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SAMPL5-DC

https://www.drugdesigndata.org/about/sampl5

The script empiricalSES.py predicts log D as in submission #49. It estimates:

  1. free energy of hydration
  2. free energy of solvation in cyclohexane
  3. cyclohexane/water partition coefficient

Requirements / dependencies

  • Works on Linux
  • Python
  • openbabel (v2.3.2 available through apt-get)
  • python-openbabel (available through apt-get)
  • python-numpy (available through apt-get)
  • MSMS (http://mgltools.scripps.edu/downloads)

Setup

  1. Download the script (empiricalSES.py)
  2. Install the dependencies
  3. Edit line 4 in empiricalSES.py to specify the path to MSMS binary

Usage examples

python /path/to/empiricalSES.py --help
python /path/to/empiricalSES.py molecule.sdf
python /path/to/empiricalSES.py mymols/*.mol2

Output example

               Molecule name, dGsol_wat, dGsol_chex, chex/wat logD
SAMPL5_074_intra_H-bond.pdb ,   -25.357,     -8.482,       -12.584
SAMPL5_074_original_conf.pdb,   -27.567,     -8.613,       -14.135