Landrum wrote:
> Hopefully you know that there is already a Cairo-based renderer in C++ and are
> modifying/improving that?
Oh. Either I didn't know about that or I'd forgotten about it. My code was
well under-way
before I heard about David's contribution and I
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 19/12/2016 10:42, Jean-Marc Nuzillard wrote:
> Thank you all!
>
> One more point:
>
> How do I get the bond indexes for which the E/Z configuration has been set?
> I seems there are no "magic" properties for bonds and no HasProp() function
> for bonds.
Iterate through the bond list and use
On 20/12/16 15:13, Yingfeng Wang wrote:
> Paolo,
>
> Thanks. I figure out this problem. The new cmake command is
>
> cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DMSVC_RUNTIME_DLL=C:/Windows/System32/msvcr100.dll
> -DRDK_USE_BOOST_SERIALIZATION=OFF -DBOOST_ROOT=C:/boost
>
On 13/07/17 18:19, Abhik Seal wrote:
Hello
I am trying to generate 3d descriptors like RDF/MORSE using with
2017.03.01 release of rdkit and i am getting an error like module'
object has no attribute 'CalcRDF' . I have Eigen3 installed as well.
Any point outs what can be the issue ?
Here is
Dear Greg,
What license(s) will you allow for Contrib code? Is the Mozilla Public License
acceptable?
Thanks,
Paul.
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On 09/05/2017 05:27, Hongbin Yang wrote:
> Hi, all,
>
> By default, rdkit uses pillow to render images when using
> rdkit.Chem.DrawMolecule. But
> the quality is not good enough, like this:
The effect you discuss is called aliasing. You want anti-aliasing.
> If memory does not fail me,
On 16/06/2017 12:08, JP wrote:
Hi Folks,
Must have been eons ago last time I posted to this mailing list. The italians have a saying
"chi non muore si rivede".
I am trying to install the RDKit (release 2017_03_2) from source, without conda, and I
thought this will be a breeze. But I am
On 09/05/2018 16:27, carlo del moro wrote:
we would like to know if it is possible to map the atom's ID of a SMILES represented substructure to the
atom sequence of a ligand contained in a pdb file. This in order to get the spatial coordinates related to
such substructure.
Depending on
On 10/05/2018 10:39, carlo del moro wrote:
I put an example for better explain my problem.
starting from a PDB representing HPE, I use RDKIT/obabel for calculate the
relative SMILES.
The three-letter-code (chemical component id) in a PDB file has meaning - it is a pointer to chemistry. The
On 29/12/2017 19:01, Drew Gibson via Rdkit-discuss wrote:
Hello, and compliments of the season to you, RDKitters :)
I'm having trouble getting the conda build of the DB package
(rdkit-postgresql95) working.
The issue I'm having occurs when trying to initialise the rdkit DB extension on
a
On 13/01/2018 18:52, Rajarshi Guha wrote:
Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query is
failing when the query SMILES is
C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3
Within [] the formal charge must be specified:
On 04/12/2019 08:28, Illimar Hugo Rekand wrote:
Hello, everyone
I was wondering if there is any reason for why aromaticity and perceived bond
orders are not set properly when using the MolFromPDB-function for RNA PDB
files, while it works perfectly for protein PDB files?
You shouldn't be
On 27/08/2020 20:15, Jason Biggs wrote:
Everything I know about C++ I learned just so that I can write a link
between an interpreted language and the rdkit, so there are definitely
some gaps in my knowledge.
What I'm trying to understand right now is the expected lifetime of an
Atom pointer
On 05/08/2020 19:44, Nikhil Maroli wrote:
I wanted to add atom types in mol2 file which is readable for
amber/leap. Is it possible with rdkit?
I did some work on CCP4 and Amber atom types a few years ago and then
converted to parm@Frosst (which I found to be a lot harder) but not to
the
On 16/11/2020 21:28, Navid Shervani-Tabar wrote:
Dear RDKit users,
I'm trying to plot a single molecule using RDKit. I use the following code
from rdkit.Chemimport Draw
from rdkitimport Chem
mol = Chem.MolFromSmiles('C1#CN2C1C2')
Chem.rdmolops.SanitizeMol(mol)
img =
On 12/03/2021 05:11, Ling Chan wrote:
Just wonder if there is any function to distinguish between a chair
ring and a boat ring?
Don't worry if there is no such utility. I can write my own geometry
detection. Just that I don't want to reinvent the wheel.
Isn't this Cremer Pople?
On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:
Sure, testosterone may be drawn as
[snip]
OK :-)
That's a top quality rendering by the way. How did you make it?
Paul.
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On 08/03/2021 13:55, Jean-Marc Nuzillard wrote:
Is it always possible to represent an organic molecule in 2D with all
necessary
configuration hints (bond wedges pointing to the front or to the back)
without introducing any explicit hydrogen atom?
No. Testosterone.
On 13/02/2021 18:15, Peter St. John wrote:
Is there any reason why RDKit says the nitrogen in beta-lactam is
SP2-hybridized? I would have assumed it should be SP3. It doesn't seem
to be the ring structure, 'C1NC1' lists all the atoms as being SP3.
>>> [(atom.GetSymbol(),
> PDB files have no bond information,
This is not true. The chemistry is specified in the Chemical Component Dictionary using the residue
identifier (so it's a reference to a chemical description, it's not embedded).
https://www.wwpdb.org/data/ccd
https://github.com/pdbeurope/ccdutils
On 13/12/2022 23:39, Thiessen, Paul (NIH/NLM/NCBI) [E] via Rdkit-discuss
wrote:
Hi folks,
I’m trying to use the MolDraw2DCairo class to generate PNG images. But
no matter what I’ve tried, including setting the ‘noFreetype’ param to
true in the c’tor, I get an empty string from
On 14/12/2022 17:37, Thomas wrote:
Is there a way to get the SMILES used to generate the molecule (NOT
the canonical one)?
Not as far as I know.
If I generate a molecule from a SMILES, a call to GetAtoms() returns
the atoms in the order of the input SMILES. I'd like to retrieve that
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