def load(pose):
"""
Load a :class:`Pose` object and return a populated :class:`Structure`
instance
Parameters
----------
pose : :class:`Pose`
PyRosetta :class:`Pose` object to convert
"""
if not Pose or not AtomID:
raise ImportError('Could not load the PyRosetta module.')
if not isinstance(pose, Pose):
raise TypeError('Object is not a PyRosetta Pose object.')
struct = Structure()
atnum = 1
conf = pose.conformation()
for resid in range(1, pose.total_residue() + 1):
res = pose.residue(resid)
resname = res.name3().strip()
chain = chr(res.chain() + ord('A') - 1)
for atno, at in enumerate(res.atoms(), start=1):
try:
atinfo = res.atom_type(atno)
atname = res.atom_name(atno).strip()
if atinfo.is_virtual():
atsym = 'EP'
else:
atsym = atinfo.element()
rmin = atinfo.lj_radius()
epsilon = atinfo.lj_wdepth()
atomic_number = AtomicNum[atsym]
mass = Mass[atsym]
except KeyError:
raise RosettaError('Could not recognize element: %s.' %
atsym)
params = dict(atomic_number=atomic_number,
name=atname,
charge=0.0,
mass=mass,
occupancy=0.0,
bfactor=0.0,
altloc='',
number=atnum,
rmin=rmin,
epsilon=epsilon)
if atinfo.is_virtual():
atom = ExtraPoint(**params)
else:
atom = Atom(**params)
atom.xx, atom.xy, atom.xz = tuple(at.xyz())
struct.add_atom(atom, resname, resid, chain, '')
atnum += 1
try:
for nbr in conf.bonded_neighbor_all_res(AtomID(
atno, resid)):
if nbr.rsd() < resid or (nbr.rsd() == resid
and nbr.atomno() < atno):
struct.bonds.append(
Bond(struct.atoms[_n_prior(pose, nbr)], atom))
except:
raise RosettaError('Could not add bonds.')
struct.unchange()
return struct
def parse(filename):
""" 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)
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 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
def parse(filename):
""" 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)
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 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
def load(pose):
"""
Load a :class:`Pose` object and return a populated :class:`Structure`
instance
Parameters
----------
pose : :class:`Pose`
PyRosetta :class:`Pose` object to convert
"""
if not Pose or not AtomID:
raise ImportError('Could not load the PyRosetta module.')
if not isinstance(pose, Pose):
raise TypeError('Object is not a PyRosetta Pose object.')
struct = Structure()
atnum = 1
conf = pose.conformation()
for resid in range(1, pose.total_residue()+1):
res = pose.residue(resid)
resname = res.name3().strip()
chain = chr(res.chain()+ord('A')-1)
for atno, at in enumerate(res.atoms(), start=1):
try:
atinfo = res.atom_type(atno)
atname = res.atom_name(atno).strip()
if atinfo.is_virtual():
atsym = 'EP'
else:
atsym = atinfo.element()
rmin = atinfo.lj_radius()
epsilon = atinfo.lj_wdepth()
atomic_number = AtomicNum[atsym]
mass = Mass[atsym]
except KeyError:
raise RosettaError('Could not recognize element: %s.'
% atsym)
params = dict(atomic_number=atomic_number, name=atname,
charge=0.0, mass=mass, occupancy=0.0,
bfactor=0.0, altloc='', number=atnum,
rmin=rmin, epsilon=epsilon)
if atinfo.is_virtual():
atom = ExtraPoint(**params)
else:
atom = Atom(**params)
atom.xx, atom.xy, atom.xz = (at.xyz()[0], at.xyz()[1], at.xyz()[2])
struct.add_atom(atom, resname, resid, chain, '')
atnum += 1
try:
for nbr in conf.bonded_neighbor_all_res(AtomID(atno,
resid)):
if nbr.rsd() < resid or (nbr.rsd() == resid
and nbr.atomno() < atno):
struct.bonds.append(
Bond(struct.atoms[_n_prior(pose, nbr)],
atom))
except:
raise RosettaError('Could not add bonds.')
struct.unchange()
return struct
