[Rdkit-discuss] How to build the RDKit for IronPython?
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[Rdkit-discuss] How to build the RDKit for IronPython?
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From: <sri...@th...> - 2010-10-20 19:49:15
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There are RDKit builds available with Standard releases of Python. But I just downloaded IronPython (hoping work with .NET, VB or C#). >>> sys.version '2.6.1 (IronPython 2.6.1 (2.6.10920.0) on .NET 2.0.50727.3603)' The RDKit I downloaded is for Python 2.5 Obviously, it is not importing in IronPython. If there is an RDKit build for IronPython, could someone point me to the source? Many Thanks Sridhar p.s. How Could I connect direct to oracle from Python2.5 to Oracle 11g? details in below thread. From: Kuntamukkula, Sridhar (Hlthcr&Science) Sent: Wednesday, October 20, 2010 2:04 PM To: rdk...@li... Subject: Re: [Rdkit-discuss] [Rdkit-devel] How to build the RDKit? Hi, I have downloaded the "Windows x86 Installer <http://prdownloads.sourceforge.net/cx-oracle/cx_Oracle-5.0.4-11g.win32- py2.5.msi?download> (Oracle 11g, Python 2.5)" to my PC and installed it. >From Python command-line, when I try to connect to oracle, I get the following error. C:\RDkit>python Python 2.5 (r25:51908, Sep 19 2006, 09:52:17) [MSC v.1310 32 bit (Intel)] on win 32 Type "help", "copyright", "credits" or "license" for more information. >>> import cx_Oracle >>> con = cx_Oracle.connect("user", "pwd", "chemdev") Traceback (most recent call last): File "<stdin>", line 1, in <module> cx_Oracle.DatabaseError: ORA-24315: illegal attribute type I have originally used the connstr=user/pwd@chemdev' and this gave me the same error as above. Then I found the above syntax in the cx_oracle_doc folder's readme.txt and am lost now. MY PC has Windows XP, Oracle is on a different server (with a TNS entry "chemdev") and I just added TNS_ADMIN Registry_entry and the path of TNS_ADMIN to the PATH env. Variable. >From a command prompt, sqlplus user/pwd@chemdev works fine. Any thoughts? Many thanks Sridhar From: nik...@no... [mailto:nik...@no...] Sent: Wednesday, October 20, 2010 2:07 AM To: Eddie Cao Cc: rdk...@li...; Kuntamukkula, Sridhar (Hlthcr&Science); rdk...@li... Subject: Re: [Rdkit-devel] How to build the RDKit? Hi Sridhar, congrats on getting things working. One more comment - maybe you want to post these kind of questions rather in the discuss than the devel list. It is much more populated and you will for sure get replies quicker. Cheers Nik Eddie Cao <cao...@gm...> 10/19/2010 11:49 PM To sri...@th... cc rdk...@li... Subject Re: [Rdkit-devel] How to build the RDKit? Hi Sridhar, Congratulations! If from rdkit import Chem gives you >>>, then it is very good sign that things are all in place. To load molecules from Oracle database, you need a database connector called cx_Oracle. After installing this module, you will be able to send SQL statement to Oracle to retrieve molecule SMILES or SDF, depending on how molecules are stored in your database. You might need to consult your database administrator. To download cx_Oracle: http://cx-oracle.sourceforge.net/ For a simple example about how to use it: http://wiki.oracle.com/page/Python Check Section 14 of the Getting Started in Python Guide for a complete list of descriptors you can calculate using RDKit: http://rdkit.org/GettingStartedInPython.pdf Regards, Eddie On Oct 19, 2010, at 2:31 PM, sri...@th... wrote: Hi Nik, Looks like I had a version issue with the RDkit I downloaded. I needed Q22010_1 for Python2.5 but I downloaded Q22009_1 in which, it was looking for Python2.5 (hardcoded path from one of the libs, looked like) when I ran the test command (hence I downloaded and installed Python2.5 and removed 2.6). Now that I have a clean install of Py2.5 and fresh download of RDkit Q22010_1 for Py2.5, the test command ran well and passed the test. I just have to go to the next step. I need to create molLogP, NumHAcceptors, NumHDonors etc.. values for a given molecule. My molecules are actually stored in an Oracle DB. So, Where do I begin? I just got your other mail. The install is set and OK now as it seems. I ran the command "from rdkit import Chem" from the command-line and it put me back to the >>> prompt, no add'l msgs. As for sending to the whole group, it was an honest mistake. I just clicked "Reply". Some other lists that I subscribed to, send to the list automagically. I realized my mistake when I didn't receive the mail back to me and fixed it in this one. Regards, Sridhar ------------------------------------------------------------------------ ------ Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev_______________________________________ ________ Rdkit-devel mailing list Rdk...@li... https://lists.sourceforge.net/lists/listinfo/rdkit-devel _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. |