示例#1
0
文件: oplsparse.py 项目: seroot/Junk
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
示例#2
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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
示例#3
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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)
示例#4
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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
示例#5
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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)
示例#6
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文件: oplsparse.py 项目: seroot/Junk
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
示例#7
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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)
示例#8
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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)
示例#9
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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)
示例#10
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文件: Main.py 项目: seroot/Junk
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)