meeko/setup.py
def init_from_obmol(self, obmol, flexible_amides=False, is_protein_sidechain=False):
        """generate a new molecule setup

            NOTE: OpenBabel uses 1-based index
        """
        # storing info
        self.mol = obmol
        self.smarts = obutils.SMARTSmatcher(self.mol)
        self.atom_true_count = self.mol.NumAtoms()
        self.init_atom()
        self.perceive_rings()
        self.init_bond(flexible_amides)
        self.mol.setup = self
        if is_protein_sidechain:
            self.ignore_backbone()
generate a new molecule setup

            NOTE: OpenBabel uses 1-based index
        
generate a new molecule setup
NOTE: OpenBabel uses 1-based index
generate a new molecule setup NOTE : OpenBabel uses 1 - based index
def init_from_obmol(self, obmol, flexible_amides=False, is_protein_sidechain=False):
        self.mol = obmol
        self.smarts = obutils.SMARTSmatcher(self.mol)
        self.atom_true_count = self.mol.NumAtoms()
        self.init_atom()
        self.perceive_rings()
        self.init_bond(flexible_amides)
        self.mol.setup = self
        if is_protein_sidechain:
            self.ignore_backbone()
def init_from_obmol ( self , obmol , flexible_amides = False , is_protein_sidechain = False ) : self . mol = obmol self . smarts = obutils . SMARTSmatcher ( self . mol ) self . atom_true_count = self . mol . NumAtoms ( ) self . init_atom ( ) self . perceive_rings ( ) self . init_bond ( flexible_amides ) self . mol . setup = self if is_protein_sidechain : self . ignore_backbone ( )
generate a new molecule setup
NOTE: OpenBabel uses 1-based index
generate a new molecule setup NOTE : OpenBabel uses 1 - based index
"""generate a new molecule setup

            NOTE: OpenBabel uses 1-based index
        """ # storing info
self
obmol
flexible_amides
is_protein_sidechain