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From: 강신원 <idk...@gm...> - 2019-07-12 07:49:17
|
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. |
From: Supreet K. <dr....@gm...> - 2016-10-02 07:34:35
|
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 |
From: Antoine L. <al...@in...> - 2010-11-12 08:44:13
|
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 |
From: Mark R. <ma...@eb...> - 2010-10-19 12:46:45
|
I made a new OrChem release (1.3) , see http://sourceforge.net/projects/orchem/files/ for details |
From: <ma...@eb...> - 2010-09-29 07:58:55
|
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 > |
From: Antoine L. <al...@in...> - 2010-09-29 07:28:31
|
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 |
From: Antoine L. <al...@in...> - 2010-09-24 12:16:19
|
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. |
From: Mark R. <ma...@eb...> - 2009-12-21 11:07:09
|
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... > > > > > |
From: Mark R. <ma...@eb...> - 2009-07-09 15:02:52
|
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. |
From: Mark R. <ma...@eb...> - 2009-07-06 14:43:19
|
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 > |
From: Matthias H. <MatthiasH@DEVGEN.COM> - 2009-07-06 14:11:50
|
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 ------------------------------------------------------------------------ ------ _______________________________________________ Orchem-devel mailing list Orc...@li... https://lists.sourceforge.net/lists/listinfo/orchem-devel _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ This e-mail and any attachments thereto may contain information which is confidential and/or protected by intellectual property rights and are intended for the sole use of the recipient(s) named above. Any use of the information contained herein (including, but not limited to, total or partial reproduction, communication or distribution in any form) by persons other than the designated recipient(s) is prohibited. If you have received this e-mail in error, please notify the sender either by telephone or by e-mail and delete the material from any computer. Any views expressed in this message are those of the individual sender, except where the sender specifies and with authority, states them to be the views of Devgen NV. Thank you for your cooperation. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ This e-mail and any attachments thereto may contain information which is confidential and/or protected by intellectual property rights and are intended for the sole use of the recipient(s) named above. Any use of the information contained herein (including, but not limited to, total or partial reproduction, communication or distribution in any form) by persons other than the designated recipient(s) is prohibited. If you have received this e-mail in error, please notify the sender either by telephone or by e-mail and delete the material from any computer. Any views expressed in this message are those of the individual sender, except where the sender specifies and with authority, states them to be the views of Devgen NV. Thank you for your cooperation. |
From: Mark R. <ma...@eb...> - 2009-07-06 13:19:50
|
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 |
From: <ma...@eb...> - 2009-06-29 17:48:09
|
> 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 |
From: John H. <j.d...@sh...> - 2009-06-29 16:18:06
|
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 |
From: Paoli F. <fp...@si...> - 2009-06-26 13:12:13
|
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. |
From: <ma...@eb...> - 2009-06-26 08:14:37
|
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 |
From: Federico P. <fp...@si...> - 2009-06-25 14:40:50
|
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. |
From: Mark R. <ma...@eb...> - 2009-06-25 11:13:44
|
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 |