def __lineToAtom(self, line):
"""put each coordinate line into atom class"""
ai = Atom()
tokens = line.strip().split()
ai.number = int(tokens[0])
ai.name = tokens[1]
ai.an = tokens[2]
ai.type1 = tokens[3]
ai.type2 = tokens[4]
ai.charge = float(tokens[5])
ai.x[0] = float(tokens[6])
ai.x[1] = float(tokens[7])
ai.x[2] = float(tokens[8])
ai.resn = int(tokens[9])
ai.resname = tokens[10]
ai.cg = int(tokens[11])
return ai
def __lineToAtom(self, line):
"""put each coordinate line into atom class"""
ai = Atom()
tokens = line.strip().split()
ai.number = int(tokens[0])
ai.name = tokens[1]
ai.an = tokens[2]
ai.type1 = tokens[3]
ai.type2 = tokens[4]
ai.charge = float(tokens[5])
ai.x[0] = float(tokens[6])
ai.x[1] = float(tokens[7])
ai.x[2] = float(tokens[8])
ai.resn = int(tokens[9])
ai.resname = tokens[10]
ai.cg = int(tokens[11])
return ai
def parser(self):
s = System()
s.pbc = v2lattice(self.a, self.b, self.c)
s.atomtypes = self.atomtypes
s.n_atoms = self.n_atoms
s.n_bonds = self.n_bonds
s.n_angles = self.n_angles
s.n_dihedrals = self.n_dihedrals
s.n_impropers = self.n_impropers
s.n_atomtypes = self.n_atomtypes
s.n_bondtypes = self.n_bondtypes
s.n_angletypes = self.n_angletypes
s.n_dihedraltypes = self.n_dihedraltypes
s.n_impropertypes = self.n_impropertypes
s.bonds = self.bonds
s.angles = self.angles
s.dihedrals = self.dihedrals
s.ffparams = self.ffparams
for i in self.coords:
# n is used to distinguish the type of data file
n = 0
for j in i:
# ignore the comments
if "#" in j:
break
n += 1
atom = Atom()
atom.an = int(i[0])
if n == 7:
# n = 7 is full type
atom.resn = int(i[1])
atom.name = self.elements[int(i[2]) - 1]
atom.element = self.elements[int(i[2]) - 1]
atom.type2 = int(i[2])
atom.charge = float(i[3])
atom.x[0] = float(i[4])
atom.x[1] = float(i[5])
atom.x[2] = float(i[6])
s.atoms.append(atom)
return s
def parser(self):
s = System()
s.pbc = v2lattice(self.a, self.b, self.c)
s.atomtypes = self.atomtypes
s.n_atoms = self.n_atoms
s.n_bonds = self.n_bonds
s.n_angles = self.n_angles
s.n_dihedrals = self.n_dihedrals
s.n_impropers = self.n_impropers
s.n_atomtypes = self.n_atomtypes
s.n_bondtypes = self.n_bondtypes
s.n_angletypes = self.n_angletypes
s.n_dihedraltypes = self.n_dihedraltypes
s.n_impropertypes = self.n_impropertypes
s.bonds = self.bonds
s.angles = self.angles
s.dihedrals = self.dihedrals
s.ffparams = self.ffparams
for i in self.coords:
# n is used to distinguish the type of data file
n = 0
for j in i:
# ignore the comments
if "#" in j:
break
n += 1
atom = Atom()
atom.an = int(i[0])
if n == 7:
# n = 7 is full type
atom.resn = int(i[1])
atom.name = self.elements[int(i[2]) - 1]
atom.element = self.elements[int(i[2]) - 1]
atom.type2 = int(i[2])
atom.charge = float(i[3])
atom.x[0] = float(i[4])
atom.x[1] = float(i[5])
atom.x[2] = float(i[6])
s.atoms.append(atom)
return s