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.
 
This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.
  
'''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'''
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'''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
  
 
  $ cp -r /mnt/nfs/home/sgu/code/interfilter .
 
  $ 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
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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.
 
On our cluster, you may source my environment.
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To filter out compounds, you may be interested in:
 
To filter out compounds, you may be interested in:
  
'''Column3''': #hydrogen bond clash + #salt bridge clash
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'''Column3: #hydrogen bond clash + #salt bridge clash'''
  
'''Column4''': #unpaired ligand donor + #unpaired ligand salt bridge
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'''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''
  
'''Column9''': #hydrogen bond + #non-ideal hydrogen bond
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'''Column9: #hydrogen bond + #non-ideal hydrogen bond'''
  
'''Column11''': #salt bridge
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'''Column11: #salt bridge'''
  
'''Column15''': interaction for you specified residue (0 means no, 1 means yes)
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'''Column15: interaction for you specified residue (0 means no, 1 means yes)'''

Revision as of 03:06, 15 February 2020

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

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

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

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
$ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt

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 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

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

Column11: #salt bridge

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