def parse(self):
"""Parse Amber PRMTOP topology file *filename*.
:Returns: MDAnalysis internal *structure* dict.
"""
formatversion = 10
with openany(self.filename) as topfile:
for line in topfile:
if line.startswith("%FLAG ATOMIC_NUMBER"):
formatversion = 12
break
if formatversion == 12:
sections = [
("ATOM_NAME", 1, 20, self._parseatoms, "_name", 0),
("CHARGE", 1, 5, self._parsesection, "_charge", 0),
("ATOMIC_NUMBER", 1, 10, self._parsesectionint, "_skip", 0),
("MASS", 1, 5, self._parsesection, "_mass", 0),
("ATOM_TYPE_INDEX", 1, 10, self._parsesectionint, "_atom_type",
0),
("NUMBER_EXCLUDED_ATOMS", 1, 10, self._parseskip, "_skip", 8),
("NONBONDED_PARM_INDEX", 1, 10, self._parseskip, "_skip", 8),
("RESIDUE_LABEL", 1, 20, self._parseatoms, "_resname", 11),
("RESIDUE_POINTER", 2, 10, self._parsesectionint, "_respoint",
11),
]
#("BOND_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("BOND_EQUIL_VALUE", 1, 5, self._parseskip,"_skip",8),
#("ANGLE_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("ANGLE_EQUIL_VALUE", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_PERIODICITY", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_PHASE", 1, 5, self._parseskip,"_skip",8),
#("SOLTY", 1, 5, self._parseskip,"_skip",8),
#("LENNARD_JONES_ACOEF", 1, 5, self._parseskip,"_skip",8),
#("LENNARD_JONES_BCOEF", 1, 5, self._parseskip,"_skip",8),
#("BONDS_INC_HYDROGEN", 2, 4, self._parsebond, "_bonds",2),
#("ANGLES_INC_HYDROGEN", 3, 3, self._parsesection, "_angles"),
#("DIHEDRALS_INC_HYDROGEN", 4, 2, self._parsesection, "_dihe"),
#("NIMPHI", 4, 2, self._parsesection, "_impr"),
#("NDON", 2, 4, self._parsesection,"_donors"),
#("NACC", 2, 4, self._parsesection,"_acceptors"),
elif formatversion == 10:
sections = [
("ATOM_NAME", 1, 20, self._parseatoms, "_name", 0),
("CHARGE", 1, 5, self._parsesection, "_charge", 0),
("MASS", 1, 5, self._parsesection, "_mass", 0),
("ATOM_TYPE_INDEX", 1, 10, self._parsesectionint, "_atom_type",
0),
("NUMBER_EXCLUDED_ATOMS", 1, 10, self._parseskip, "_skip", 8),
("NONBONDED_PARM_INDEX", 1, 10, self._parseskip, "_skip", 8),
("RESIDUE_LABEL", 1, 20, self._parseatoms, "_resname", 11),
("RESIDUE_POINTER", 2, 10, self._parsesectionint, "_respoint",
11),
]
#("BOND_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("BOND_EQUIL_VALUE", 1, 5, self._parseskip,"_skip",8),
#("ANGLE_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("ANGLE_EQUIL_VALUE", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_PERIODICITY", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_PHASE", 1, 5, self._parseskip,"_skip",8),
#("SOLTY", 1, 5, self._parseskip,"_skip",8),
#("LENNARD_JONES_ACOEF", 1, 5, self._parseskip,"_skip",8),
#("LENNARD_JONES_BCOEF", 1, 5, self._parseskip,"_skip",8),
#("BONDS_INC_HYDROGEN", 2, 4, self._parsebond, "_bonds",2),
#("ANGLES_INC_HYDROGEN", 3, 3, self._parsesection, "_angles"),
#("DIHEDRALS_INC_HYDROGEN", 4, 2, self._parsesection, "_dihe")]
#("NIMPHI", 4, 2, self._parsesection, "_impr"),
#("NDON", 2, 4, self._parsesection,"_donors"),
#("NACC", 2, 4, self._parsesection,"_acceptors")]
# Open and check top validity
# Reading header info POINTERS
with openany(self.filename) as topfile:
next_line = topfile.next
header = next_line()
if header[:3] != "%VE":
raise ValueError(
"{} is not a valid TOP file. %VE Missing in header".format(
topfile))
title = next_line().split()
if not (title[1] == "TITLE"):
raise ValueError(
"{} is not a valid TOP file. 'TITLE' missing in header".
format(topfile))
while header[:14] != '%FLAG POINTERS':
header = next_line()
header = next_line()
topremarks = [next_line().strip() for i in xrange(4)]
sys_info = [int(k) for i in topremarks for k in i.split()]
structure = {}
final_structure = {}
try:
for info in sections:
self._parse_sec(sys_info, info, next_line, structure,
final_structure)
except StopIteration:
raise ValueError("The TOP file didn't contain the minimum"
" required section of ATOM_NAME")
# Completing info respoint to include all atoms in last resid
structure["_respoint"].append(sys_info[0])
structure["_respoint"][-1] = structure["_respoint"][-1] + 1
atoms = [
None,
] * sys_info[0]
j = 0
segid = "SYSTEM"
for i in range(sys_info[0]):
charge = convert(structure["_charge"][i], 'Amber',
flags['charge_unit'])
if structure["_respoint"][j] <= i + 1 < structure["_respoint"][j +
1]:
resid = j + 1
resname = structure["_resname"][j]
else:
j += 1
resid = j + 1
resname = structure["_resname"][j]
mass = structure["_mass"][i]
atomtype = structure["_atom_type"][i]
atomname = structure["_name"][i]
#segid = 'SYSTEM' # does not exist in Amber
atoms[i] = Atom(i, atomname, atomtype, resname, resid, segid, mass,
charge)
final_structure["_atoms"] = atoms
final_structure["_numatoms"] = sys_info[0]
return final_structure
def parse(self):
"""Parse Amber PRMTOP topology file *filename*.
:Returns: MDAnalysis internal *structure* dict.
"""
formatversion = 10
with openany(self.filename) as topfile:
for line in topfile:
if line.startswith("%FLAG ATOMIC_NUMBER"):
formatversion = 12
break
if formatversion == 12:
sections = [
("ATOM_NAME", 1, 20, self._parseatoms, "_name", 0),
("CHARGE", 1, 5, self._parsesection, "_charge", 0),
("ATOMIC_NUMBER", 1, 10, self._parsesectionint, "_skip", 0),
("MASS", 1, 5, self._parsesection, "_mass", 0),
("ATOM_TYPE_INDEX", 1, 10, self._parsesectionint, "_atom_type", 0),
("NUMBER_EXCLUDED_ATOMS", 1, 10, self._parseskip, "_skip", 8),
("NONBONDED_PARM_INDEX", 1, 10, self._parseskip, "_skip", 8),
("RESIDUE_LABEL", 1, 20, self._parseatoms, "_resname", 11),
("RESIDUE_POINTER", 2, 10, self._parsesectionint, "_respoint", 11),
]
#("BOND_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("BOND_EQUIL_VALUE", 1, 5, self._parseskip,"_skip",8),
#("ANGLE_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("ANGLE_EQUIL_VALUE", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_PERIODICITY", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_PHASE", 1, 5, self._parseskip,"_skip",8),
#("SOLTY", 1, 5, self._parseskip,"_skip",8),
#("LENNARD_JONES_ACOEF", 1, 5, self._parseskip,"_skip",8),
#("LENNARD_JONES_BCOEF", 1, 5, self._parseskip,"_skip",8),
#("BONDS_INC_HYDROGEN", 2, 4, self._parsebond, "_bonds",2),
#("ANGLES_INC_HYDROGEN", 3, 3, self._parsesection, "_angles"),
#("DIHEDRALS_INC_HYDROGEN", 4, 2, self._parsesection, "_dihe"),
#("NIMPHI", 4, 2, self._parsesection, "_impr"),
#("NDON", 2, 4, self._parsesection,"_donors"),
#("NACC", 2, 4, self._parsesection,"_acceptors"),
elif formatversion == 10:
sections = [
("ATOM_NAME", 1, 20, self._parseatoms, "_name", 0),
("CHARGE", 1, 5, self._parsesection, "_charge", 0),
("MASS", 1, 5, self._parsesection, "_mass", 0),
("ATOM_TYPE_INDEX", 1, 10, self._parsesectionint, "_atom_type", 0),
("NUMBER_EXCLUDED_ATOMS", 1, 10, self._parseskip, "_skip", 8),
("NONBONDED_PARM_INDEX", 1, 10, self._parseskip, "_skip", 8),
("RESIDUE_LABEL", 1, 20, self._parseatoms, "_resname", 11),
("RESIDUE_POINTER", 2, 10, self._parsesectionint, "_respoint", 11),
]
#("BOND_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("BOND_EQUIL_VALUE", 1, 5, self._parseskip,"_skip",8),
#("ANGLE_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("ANGLE_EQUIL_VALUE", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_FORCE_CONSTANT", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_PERIODICITY", 1, 5, self._parseskip,"_skip",8),
#("DIHEDRAL_PHASE", 1, 5, self._parseskip,"_skip",8),
#("SOLTY", 1, 5, self._parseskip,"_skip",8),
#("LENNARD_JONES_ACOEF", 1, 5, self._parseskip,"_skip",8),
#("LENNARD_JONES_BCOEF", 1, 5, self._parseskip,"_skip",8),
#("BONDS_INC_HYDROGEN", 2, 4, self._parsebond, "_bonds",2),
#("ANGLES_INC_HYDROGEN", 3, 3, self._parsesection, "_angles"),
#("DIHEDRALS_INC_HYDROGEN", 4, 2, self._parsesection, "_dihe")]
#("NIMPHI", 4, 2, self._parsesection, "_impr"),
#("NDON", 2, 4, self._parsesection,"_donors"),
#("NACC", 2, 4, self._parsesection,"_acceptors")]
# Open and check top validity
# Reading header info POINTERS
with openany(self.filename) as topfile:
next_line = topfile.next
header = next_line()
if header[:3] != "%VE":
raise ValueError("{} is not a valid TOP file. %VE Missing in header".format(topfile))
title = next_line().split()
if not (title[1] == "TITLE"):
raise ValueError("{} is not a valid TOP file. 'TITLE' missing in header".format(topfile))
while header[:14] != '%FLAG POINTERS':
header = next_line()
header = next_line()
topremarks = [next_line().strip() for i in xrange(4)]
sys_info = [int(k) for i in topremarks for k in i.split()]
structure = {}
final_structure = {}
try:
for info in sections:
self._parse_sec(sys_info, info, next_line,
structure, final_structure)
except StopIteration:
raise ValueError("The TOP file didn't contain the minimum"
" required section of ATOM_NAME")
# Completing info respoint to include all atoms in last resid
structure["_respoint"].append(sys_info[0])
structure["_respoint"][-1] = structure["_respoint"][-1] + 1
atoms = [None, ]*sys_info[0]
j = 0
segid = "SYSTEM"
for i in range(sys_info[0]):
charge = convert(structure["_charge"][i],
'Amber',
flags['charge_unit'])
if structure["_respoint"][j] <= i+1 < structure["_respoint"][j+1]:
resid = j + 1
resname = structure["_resname"][j]
else:
j += 1
resid = j + 1
resname = structure["_resname"][j]
mass = structure["_mass"][i]
atomtype = structure["_atom_type"][i]
atomname = structure["_name"][i]
#segid = 'SYSTEM' # does not exist in Amber
atoms[i] = Atom(i, atomname, atomtype, resname, resid, segid, mass, charge)
final_structure["_atoms"] = atoms
final_structure["_numatoms"] = sys_info[0]
return final_structure
def _assert_almost_equal_convert(value, u1, u2, ref):
assert_almost_equal(units.convert(value, u1, u2), ref,
err_msg="Conversion {0} --> {1} failed".format(u1, u2))
