Adrian,
On Nov 21, 2007 7:12 PM, Adrian Schreyer adr...@cryst.bioc.cam.ac.uk wrote:
I think there might be something going wrong with the hydrophobe feature
definition, or to be more precise, with the implementation.
Using the linking amino acid Alanine as an example, the C atom will be
Hi Adrian,
What kind of molecules are you feeding to my poor software? sheesh!
:-)
The first SMILES is not valid. | is not a legal character in a
SMILES string, so that's correct behavior.
The second SMILES is valid and can be parsed successfully by the
RDKit, but it cannot be sanitized:
m =
Hi Christos,
This has reached a level of complication that such a simple task
doesn't deserve. I shouldn't have pointed you at the code at the end
of MolDrawing.py, that's messy and unclear. Sorry.
The attached file takes two arguments: smiles and a filename and
produces an image file with that
Dear Christos,
There is a big hole in the docs around the db support. But the db
stuff does work and is something I use all the time (so it's very
actively maintained). There are some convenience utilities associated
with DBs and molecules coming in the next release (middle of Dec,
probably). The
Dear RDKit folks,
I had hoped to have a release of the RDKit finished in December. That
obviously didn't happen and I'd like to explain why.
In November I did some canonicalization torture tests[1] and found a
couple of bugs in the generation of canonical smiles for symmetric
molecules and
I'm very happy to announce that the next version of the RDKit
(Jan2008_1). This release took longer than I wanted to get done
(witness the date!), but it's finally here.
The release notes are below. There are some fairly big and important
changes, so please at least skim them.
The source release
Hi Markus,
This does look like a bug. Thanks for reporting it.
I'll be away for the weekend starting tomorrow, but I'll look at it next week.
Regards,
-greg
On Wed, Mar 19, 2008 at 9:31 PM, markus m.koss...@tu-bs.de wrote:
Hi there, it's me again... :-)
As you asked me to post things
Dear all,
On Sat, Mar 29, 2008 at 12:57 PM, Noel O'Boyle baoille...@gmail.com wrote:
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
On Thu, Apr 3, 2008 at 4:15 PM, Adrian Schreyer ams...@cam.ac.uk wrote:
After a couple of hours work on comparing molecules with RDKit I
noticed that the algorithm is apparently struggling with structures
that consist of a repetitive substructure, such as linear alkanes
(azelaic acid
Hi Adrian,
On Tue, Apr 8, 2008 at 5:06 PM, Adrian Schreyer ams...@cam.ac.uk wrote:
I was wondering what would be the best way in RDKit to represent
molecules with a metal complex in SMILES, for instance heme.
Apparently different programs use different approaches, CACTVS uses a
Hi Noel,
You already figured out the problem with the chirality of
chlorobromomethane, but I want to clarify a couple of things below.
On Mon, Apr 14, 2008 at 12:50 PM, Noel O'Boyle baoille...@gmail.com wrote:
I'm trying to specify the chirality of the carbon in
chlorobromomethane, but
Dear all,
After fixing a couple of small bugs and making some other changes, I
just tagged a second release candidate for the May 2008 release:
http://rdkit.svn.sourceforge.net/svnroot/rdkit/tags/Release_May2008_1RC2
Release notes are here:
On Thu, May 22, 2008 at 9:19 PM, TJ O'Donnell t...@acm.org wrote:
I'm new to RDKit and have had good success so far
building it under linux and installing it on windows.
Some of the tests fail (only tested under linux).
I can try to get that resolved later.
I'm happy to help as you try and
Hi Noel,
On Fri, May 23, 2008 at 2:50 PM, Noel O'Boyle baoille...@gmail.com wrote:
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:
On Fri, May 23, 2008 at 4:22 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
On May 23, 2008, at 9:52 AM, Greg Landrum wrote:
As an aside: SDF is a very inefficient storage mechanism for
multi-conf SD files: there's a lot of duplicated information. The
RDKit supports a format called
Dear all,
On Tue, Jul 22, 2008 at 11:40 AM, Evgueni Kolossov ekolos...@gmail.com wrote:
Hi,
If anybody interested, I have made single RDKit.sln as well as separate
solutions for each dll in RDKit for Visual Studio 2005. All builds OK.
If people are interested in this, and Evgueni agrees, I
On 8/6/08, Noel O'Boyle baoille...@gmail.com 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, it's 50%
slower if you use cinfony (which
On Mon, Aug 11, 2008 at 2:24 PM, Evgueni Kolossov ekolos...@gmail.com wrote:
Hi Greg,
ROMol::getPropList() will return not only properties from the SDFile but
also some default properties.
Is there way(param) to get only properties loaded from the file?
There's no simple solution at the
Dear Evgueni,
I checked in some changes this morning that added two optional
arguments to ROMol.getPropList() includePrivate and includeComputed.
These behave the same in C++ as they do in Python. The default
behavior is the same as before: to show all properties.
-greg
On Mon, Aug 11, 2008 at
Dear Robert,
This is a general-interest question so I'm also sending my reply to
the mailing list.
On Wed, Aug 13, 2008 at 10:12 PM, Robert DeLisle rkdeli...@gmail.com wrote:
I'm a new user of RDKit - may I congratulate you on an excellent package. I
look forward to using it in the future.
Dear Markus,
On Fri, Aug 15, 2008 at 1:23 PM, markus m.koss...@tu-bs.de wrote:
Dear all,
as there is so much Geometry functionality within the RDKit, I wonder if
it provides
a function that computes the DistanceMatrix of a list of Point3D Objects.
If RDKit does not have this functionality,
Dear Evgueni,
this is a general interest answer, so I'm directing it to the mailing list.
On Fri, Aug 15, 2008 at 11:56 AM, Evgueni Kolossov
ekolos...@btinternet.com wrote:
I need to understand a little bit more about RingInfo.
For a given atom I got:
- the number of rings atom involved
Dear Evgueni,
2008/8/17 Evgueni Kolossov ekolos...@gmail.com
Thanks Greg,
But this is not enough:
unsigned int minRingSize=ringInfo-
minAtomRingSize(atomIdx);
for(VECT_INT_VECT_CI ringIt=ringInfo-atomRings().begin();
ringIt!=ringInfo-atomRings().end();++ringIt){
On Mon, Aug 18, 2008 at 2:55 PM, Evgueni Kolossov ekolos...@gmail.com wrote:
Another question: getAllRotatableBonds(RDKit::ROMol mol) - will this take
in account hydrogens or not?
I think you're talking about the function that's in :
.../Code/GraphMol/Depictor/DepictUtils.h
That looks for
On Mon, Aug 18, 2008 at 8:15 PM, Evgueni Kolossov ekolos...@gmail.com wrote:
Thanks Greg,
Will this give the SHORTEST distance?
Yes. As the header file says, it uses the all-pairs shortest paths algorithm.
-greg
Dear Andy,
On Wed, Aug 20, 2008 at 11:40 PM, Andrew Fant f...@moleculargeek.com wrote:
I tried to build the May 2008 release tarball today on a centos 4.6
system with gcc-3 and boost 1.36.0, and ran into a C++ problem that is
beyond my ken.
I haven't tried boost 1.36.0 yet, so you're breaking
Hi Markus,
On Thu, Aug 21, 2008 at 1:34 PM, markus m.koss...@tu-bs.de wrote:
Hi,
somehow I do not get the way RDKit organizes the IDs of conformers:
Yes, the way conformers is handled is confusing at first.
First I'll show you how to do what I think you were trying to do, then
I'll try and
Markus,
On Thu, Aug 21, 2008 at 3:48 PM, markus m.koss...@tu-bs.de wrote:
O.K,
Conformer IDs and Indices are not the same, that's what I got wrong.
Just to get certain on a detail:
Calling GetConformers() returns the List of Conformers in a defined order,
doesn't it?
It's a tuple, not a
On Wed, Sep 3, 2008 at 8:26 AM, Evgueni Kolossov ekolos...@gmail.com wrote:
I can accept explanation for aromaticity but for structure 11 it will be
good to have ability to read it with warning for example. All structure
editors can read it!
If you want to be able to handle molecules that are
This evening I checked in a bunch of changes (mostly to Jamfiles) that
allow the RDKit to be built under Mac OS X (at least under version
10.5.4). All the unit tests pass except for Numeric/EigenSolvers; I'm
looking into that one.
I am a very, very long way from being a Mac OS X expert, but
On Mon, Sep 8, 2008 at 3:54 PM, Peter Harley pj...@cam.ac.uk wrote:
On Sep 8 2008, Greg Landrum wrote:
Copying in the Externals folder from the May release is hazardous, but
it might work. Regardless, it shouldn't cause the problem that you are
seeing with point not being built.
I thought
Dear Evgueni,
Sorry for the slow reply; I'm in intermittent email contact until the
end of the week.
On Wed, Sep 10, 2008 at 11:38 AM, Evgueni Kolossov ekolos...@gmail.com wrote:
I am trying to use your function to calculate Balaban index J:
doubel dResult =
Dear Evgueni,
On Thu, Sep 11, 2008 at 9:40 AM, Evgueni Kolossov ekolos...@gmail.com wrote:
Can you please describe (or forward me to description) what rules you
applied for fragmentation process. Can they be modified, etc.
I'm not 100% sure which fragmentation process you are talking about,
Dear Andy,
On Mon, Sep 15, 2008 at 11:22 PM, Andrew Fant f...@moleculargeek.com wrote:
I'm building rdkit on an ubuntu 8.04 lts intel pc and am running into a
really annoying link error. For several reasons, I'm using a hand-built
atlas that works with the other applications, but any time one
Dear all,
I'm really happy to announce that this morning I tagged the Q3 2008
release candidate:
https://rdkit.svn.sourceforge.net/svnroot/rdkit/tags/Release_Q32008_1RC1
(browseable at:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q32008_1RC1)
Source and binary distributions (for
[heh, worse than sending a message without an attachment is hitting
send before the message is done and sending a message without text...
sorry]
On Wed, Oct 15, 2008 at 7:59 PM, Robert DeLisle rkdeli...@gmail.com wrote:
As you know, I've been working with descriptors in RDKit, and I think I've
On Fri, Oct 17, 2008 at 12:07 PM, Noel O'Boyle baoille...@gmail.com wrote:
Hmmm...sounds like something that is not specific to RDKit...I might
think about adding this to cinfony. Especially if you send a patch :-)
I agree with Noel, this is something generally interesting that's not
Dear Kirk,
On Sat, Oct 18, 2008 at 1:18 AM, Robert DeLisle rkdeli...@gmail.com wrote:
I notice within the Python API that RDKit has the ability to communicate
with PyMol. I have not, however, been able to find an example and haven't
quite figured it out on my own. Could you provide an
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://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap_help.html
They even include a bit of help and some examples for using that
interface from Python:
I wanted to make one more post on this topic, ask a couple questions
(at the bottom of the post), and give people a few days to comment
before I regenerate the regression test data and commit a change for
this bug.
On Wed, Oct 15, 2008 at 8:19 PM, Hans Purkey hans.pur...@gmail.com wrote:
If the
On Tue, Oct 28, 2008 at 5:38 PM, Robert DeLisle rkdeli...@gmail.com wrote:
I agree with Nik an additional 2 pence. In fact, while reading Greg's
original note, my thoughts were essentially identical to Nik's comments.
Excellent. Here's an altered proposal based on Nik's comments.
The
On Wed, Oct 29, 2008 at 4:36 PM, Robert DeLisle rkdeli...@gmail.com wrote:
Another 2 pence. Nik is clearly hijacking my thoughts.
I had the same thoughts on fluoro - include a flag that would allow/disallow
counting fluorine at all, and reduce it to aromatic fluorine only.
Ok, I can go along
On Mon, Nov 3, 2008 at 4:19 AM, Robert DeLisle rkdeli...@gmail.com wrote:
I could go with the AcceptorsPlusFluorines() function option. Either way
works for me.
Another thought I had that would likely required more work would be to allow
the import of custom definitions. If I could import a
On Wed, Nov 12, 2008 at 6:21 PM, Igor Filippov [Contr]
ig...@helix.nih.gov wrote:
Has anyone reported a successful build in MinGW environment?
I'm getting some obscure error messages, the log file is attached.
I've been meaning for a while now to look into doing a mingw build. I
will give it a
Dear all,
In case anyone is interested: I did some modifications to the build
system to allow the RDKit to be built on windows using MinGW.
Since there were a lot of changes, I did this work on a branch:
https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/mingwBuild_15Nov2008
There are
:
$ pwd
/home/Administrator/rdkit-mingw
Igor
On Mon, 2008-11-17 at 17:56 +0100, Greg Landrum wrote:
It looks to me like there's an environment variable that's set incorrectly.
For what it's worth, here are my RDBASE and BOOST variables:
BOOSTHOME and BOOST_BUILD_PATH are both c
Dear Noel,
On Fri, Nov 21, 2008 at 1:08 PM, Noel O'Boyle baoille...@gmail.com wrote:
I was wondering whether RDKit has been successfully compiled on a Mac.
The Q3 release (and current svn version, of course) do build (and
work!) on MacOS.
I need to do a wiki entry with build instructions, but
, 2008 at 5:11 AM, Andrew Dalke da...@dalkescientific.com wrote:
On Nov 21, 2008, at 9:20 AM, Greg Landrum wrote:
The Q3 release (and current svn version, of course) do build (and
work!) on MacOS.
I've compiled it on my 10.4 machine but it required some changes that
Greg put into svn and which
Dear Kirk,
On Fri, Nov 21, 2008 at 12:38 AM, Robert DeLisle rkdeli...@gmail.com wrote:
After running through the process with exception handling in place I was
able to isolate 10 structures that were being problematic. All of them had
at least one bond designated as 0 order in the SD file -
On Mon, Nov 24, 2008 at 3:05 PM, Andrew Dalke da...@dalkescientific.com wrote:
Greg:
Please let me know if you want me to edit, rewrite, or remove your
name. :-)
No worries; not a problem.
But why is there so much green and blue text? ... Ahh, WikiMarkup.
yeah, the google wiki formatter
On Mon, Nov 24, 2008 at 5:11 PM, Robert DeLisle rkdeli...@gmail.com wrote:
Fantastic! Thanks, Greg!
After I got things working I've been able to generate a database and do some
preliminary searches. I'm impressed at how quickly I can search ~100,000
compounds with SMARTS patterns. I have a
On Tue, Nov 25, 2008 at 9:23 PM, Igor Filippov i...@mps.ohio-state.edu wrote:
The first includes some changes to the build system that allow the
RDKit to be built using the mingw system on windows. If you don't know
what this means, it's probably not important to you, so don't worry
about it.
On Wed, Nov 26, 2008 at 8:11 PM, Igor Filippov [Contr]
ig...@helix.nih.gov wrote:
I have followed the process, everything except for the very last step
seems to have worked out Ok.
I'm attaching the error log from
bjam --toolset=gcc --without-python all-libraries
(done in rdkit-svn/Code)
Noel,
I'm not enough of a Mac person (yet?) to know what the compelling case
is for installing/using the fink python instead of the system version.
Aside from being able to install instead of build pycairo, what's the
argument for it?
I'm pretty conservative when it comes to installing on
On Wed, Nov 26, 2008 at 10:07 PM, Igor Filippov [Contr]
ig...@helix.nih.gov wrote:
I tried that, also with adding --prefix=/home... to both boost and RDKit
bjam run options but it's still the same error. I wonder where does it
get c:/ prefix...
No clue. Is there a mingw/msys configuration
On Thu, Nov 27, 2008 at 10:34 PM, Noel O'Boyle baoille...@gmail.com 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. So if you want any other extensions
you're out of luck.
Dear all,
When I made the changes to the handling of stereochemistry in the Q3
2008 release of the RDKit, I attempted to get the canonicalization of
ring stereochemistry specifications (i.e. things like the molecule
encoded by the SMILES c...@h]1cc[c@@H](C)CC1) right. I knew that it
was unlikely
Dear Igor,
On Fri, Dec 26, 2008 at 6:56 PM, Igor Filippov [Contr]
ig...@helix.nih.gov wrote:
Dear Greg,
I was wondering if you could give a hint as to how accomplish the
following: I am trying to remove all the disconnected fragments from a
molecule smaller than a certain threshold number of
Dear all,
I just tagged a release candidate for the Q4 2008 release in svn:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q42008_1RC1/
I also uploaded a source tarball to the google code project page:
http://rdkit.googlecode.com/files/RDKit_Q42008_RC1.tgz
The release notes are at
Dear Marshall,
I believe that the build problems you are having are due to a bad
interaction between the boost build system and the way mount points
are set up on your machine.
Here's the evidence:
On Thu, Jan 8, 2009 at 7:42 PM, Marshall Levesque
marsh...@emolecules.com wrote:
I get these
Dear Marshall,
On Wed, Jan 14, 2009 at 1:29 AM, Marshall Levesque
marsh...@emolecules.com wrote:
/home/marshall/boost_1_37_0/boost/type_traits/detail/cv_traits_impl.hpp:37:
internal compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067
Please submit a full bug report,
Since this
Dear all,
I'm very happy to announce that the next version of the RDKit --
Q42008_1 -- is released.
The release notes are below.
The source release and a windows binary are on the sourceforge downloads page:
Thanks for the additional information Marshall.
After a bit of poking around, it looks like it's a compiler bug that
can possibly be worked around:
http://mail.python.org/pipermail/cplusplus-sig/2008-April/013116.html
Please try adding:
toolsetgcc:cflags-DBOOST_PYTHON_NO_PY_SIGNATURES
to
Dear all,
I'm exploring options for making the python bindings for the RDKit
easier to install in binary form. Specifically I'm trying to get
everything working with distutils and easy_install. If we can get this
working, end-user installation of the RDKit on supported systems
(linux, macos-x,
As part of my effort to make the RDKit easier to install, a very
long-standing item on my ToDo list has come back up: setting the
python code up as a python package.
In order to make this work, I need to change the way the code is
imported. Instead of:
import Chem
the correct way of doing an
On Sun, Jan 25, 2009 at 11:39 AM, Noel O'Boyle baoille...@gmail.com wrote:
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?
Hi Noel,
On Fri, Jan 30, 2009 at 10:31 AM, Noel O'Boyle baoille...@gmail.com wrote:
Am I right in saying that there are no 3D descriptors in RDKit? That
they're all either 1D or 2D?
Not completely. The feature map and feature-map vector code is a 3D
descriptor. One could argue that the
Dear all,
I've got a version of the new, theoretically easier to install, RDKit
distribution ready for testing.
If you're feeling adventurous, you can get the new distribution from a branch:
https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/EasyInstall_24Jan2009
Build/installation
Hi Andrew,
I'll start with your question and then elaborate a bit:
On Mon, Feb 9, 2009 at 1:54 AM, Andrew Dalke da...@dalkescientific.com wrote:
Hmm, I haven't asked a question yet Greg? How did RDKit manage to
be the only one I found which uses branching in the fingerprint
generation
Andrew,
On Mon, Feb 9, 2009 at 11:26 AM, Andrew Dalke da...@dalkescientific.com wrote:
Greg:
I must admit that I find the use of branched paths somehow more
pleasing. If you don't include either branching or more detail about
atom identity in the hashing, then it seems like you'd get 100%
On Mon, Feb 9, 2009 at 11:57 AM, Andrew Dalke da...@dalkescientific.com wrote:
If you do find yourself cursing the speed of the fingerprint
generation, it might be worth taking a look at using the alternate RNG
that is applied in the layered fingerprint code (line 229 of
Fingerprints.cpp).
Dear all
Andrew's question about fingerprints hit me at the right time: I had
just finished doing some optimization work on the RDKit substructure
search machinery (removing the vflib dependency). The details are
here:
http://code.google.com/p/rdkit/wiki/SubgraphIsomorphismOptimization
It would
Hi Evgueni,
On Tue, Feb 10, 2009 at 9:48 PM, Evgueni Kolossov ekolos...@gmail.com wrote:
I am moving into Visual Studio 2008 and updated project giving me a lot of
unresolved externals in RDKit libs.
Should I just recompile RDKit (but cannot see what difference it will make)
or I need for
, Evgueni Kolossov ekolos...@gmail.com wrote:
Yes,
This is why I am talking about new boost version...
It refer to libraries of RDKit built with the old version.
Regards,
Evgueni
2009/2/11 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
On Wed, Feb 11, 2009 at 4:38 PM, Evgueni Kolossov
Dear all,
If you are using the RDKit from C++, please take a look at this wiki
page, which describes an upcoming change to the API of ROMols:
http://code.google.com/p/rdkit/wiki/ChangingGraphProperties
If you use the code from Python, this does not affect you.
Best Regards,
-greg
Dear Evgueni,
On Thu, Feb 12, 2009 at 10:22 AM, Evgueni Kolossov ekolos...@gmail.com wrote:
Thank you very much - it all works now.
Glad to hear it.
Another question - I still have boost 1.35 and I have noticed you are using
1.36. I want to pick up the latest dev. from svn and according to
On Thu, Feb 12, 2009 at 11:53 AM, Evgueni Kolossov ekolos...@gmail.com wrote:
I have noticed a new version of bjam as well (3.1.17).
have you tryed it?
Yes, that's what I've been using: it works without problems.
I should do a table/matrix of the versions of compilers, OSs, boost
versions,
On Thu, Feb 12, 2009 at 2:55 PM, Andrew Dalke da...@dalkescientific.com wrote:
On Feb 12, 2009, at 8:46 AM, Greg Landrum wrote:
I'm either not understanding completely or I disagree. The queries
were constructed by fragmenting the molecules I searched through, so
I'd expect lots
On Fri, Feb 13, 2009 at 11:21 PM, Andrew Dalke
da...@dalkescientific.com wrote:
On Feb 13, 2009, at 9:14 PM, TJ O'Donnell wrote:
Yes, INnChI is unique across different packages. This is because
there is one definitive source for the code and algorithm. This was
a design goal of InChI.
Or
George,
I don't see any obvious problems with your simple example and do not
have easy access to a windows machine at the moment. I will give it a
try next week; In the meantime maybe someone else who uses windows can
comment?
- greg
On e2/20/09, George Oakman oakm...@hotmail.com wrote:
Hi
Dear Cheng,
On Sat, Feb 21, 2009 at 11:54 PM, Cheng Wang cheng...@hotmail.com wrote:
I am a newcomer to RDKit and I just start to read the getting start file and
the manual.
What I want to do is to provide a list of species with SMILES and then have
RDKit identify
all the isomers among the
Dear Cheng,
On Sun, Feb 22, 2009 at 9:33 PM, Cheng Wang cheng...@hotmail.com wrote:
Nowadays we use some large detailed mechanisms to study combustion
behavior. These
mechanisms normally involve hundreds (sometimes over 1000) species including
a lot of
large hydrocarbons (more than 6 Cs).
On Fri, Feb 27, 2009 at 10:08 AM, Noel O'Boyle baoille...@gmail.com wrote:
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...
Thanks for the offer.
What I tried is to use the python distutils to create either a tar
Dear Marshall,
On Wed, Mar 4, 2009 at 8:34 AM, Marshall Levesque
marsh...@emolecules.com wrote:
Does the number 1 after I try to optimize the molecule mean that there was
an error?
###
m =
Chem.MolFromSmiles('Clc1ccc(C=CC(=O)OC(P(=O)(OC2CC(CCC2C)C(C)C)OC2CC(CCC2C)C(C)C)c2cccnc2)c(Cl)c1')
Dear George,
On Wed, Mar 4, 2009 at 6:15 PM, George Oakman oakm...@hotmail.com wrote:
Hi all,
I have noticed that the MACCS Fingerprints are only available via the Python
framework. Has anyone implemented a C++ version on RDKit already?
Not that I'm aware of, but it would be something useful
Dear Marshall,
On Wed, Mar 4, 2009 at 7:01 PM, Marshall Levesque
marsh...@emolecules.com wrote:
I have written a script to automate converting compounds from a 2D SD file
into a 3D, optimized SD file. With the compounds I'm testing with, I get a
hangup in python that has to be killed. I'm
Dear all,
Yesterday I checked in an implementation of the BRICS molecular
fragmentation algorithm that came out of Matthias Rarey's group last
year (http://dx.doi.org/10.1002/cmdc.200800178).
The code is in: $RDBASE/rdkit/Chem/BRICS.py
One particularly useful feature of this implementation is
Dear Charlie,
On Wed, Mar 11, 2009 at 12:52 PM, charlie zhu zh.char...@gmail.com wrote:
Thanks for reply. I also think SDView is most needed and common used
GUI part.
I use SDView pretty frequently, so there is some incentive for me to
get it more up to date. It's just a matter of finding the
Dear all,
I added a page to the wiki with a table providing information about
successful RDKit builds:
http://code.google.com/p/rdkit/wiki/WorkingBuilds
If you have contributions to this table, please either send them to
the rdkit-devel list (don't worry if you aren't subscribed, I will
approve
Dear all,
This morning I uploaded some beta binary packages to the google code
download page:
http://code.google.com/p/rdkit/downloads/list
I haven't had a chance to do installation instructions yet, but you
can probably figure out where the linux and mac tarballs should be
extracted by looking
On Wed, Mar 18, 2009 at 3:39 AM, Andrew Dalke da...@dalkescientific.com wrote:
On Mar 12, 2009, at 5:49 PM, Greg Landrum wrote:
The thing I don't know how to do, and that I suspect would be
considerably
more effort, but that would also be very cool, would be to add
chemistry functionality
Dear all,
I just tagged the Q1 2009 release of the RDKit in svn:
https://rdkit.svn.sourceforge.net/svnroot/rdkit/tags/Release_Q12009_1beta3
There's a source tarball on the google code page:
http://code.google.com/p/rdkit/downloads/detail?name=RDKit_Q12009_1beta3.tgz
If no big problems show up,
Dear Evgueni,
On Thu, Mar 26, 2009 at 4:27 PM, Evgueni Kolossov ekolos...@gmail.com wrote:
What is the maximum length of RDKFingerprintMol?
hmm... good question. I guess the theoretical limit is somewhere
around 2^31, but it wouldn't be practical to do fingerprints that size
since the densities
Dear George,
I'd suggest you find whatever package exists for Red Hat that includes
a pre-built BLAS and LAPACK. I wouldn't recommend building them
yourself.
-greg
On Thu, Mar 26, 2009 at 4:11 PM, George Oakman oakm...@hotmail.com wrote:
Hi all,
I decided to take a vacation from Windows for
Dear Evgueni,
On Thu, Mar 26, 2009 at 6:22 PM, Evgueni Kolossov ekolos...@gmail.com wrote:
I understood that default it set to 2048 and default density set to 0.0 with
minimum size set default to 128, minPath to 1, maxPath to 7, and
nBitsPerHash to 4.
Can you please justify this selection for
On Thu, Mar 26, 2009 at 6:28 PM, George Oakman oakm...@hotmail.com wrote:
Hi Greg,
Thanks.
Do you know which version is required?
As long as it's compatible with your c++ compiler, I don't think it
should make much difference.
-greg
Dear Markus,
I'm impressed that you managed to get as far as you did with this. The
code for accessing pubmed wasn't really designed for what you're
doing, but you've somehow made it mostly work. My compliments. :-)
On Thu, Mar 26, 2009 at 8:33 AM, markus kossner m.koss...@tu-bs.de wrote:
Hi
Hi George,
On Fri, Mar 27, 2009 at 6:52 PM, George Oakman oakm...@hotmail.com wrote:
Thanks. I guess the easiest would be to upgrade my Red Hat distribution,
which would come with a more recent gcc and BLAS library. Unfortunately I
can't do that as it is my current 'minimum requirement' build
Dear Igor,
On Fri, Mar 27, 2009 at 8:21 PM, Igor Filippov [Contr]
ig...@helix.nih.gov wrote:
I have to say - I always need to find that webpage with a little note
somewhere half down the middle that mentions how to compile with bjam on
64-bit systems. Would it be possible to make this option
On Wed, Apr 1, 2009 at 8:37 PM, George Oakman oakm...@hotmail.com wrote:
Can delocalized bonds be represented using SMILES strings? (this might be a
silly question, please excuse my limited level of understanding of this
domain).
It's not a particularly silly question, but the answer is still
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