Hi All,
I wonder whether following procedure is doable within CDK..
Read a SDF file and write a gamess input file (i know I can write a gaussian
input file) - CDK
Call gamess to run an optimization (using separate java code)
Read in optimized geometry and (electrostatic potentials) from gamess
Hi All,
When I render molecules using CDK, carbon carbon bonds appear in black for most
molecules, gray for some. Why do bonds appear in gray for some? Is there a way
to fix this?
Lochana
--
All the data continuously
Hi All,
I was trying to use SMARTSQueryTool to match all aliphatic and aromatic N with
4 connections.
[$([NX4+]),$([nX4+])]
The molecules were read from PubChem SDF files. The query gives me only
aliphatic, it also gives me things with 3 bonds say N connected to a =O and 2
others ?
I read in a sdf.gz file downloaded from pubchem using IteratingMDLReader to a
LinkedList of IAtomContainer
The file contains 576 structures. However when I write it using SDFWriter I can
see only 574. Inside the SDF file I can only see half of 575 recored and none
of 576. MDLV2000 writer
The problem was with forgetting to add writer.close()
It fixed the problem.
public static void writeSDF() throws IOException, CDKException, Exception
{
String filename = /Users/lochana/Desktop/test.sdf;
SDFWriter writer = new SDFWriter(new FileWriter(new File(filename)));
What does model.set(BasicSceneGenerator.ShowMoleculeTitle.class,true); do ??
Is it possible to display a molecule title or a text string on the rendered
molecule??
Thanks.
Lochana--
The demand for IT networking
Can you create a MDL V2000 molfile with FC(Cl)BrI as compound, make
sure it has the stereo field, *and* let me know if that file
represents the R or S species? Then I will write a patch to add this
functionality.
Attached compound CID_79058.sdf is S isomer of FC(Cl)BrH downloaded from
pubchem.
I have a sdf file with abbreviated amino acids..The CDK SDF readers seem to
read this molecule but fails to write it back in SDF format..Is there anyway to
expand these abbreviations?? Any other library or workaround?? The SDF is
attached. Thanks.
abbrAA.sdf
Description: Binary data
Hi All,
Is it possible to fragment a molecule based on set of rules using CDK??
Here is an example rule from a paper:
Molecules containing an amine group with (at least) an ethylene or substituted
ethy- lene group separating the nitrogen atom from other functional groups,
will cleave and
Hi All,
I found CDK molecular descriptor engine hangs with
org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
I tried it with my own code and Rajarshi's descriptor engine UI program
(Electronic -- Ionization Potential)
Thanks.
Lochana
A small utility program to convert data fields in a SDF file to an Excel sheet
(xslx)..
http://www.scientisoft.com/software--
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here
Hi All,
I want to combine atom type E-state indices to generate new descriptors (to
describe certain functional groups). Is this possible with CDK? If so how do I
get the E-States for an iAtomContainer??
Thanks.
Hi All,
Is there new developments in porting Padel descriptors to CDK? We rely on
Molconn E-State descriptors for some QSPR models in our program MolFInd (to be
released soon)
The major limitation for us to make the program completely free
is unavailability of Estate descriptors in CDK. It
I figured integrating PaDEL with our program to calculate e-states is not that
difficult. If anyone is interested it is a matter of adding
libPaDEL-Descriptor.jar to your project and writing a couple of lines.
From: lochana menikarachchi locha...@yahoo.com
What is the boolean[] doubleBondConfiguration in chiralSMILES generator??
Thanks.
Lochana--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed
Hi,
Is it possible to create a custom fingerprint using CDK?
Thanks.
Lochana--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT
Hi Nina,
I did try the RandomAccessSDFReader. It took few minutes to build the index for
an SD file with 50,000 structures. What I am saying is what ever MarvinView
does to build index (if it is using an index) is much faster. I am wondering
how it does that.
Joos,
You are right. I should use a local database instead of SD files...
Lochana
From: Joos Kiener j...@sunrise.ch
To: lochana menikarachchi locha...@yahoo.com
Cc: cdk-user@lists.sourceforge.net cdk-user@lists.sourceforge.net
Sent: Thursday, September 19
If it doesn't hurt why not leave it. I will help me to make my program a lot
more open source. Right now I am using marvin because it retains this
information.
From: John May john...@ebi.ac.uk
To: lochana menikarachchi locha...@yahoo.com
Cc: cdk-user
What is the recommended method for storing IAtomContainers in a database.
Serialize? MDL Strings?
Is there anyway to get the MDLV2000 representation as a String from
IAtomContainer?? --
October Webinars: Code for
Hi,
I need to match a set of fragments (substructures) of a target molecule to the
target. Each fragment will be matched once. As I match the fragments, a weight
(score) will be assigned to the matched atoms in the target. This weight will
be incremented as more fragments are matched. Finally,
Hi All,
I tried adding ebi maven repository to Netbeans 7.4.
http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo
It doesn't show any version after 1.4.13 in netbeans??
I can see 1.5.5 when I go to the url. Any idea why those versions aren't
showing up..
Thanks.
the LGPL -
https://www.gnu.org/licenses/lgpl-java.html. I might add that to the README
actually.
J
On 28 Mar 2014, at 06:17, Egon Willighagen egon.willigha...@gmail.com wrote:
Hi Lochana,
On Fri, Mar 28, 2014 at 3:43 AM, lochana menikarachchi
locha...@yahoo.com wrote:
Is there any reason
I observed the same behavior as this.. http://sourceforge.net/p/cdk/bugs/1197/
public static String iAtomContainerListToSDFString(ListIAtomContainer
mfSDF) throws FileNotFoundException, CDKException, IOException
{
StringWriter sw = new StringWriter();
BufferedWriter bw = new
Do we have an MMFF94 based energy minimizer in the CDK?
Thanks.
Dr. Lochana C. Menikarachchi
Senior Lecturer,
Department of Pharmacy,
Faculty of Allied Health Sciences,
University of Peradeniya
___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
25 matches
Mail list logo