Dear,
Can the OBConversion class treat an input sd-file as a multi-
conformational file and hence automatically generate molecules that
contain more than set of coordinates?
More specifically, when reading an sd-file, can the OBConversion class
'detect' whether subsequent molecules are identi
> On Wed, Jul 7, 2010 at 6:54 PM, Geoffrey Hutchison
> wrote:
>>> isomorph code (identity checking), so in the meanwhile we would have
>>> to specify a convention such as all molecules with the same title
>>> are
>>> the same.
>>
>> I've been thinking about this for a while. The easiest detectio
ource software development,
and provides its clients with a wide variety of computational
chemistry-based lead discovery services, including Open Babel support,
training and code development. Please visit www.silicos.com for more
details.
Kind regards,
Hans De Winter
Silic
All,
a client of us is looking for a tool to perform compound library
enumerations by defining the building blocks and some general reaction
schemes. The client has access to Pipeline Pilot in which this kind of
stuff can be done, but for the particular project in mind it would be
very con
re details, download
instructions and documentation.
Kind regards,
Hans De Winter
Silicos NV
--
Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
Be part of this innovative community and reach millions
.
Please visit Silicos' website at www.silicos.com for more details,
download instructions and documentation.
Kind regards,
Hans De Winter
Silicos NV
--
Start uncovering the many advantages of virtual appliance
Dear,
Silicos NV is pleased to announced today the release of its new open
source software tool called PIRAMID under the General Public License
(GPL) v2. PIRAMID has been written on top of Open Babel's C++ API.
PIRAMID is a shape-based alignment tool for the alignment of pairs of
molecule
All,
maybe a simple question but I couldn't figure it out: which OB C++
method/class should I use to remove all stereochemical (implicit or
explicit) information from a molecule? I want to modify the molecule
in such way that stereochemistry is removed completely and that, if I
convert the
leted using OBMol::DeleteData(unsigned int type).
The type is OBGenericDataType::StereoData (27). In python this is
openbabel.StereoData."
Thx to all!
Hans
On Nov 8, 2010, at 15:16 , Craig A. James wrote:
> On 11/8/10 12:55 AM, Hans De Winter wrote:
>> maybe a simple question but I
> obspectrophore = "/usr/local/bin/obspectrophore"
> template_call = "obspectrophore +' -i 1eve_ligand.mol >
> template.txt"
> os.system(template_call)
>
> My Questions:
> 1) Is there a more convenient way to get an output file than the
> '>template.txt' option?
I'm sure there must be ways, p
> 18) There are some minor problems with the spectrophoretest.cpp
> test01. (I didn't review all of the tests.)
>
> In
>
> OB_REQUIRE( (r[13] > 3.470) && (r[13] < 3.472) );
> OB_REQUIRE( (r[14] > 6.698) && (r[14] < 6.800) );
> OB_REQUIRE( (r[15] > 9.485) && (r[15] < 9.487) );
>
> the li
Hi All,Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in such way that the bond orders are no longer dependent on the way the molecule was entered? For example, the two smiles representations of the indole ring, N1C=CC2=C1C=CC=C2 and N1C=CC2=CC=CC=C12, lead to differences in
Hi all,
What am I doing wrong in the following code:
#include
#include
#include
#include
int main (int argc, char * const argv[])
{
OpenBabel::OBMol mol;
OpenBabel::OBConversion smi2mol;
smi2mol.SetInFormat("smi");
OpenBabel::OBConversion mol2can;
mol2can.SetOutFormat("can");
All,
I'm using the OB C++ API and I wwas wondering whether there is a way
to retrieve bot Kekule structure from an aromatic system (if there are
two Kekule's)? For example, I would like to get access to both Kekule
forms of the aromatic indole ( c1ccc2c(c1)[nH]cc2 ), hence
[NH]1C=CC2=CC=CC
Hi Geoff,
I'll have a look into it - I'll keep you updated.
Hans
On Dec 1, 2010, at 22:25 , Geoffrey Hutchison wrote:
>
> On Nov 30, 2010, at 10:21 AM, Igor Filippov [Contr] wrote:
>
>> I would be very interested in this too, if it's possible in a general
>> case.
>
> There is not currently a m
tics tools have been
brought into the open source domain by Silicos, including SIEVE,
PHARAO, PIRAMID, and OBSPECTROPHORE, the latter being part of Open
Babel 2.3.
For more information about ProfiLIB, or any other tools or services,
please contact Silicos at i...@silicos.com.
Kind re
tics tools have been
brought into the open source domain by Silicos, including SIEVE,
PHARAO, PIRAMID, and OBSPECTROPHORE, the latter being part of Open
Babel 2.3.
For more information about ProfiLIB, or any other tools or services,
please contact Silicos at i...@silicos.com.
Kind re
chemoinformatics tools have been
brought into the open source domain by Silicos, including SIEVE,
PHARAO, PIRAMID, and OBSPECTROPHORE, the latter being part of Open
Babel 2.3.
For more information about STRIPPER or any other tools, please contact
Silicos at i...@silicos.com.
Kind r
hx in advance.
Hans De Winter
Silicos NV
--
Colocation vs. Managed Hosting
A question and answer guide to determining the best fit
for your organization - today and in the future.
http://p.sf.net/sfu/internap-
Hi,I just encountered a promising tool called MyChem ( http://mychem.sourceforge.net ) which is an extension for MySQL to handle chemical data within MySQL. According the manual it seems very interesting (it is linked against OpenBabel), but I'm struggling to install it working on my Mac OS X syste
Hi,Silicos-it is pleased to announce the release of its renewed website (www.silicos-it.com) from which 5 open source packages (LGPL license) can be downloaded:- Filter-it is a program for filtering molecules with unwanted properties out of a set of molecules. The program comes with a number of pre
Hi,Rdk-it can now be downloaded from our website (www.silicos-it.com). Rdk-it is a package of Python tools and functions that have been build on top of the open source chemoinfomatics toolkit RDKit. The current version of Rdk-it contains Qed, a Python function and standalone tool to calculate the '
Hi,in order to avoid confusion (we originally didn't made the link, although it is rather obvious though), we decided to change the name Rdk-it into Biscu-it. Please feel free to check out the free code at www.silicos-it.com- Hans
www.silicos-it.comA division of Imacosi bvbaDe Roskam 35,2970 Schild
Hi all,Align-it 1.0.3 has been released as of today. Align-it is using the Open Babel C++ as its core API.Align-it is an open source tool for the alignment of database molecules to a reference compound using pharmacophore matches. You can download the new release from the website of Silicos-it (www
> I do think there is a tremendous amount of interest in such a database and
> would be happy to help compile and/or maintain such a resource. I've been
> focusing on the simplified end (e.g., reactions similar to those linked by
> David).
Not really a contribution in answering the question, bu
Hi all,
has anyone already has experience with compiling OpenBabel 2.3.2 under OS X
10.9 (Maverick)?
I tried it (after installing the XCode and Developer tools, as well as cmake
and pkg-config from Homebrew) and got the following:
In file included from
/usr/local/src/openbabel-2.3.2/include/o
Geoff,
even the master gives me the same issue:
Here is the output from the cmake .. command:
hans$ export EIGEN=/usr/local/src/eigen-eigen-b23437e61a07
hans$ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/openbabel
-DEIGEN2_INCLUDE_DIR=$EIGEN ..
-- Using included inchi library.
-- Found LibXml2: /usr
Thanks Matt,
your homebrew alternative works perfect!
Hans
On 31 Oct 2013, at 16:39, Matt Swain wrote:
> I am also having this problem when compiling on Mavericks. I believe it is
> because Mavericks changes the default C++ library from libstdc++ to libc++.
>
> libc++ provides a C++11 libra
Dear Geoff,for your convenience, I’ve included my CMakeCache.txt file from the build directory.# This is the CMakeCache file.
# For build in directory: /usr/local/src/openbabel-2.3.2/build
# It was generated by CMake: /usr/local/Cellar/cmake/2.8.12/bin/cmake
# You can edit this file to change value
Hi,
in principle there should be no restriction on the under limit for the number
of atoms, so I can’t recall exactly why we did put this 'atoms < 3’ restriction
in the code in first instance. So I guess you can safely remove this check and
replace it with a lower limit like 1 or so.
Hans
On
30 matches
Mail list logo
