[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

Re: [Dev] WSO2 Committers += Gayan Gunaratne

: rajkumarr.com ___ Dev mailing list Dev@wso2.org http://wso2.org/cgi-bin/mailman/listinfo/dev -- Lochana Menikarachchi Senior Tech Lead WSO2 Inc. ___ Dev mailing list Dev@wso2.org http://wso2.org/cgi

Re: [Architecture] Machine Learner - Proposed UX

887816 e: dhanu...@wso2.com w: http://www.wso2.com -- Lochana Menikarachchi Senior Tech Lead WSO2 Inc. ___ Architecture mailing list Architecture@wso2.org https://mail.wso2.org/cgi-bin/mailman/listinfo/architecture

Re: [Architecture] Machine Learner - Proposed UX

, and then have a tab inside to see all algos to select one, and another tab to help selecting one algo from recommendations. Regards Suho On Wed, Dec 17, 2014 at 12:38 PM, Lochana Menikarachchi loch...@wso2.com wrote: In step 8/9, we ask the questions by default. The user has the option

one hot encoding

Do we have one-hot encoding in spark MLLib 1.1.1 or 1.2.0 ? It wasn't available in 1.1.0. Thanks. - To unsubscribe, e-mail: dev-unsubscr...@spark.apache.org For additional commands, e-mail: dev-h...@spark.apache.org

[Dev] Carbon 4.3.0 snapshot based server hangs

-- Lochana Menikarachchi Senior Tech Lead WSO2 Inc. ___ Dev mailing list Dev@wso2.org http://wso2.org/cgi-bin/mailman/listinfo/dev

Re: packaging spark run time with osgi service

-spark-user-list.1001560.n3.nabble.com/Packaging-a-spark-job-using-maven-td5615.html On Mon, Dec 1, 2014 at 4:28 PM, Lochana Menikarachchi locha...@gmail.com mailto:locha...@gmail.com wrote: I have spark core and mllib as dependencies for a spark based osgi service. When I call the model

spark osgi class loading issue

We are trying to call spark through an osgi service (with osgifyed version of assembly.jar). Spark does not work (due to the way spark reads akka reference.conf) unless we switch the class loader as follows. Thread.currentThread().setContextClassLoader(JavaSparkContext.class.getClassLoader());

Re: packaging spark run time with osgi service

-maven-td5615.html On Mon, Dec 1, 2014 at 4:28 PM, Lochana Menikarachchi locha...@gmail.com mailto:locha...@gmail.com wrote: I have spark core and mllib as dependencies for a spark based osgi service. When I call the model building method through a unit test (without osgi) it works

[Dev] Accessing a DB through bundle starter

.carbon.context.internal.CarbonContextDataHolder$CarbonInitialJNDIContext.lookup(CarbonContextDataHolder.java:705) at javax.naming.InitialContext.lookup(InitialContext.java:411) at org.wso2.carbon.ml.model.DatabaseHandler.getDatabaseHandler(DatabaseHandler.java:62) -- Lochana Menikarachchi Senior Tech Lead WSO2 Inc

Re: [Dev] Accessing a DB through bundle starter

, Lochana Menikarachchi loch...@wso2.com wrote: Is it possible access a database within osgi bundle's start method? public void start(BundleContext context) throws Exception { ModelService modelService = new ModelService(); context.registerService

[Dev] Carbon 4.3.0-SNAPSHOT intermittent error

) at java.lang.Thread.run(Thread.java:745) -- Lochana Menikarachchi Senior Tech Lead WSO2 Inc. ___ Dev mailing list Dev@wso2.org http://wso2.org/cgi-bin/mailman/listinfo/dev

Re: [Dev] Carbon 4.3.0-SNAPSHOT intermittent error

Correction.. I get this with a Carbon 4.3.0-SNAPSHOT based product.. I have ldap, carbon remote user management features and jaggery features installed in it. On Wed, Nov 5, 2014 at 9:26 AM, Lochana Menikarachchi loch...@wso2.com wrote: I run into this error intermittently

Re: [Dev] Carbon 4.3.0-SNAPSHOT intermittent error

, 2014 at 9:49 AM, Lochana Menikarachchi loch...@wso2.com wrote: Correction.. I get this with a Carbon 4.3.0-SNAPSHOT based product.. I have ldap, carbon remote user management features and jaggery features installed in it. This is a known issue in 4.3.0. I think the jaggery feature is causing

[Dev] jaggery for 4.3.0-SNAPSHOT

Hi, Need to bundle jaggery feature with the carbon 4.3.0-SNAPSHOT based product we are building. What is the repo and what are the features required? Thanks. -- Lochana Menikarachchi Senior Tech Lead WSO2 Inc. ___ Dev mailing list Dev@wso2.org http

label points with a given index

SparkConf conf = new SparkConf().setAppName(LogisticRegression).setMaster(local[4]); JavaSparkContext sc = new JavaSparkContext(conf); JavaRDDString lines = sc.textFile(some.csv); JavaRDDLabeledPoint lPoints = lines.map(new CSVLineParser()); Is there anyway to parse an index

Re: label points with a given index

Figured constructor can be used for this purpose.. On 10/24/14 7:57 AM, Lochana Menikarachchi wrote: SparkConf conf = new SparkConf().setAppName(LogisticRegression).setMaster(local[4]); JavaSparkContext sc = new JavaSparkContext(conf); JavaRDDString lines = sc.textFile(some.csv

Re: [Dev] jaggery file upload

standard to write to files and read files. Cheers~ On Tue, Oct 7, 2014 at 12:41 PM, Lochana Menikarachchi loch...@wso2.com wrote: Is there any reason to restrict file system operations (why not outside Jaggery application context root) ? http://jaggeryjs.org/documentation.jag?api=file

Re: [Dev] jaggery file upload

saving a file to a specific path is inadvisable cause paths will depend upon deploying machine. Can you elaborate more on the requirement - where we can give a solution? Cheers~ On Tue, Oct 7, 2014 at 10:50 AM, Lochana Menikarachchi loch...@wso2.com wrote: Unfortunately, that's not going

Re: [Dev] jaggery file upload

to store the files. Adding @sameeraM to the thread. Cheers~ On Tue, Oct 7, 2014 at 12:09 PM, Lochana Menikarachchi loch...@wso2.com wrote: Hi, File uploading brings about a number of issues in scalability. For example - if we upload files to the deployments directory- it's not going

Re: [Dev] jaggery file upload

Is there any reason to restrict file system operations (why not outside Jaggery application context root) ? http://jaggeryjs.org/documentation.jag?api=file On Tue, Oct 7, 2014 at 12:20 PM, Lochana Menikarachchi loch...@wso2.com wrote: We need to support file uploading to a server location

[Dev] jaggery file upload

file.saveAs(String targetLocation); this saves a given file relative to the Jaggery application context root Is there anyway to save the file according to absolute path? Thanks. -- Lochana Menikarachchi Senior Tech Lead WSO2 Inc. ___ Dev mailing list

Re: [Dev] jaggery file upload

, '/').replace(/^[\/]/g, ''); return parent + MODULE_PATH + path; }; [1] https://github.com/Madhuka/sugarcane/blob/master/core/sugarcane/scripts/engine/test.js On Tue, Oct 7, 2014 at 9:37 AM, Lochana Menikarachchi loch...@wso2.com wrote: -- Cheers, Madhuka Udantha http

Re: [Dev] jaggery file upload

lean . enterprise . middleware On Tue, Oct 7, 2014 at 10:29 AM, Lochana Menikarachchi loch...@wso2.com wrote: Dilan, There is a specific requirement.. We need to upload a file to a given location Madhuka, That method returns absolute path.. What I want is to upload a file to a given location

Hyper Parameter Tuning Algorithms

Found this thread from April.. http://mail-archives.apache.org/mod_mbox/spark-user/201404.mbox/%3ccabjxkq6b7sfaxie4+aqtcmd8jsqbznsxsfw6v5o0wwwouob...@mail.gmail.com%3E Wondering what the status of this.. We are thinking about implementing these algorithms.. Would be a waste if they are already

Hyper Parameter Optimization Algorithms

Hi, Is there anyone who works on hyper parameter optimization algorithms? If not, is there any interest on the subject. We are thinking about implementing some of these algorithms and contributing to spark? thoughts? Lochana

[orientdb] orientdb 1.6.4 - sorting question

I have a set of scores in a cluster. Ex: scores property = 1.25, 0.6, 0.6, 0, 0, 0 I would like to assign a rank for each score rank Property = 1, 3, 3, 6, 6, 6 I can do this by doing a ORDER BY SQL and assigning the rank by going through the list, but, it is not memory efficient. What is

[orientdb] Re: orientdb 1.6.4 - sorting question

= m; j++) { results.get(j).field(cidRank, someScore); results.get(j).save(); } does not work..Nothing gets saved?? On Thursday, April 17, 2014 5:12:12 PM UTC-4, Lochana Menikarachchi wrote: I have a set of scores in a cluster. Ex

[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,

[Jmol-developers] Reading a gaussian log file with Jmol API

Hi Everyone, How do you read the last coordinates set and charges from a gaussian log file.   Can somebody provide a code example? I have Jmol.jar in the class path. I am not looking for visualization options. I just need to read the data into my java program.  Should I be using Jmol.jar or

[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.

[Jmol-users] jmol api antialiasDisplay

How do I set antialiasDisplay  to True using jmol api. I couldn't find it on jmol java docs. Thanks. Lochana -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary

[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

Re: [Jmol-users] Jmol for iPads?

openSoft's IMolView for ipad - pretty fast and responsive http://www.molsoft.com/iMolview.html   From: Philip Bays pb...@saintmarys.edu To: jmol-users@lists.sourceforge.net Sent: Friday, March 23, 2012 4:41 PM Subject: Re: [Jmol-users] Jmol for iPads? At

[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

[Jmol-users] JmolViewer

Hi All, I was looking for a JmolViewer jar file that I can embed in a stand alone application. I can see JMol application and applet viewer in the downloads but not a jar file that can be used for developing a stand alone application. How do I go about this?? Thanks. Lochana

[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