def __init__(self):
Molecule.__init__(self)
self.molid = Molecule.molid
self.nor = 0 # Number of residues in a ligand; WILL ALWAYS BE 1
self.resids = [] # List of residue ids of a ligand
self.atmidx = [] # List of atom indices from the input file
self.residue = {} # Information about each residue. Key: Residue id.
def __init__(self):
Molecule.__init__(self)
self.molid = Molecule.molid
self.nor = 0 # Number of residues in a protein
self.resids = [] # List of residue ids of a protein
self.atmidx = [] # List of atom indices
self.residue = {} # Information about each residue. Key: Residue id.
self.chain_break = False # This will be True if chain breaks are encountered
def __init__(self, name=None, ff=None, sym=False, g_settings=None, m_settings=None, multipoles=None, ls_jobs=['w', 'non-w']):
GM_logger.info("Creating MoleculeOnGrid instance")
Molecule.__init__(self, name=name, ff=ff, sym=sym, settings=m_settings, multipoles=multipoles)
self.grid = grid.Grid(molecule_name=name, settings=g_settings)
self.grid_coordinates = self.grid.get_coordinates()
reference = {}
reference['non-w'] = self.grid.get_properties(property_name='esp', theory='reference')
try:
reference['w']= reference['non-w']*np.sqrt(self.grid.weights)
except AttributeError:
pass
self.A = {}
self.set_A(ls_jobs)
self.LS = {}
for key, A in self.A.items():
self.LS[key] = LeastSquares(name=key, A=A, b=reference[key])
def __init__(self, name):
Molecule.__init__(self, name)
def __init__(self, name): Molecule.__init__(self,name) self.location = self.getMaxEntityId() + 1