Difference between revisions of "UCSF Strain Filtering"

From DISI
Jump to: navigation, search
(Created page with "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 ...")
 
Line 6: Line 6:
 
  $ conda create -c rdkit -n my-rdkit-env rdkit
 
  $ conda create -c rdkit -n my-rdkit-env rdkit
 
  $ 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:
 +
$ 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.

Revision as of 17:51, 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. 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.