Difference between revisions of "Interaction Filtering"

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This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.
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This is Interaction Filtering version 1.1 (20200601). Please copy the code to your current directory.
  
 
  $ cp -r /mnt/nfs/home/sgu/code/interfilter .
 
  $ cp -r /mnt/nfs/home/sgu/code/interfilter .
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'''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''
 
'''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''
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'''Column5: #unpaired ligand acceptor'''
  
 
'''Column9: #hydrogen bond'''
 
'''Column9: #hydrogen bond'''
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'''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''
 
'''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''
  
  $ awk '$3==0 && $4==0 && $9+$11>0' poses_noResidue_interaction_analysis.txt > filtered.txt
+
  $ awk '$3==0 && $4==0 && $5<=3 && $9+$11>0' poses_noResidue_interaction_analysis.txt > filtered.txt
  $ awk '$3==0 && $4==0 && $9+$11>0 && $15>0' poses_ASP115A_interaction_analysis.txt > filtered.txt
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  $ awk '$3==0 && $4==0 && $5<=3 && $9+$11>0 && $15>0' poses_ASP115A_interaction_analysis.txt > filtered.txt

Revision as of 02:33, 18 June 2020

This is Interaction Filtering version 1.1 (20200601). Please copy the code to your current directory.

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

FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh

To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: 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
$ source /nfs/soft/openeye/license.csh

Running the code:

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

If you want to have/avoid the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):

In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.

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

If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):

$ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot
An example of paired interaction plot
An example of unpaired interaction 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: #hydrogen bond clash + #salt bridge clash

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

Column5: #unpaired ligand acceptor

Column9: #hydrogen bond

Column11: #salt bridge

Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)

$ awk '$3==0 && $4==0 && $5<=3 && $9+$11>0' poses_noResidue_interaction_analysis.txt > filtered.txt
$ awk '$3==0 && $4==0 && $5<=3 && $9+$11>0 && $15>0' poses_ASP115A_interaction_analysis.txt > filtered.txt