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
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s Team, WSO2 Inc.
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Senior Tech Lead
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>>
>> Cheers
>>
>>
>> On Thu, Dec 18, 2014 at 8:51 AM, Dhanuka De Silva
>> wrote:
>>>
>>> Suho's comment makes sense. Lets see what we can do about it without
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
> wrote:
>
>> In step 8/9, we ask the questions by defau
Wizard Step 4)
>
> ML-10-Wizard-Step-5-final
> (Modify parameters for the selected Algorithm - Wizard Step 5)
>
> Cheers
>
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> Dhanuka De Silva
> m: +94 773 887816
> e: dhanu...@wso2.com
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Senior Tech Lead
WSO2 Inc.
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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.
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Lochana Menikarachchi
Senior Tech Lead
WSO2 Inc.
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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());
ache-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
mailto:locha...@gmail.com>> wrote:
I have spark core and mllib as dependencies for a spark based osgi
service. When I call the model
using-maven-td5615.html
On Mon, Dec 1, 2014 at 4:28 PM, Lochana Menikarachchi
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 OK. Whe
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 OK. When I call it through the osgi service,
nothing happens. I tried adding spark assembly jar. Now it throws
following error..
An err
, Lochana Menikarachchi
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(Mod
at
org.wso2.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 Tec
2014 at 9:49 AM, Lochana Menikarachchi
> 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
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
wrote:
>
> I run into this error intermittently.. Is there a solution fo
java.lang.Thread.run(Thread.java:745)
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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.
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http
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);
JavaRDD lines = s
SparkConf conf = new
SparkConf().setAppName("LogisticRegression").setMaster("local[4]");
JavaSparkContext sc = new JavaSparkContext(conf);
JavaRDD lines = sc.textFile("some.csv");
JavaRDD lPoints = lines.map(new CSVLineParser());
Is there anyway to parse an index to a function.
tation.
>>
>> Also I think you need to read this file from a Java component. For that -
>> you can use the absolute path to the web app itself (again the same method
>> as above -abstract the implementation)
>>
>> @SameeraM @SameeraP remember the file server d
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
wrote:
> We need to support file uploading to a server location (for testing
r use HDFS/RDMS to store the files. Adding @sameeraM to the
> thread.
>
> Cheers~
>
> On Tue, Oct 7, 2014 at 12:09 PM, Lochana Menikarachchi
> wrote:
>
>> Hi,
>>
>> >>File uploading brings about a number of issues in scalability. For
>> example -
these files across the cluster if DepSync
> enabled). Also 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, 20
gt; WSO2 Inc. <http://wso2.com/>
> Mobile: +94775149066
> lean . enterprise . middleware
>
> On Tue, Oct 7, 2014 at 10:29 AM, Lochana Menikarachchi
> wrote:
>
>> Dilan, There is a specific requirement.. We need to upload a file to a
>> given location
>> Ma
('carbon.home')).replace(/[\\]/g,
> '/').replace(/^[\/]/g, '');
> return parent + MODULE_PATH + path;
> };
>
> [1]
> https://github.com/Madhuka/sugarcane/blob/master/core/sugarcane/scripts/engine/test.js
> On Tue, O
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.
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Lochana Menikarachchi
Senior Tech Lead
WSO2 Inc.
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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
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
---
List results = db.query(new OSQLSynchQuery("SELECT *
FROM FilteredCompounds ORDER BY cidScore DESC"));
this works
but replacing * with @rid as realRID does not work..
On Thursday, April 17, 2014 5:12:12 PM UTC-4, Lochana Menikarachchi wrote:
>
> I have a set of scores in a
for (int j = start; j <= 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 h
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 th
I observed the same behavior as this.. http://sourceforge.net/p/cdk/bugs/1197/
public static String iAtomContainerListToSDFString(List
mfSDF) throws FileNotFoundException, CDKException, IOException
{
StringWriter sw = new StringWriter();
BufferedWriter bw = new BufferedWriter
; -
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 wrote:
Hi Lochana,
>
>On Fri, Mar 28, 2014 at 3:43 AM, lochana menikarachchi
> wrote:
>
>Is there any reason to distribute CDK under LGPL lice
Is there any reason to distribute CDK under LGPL license? Why not apache
license? Also, did you guys thought about incubating CDK as an apache project??--
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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.
Lochana
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 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 Jmol
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 Performa
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
To: lochana menikarachchi
Cc: "cdk-user@lists.sourceforge.net"
My biggest concern is the charge column. One of our programs uses a proprietary program that relies on this information. From: John May To: lochana
menikarachchi Cc: "cdk-user@lists.sourceforge.net" Sent: Friday, September 20, 2013 4:11 PM Subject: Re: [Cdk-user] Charge and Stereo
Was this issue addressed in a later patch?
http://www.mail-archive.com/cdk-user@lists.sourceforge.net/msg02347.html
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Joos,
You are right. I should use a local database instead of SD files...
Lochana
From: Joos Kiener
To: lochana menikarachchi
Cc: "cdk-user@lists.sourceforge.net"
Sent: Thursday, September 19, 2013 9:37 AM
Subject: Re: [Cdk-user] Reading larg
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.
Lochana---
Hi Everyone,
I need to quickly load 5-10 molecules to a jTable from a large SD file(say 1
million structures). The table needs to be updated by loading only 5-10
structures as the user scrolls down the table. I tried various SDF readers in
CDK. Iterating reader, RandomAccessSDFReader but, they
Hi,
Is it possible to create a custom fingerprint using CDK?
Thanks.
Lochana--
Live Security Virtual Conference
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What is the boolean[] doubleBondConfiguration in chiralSMILES generator??
Thanks.
Lochana--
Live Security Virtual Conference
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threat landscape has changed
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
To: "cdk
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 see
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.
Lochana---
How do I set antialiasDisplay to True using jmol api. I couldn't find it on
jmol java docs.
Thanks.
Lochana
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monitoring Big Data applications. Try Boundary
A small utility program to convert data fields in a SDF file to an Excel sheet
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openSoft's IMolView for ipad - pretty fast and responsive
http://www.molsoft.com/iMolview.html
From: Philip Bays
To: jmol-users@lists.sourceforge.net
Sent: Friday, March 23, 2012 4:41 PM
Subject: Re: [Jmol-users] "Jmol" for iPads?
At the ACS meeting last
Following code run into concurrent modification exception when ran in more than
1 thread. Any ideas??
ExecutorService eservice = Executors.newFixedThreadPool(threads);
CompletionService > cservice = new
ExecutorCompletionService > (eservice);
int k=0;
for (IAtomCo
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
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 lo
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
-
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
--
> 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
pubch
I have noticed either cdk MDLV2000 reader or sdf writer looses some information
in the sdf file. (column 7) This breaks compatibility with other programs that
rely on this information. Both oechem and marvin keep all information in sdf.
Is there anyway to solve this. Is it a limitation in the C
Is it possible to read partial charges contained in PubChem 3D SDF files using
MDLV2000 Reader ??
>
29
1 -0.36
10 0.08
11 0.09
12 -0.15
13 -0.15
14 -0.15
15 0.08
16 -0.15
17 -0.15
18 -0.15
19 0.63
2 -0.53
20 0.28
21 0.15
22 0.15
23 0.15
24 0.15
25 0.15
26 0.15
27 0.15
28 0.45
3 -0.57
32 0.5
4 -0
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.
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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)));
I read in a sdf.gz file downloaded from pubchem using IteratingMDLReader to a
LinkedList of
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 on the other han
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 ?
Thank
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 g
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
Any new developments and stable versions of Elemental formula to Structure
Generator Classes in CDK ??
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