def pdb4all2parmed(structure: 'PDB') -> 'Structure':
structure.guess_elements()
struc_pmd = Structure()
for a in structure.pdb:
atom = Atom(atomic_number=Ptable[a['element']]['N'],
name=a['name'],
number=a['serial'])
struc_pmd.add_atom(atom=atom,
resname=a['resName'],
resnum=a['resSeq'],
chain=a['chainID'],
segid=a['segment'])
struc_pmd.coordinates = structure.xyz
struc_pmd.assign_bonds()
return struc_pmd
def parse(filename, skip_bonds=False):
""" Parses a Gromacs GRO file
Parameters
----------
filename : str or file-like
Name of the file or the GRO file object
skip_bonds : bool, optional
If True, skip trying to assign bonds. This can save substantial time
when parsing large files with non-standard residue names. However,
no bonds are assigned. This is OK if, for instance, the GRO file is
being parsed simply for its coordinates. This will also reduce the
accuracy of assigned atomic numbers for typical ions. Default is
False.
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)
line_parser = _AtomLineParser()
for i, line in enumerate(fileobj):
if i == natom: break
try:
atom, resname, resnum = line_parser.read(line)
except (ValueError, IndexError):
raise GromacsError('Could not parse the atom record of '
'GRO file %s' % filename)
struct.add_atom(atom, resname, resnum)
else:
# If no box exists, the break did not hit, so line still
# contains the last atom (which cannot be interpreted as a box).
# This wipes out line (IFF fileobj reached the line)
line = fileobj.readline()
if i+1 != natom:
raise GromacsError('Truncated GRO file. Found %d of %d '
'atoms' % (i+1, natom))
# 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()
# Assign bonds (and improved element guesses)
if not skip_bonds:
struct.assign_bonds()
return struct
def parse(filename, skip_bonds=True):
""" Read a PQR file and return a populated `Structure` class
Parameters
----------
filename : str or file-like
Name of the PQR file to read, or a file-like object that can iterate
over the lines of a PQR. Compressed file names can be specified and
are determined by file-name extension (e.g., file.pqr.gz,
file.pqr.bz2)
skip_bonds : bool, optional
If True, skip trying to assign bonds. This can save substantial time
when parsing large files with non-standard residue names. However,
no bonds are assigned. This is OK if, for instance, the PQR file is
being parsed simply for its coordinates. Default is False.
Returns
-------
structure : :class:`Structure`
The Structure object initialized with all of the information from
the PDB file. No bonds or other topological features are added by
default.
"""
if isinstance(filename, string_types):
own_handle = True
fileobj = genopen(filename, 'r')
else:
own_handle = False
fileobj = filename
struct = Structure()
# Add metadata fields
modelno = 1 # For PDB files with multiple MODELs
atomno = 0
coordinates = []
all_coordinates = []
# Support hexadecimal numbering like that printed by VMD
try:
for line in fileobj:
words = line.split()
if words[0] in ('ATOM', 'HETATM'):
atomno += 1
if len(words) == 10:
_, num, nam, res, resn, x, y, z, chg, rad = words
chn = ''
elif len(words) >= 11:
_, num, nam, res, chn, resn, x, y, z, chg, rad = (
words[i] for i in range(11))
# If the radius is not a float (but rather a letter,
# like the element or something), then the chain might
# be missing. In this case, shift all tokens "back" one
# and empty the chn string
try:
float(rad)
except ValueError:
resn, x, y, z, chg, rad = chn, resn, x, y, z, chg
else:
raise ValueError('Illegal PQR record format: expected '
'10 or 11 tokens on the atom line')
x, y, z = float(x), float(y), float(z)
chg, rad = float(chg), float(rad)
resn, num = int(resn), int(num)
elem = element_by_name(nam) # Yuck
atomic_number = AtomicNum[elem]
mass = Mass[elem]
if nam in ('EP', 'LP'): # lone pair
atom = ExtraPoint(atomic_number=atomic_number, name=nam,
charge=chg, mass=mass, number=num,
solvent_radius=rad)
else:
atom = Atom(atomic_number=atomic_number, name=nam,
charge=chg, mass=mass, number=num,
solvent_radius=rad)
atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
if modelno == 1:
struct.add_atom(atom, res, resn, chn)
else:
try:
orig_atom = struct.atoms[atomno-1]
except IndexError:
raise PDBError('Extra atom in MODEL %d' % modelno)
if (orig_atom.residue.name != res.strip()
or orig_atom.name != nam.strip()):
raise PDBError('Atom %d differs in MODEL %d [%s %s '
'vs. %s %s]' % (atomno, modelno,
orig_atom.residue.name,
orig_atom.name, res, nam))
coordinates.extend([atom.xx, atom.xy, atom.xz])
elif words[0] == 'ENDMDL':
# End the current model
if len(struct.atoms) == 0:
raise PDBError('MODEL ended before any atoms read in')
modelno += 1
if len(struct.atoms)*3 != len(coordinates):
raise PDBError(
'Inconsistent atom numbers in some PDB models')
all_coordinates.append(coordinates)
atomno = 0
coordinates = []
elif words[0] == 'MODEL':
if modelno == 1 and len(struct.atoms) == 0: continue
if len(coordinates) > 0:
if len(struct.atoms)*3 != len(coordinates):
raise PDBError('Inconsistent atom numbers in '
'some PDB models')
warnings.warn('MODEL not explicitly ended', PDBWarning)
all_coordinates.append(coordinates)
coordinates = []
modelno += 1
atomno = 0
elif words[0] == 'CRYST1':
a, b, c = (float(w) for w in words[1:4])
try:
A, B, C = (float(w) for w in words[4:7])
except ValueError:
A = B = C = 90.0
struct.box = [a, b, c, A, B, C]
finally:
if own_handle: fileobj.close()
struct.unchange()
if not skip_bonds:
struct.assign_bonds()
if coordinates:
if len(coordinates) != 3*len(struct.atoms):
raise PDBError('bad number of atoms in some PQR models')
all_coordinates.append(coordinates)
struct._coordinates = np.array(all_coordinates).reshape(
(-1, len(struct.atoms), 3))
return struct
