Using eMolFrag

Command line: "/Path_to_Python/python /Path_to_scripts/ -i /Path_to_input_directory/ -o /Path_ro_output_directory/ -p Number_of_cores -m Output_selection -c Output_format".

  1. /Path_to_Python/python : Can be simplified as python ignoring the absolute path.
  2. /Path_to_scripts/ : Main path to the scripts, relative path is also OK.
  3. /Path_to_input_directory/ : Path of the directory which contains input mol2 files, relative path is also OK.
  4. /Path_to_output_directory/ : Path of the directory for output, relative path is also OK.
  5. Number-of-cores : Number of processes created in parallel. It is better to set this parameter no larger than the number of cores available on the system/node/cluster.
  6. Output_selection : Choose to remove redundancy in output fragments (or not), keep temporary files (or not).
  7. Output_format : Extensive or simple output format.

Example: "Extract fragments from test-set100 ".

1)Downlaod test-set100.tar.gz and unpack at a directory such as TestEMolFrag/

[foo]$ mkdir TestEMolFrag/ # any folder name you want

[foo]$ cp /.../test-set100.tar.gz TestEMolFrag/

[foo]$ cd TestEMolFrag/

[TestEMolFrag]$ tar xzf test-set100.tar.gz # unpack input data set

2)Set the path

  • use absolute path
  • assuming that path to is /.../eMolFrag_2016_07_23_01/
  • assuming that path to pkcombu is /.../pkcombu

[TestEMolFrag]$ python /.../ # run Configure path, use absolute path

[TestEMolFrag]$ # step 1: assuming that path to is /.../eMolFrag_2016_07_23_01/, type: /.../eMolFrag_2016_07_23_01/

[TestEMolFrag]$ # step 2: assuming that path to pkcombu is /.../pkcombu, type: /.../pkcombu


  • input molecules: test-set100
  • Output directory should be provided
  • use absolute paths

[TestEMolFrag]$ python /.../eMolFrag_2016_07_23_01/ -i /.../TestEMolFrag/test-set100/ -o /.../TestEMolFrag/output-testset100-1/ -p 16 -m 0 -c 0

[TestEMolFrag]$ # check the output

© Michal Brylinski
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