Difference between revisions of "UCSF Strain Filtering"

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  $ conda activate my-rdkit-env
 
  $ conda activate my-rdkit-env
  
Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2. For example:
+
Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:
 
  $ python3 Torsion_Strain.py test1.db2.gz
 
  $ python3 Torsion_Strain.py test1.db2.gz
 
  $ python3 Torsion_Strain.py test2.mol2
 
  $ python3 Torsion_Strain.py test2.mol2
  
 
The output is a csv file, containing the strain energy and detailed information for each compound in mol2 or each conformation in db2.
 
The output is a csv file, containing the strain energy and detailed information for each compound in mol2 or each conformation in db2.
 +
You may be most interested in the first two columns of the output, otherwise please refer to the detailed comments in the Torsion_Strain.py.

Revision as of 18:06, 6 January 2020

This is the 1st version of UCSF strain filtering. Please copy the code to your current directory.

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

To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html On our cluster, you only need to type:

$ conda create -c rdkit -n my-rdkit-env rdkit
$ conda activate my-rdkit-env

Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:

$ python3 Torsion_Strain.py test1.db2.gz
$ python3 Torsion_Strain.py test2.mol2

The output is a csv file, containing the strain energy and detailed information for each compound in mol2 or each conformation in db2. You may be most interested in the first two columns of the output, otherwise please refer to the detailed comments in the Torsion_Strain.py.