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how to import solvent accessible surface area as a feature in pyemma? #1586
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Hi Satyajit Khatua, |
Hi,
Thank you for the quick response. I will try to import the sasa as you have mentioned. Will report you back.
Thanks again,
Satyajit Khatua
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From: Tim Hempel ***@***.***>
Sent: Monday, January 2, 2023 5:10:22 PM
To: markovmodel/PyEMMA ***@***.***>
Cc: satyajitkhatua09 ***@***.***>; Author ***@***.***>
Subject: Re: [markovmodel/PyEMMA] how to import solvent accessible surface area as a feature in pyemma? (Issue #1586)
Hi Satyajit Khatua,
you can use mdtraj to compute the SASA using their implementation of the Shrake-Rupley algorithm. It's documented here<https://www.mdtraj.org/1.9.8.dev0/api/generated/mdtraj.shrake_rupley.html>. This function computes the SASA from an mdtraj-Trajectoryobject, which is exactly what you need in order to implement your own custom feature. There's an example on how to do that here #1566 (comment)<#1566 (comment)>, can you use that as a template?
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Hi, I have tried to calculate the SASA feature in these two different instances. The problems are attached herewith. I actually intended to calculate the SASA value for the ligand molecule, not all of the residues. That is where I am getting the errors. Can you help me with this? I have tried importing different options inside mdtraj.shrake_rupley() function. It seems nothing is working for me. With regards, |
The function call def custom_function(traj, ligand_resid=FIXME):
# compute ligand sasa and select ligand
# returns array with length n_frames
ligand_sasa = mdtraj.shrake_rupley(traj, mode='residue')[:, ligand_resid]
# expand dimension to (n_frames, 1) as required by pyemma and return
return ligand_sasa[:, None] |
Hi,
Thanks a lot. I have got the ligand sasa as per your suggestion.
With regards,
Satyajit Khatua
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From: Tim Hempel ***@***.***>
Sent: Tuesday, January 3, 2023 9:04:21 PM
To: markovmodel/PyEMMA ***@***.***>
Cc: satyajitkhatua09 ***@***.***>; Author ***@***.***>
Subject: Re: [markovmodel/PyEMMA] how to import solvent accessible surface area as a feature in pyemma? (Issue #1586)
The function call shrake_rupley(traj, mode='residue') returns an array of shape (n_frames, n_residues) that contains the SASA per residue for each time frame. You can select the SASA of your ligand if you know which residue-index your ligand has (make sure to use 0-based residue indexing as this is a numpy array). The code inside the function could look something like this: (CAUTION: I didn't check if it works! Please let me know if it does.)
def custom_function(traj, ligand_resid=FIXME):
# compute ligand sasa and select ligand
# returns array with length n_frames
ligand_sasa = mdtraj.shrake_rupley(traj, mode='residue')[:, ligand_resid]
# expand dimension to (n_frames, 1) as required by pyemma and return
return ligand_sasa[:, None]
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Hi,
For one ligand unbinding, I want to use SASA as one of my CVs. Is there a way to import this feature in PyEMMA? If yes, can you tell me how to do that? This may be a simple question, but I am unable to include this feature. Please help.
WIth regards,
Satyajit Khatua
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