Feature requests

Python Prescription - Virtual Screening Tool

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Feature requests

Postby wrmartin » Sat Nov 08, 2014 12:26 am

Hello Sargis,

I've been using your software for some virtual screening and have come across a few things I would like to suggest:

1) Allow data to be exported as something other than .csv. I recently used a somewhat large (10k ligands) database, all of which used IUPAC for naming. Of course, this created an issue when exporting as a .csv.

2) Exporting conformations. Right now, if I find a conformation I want to do further work on (say, QM/MM), I have to load it into ADT to give myself a reasonable starting point. It would be nice to be able to select a conformation in PyRx and export it to .pdb and avoid that step.

Thanks in advance.
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Re: Feature requests

Postby sargis » Sat Nov 08, 2014 5:41 pm

Hello Martin,

Thank you for the message. I'm glad to hear you have been using PyRx for virtual screening and appreciate feature requests.

wrmartin wrote:1) Allow data to be exported as something other than .csv. I recently used a somewhat large (10k ligands) database, all of which used IUPAC for naming. Of course, this created an issue when exporting as a .csv.

This is a bit tricky, as I can't think of better way of exporting other than .csv at the moment. I would be happy to hear about other formats that would work better for this case. It might be better to replace IUPAC names with chemical formulas to make it more compact. If you have used Open Babel widget to import these ligands, there is this line in PyRx/traitedBabel.py that sets the names:
Code: Select all
self.title = os.path.split(OBMol.GetTitle())[1]

You can replace this with
Code: Select all
self.title = OBMol.GetFormula()

This way it won't require additional pre or post processing to make exported csv smaller. traitedBabel.py is located under C:\Program Files (x86)\PyRx\$Version\Lib\site-packages\PyRx on Windows.

wrmartin wrote:2) Exporting conformations. Right now, if I find a conformation I want to do further work on (say, QM/MM), I have to load it into ADT to give myself a reasonable starting point. It would be nice to be able to select a conformation in PyRx and export it to .pdb and avoid that step.

To do this in PyRx, please select a conformation in PyRx, right-click on the molecule under Navigator -> Molecules and select Save as PDB. There are many nice features in ADT that's not implemented in PyRx to avoid duplication. However, I'd happy to implement any feature requests that would make PyRx a better tool.

Thank you for using PyRx!
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Re: Feature requests

Postby wrmartin » Sun Nov 09, 2014 4:48 am

I agree that a .csv is typically just fine, and usually the "best" way to do it. My thought would be an option to select the delimeter and save as a text file. Once the .txt is opened in excel, it should prompt for input with regards to what the delimiter is. On your end it could even be a user inputed value, as it can be in excel as well.

For the second question, I wasn't clear. I meant the docked complex, molecule and ligand.

Thank you for the prompt response!
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Re: Feature requests

Postby sargis » Sun Nov 09, 2014 5:15 am

Thank you, those are good feature requests. Sorry I didn't get them initially.

1) I'm thinking to have a GUI somewhere under Edit -> Preferences so that users can select the delimiter when saving cvs file. I'll need to read https://docs.python.org/2/library/csv.html more carefully to make a GUI for this in PyRx.

2) I'll work on options for saving the docked complex (molecule and ligand) in the next release of PyRx.

Thank you for the much appreciated feedback.
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Re: Feature requests

Postby wrmartin » Sun Nov 09, 2014 9:05 pm

Great! Thanks for taking the time to respond. If it makes it any easier, I think you actually want to save as a .txt file when changing the delimiter. I'm not entirely certain, but I think excel automatically assumes commas when the extension is .csv. When opening a .txt, excel prompts if the file is delimited or "fixed width", and after selecting delimited, asks to select the delimiter from a few options, or custom.

Hopefully that made sense.
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