Python simple_unknowns Examples

Example #1

File: hetatm.py Project: Almad/pymol

def generate(model, topology= None, forcefield = None ):
    
    add_bonds(model,topology=topology,forcefield=forcefield)
    connected = model.convert_to_connected()
    add_hydrogens(connected,topology=topology,forcefield=forcefield)
    place.simple_unknowns(connected)
    return connected.convert_to_indexed()

Example #2

def generate(model, topology=None, forcefield=None):

    add_bonds(model, topology=topology, forcefield=forcefield)
    connected = model.convert_to_connected()
    add_hydrogens(connected, topology=topology, forcefield=forcefield)
    place.simple_unknowns(connected)
    return connected.convert_to_indexed()

Example #3

File: protein.py Project: dprada/pymol-open-source

def generate(model, forcefield = protein_amber, histidine = 'HIE',
                 skip_sort=None, bondfield = bond_amber ):

    strip_atom_bonds(model) # remove bonds between non-hetatms (ATOM)
    add_bonds(model,forcefield=forcefield)   
    connected = model.convert_to_connected()
    add_hydrogens(connected,forcefield=forcefield,skip_sort=skip_sort)
    place.simple_unknowns(connected,bondfield = bondfield)
    return connected.convert_to_indexed()

Example #4

File: protein.py Project: wangdang511/pymol-open-source

def generate(model, forcefield = protein_amber, histidine = 'HIE',
                 skip_sort=None, bondfield = bond_amber ):

    strip_atom_bonds(model) # remove bonds between non-hetatms (ATOM)
    add_bonds(model,forcefield=forcefield)   
    connected = model.convert_to_connected()
    add_hydrogens(connected,forcefield=forcefield,skip_sort=skip_sort)
    place.simple_unknowns(connected,bondfield = bondfield)
    return connected.convert_to_indexed()