Difference between revisions of "Strain Filtering"

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This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.
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This is Strain Filtering version 1.1 (20200218). Please copy the code to your current directory.
 
  $ cp -r /mnt/nfs/home/sgu/code/strainfilter .
 
  $ cp -r /mnt/nfs/home/sgu/code/strainfilter .
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 +
Furthermore, if you don't want to include the strain from hydrogens, you can try this version:
 +
$ cp -r /mnt/nfs/home/sgu/code/noh .
 +
  
 
To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html
 
To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html
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You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.
 
You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.
  $ awk -F"," '$2<6.5 && $6<1.8' test2_Torsion_Strain.csv
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  $ awk -F"," '$2>0 && $2<6.5 && $6<1.8' test2_Torsion_Strain.csv > filtered.csv
 
This example uses awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8.
 
This example uses awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8.

Latest revision as of 13:55, 17 June 2020

This is Strain Filtering version 1.1 (20200218). Please copy the code to your current directory.

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

Furthermore, if you don't want to include the strain from hydrogens, you can try this version:

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


To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html

On our cluster, you may source my environment.

$ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh
$ conda activate my-rdkit-env

Currently, the code can handle db2/db2.gz and mol2 inputs. For example:

$ python Torsion_Strain.py test1.db2.gz
$ python Torsion_Strain.py test2.mol2

The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.

You may be interested in Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy), from which you can choose different thresholds to filter compounds. e.g.

$ awk -F"," '$2>0 && $2<6.5 && $6<1.8' test2_Torsion_Strain.csv > filtered.csv

This example uses awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8.