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Bill LaidigBill Laidig 

Python example(s) of molecular manipulation


I have been looking at the example protocols for python in PP v.  I see how to do things properties, parameters and globals, but not how to manipulate the the molecule object arrays (like the chem. toolkit in perl).  I was trying to write a COSMO file reader in python and could not figure out how to create the molecule object or how to push coordinates and atom types into the appropriate arrays.  Does anyone have any examples of doing this (I read the documentation, but couldn't find anything about this except how to generate node objects).

Hi Bill,

Are you talking about COSMOlogic (COSMOtherm, COSMOconf, etc)?  If you are I have a series of protocols that take a molecule, parameterise it in COSMOconf and then this is passed on to a COSMOtherm protocol.  

Happy to discuss more if this is relevant.

Bill LaidigBill Laidig
Hi Murray,

Yes, I am talking about reading COSMOlogic *.cosmo files. Thanks for the protocol offer, but I don't think we need that since we have our own internal protocol at P&G.  What I was trying to do was 2 fold:

1. Read in the segment charges and some them into atomic response charges.  This is to help with selecting the best fragments to use in MCOS files.  I am currently doing this in Excel and its a pain.
2. Learn how to write python components especially ones that manipulate molecules.

It's good to know other folks here use COSMOlogic products,

Bill LaidigBill Laidig
I asked this question to Biovia Support and this is their response (edited):

Currently we do not have a molecular toolkit for use in Python like we do in Perl.  PilotScript also has functions to a rich set of functionality available in the Perl toolkit. 

I requested this feature be added.