def read(self, line):
""" Reads a line
Parameters
----------
line : str
A line with an atom record from a GRO file
Returns
-------
atom, resname, resnum : Atom, str, int
The Atom instance, residue name, and residue number containing the
atom
"""
resnum = int(line[:5])
resname = line[5:10].strip()
atomname = line[10:15].strip()
elem = element_by_name(atomname)
atomic_number = AtomicNum[elem]
mass = Mass[elem]
atnum = int(line[15:20])
if atomic_number == 0:
atom = ExtraPoint(name=atomname, number=atnum)
else:
atom = Atom(atomic_number=atomic_number, name=atomname,
number=atnum, mass=mass)
if self._digits is None:
self._pdeci = line.index('.', 20)
self._ndeci = line.index('.', self._pdeci+1)
self._digits = self._ndeci - self._pdeci
atom.xx, atom.xy, atom.xz = (
float(line[20+i*self._digits:20+(i+1)*self._digits])*10
for i in range(3)
)
wbeg = 20 + self._digits * 3
wend = wbeg + self._digits
if line[wbeg:wend].strip():
atom.vx, atom.vy, atom.vz = (
float(line[wbeg+i*self._digits:wend+i*self._digits])*10
for i in range(3)
)
return atom, resname, resnum
def parse(filename):
""" Parses a Gromacs GRO file
Parameters
----------
filename : str or file-like
Name of the file or the GRO file object
Returns
-------
struct : :class:`Structure`
The Structure instance instantiated with *just* residues and atoms
populated (with coordinates)
"""
struct = Structure()
if isinstance(filename, string_types):
fileobj = genopen(filename, 'r')
own_handle = True
else:
fileobj = filename
own_handle = False
try:
# Ignore the title line
fileobj.readline()
try:
natom = int(fileobj.readline().strip())
except ValueError:
raise GromacsError('Could not parse %s as GRO file' % filename)
digits = None
for i, line in enumerate(fileobj):
if i == natom: break
try:
resnum = int(line[:5])
resname = line[5:10].strip()
atomname = line[10:15].strip()
elem = element_by_name(atomname)
atomic_number = AtomicNum[elem]
mass = Mass[elem]
atnum = int(line[15:20])
if atomic_number == 0:
atom = ExtraPoint(name=atomname, number=atnum)
else:
atom = Atom(atomic_number=atomic_number, name=atomname,
number=atnum, mass=mass)
if digits is None:
pdeci = line.index('.', 20)
ndeci = line.index('.', pdeci+1)
digits = ndeci - pdeci
atom.xx, atom.xy, atom.xz = (
float(line[20+i*digits:20+(i+1)*digits])*10
for i in range(3)
)
i = 4
wbeg = (pdeci-4)+(5+ndeci)*(i-1)
wend = (pdeci-4)+(5+ndeci)*i
if line[wbeg:wend].strip():
atom.vx, atom.vy, atom.vz = (
float(line[(pdeci-3)+(6+ndeci)*i:
(pdeci-3)+(6+ndeci)*(i+1)])*10
for i in range(3, 6)
)
except (ValueError, IndexError):
raise GromacsError('Could not parse the atom record of '
'GRO file %s' % filename)
struct.add_atom(atom, resname, resnum)
# Get the box from the last line if it's present
if line.strip():
try:
box = [float(x) for x in line.split()]
except ValueError:
raise GromacsError('Could not understand box line of GRO '
'file %s' % filename)
if len(box) == 3:
struct.box = [box[0]*10, box[1]*10, box[2]*10,
90.0, 90.0, 90.0]
elif len(box) == 9:
# Assume we have vectors
leng, ang = box_vectors_to_lengths_and_angles(
[box[0], box[3], box[4]]*u.nanometers,
[box[5], box[1], box[6]]*u.nanometers,
[box[7], box[8], box[2]]*u.nanometers)
a, b, c = leng.value_in_unit(u.angstroms)
alpha, beta, gamma = ang.value_in_unit(u.degrees)
struct.box = [a, b, c, alpha, beta, gamma]
finally:
if own_handle:
fileobj.close()
return struct
