ember 2015 at 15:03, Greg Landrum wrote:
> Agreed. If you set the bond wedging explicitly it should be preserved.
>
> Here's the issue, which includes links to the commits with the fix (that's
> now checked in):
> https://github.com/rdkit/rdkit/issues/611
>
> -greg
&
Hi all,
I'd like to capture error messages during SMILES parsing, but am having
trouble getting this to work.
The following code raises an AssertionError, for example. Is there
something here I'm missing? I'm using this from a Windows 7 conda
environment, Python 2.7 64-bit, RDKit 2017.03.3, but a
) instead read().
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-09-08 15:51 GMT+02:00 Noel O'Boyle :
>
>> Hi all,
>>
>> I'd like to capture error messages during SMILES parsing, but am having
>&g
Any chance of more info on what RDkit contains? E.g. an API, or a
website. Although Open Source projects are infamous for incomplete
documentation, you seem to have taken this to an extreme :-)
I'm involved in other open source cheminformatics packages (via the
BlueObelisk, with varying degrees of
ow on.
Don't worry about it. Hope you had a good holiday.
> On 8/27/07, Noel O'Boyle wrote:
> > Any chance of more info on what RDkit contains? E.g. an API, or a
> > website. Although Open Source projects are infamous for incomplete
> > documentation, you seem to
On 13/09/2007, Greg Landrum wrote:
> On 9/13/07, Noel O'Boyle wrote:
> > So on to the questions:
> > (1) Can I believe my eyes? Is this really open source? A lot of the
> > Python code has a very restrictive copyright statement right at the
> > start (see Windows
> Well...don't worry about the publicisation...you can leave that to me
> (I feel a blog post coming on :-) )
As promised, here's a blog post:
http://baoilleach.blogspot.com/2007/09/rdkit-not-just-yet-another.html
Noel
Several of the blue-obelisk projects are currently moving to CMake
right about now...
Noel
I am finding it difficult to read an SDF file. The following program
(on Windows):
for mol in Chem.SDMolSupplier("head.sdf"):
print mol
gives the following error:
runtime error R6025
- pure virtual function call
I'm using the Jan2008 release, with numpy instead of Numeric (if that
makes
Does RDKit make the molecular weight available somewhere? - I just
can't find it anywhere.
Noel
I've been looking into depiction in RDKit. It uses sping, which
unfortunately looks like it's not very up to date. I know that BKChem
has moved from sping to pycairo. At the moment, is it actually
possible to make a PNG with RDKit?
Noel
ail from
the list - you should probably cc me in future (I suffer from
one-too-many mailing lists).
Regards,
Noel
On 01/04/2008, Noel O'Boyle wrote:
> I've been looking into depiction in RDKit. It uses sping, which
> unfortunately looks like it's not very up to date. I know that BKChem
> has moved from sping to pycairo. At the moment, is it actually
> possible to make a PNG with RDKit?
>
>
> Noel
>
I've been trying to get my head around what's happening when I read
and write isomeric smiles. As a user, I hope that the same molecule
will also have the same isomeric SMILES. However, look at the
following examples using cinfony which read a SMILES string and write
an isomeric SMILES string...
I
I think I've been misunderstanding the square brackets. I need to
RTFM, I think, after which I'll post here again if still confused.
Noel
On 14/04/2008, Noel O'Boyle wrote:
> I've been trying to get my head around what's happening when I read
> and write isomeric
And (egg on face) chlorobromomethane isn't chiral in the first
place...what was I thinking?
On 14/04/2008, Noel O'Boyle wrote:
> I've been trying to get my head around what's happening when I read
> and write isomeric smiles. As a user, I hope that the same molecule
If I found a bug earlier, it was completely by accident. The following
though I think is also a bug. I find that I can invert the
stereocenter by adding and removing Hs.
>>> mol = rdk.readstring("smi", "C[C@@H](O)(Cl)c1c1")
>>> mol.write("iso")
'C[C@@H](O)(Cl)c1c1'
>>> mol.addh()
>>> mol.w
Wait a second, that molecule has five substituents on the isomeric C.
But I think we share the blame again this time, Greg, because I took
that structure from the RDKit Python tutorial Section 2.3. :-)
Noel
On 14/04/2008, Noel O'Boyle wrote:
> If I found a bug earlier, it was compl
I am running into trouble building a molecule from scratch. Let's say
the molecule represented by "F/C=C/F" (taken from the Daylight SMILES
tutorial). Here's the code to build it (according to me):
import Chem
# Set some lookups
_bondtypes = {1: Chem.BondType.SINGLE,
2: Chem.BondTyp
On 15/04/2008, Greg Landrum wrote:
> The problem is here. I shouldn't even have exposed SetStereo to
> Python. To indicate bond stereochemistry, you need to set the
> directionalities of the neighboring single bonds. So you'd do:
> [13] >>> rdmol.GetBondWithIdx(0).SetBondDir(Chem.BondDir.ENDUPR
I've done it again :-/
>>> print Chem.MolToMolBlock(Chem.MolFromSmiles(""))
Traceback (most recent call last):
File "", line 1, in
RuntimeError: Pre-condition Violation
Noel
t; 0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 3 4 1 0
> M END
>
>
> On Tue, Apr 22, 2008 at 1:25 PM, Noel O'Boyle wrote:
> > I've done it again :-/
> >
> > >>> print Ch
On 22/04/2008, Greg Landrum wrote:
> Hi Noel,
>
>
> On Tue, Apr 22, 2008 at 2:48 PM, Noel O'Boyle wrote:
> > Yes, I should have said - I'm using the latest release on Windows.
> >
> >
>
>
> By latest release do you mean the Jan2008 release or
I threw together a Python script to compare the data files of OB and
RDKit to see whether they contained the same figures. I haven't yet
looked at the paper to verify these, but here are the preliminary
results:
MR
In OB, not in RDKit: set([-0.57542])
In RDKit, not in OB: set([5.753899
I'm a bit confused by how RDKit calculates the 2D coordinates. I use
AllChem.Compute2DCoords(mol, clearConfs = False) to calculate the 2D
coordinates.
Given an SD file containing a 2D depiction, RDKit appears to use those
coordinates rather than generating its own. Can you confirm that this
is the
On 24/04/2008, Greg Landrum wrote:
> Hi Noel,
>
>
> On Thu, Apr 24, 2008 at 12:03 PM, Noel O'Boyle wrote:
> > I'm a bit confused by how RDKit calculates the 2D coordinates. I use
> > AllChem.Compute2DCoords(mol, clearConfs = False) to calculate the 2D
>
way to catch typos.
>
>
> On Thu, Apr 24, 2008 at 9:03 AM, Noel O'Boyle wrote:
> > MR
> > In OB, not in RDKit: set([-0.57542])
> > In RDKit, not in OB: set([5.75389998])
>
>
> This is Me1 and is correct in the RDKit.
>
FYI - the bug below is also exhibited by RDKit.
-- Forwarded message --
From: Steve Constable
Date: 2008/5/1
Subject: [Open Babel] Hydrogen adder error?
To: openbabel-disc...@lists.sourceforge.net
Hello,
I'm working with openbabel 2.1.1, and I'm having an issue with the
OBMol::
I think I spoke too soon. Looks like it's not a bug...
-- Forwarded message --
From: Tim Vandermeersch
Date: 2008/5/1
Subject: Re: [Open Babel] Hydrogen adder error?
To: Steve Constable
Cc: openbabel-disc...@lists.sourceforge.net
This doesn't work in trunk, when you place an at
There are still a lot of people out there using Py2.4. It would be
nice to see two versions of RDKit on Windows; one for Py2.4, one for
Py2.5. Current download figures for openbabel-python indicate a 2:1
Py2.5:Py2.4 userbase.
Noel
I hope it's on Greg's to do list also, but there is a compiled version
of Numeric for Py2.5 available from the following link:
http://www.pygame.org/download.shtml
2008/5/22 TJ O'Donnell :
> I'm new to RDKit and have had good success so far
> building it under linux and installing it on windows.
>
I've just tried to build on Linux and I've left some comments on your
build under Linux page...
2008/5/22 Greg Landrum :
> On Thu, May 22, 2008 at 9:19 PM, TJ O'Donnell wrote:
>> I'm new to RDKit and have had good success so far
>> building it under linux and installing it on windows.
>> Some of
If I run bjam in /Code/GraphMol/Wrap, I get:
...found 4999 targets...
...updating 9 targets...
gcc.link.dll ../bin/gcc-4.1.2/release/threading-multi/libGraphMol.so
/usr/bin/ld: cannot find -lblas
collect2: ld returned 1 exit status
"g++"-o "../bin/gcc-4.1.2/release/threading-multi/libGrap
It might be good also if the build system complained at this point by
dying horribly...
2008/5/23 Greg Landrum :
> Hi Noel,
>
> On Fri, May 23, 2008 at 2:50 PM, Noel O'Boyle wrote:
>> If I run bjam in /Code/GraphMol/Wrap, I get:
>>
>> ...found 4999 tar
2008/7/15 markus :
> Hi there,
> here's a compiling problem when trying to setup the latest trunk:
> I wrote a small sh-script for (re-)installing RDKit on Ubuntu. This script
> worked very well, until I tried to get the latest trunk on Friday.
> For anti-spam-reasons I attached the script whic
I would be happy if you just concentrated on updating the
documentation for the current supported builds so that they're
self-contained and foolproof. I'm thinking here mainly of the Windows
build - what boost stuff do I need to download exactly? Also, the
Linux build tells me to read the boost doc
I think it's built fine, but initially it couldn't find find boost-build.jam.
I needed to set a new environment variable BOOST_ROOT="%BOOSTHOME%"
Note the quotation marks (I've got spaces in the path for BOOSTHOME).
Here's the batch file I used to set the variables:
@echo off
set RDBASE=C:\Docume
2008/7/21 Greg Landrum :
> The problem with bjam not being able to find boost-build.jam is
> because your BOOST_BUILD_PATH is set incorrectly; it should be set to
> "%BOOSTHOME%"; then you won't need BOOST_ROOT.
So, you're saying that I don't need anyt of the BOOST variables to
point to the compil
For purposes of timing comparison (C++ API vs. using Boost.Python), is
there any operation available from the C++ API that takes about 0.5
seconds per molecule? I've tried to slow down the Forcefield
Optimization by reducing the tolerances but it's much too fast still.
Noel
I'm getting some strange results when I compare the timing for using
cinfony to access RDKit, compared to writing the equivalent C++
program. Basically, for iteration over a very large SDF file, it's 50%
slower if you use cinfony (which simply calls SDMolSupplier and
'yields' the results).
I'm usi
2008/8/6 Greg Landrum :
> On 8/6/08, Noel O'Boyle wrote:
>> I'm getting some strange results when I compare the timing for using
>> cinfony to access RDKit, compared to writing the equivalent C++
>> program. Basically, for iteration over a very large SDF file
Looks like I forgot to correct the PYTHONPATH. My figures are now in
agreement with yours...
2008/8/6 Noel O'Boyle :
> 2008/8/6 Greg Landrum :
>> On 8/6/08, Noel O'Boyle wrote:
>>> I'm getting some strange results when I compare the timing for using
>>
EmbedMolecule. I recommend you read the PDF supplied with RDKit.
2008/8/8 Evgueni Kolossov :
> Thanks - this is kind of works.
> Unfortunately there is no atomic coordinates generated - how we can do this?
> Otherwise it will display just single dot.
>
> Regards,
> Evgueni
>
>
> 2008/8/8 Igor Fili
Perhaps I misunderstand. Are you looking for a fast Python solution to
creating a distance matrix? If so, you might want to use numpy (which
uses C extensions), where the distance between two vectors x, y is
simply sqrt(sum((x-y)**2)). See
http://projects.scipy.org/pipermail/numpy-discussion/2007-A
Hmmm...sounds like something that is not specific to RDKit...I might
think about adding this to cinfony. Especially if you send a patch :-)
Noel
2008/8/17 markus :
> Hi There,
> I wonder if it could be possible to access the Pubchem Power User
> Gateway directly via RDKit.
> As there is already s
Also see BioPython. It has some wrappers around NCBI's functionality
already, but I haven't looked at using it with PubChem...
2008/10/18 Greg Landrum :
> Hi Markus,
>
> I did a bit of exploring of the Pubchem Power User Gateway this
> morning and discovered that they have a SOAP interface:
> http
Hello Greg,
I was wondering whether RDKit has been successfully compiled on a Mac.
Noel
FYI, Stephan Nagy (of Tripos??) just said the following on FF
(http://friendfeed.com/snagy/discussion):
Tripos will be releasing some sln parsing and generation code for Java
and C. There is a formal grammar that will also be made available with
the release of those APIs. The current plan is to ma
Hello Greg,
To make life difficult, I've been trying to build RDKit on MacOSX 10.5
but using the Fink-installed python2.5 and numpy (note: I'm using Fink
unstable):
I'm a newbie to MacOSX. Fink is one of two options (also tried
MacPorts - didn't work well enough) for package-managed installation
I now realise there is a third option for me. I could install cairo
with Fink, and then try to compile pycairo for the System Python using
the Fink installed libraries...hmmm...
2008/11/27 Noel O'Boyle :
> Hello Greg,
>
> To make life difficult, I've been trying to build R
installing on unstable platforms. :-)
>
> -greg
>
> On Thu, Nov 27, 2008 at 10:10 AM, Noel O'Boyle wrote:
>>
>> To make life difficult, I've been trying to build RDKit on MacOSX 10.5
>> but using the Fink-installed python2.5 and numpy (note: I'm using
2008/11/28 Greg Landrum :
> On Thu, Nov 27, 2008 at 10:34 PM, Noel O'Boyle wrote:
>> than installs them. The Sytem Python comes with PIL, Tkinter,
>> wxPython, Numpy and Matplotlib. And that's it. There doesn't seem to
>> be a package manager for Macs.
Please make it all lowercase. It's very difficult to remember a
mixture of upper and lower case. I think they've done with the
standard libraries in Py3.0. Now Tkinter is tkinter, etc.
But why pyrdkit? Why not rdkit?
- Noel
2009/1/25 Greg Landrum :
> As part of my effort to make the RDKit easier
Hello Greg,
Am I right in saying that there are no 3D descriptors in RDKit? That
they're all either 1D or 2D?
- Noel
2009/2/13 George Oakman :
> Hi,
>
> Thanks a lot for the speedy response.
>
> Yes, this is what I was suspecting - slightly different conventions (in this
> case probably to do with which branch to deal with first) will lead to
> different results.
>
> The book I was referring to is An Introduction
2009/2/17 Andrew Dalke :
> On Feb 17, 2009, at 9:18 AM, George Oakman wrote:
>> Does someone know if I can assume that the canonical SMILES of
>> RDKit are the same as the Open Babel ones?
You can assume they are not the same. No attempt has been made to make
them consistent.
> I wouldn't assume
Yes - I was wondering how you were going to pull off the Windows
release. If you want someone to bounce ideas off, get in touch...
2009/2/27 Greg Landrum :
> Dear all,
>
> I've merged the contents of the EasyInstall branch of the RDKit code
> onto the trunk. This has some consequences for those us
ew=markup
The extension modules in this case are not built with distutils and
yet it all works. It's also possible to set some environment variables
at this time, if necessary. See the postinstall.py script in the same
directory.
- Noel
2009/2/27 Greg Landrum :
> On Fri, Feb 27, 2009 at 10:08 A
Hello Greg,
Hope you had a good holiday.
Looking at the download figures from OB Python since Aug 09, the vast
majority of users are now using Python 2.6 (on Windows at least!).
Wearing my cinfony hat, is there any chance that the next windows
release of RDKit will target 2.6 (or better still, bo
Hello Greg,
In anticipation of the Spring ACS meeting, I'm updating cinfony.
It's great to finally see an RDKit release with support for Python 2.6
on Windows. It's also a zip file, which is Windows-friendly. However,
it's a 'zip bomb', which can cause some problems - you might want to
fix that.
Just saw that you're preparing a new release. I guess you can ignore
the comments below except for the praise. :-) I'll try the new
version...
- Noel
2010/1/24 Noel O'Boyle :
> Hello Greg,
>
> In anticipation of the Spring ACS meeting, I'm updating cinfony.
>
>
2010/1/24 Greg Landrum :
> aOn Sun, Jan 24, 2010 at 7:04 PM, Noel O'Boyle wrote:
>> Just saw that you're preparing a new release. I guess you can ignore
>> the comments below except for the praise. :-) I'll try the new
>> version...
>>
>
> Thanks fo
Hello Greg,
Just tried the Q4 .tar.gz for Windows. It seems to be missing several
.pyd files. In particular, it is missing rdBase.pyd so that the
following error occurs:
>>> from rdkit import Chem
Traceback (most recent call last):
File "", line 1, in
File "C:\Tools\cinfony\cinfony-0.9\cinfo
2010/1/25 Greg Landrum :
> Hi Noel,
>
> On Sun, Jan 24, 2010 at 9:45 PM, Noel O'Boyle wrote:
>> Hello Greg,
>>
>> Just tried the Q4 .tar.gz for Windows. It seems to be missing several
>> .pyd files. In particular, it is missing rdBase.pyd so that the
>
Hi Cedric,
There will be a new version of cinfony released in the coming week
(and a talk to follow at the ACS, the following week). This supports
the latest version of RDKit. I also promise to set up a proper mailing
list where enquiries of this sort can be sent (sorry Greg).
- Noel
Original me
On 19 March 2010 13:53, Cedric MORETTI wrote:
> Hi
>
> I have a question with RDKIT…
>
> There are tools of dataminning in RDKIT??
>
> I don’t find these tools…
>
>
>
> Other question
>
> When the news version to cinfony is available?
>
> The next week???
Cinfony 1.0a is available at http://cinfo
Hello Greg,
I'm trying to follow the instructions at
http://code.google.com/p/rdkit/wiki/BuildingWithCmake on an Ubuntu
9.04 system.
(1) I downloaded a boost source version.
(http://sourceforge.net/projects/boost/files/boost/1.42.0/boost_1_42_0.tar.gz/download)
(2) I extracted it and tried "bjam
te: I haven't tested the RDKit with boost 1.42, but I don't
> anticipate any major problems.
>
> -greg
>
> On Wed, Mar 31, 2010 at 8:46 AM, Noel O'Boyle wrote:
>> Hello Greg,
>>
>> I'm trying to follow the instructions at
>> http://code.g
On 1 April 2010 14:49, Greg Landrum wrote:
> Dear Noel,
>
> On Thu, Apr 1, 2010 at 2:09 AM, Noel O'Boyle wrote:
>> Ok, I had to run the following after unzipping boost:
>>
>> ./bootstrap.sh --with-libraries=python --prefix=/home/user/Tools/cinfony/tree
>>
On 1 April 2010 14:53, Noel O'Boyle wrote:
> On 1 April 2010 14:49, Greg Landrum wrote:
>> Dear Noel,
>>
>> On Thu, Apr 1, 2010 at 2:09 AM, Noel O'Boyle wrote:
>>> Ok, I had to run the following after unzipping boost:
>>>
>>> ./bootstrap
Since the world's attention has been drawn to this, maybe I'd better
sort this out now :-)
On 20 April 2010 19:04, Andrew Dalke wrote:
> On Apr 20, 2010, at 6:56 PM, Geoffrey Hutchison wrote:
>> Feel free to "steal" the CMake from Open Babel. See scripts/CMakeLists.txt.
>> A few weeks ago, we us
On 20 April 2010 19:20, Geoffrey Hutchison wrote:
>
> On Apr 20, 2010, at 2:04 PM, Andrew Dalke wrote:
>
>> In trying to get OpenBabel to compile on my Mac last week, working with Noel
>> on this, I found that this part of the OB configuration for the Mac doesn't
>> work quite right.
>> I expect
I'll look into this as soon as possible.
On 30 April 2010 10:24, Cedric MORETTI wrote:
> Tks you Greg for your answer.
>
> If my brain is good, I'm remember that Noel O'Boyle (the cinfony creator's)
> subscribed to RDKIT mailing-list so maybe he could
You should be able to accomplish the same with "cmake
-DBoost_USE_STATIC_LIBS=OFF".
On 25 June 2010 04:58, Kei Taneishi wrote:
> Hi Christian,
>
> I'm using dynamic linking to libboost_regex.
> At first, edit $RDBASE/Code/GraphMol/SLNParse/CMakeLists.txt as below.
>
>
On 1 July 2010 13:43, Evgueni Kolossov wrote:
> Dear Greg,
>
> I was sure bison and flex are part of cygwin installation but cannot find
> executables.
> Can you suggest anything?
Run cygwin setup, and type bison into the search box.
> Regards,
> Evgueni
>
> On 1 July 2010 13:06, Greg Landrum w
On 1 July 2010 19:52, Greg Landrum wrote:
> Dear Cedric,
>
> On Thu, Jul 1, 2010 at 10:52 AM, Cedric MORETTI
> wrote:
>> Hello all,
>>
>> I have a little question.
>>
>> I don’t arrive to read 2 SDF files with RDKIT when I use the for loop.
>>
>> I explain
>>
>> I have a first sdf files with 1 pr
On 1 July 2010 20:15, Greg Landrum wrote:
> On Thu, Jul 1, 2010 at 9:01 PM, Noel O'Boyle wrote:
>>>
>>> I think what you want is something like the following:
>>>
>>> suppl1 = Chem.SDMolSupplier('file1.sdf')
>>> suppl2 = Chem.S
On 5 July 2010 21:33, Gianluca Sforna wrote:
> Hi all,
> after spending some time to prepare a Fedora package I have a couple
> remarks/suggestions I'd like to discuss with you in order to make the
> process easier for all the distributions around.
>
> Versioning - package manager programs (this i
On 28 July 2010 15:04, Evgueni Kolossov wrote:
> Dear Greg,
>
> I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go
> through the configuration stage with CMake:
>
> CMake Error at C:/Program Files/CMake
> 2.8/share/cmake-2.8/Modules/FindBoost.cmake:910 (message):
> Unable to
;
> On 28 July 2010 15:07, Noel O'Boyle wrote:
>>
>> On 28 July 2010 15:04, Evgueni Kolossov wrote:
>> > Dear Greg,
>> >
>> > I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go
>> > through the configuration stage wit
Hi all,
I'm updating cinfony and using the latest RDKit Release
(RDKit_2010_12_1, the binary Python 2.6 release), but "from rdkit
import Chem" is causing Python to crash (on Windows 7) as below. I've
tried with and without RDBASE defined.
Can someone confirm that it works for them?
- Noel
=
On 31 March 2011 12:45, Greg Landrum wrote:
> On Thu, Mar 31, 2011 at 8:51 AM, James Davidson
> wrote:
>>
>>
>> It then ocurred to me that it could have been an incompatibility with an
>> earlier Numpy version(?) Would this be involved at the point of import?
>> The version I reinstalled was 1.
On 31 March 2011 13:13, Noel O'Boyle wrote:
> On 31 March 2011 12:45, Greg Landrum wrote:
>> On Thu, Mar 31, 2011 at 8:51 AM, James Davidson
>> wrote:
>>>
>>>
>>> It then ocurred to me that it could have been an incompatibility with an
>>
Hi Greg,
With the deprecation of the AvailDescriptors module, it seems that the
only way to get the list of descriptors is:
len(Descriptors._descList)
I don't like accessing hidden attributes; is there some better way to do this?
- Noel
---
I notice that _descList is missing at least the molecular formula and
molecular weight. What I'm really looking for is a replacement for
descDict in the original AvailDescriptors module.
- Noel
On 31 March 2011 18:28, Noel O'Boyle wrote:
> Hi Greg,
>
> With the
Hi Greg,
You mentioned that there is a Jar file and associated shared library
for RDKit in the KNIME repository. Unfortunately, they don't provide
access except on request (see http://tech.knime.org/node/20231 for
example). Could you make these available somewhere or include them in
a future relea
Hello all,
I've just released Cinfony 1.1 with support for RDKitl 2011.09. New in
this release is support for Indigo and OPSIN.
If you are interested in writing Python scripts that have access to
several cheminformatics toolkits using the same API (CDK, Open Babel,
Indigo, RDKit and OPSIN are all
Hi Greg,
Is there any way to retrieve the SMILES atom order after generating a
SMILES string, and if not, is this something that could easily be
added (I might try a patch)? This is useful to store additional
information relating to particular atoms in the comment field.
Regards,
Noel
---
Great. So if I understand you correctly, it is currently accessible from C++.
- Noel
On 11 June 2013 10:26, Greg Landrum wrote:
> Noel,
>
> On Tue, Jun 11, 2013 at 10:49 AM, Noel O'Boyle wrote:
>>
>>
>> Is there any way to retrieve the SMILES atom order after ge
Hi Greg,
There's an option you can use when generating the Doxygen docs that
creates a nice Javascript search function. I find this very useful
with other docs (see top right of http://openbabel.org/api/2.3/ for
example). Any chance you might use this in future?
The option is SEARCHENGINE.
Regar
Hi Greg,
This isn't really a bug report, just an FYI that may be helpful. I've
been using Boost 1.49 until now to compile RDKit, but this is now too
old. Specifically, the FMCS code chokes on it.
Also, I've been compiling on Windows with mingw-w64 (the fork of
MinGW), and I needed to comment out
from 'std::pair<_Ty1,_Ty2>' to 'const
std::pair<_Ty1,_Ty2> &'
This looks like an MSVC versus Boost issue rather than anything
related to RDKit.
Regards,
- Noel
On 21 May 2015 at 03:22, Greg Landrum wrote:
> Hi Noel,
>
> On Wed, May 20, 2015 at 10:54 AM
Hey Greg,
I hope you had a good meeting.
I was wondering whether it is possible to set the location of depicted
wedge/hashes in a MOL file output.
Right now, it seems that I can call WedgeHashBonds and that tells me
where the wedge or hashes are via GetBondDir() (although I am still a
bit confus
You are assuming that CHI_TETRAHEDRAL_CW means "R" and v.v. for "S". I
don't think that's correct.
On 8 September 2015 at 12:58, Michał Nowotka wrote:
> Hi,
>
> I'm comparing stereo centers assigned by ChemAxon JChem and RDKit.
>
> The code would be:
>
> #-
Hi all,
I'll keep it short: we're currently recruiting for a Cheminformatician at
Sosei Heptares. We have no specific grade in mind - you could be just
finishing your PhD, or be much more experienced. Here's the link for more
details:
https://cezanneondemand.intervieweb.it/heptares/jobs/cheminform
"Every valid SMILES is also a valid SMARTS": I think this is one of John
May's lines, which I was never keen on as it makes people think that if you
treat a SMILES as a SMARTS that it will match the original SMILES. It
mostly will, but I think you have found the difference between the SMILES
and SM
There are other more subtle changes that can affect the aromaticity, e.g.
changing a bond order, the charge, or the atomic number of an atom. IMO,
the user needs to take responsibility for knowing if aromaticity might be
invalidated, and perform the appropriate actions. The alternative is for
the t
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