Difference between revisions of "Interaction Filtering"

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(Created page with "This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory. $ cp -r /mnt/nfs/home/sgu/code/interfilter . To run the code, yo...")
 
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To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html
 
To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html
 +
 
On our cluster, you may source my environment.
 
On our cluster, you may source my environment.
 
  $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh
 
  $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh
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The output is a txt file, containing 15 columns:
 
The output is a txt file, containing 15 columns:
 
1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue
 
1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue
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To filter out compounds, you may be interested in:
 
To filter out compounds, you may be interested in:
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Column3: # of hydrogen bond clash + # of salt bridge clash
 
Column3: # of hydrogen bond clash + # of salt bridge clash
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Column4: # of unpaired ligand donor + # of unpaired ligand salt bridge
 
Column4: # of unpaired ligand donor + # of unpaired ligand salt bridge
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Column9: # of hydrogen bond + non-ideal hydrogen bond
 
Column9: # of hydrogen bond + non-ideal hydrogen bond
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Column11: # of salt bridge
 
Column11: # of salt bridge
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Column15: interaction for you specified residue (0 means no, 1 means yes)
 
Column15: interaction for you specified residue (0 means no, 1 means yes)

Revision as of 17:11, 11 February 2020

This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.

$ cp -r /mnt/nfs/home/sgu/code/interfilter .

To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html

On our cluster, you may source my environment.

$ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh
$ conda activate oepython
$ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt

If you find any version conflicts between python 3.7 and 2.7. You may comment in the ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh

Running the code:

$ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2

If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):

$ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A

If you want to plot the paired/unpaired interaction (figure generation is slower, but several thousand should be fine):

$ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot

The output is a txt file, containing 15 columns: 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue

To filter out compounds, you may be interested in:

Column3: # of hydrogen bond clash + # of salt bridge clash

Column4: # of unpaired ligand donor + # of unpaired ligand salt bridge

Column9: # of hydrogen bond + non-ideal hydrogen bond

Column11: # of salt bridge

Column15: interaction for you specified residue (0 means no, 1 means yes)