hemahecodes

from rdkit.Chem import rdchem
from rdkit import Chem

# Import molecules
core = Chem.MolFromPDBFile('../FFF/core.pdb')
fragment = Chem.MolFromPDBFile('../FFF/fragment.pdb')

# Merge both molecules
combo = Chem.CombineMols(core,fragment)

hemahecodes

SCHRODINGER="Path to Schrodinger"
$SCHRODINGER/utilities/glide_sort actives.maegz  -o actives_sorted.mae -R
$SCHRODINGER/utilities/glide_sort decoys.maegz  -o decoys_sorted.mae -R
$SCHRODINGER/glide_merge actives_sorted.mae decoys_sorted.mae -o glide_results.mae -R
$SCHRODINGER/run enrichment.py 

hemahecodes

import schrodinger
from schrodinger.analysis.enrichment import calculator
efcalc = calculator.Calculator(
    actives = "actives.txt",            # Active titles, one per line.
    results = "glide_docking_results.mae",        # Glide pv file.
    total_decoys = 1093 # Number of decoys
)
efcalc.report()                    # Print default report to standard out.
efcalc.savePlot()                  # Create default graph png.
print(efcalc.calcBEDROC(alpha=20)) # Print the BEDROC metric value

hemahecodes

import sys

class PDBAtom:
    """
    It defines a PDB Atom object.
    """
    def __init__(self, line):
        self.type = self._get_type(line)  # from columns 1-7
        self.ser_num = self._get_serial_number(line)  # from columns 7-11
        self.at_name = self._get_atom_name(line)  # from columns 13-16