Interaction Filtering: Difference between revisions
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$ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot | $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot | ||
[[Pair.png|thumb|center|500px|An example of paired interaction plot]] | [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]] | ||
[[Unpair.png|thumb|center|500px|An example of unpaired interaction plot]] | [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]] | ||
The output is a txt file, containing 15 columns: | The output is a txt file, containing 15 columns: |
Revision as of 00:19, 12 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 can be slow, 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)