def get_angles(angle,opls):
""" Gets the angles from a given opls file and assigns them to the relevant
angle objects from the parse file. Is a void method
Keyword Arguments:
angle - The list of angle objects to add attributes to
opls - The opls angle objects from the opls file
"""
#PROBABLY SLIGHTLY INCORRECT TODO
a_master = p.find_atom_by_id(angle.Angle_master).bond_id
a_slave1 = p.find_atom_by_id(angle.Angle_slave1).bond_id
a_slave2 = p.find_atom_by_id(angle.Angle_slave2).bond_id
if a_slave1 == "" or a_slave2 == "":
return
for i in range(0,len(opls)):
if a_slave1 <= a_slave2:
oplsList = [a_slave1,a_master,a_slave2]
if oplsList[0] == opls[i].angle_slave1 and oplsList[1] == opls[i].angle_master and oplsList[2] == opls[i].angle_slave2:
angle.Angle_equib_len = opls[i].equib_len
angle.Angle_force_const = opls[i].force_const
elif a_slave2 < a_slave1:
oplsList = [a_slave2,a_master,a_slave1]
if oplsList[0] == opls[i].angle_slave2 and oplsList[1] == opls[i].angle_master and oplsList[2] == opls[i].angle_slave1:
angle.Angle_equib_len = opls[i].equib_len
angle.Angle_force_const = opls[i].force_const
def is181(atom,opls):
number = 180
if atom.atom_type == "N":
if atom.Num_Bonds == 3:
if p.find_atom_by_id(atom.Atom_Bonds[0]).atom_type == "C" and p.find_atom_by_id(atom.Atom_Bonds[1]).atom_type == "C" and p.find_atom_by_id(atom.Atom_Bonds[2]).atom_type == "C":
assign_atom_vars(atom,number,opls)
return True
return False
def is17(atom,opls):
number = 16
if atom.atom_type == "C":
if atom.Num_Bonds == 3:
bondList = [p.find_atom_by_id(atom.Atom_Bonds[0]).atom_type,p.find_atom_by_id(atom.Atom_Bonds[1]).atom_type,p.find_atom_by_id(atom.Atom_Bonds[2]).atom_type]
if "C" in bondList:
bondList.remove("C")
if "C" in bondList and "H" in bondList:
assign_atom_vars(atom,number,opls)
def is10(atom,opls):
number = 9
if atom.atom_type == "C":
if atom.Num_Bonds == 4:
bondList = [p.find_atom_by_id(atom.Atom_Bonds[0]),p.find_atom_by_id(atom.Atom_Bonds[1]),p.find_atom_by_id(atom.Atom_Bonds[2]),p.find_atom_by_id(atom.Atom_Bonds[3])]
bondList.sort()
if bondList[0].atom_type == "C" and bondList[1].atom_type == "H" and bondList[2].atom_type == "H" and bondList[3].atom_type == "H":
assign_atom_vars(atom,number,opls)
return True
return False
def is13(atom,opls):
number = 12
if atom.atom_type == "C" and atom.Num_Bonds == 4:
bondList = [p.find_atom_by_id(atom.Atom_Bonds[0]).atom_type,p.find_atom_by_id(atom.Atom_Bonds[1]).atom_type,p.find_atom_by_id(atom.Atom_Bonds[2]).atom_type,p.find_atom_by_id(atom.Atom_Bonds[3]).atom_type]
if "H" in bondList:
bondList.remove("H")
if "H" in bondList:
bondList.remove("H")
if "C" in bondList:
bondList.remove("C")
if "N" in bondList:
assign_atom_vars(atom,number,opls)
elif "C" in bondList:
assign_atom_vars(atom,number,opls)
def get_bond(aBond,opls):
""" Sets the equil_len and force constant for each bond. No returns, is void.
Keyword Arguments:
aBond - The list of bonds to set the opls values
opls - The list of opls bond values created by getBonds
"""
master_id = p.find_atom_by_id(aBond.bond_master).bond_id
slave_id = p.find_atom_by_id(aBond.bond_slave).bond_id
if slave_id == "":
return
for i in range(0,len(opls)):
if master_id == opls[i].bond_master and slave_id == opls[i].bond_slave:
aBond.bond_force_const = opls[i].force_const
aBond.bond_equib_len = opls[i].equib_len
elif master_id == opls[i].bond_slave and slave_id == opls[i].bond_master:
aBond.bond_force_const = opls[i].force_const
aBond.bond_equib_len = opls[i].equib_len
def is178(atom,opls):
number = 177
if atom.atom_type == "O" and atom.Num_Bonds == 1:
if p.find_atom_by_id(atom.Atom_Bonds[0]).atom_type == "C":
assign_atom_vars(atom,number,opls)
def is177(atom,opls):
number = 176
if atom.atom_type == "C" and atom.Num_Bonds == 3:
bondList = [p.find_atom_by_id(atom.Atom_Bonds[0]).atom_type,p.find_atom_by_id(atom.Atom_Bonds[1]).atom_type,p.find_atom_by_id(atom.Atom_Bonds[2]).atom_type]
if "C" in bondList and "N" in bondList and "O" in bondList:
assign_atom_vars(atom,number,opls)
def is26(atom,opls):
number = 25
if atom.atom_type == "S" and atom.Num_Bonds == 2:
if p.find_atom_by_id(atom.Atom_Bonds[0]).atom_type == "C" and p.find_atom_by_id(atom.Atom_Bonds[1]).atom_type == "C":
assign_atom_vars(atom,number,opls)
opls_atoms = op.create_opls_atom(opls_atom_ids,opls_van,opls_partial)
#op.print_opls_atoms(opls_atoms)
opls_bonds = op.create_opls_bond(opls_bond)
#op.print_opls_bonds(opls_bonds)
opls_angles = op.create_opls_angle(opls_angle)
#op.print_opls_angles(opls_angles)
#get opls molecules
for i in range(0,len(atom)):
tm.get_molecule(atom[i],opls_atoms)
#get opls bonds
for i in range(0,len(bond)):
if p.find_atom_by_id(bond[i].bond_master).atom_type == "H" or p.find_atom_by_id(bond[i].bond_slave).atom_type == "H":
continue
op.get_bond(bond[i],opls_bonds)
#get opls angles
for i in range(0,len(AngleList)):
op.get_angles(AngleList[i],opls_angles)
#print again to see the opls changes, this time printing the extra info
#p.print_atoms(atom,True)
#p.print_bonds(bond,True)
#p.print_angles(AngleList,True)
#count the atoms found earlier by get_molecule
tester.count_atoms(opls_atoms,atom)