orchem-devel — developers' discusion on OrChem

[Orchem-devel] verify failed with Pubchem mol data in oracle 12g

[강신원 <idk...@gm...>]

 Hello, I'm Shinwon Kang.

I am making a simple chemical substructure search service prototype with
OrChem and PubChem chemical data.

In the installing phase, it failed to verify orchem installing.

But, other sample from internet was successful.

I attached a failed output and a successful output file.

   - Fail: pubchem_verify_result.txt
   - Sucess: verify_sccess.txt


how to solve this problem?

and,

I checked out orchem srouce from cvs repository and test
uk.ac.ebi.orchem.test.VerifyOrchem.verify(String) method.

When does not call fixCarbonHCount(Molecule) method, it is succeded to
generate a SMILES.

Please help me.

[Orchem-devel] Supreet Kaur studying masters in chemistry fascinated to learn more about OrChem

[Supreet K. <dr....@gm...>]

Hey!

hope you guys are doing great,
my name is Supreet Kaur studying masters in chemistry
while I was going through project OrChem I was fascinated
to know how popular oracle db was used to develop OrChem
coz in oracle i have little knowledge  and wanna learn more
about your project kindly help me understand more about the project.
even i want to contribute to the project if i could understand about the
project.

more over i wanted to know whether there is any ready to use VM or  docker
or demo  page online to get hands on experience of the project. coz i
am just an amateur programmer as i am just a silly chemistry majors.
i am failing to prepare run time environment since 4 weeks . kindly help me
out in this regard as your helping hand will be highly appreciated

with love
Supreet Kaur

[Orchem-devel] Questions about the new Release 1.3

[Antoine L. <al...@in...>]

Hi Mark,

I have some questions about the new OrChem release:

Upgrade procedure:
I have already install the previous version. By installing the new
release, I simply do the installation procedure once again ? Or do I
have to remove something before ?

In the list of new features of this release you write

- Exact search option. What do you mean ?

- Added CDK functionality available through package calculate.plsql
(generate
  formula, charge, mass) : greate !

- Accept SMILES as molecular base data for fingerprinting/searching:
does it means that I can now only work with smiles code  ? and that I
can completelly remove mol file ?


Search of complexes:
if I have complex of molecules (in SMILES separated by a ".") like :
O=C(NC1CC(CCC1)C3CCCCC3C2CCCCC2)C(=O)NC4CCCCC4.C1CCCCC1C3CCCC2CCCCC23
It means I have in fact two molecules that are store together under the
same compount ID:
O=C(NC1CC(CCC1)C3CCCCC3C2CCCCC2)C(=O)NC4CCCCC4
and
C1CCCCC1C3CCCC2CCCCC23

How do you deal with this ?


Thanks for your help.

Regards,

Antoine

[Orchem-devel] New release

[Mark R. <ma...@eb...>]

I made a new OrChem release (1.3) , see 
http://sourceforge.net/projects/orchem/files/ for details

Re: [Orchem-devel] orchem web app

[<ma...@eb...>]

hi Antoine,

yes, it does mean that, but it has not officially been released (I think
you're looking at a cvs development version of OrChem). If you set it to
'Y' as a database argument it should give the exact result back.
Do you have the latest version installed in the database? If so, let me
know what you query for and what is in your result set (in SMILES format)
so I can see if something is not working properly.

When I'm back at work (I'm on leave this week) I will start on a new
release which will include a few new features like the exact search and
the requests you made earlier.

best regards,
Mark


> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Orchem-devel mailing list
> Orc...@li...
> https://lists.sourceforge.net/lists/listinfo/orchem-devel
>


>  Hi,
>
> What does in the web app the "Exact match ?" parameter means ? I would
> interpret this as the identity search. But it seems not to be the case
> as many structures can be returned.
>
> thanks for your help
>
> Antoine
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Orchem-devel mailing list
> Orc...@li...
> https://lists.sourceforge.net/lists/listinfo/orchem-devel
>

[Orchem-devel] orchem web app

[Antoine L. <al...@in...>]

 Hi,

What does in the web app the "Exact match ?" parameter means ? I would
interpret this as the identity search. But it seems not to be the case
as many structures can be returned.

thanks for your help

Antoine

[Orchem-devel] OrChem: Webapp example : problem by applet loading

[Antoine L. <al...@in...>]

Hi,

I have some questions.

Question  1) 
After having checkout the Orchem projekt from svn, create the property
file [1] , I could build without problem the war file. Than I try to
deploy it in Tomacat and in JBoss. This worked also fine. I can search
SMILES. The only problem is with the loading of the applet. Something is
wrong with the class loader. It say always :

charger : classe
org.openscience.jchempaint.applet.JChemPaintEditorApplet introuvable.
java.lang.ClassNotFoundException:
org.openscience.jchempaint.applet.JChemPaintEditorApplet
    at sun.plugin2.applet.Applet2ClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.plugin2.applet.Plugin2ClassLoader.loadCode(Unknown Source)
    at sun.plugin2.applet.Plugin2Manager.createApplet(Unknown Source)
    at
sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown
Source)
    at java.lang.Thread.run(Unknown Source)
Exception : java.lang.ClassNotFoundException:
org.openscience.jchempaint.applet.JChemPaintEditorApplet

I try it in Firefoxe and Explorer. the same apend. Something get wrong
with the <applet> tag and the classloader. I have so 0 experience with
jsp. I have check: the jar containing JChemPaintEditorApplet
jchempaint-applet-core.jar is there.  Any idea what's goes wrong ?
By my version the JSP snippet looks like:

<applet code="org.openscience.jchempaint.applet.JChemPaintEditorApplet" 
	archive="jchempaint/jchempaint-applet-core.jar" 
	id="editor"
	name="editor" 
	width="700" 
	height="500">
<param name="impliciths" value="true"></param>
<param name="codebase_lookup" value="false"/>
<param name="onLoadTarget" value="statusFrame"></param>
<param name="image" value="hourglass.gif"></param>
<param name="boxborder" value="false"></param>
<param name="centerimage" value="true"></param>
</applet>

Question  2) 
An other basic oracle question: when I tell orchem (in the parameter
table) that it has to take a specific table can I do this to a table
that is in an other shema ? Do I have the right to do this ? Or do I
have to setup this right specifically in oracle ? How it looks like in
the parameter table ? simply schemaname. tablename ? 


Question  3) 
How can I calculate the molecular mass and the empirical formula (like
C6O6H12) of a molecule using the cartridge ?



Thanks for your help

Antoine



[1] by the way in the properties/README you say that we have to create
the directory "my_local_properties". Is it not "my_local_copies" ? I
would also add that it has to be created in the "properties" directory.

Re: [Orchem-devel] problem on orchem

[Mark R. <ma...@eb...>]

Hello Wu hao,

thanks for installing OrChem. I had a look at your mol files. It looks
to me the they may not be formatted as the CDK expects. The
specification for MDL files is at
www.symyx.com/downloads/public/ctfile/ctfile.pdf

I attached an example program 'test.sql' with Methane taken from ChEbi:
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16183

If I run that script, OrChem works fine (the first time you see some
warnings, that's standard). Could you try to run it on sql*plus?

You could compare the Molfile attached to the Molfiles you use. It's all
quite sensitive to have data at exactly the right position.

best regards,
Mark


> dear Mark Rijnbeek
> 
>  
> 
> i just finished installtion of orchem
>  
> however,when i execute
> /select orchem_utils.verify_orchem(15) from dual;/
> an error returns
> /OKAY: compound found with primary key 15
> ERRORError while parsing line 4: M  EN/
>  
> *I tried several input format for methene, but none of them works
> could you tell me where i do it wrong?
> thank you very much
> * 
> here's what i'v tried
> 0.0000 0.0000 0.0000 C 0 0 0 0 0
> M RAD 1 1 2
> M END
>  
> 1 0 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0
> M RAD 1 1 2
> M END
>  
> 4 3 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0
> 1 2 1 0 0 0
> 1 3 1 0 0 0
> 1 4 1 0 0 0
> M RAD 1 1 2
> M END
>  
> 
> OpenBabel12210909062D
> 
> 1 0 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0
> M RAD 1 1 2
> M END
>  
> sincerely,Wu
>  
> 
> --------------------------
> Wu Hao
> Assistant Professor
> Institute of Process Engineering, 
> Chinese Academy of Sciences
> ha...@ho... 
> 
> 
> 
> 
> 

Re: [Orchem-devel] News: First Function

[Mark R. <ma...@eb...>]

Hi Federico,
> I finished my first procedure to convert Molfile to SMILES. It works!!
>   
Good stuff !
> I'm using your utility to test and reload the java class into database.
>   
You mean VerifyOrchem.java? Ok.
> I'm trying to follow your indication and your organization. Do you
> prefer that a commit the project frequently or less frequently? 
>
>   
I'd prefer you to commit frequently, so go ahead.

Just to check: whenever you add new Java stored procedures, group them 
logically together in (a) PL/SQL package(s).
Like the existing packages serve a specific purpose for similarity and 
substructure searching.
The same goes for the Java package tree, you may want to add any new 
classes in their own Java package.

By the way - did you get the unit test to work, as described on 
http://orchem.sourceforge.net/developers.html?
Someone else had trouble getting it to work, a java.sql.SQLException: 
"Io exception: Connection reset" when loading the unit test data. Just 
curious if you had seen the same.

Mark.

Re: [Orchem-devel] The 2009 International Oracle Life Sciences and Healthcare User Group Meeting

[Mark R. <ma...@eb...>]

We are all passive lurkers to some extent; with regards to your 
question, see:
http://sourceforge.net/projects/chemdb/
So - OrChem (hence the "Or" bit) is specifically for Oracle. Mychem and 
Pgchem target the other databases. We don't share source code, the other 
two do not use CDK and had been already built when I started work on 
OrChem. Also they're not Java based like OrChem, but written in C++. I'm 
actually not sure what the ChemiSQL federation entitles ;)


> Hello,
>
> I'm just a passive lurker on this list ;-)
> I was wondering if OrChem will also support or work with open-source
> databases like MySQL or Postgresql?
> Or is it really dependent on the Oracle cartridge technology?
>
> Cheers,
> Matthias
>   

Re: [Orchem-devel] The 2009 International Oracle Life Sciences and Healthcare User Group Meeting

[Matthias H. <MatthiasH@DEVGEN.COM>]

Hello,

I'm just a passive lurker on this list ;-)
I was wondering if OrChem will also support or work with open-source
databases like MySQL or Postgresql?
Or is it really dependent on the Oracle cartridge technology?

Cheers,
Matthias
 

-----Original Message-----
From: Mark Rijnbeek [mailto:ma...@eb...] 
Sent: Monday, July 06, 2009 4:19 PM
To: orc...@li...; Caffeine
Subject: [Orchem-devel] The 2009 International Oracle Life Sciences and
Healthcare User Group Meeting



Fyi, I'm giving a talk on OrChem at the OLSUG: 
http://www.olsug.org/wiki/index.php?title=Main_Page

It may be of interest to you - there are some chemoinformatics talks 
from  Accelrys and Biochemfusion. There's also a Knime workshop it
seems.
Would be nice to get a paper published on OrChem beforehand, I'm sort of

halfway there.

Mark


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Orc...@li...
https://lists.sourceforge.net/lists/listinfo/orchem-devel
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Any views expressed in this message are those of the individual
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Thank you for your cooperation.

[Orchem-devel] The 2009 International Oracle Life Sciences and Healthcare User Group Meeting

[Mark R. <ma...@eb...>]

Fyi, I'm giving a talk on OrChem at the OLSUG: 
http://www.olsug.org/wiki/index.php?title=Main_Page

It may be of interest to you - there are some chemoinformatics talks 
from  Accelrys and Biochemfusion. There's also a Knime workshop it seems.
Would be nice to get a paper published on OrChem beforehand, I'm sort of 
halfway there.

Mark

Re: [Orchem-devel] Privileges for Oracle users - help

[<ma...@eb...>]

> Can anyone tell me how to change the user privileges for
>     everything required - views, procedures, Java, etc. I can do this as
>     SYS, but would prefer to do it all as a seperate user.
>     John
>

Hi John

you're supposed to let the "orchem" user account own the objects required,
not SYS. I hope that was clear from my documentation, if not let me know
how I might rephrase that.

So you can discard those objects owned by SYS (drop them, or just leave
them lying around)

Create a new account, say ORCHEM, if you don't have such an account yet.

With SYS, grant RESOURCE and CONNECT to ORCHEM.

This gives ORCHEM enough privileges to install the objects in its own
'schema' (schema means user realm in Oracle).
Then, as ORCHEM, create the tables, views and load the java.

Btw - as a start, you can instead start with setting up the unit test
environment. See documentation pages. This works from a CVS checkout, and
not only sets up Orchem in your database but also installs a little table
with a compound sample to test with.

good luck !
Mark

[Orchem-devel] Privileges for Oracle users - help

[John H. <j.d...@sh...>]

Can anyone tell me how to change the user privileges for 
    everything required - views, procedures, Java, etc. I can do this as 
    SYS, but would prefer to do it all as a seperate user.
    John

Re: [Orchem-devel] [Re: Good begin for me!]

[Paoli F. <fp...@si...>]

Super!!! 
I will prepare the environment to develop as soon as possible. 

Federico


-----Original Message-----
From: ma...@eb... [mailto:ma...@eb...] 
Sent: Friday, June 26, 2009 10:14 AM
To: orc...@li...
Subject: [Orchem-devel] [Re: Good begin for me!]




Hi Federico,

thanks for taking up orchem, glad you like it! Of course you could begin
to develop functionality. To keep track of things, could you state the
feature(s) you plan to work on in sourceforge?
Go to Tracker/Feature requests, create a feature and assign it to
yourself. A bit fake, but in that way we can keep track of things.

You will need to check out orchem  from cvs and work from there. I use
Jdeveloper myself to code Java. There's also a build.xml file for ant to
compile/build things from the command line.

The idea behind orchem is to use the CDK where possible. The features
you mention can probably be done with the CDK.
It's useful for you then to have a CDK checkout, read more on
https://sourceforge.net/apps/mediawiki/cdk/index.php?title=Development_w
ith_Git
You can browse the CDK source code for examples how-to do things.
Especially the /test directory with Junit tests contains many examples.
If you get stuck, you can post questions to the cdk user list.

In the end, you'd create Java classes on top of the CDK and wrap these
as stored procedures. If you get to that point, contact me. We need to
find a new Java package name that makes sense, and will probably need to
create one more more new pl/slq packages to bundle the new Java stored
procedures. I'd like to keep an eye on the organization of the source
code, to see what goes where.

thanks!
Mark

---------------------------- Original Message
----------------------------
Subject: Good begin for me!
From:    "Federico Paoli" <fp...@si...>
Date:    Thu, June 25, 2009 19:01
To:      "Mark Rijnbeek" <ma...@eb...>
------------------------------------------------------------------------
--

Hi Mark,
I'm very happy to help you and your team to test the orchem cartridge,
also because is very good work!!

How do you think we could continue this "collaboration"?

For examples I should need some other functions:
- convert format
- calculation properties
- ecc...

...and I have other ideas.....

Do you prefer that I have to continue the test? ... or Do you prefer I
could begin to develop some functions?

Thanks
Federico




Federico Paoli
Responsabile - Information Technology
Siena Biotech S.p.A.
Strada del Petriccio e Belriguardo, 35
53100 Siena - ITALY
Tel: (+39) 0577 381 418
Fax: (+39) 0577 381 208
fp...@si...
www.sienabiotech.it


 

Federico Paoli
Responsabile - Information Technology
Siena Biotech S.p.A.
Strada del Petriccio e Belriguardo, 35
53100 Siena - ITALY
Tel: (+39) 0577 381 418
Fax: (+39) 0577 381 208
fp...@si...
www.sienabiotech.it 






This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited.

[Orchem-devel] [Re: Good begin for me!]

[<ma...@eb...>]

Hi Federico,

thanks for taking up orchem, glad you like it! Of course you could begin
to develop functionality. To keep track of things, could you state the
feature(s) you plan to work on in sourceforge?
Go to Tracker/Feature requests, create a feature and assign it to
yourself. A bit fake, but in that way we can keep track of things.

You will need to check out orchem  from cvs and work from there. I use
Jdeveloper myself to code Java. There's also a build.xml file for ant to
compile/build things from the command line.

The idea behind orchem is to use the CDK where possible. The features you
mention can probably be done with the CDK.
It's useful for you then to have a CDK checkout, read more on
https://sourceforge.net/apps/mediawiki/cdk/index.php?title=Development_with_Git
You can browse the CDK source code for examples how-to do things.
Especially the /test directory with Junit tests contains many examples. If
you get stuck, you can post questions to the cdk user list.

In the end, you'd create Java classes on top of the CDK and wrap these as
stored procedures. If you get to that point, contact me. We need to find a
new Java package name that makes sense, and will probably need to create
one more more new pl/slq packages to bundle the new Java stored
procedures. I'd like to keep an eye on the organization of the source
code, to see what goes where.

thanks!
Mark

---------------------------- Original Message ----------------------------
Subject: Good begin for me!
From:    "Federico Paoli" <fp...@si...>
Date:    Thu, June 25, 2009 19:01
To:      "Mark Rijnbeek" <ma...@eb...>
--------------------------------------------------------------------------

Hi Mark,
I'm very happy to help you and your team to test the orchem cartridge,
also because is very good work!!

How do you think we could continue this "collaboration"?

For examples I should need some other functions:
- convert format
- calculation properties
- ecc...

...and I have other ideas.....

Do you prefer that I have to continue the test? ... or Do you prefer I
could begin to develop some functions?

Thanks
Federico




Federico Paoli
Responsabile - Information Technology
Siena Biotech S.p.A.
Strada del Petriccio e Belriguardo, 35
53100 Siena - ITALY
Tel: (+39) 0577 381 418
Fax: (+39) 0577 381 208
fp...@si...
www.sienabiotech.it

Re: [Orchem-devel] Orchem developer list

[Federico P. <fp...@si...>]

OK! I will use this list!

My Test with parallel function. 

SQL> @subpar.sql
Enter value for smiles: CCO

PL/SQL procedure successfully completed.

Elapsed: 00:00:00.18
Enter value for topn: null
old   1:  select count(*) from table
(orchem_subsearch_par.search(:key,&topn,'N'))
new   1:  select count(*) from table
(orchem_subsearch_par.search(:key,null,'N'))

  COUNT(*)
----------
    242602

Elapsed: 00:01:17.33
SQL> /







On Thu, 2009-06-25 at 12:13 +0000, Mark Rijnbeek wrote:

> I just tested the list orc...@li..., it seems to 
> work now.
> 
> If you're still interested, stay on the list, otherwise unsubscribe.
> John and Federico, I suggest you use this list for questions/suggestions 
> regading OrChem, rather than sending them to my Ebi email address.
> 
> cheers,
> Mark
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Orchem-devel mailing list
> Orc...@li...
> https://lists.sourceforge.net/lists/listinfo/orchem-devel

 

Federico Paoli
Responsabile - Information Technology
Siena Biotech S.p.A.
Strada del Petriccio e Belriguardo, 35
53100 Siena - ITALY
Tel: (+39) 0577 381 418
Fax: (+39) 0577 381 208
fp...@si...
www.sienabiotech.it 






This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited.

[Orchem-devel] Orchem developer list

[Mark R. <ma...@eb...>]

I just tested the list orc...@li..., it seems to 
work now.

If you're still interested, stay on the list, otherwise unsubscribe.
John and Federico, I suggest you use this list for questions/suggestions 
regading OrChem, rather than sending them to my Ebi email address.

cheers,
Mark