[Cdk-user] MMFF94 based energy minimizer

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

[Cdk-user] cdk 1.4.19 SDFWriter with StringWriter

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

Re: [Cdk-user] CDK License

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

[Cdk-user] cdk ebi maven repository

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.

[Cdk-user] Substructure matching

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,

[Cdk-user] Storing IAtomContainers in a Database

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

Re: [Cdk-user] Charge and Stereo Columns in SD Files

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

[Cdk-user] Reading large SD Files

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.

Re: [Cdk-user] Reading large SD Files

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

[Cdk-user] Custom Fingerprint

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

[Cdk-user] chiral SMILES

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

Re: [Cdk-user] Padel_Estate_Descriptors

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

[Cdk-user] Padel_Estate_Descriptors

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

[Cdk-user] E-State

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.

[Cdk-user] sdf2Excel

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

[Cdk-user] IPMolecularLearningDescriptor hangs

 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

[Cdk-user] Fragmenting Molecules based on set of rules

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

[Cdk-user] Abbreviated Amino Acids in SDF

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

[Cdk-user] SDF Problem

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.

[Cdk-user] Display Molecule Name

 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

[Cdk-user] SDFWriter problem

 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

[Cdk-user] SDFWriter

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)));  

[Cdk-user] SMARTS Matching

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 ?

[Cdk-user] Rendered Bonds in Gray

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

[Cdk-user] Read Write Gaussian and Gamess

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