Example #1
0
 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.
Example #2
0
 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])
Example #4
0
 def __init__(self, name):
     Molecule.__init__(self, name)
Example #5
0
	def __init__(self, name):
		Molecule.__init__(self,name)
		self.location = self.getMaxEntityId() + 1