def writePQRStream(stream, atoms, **kwargs):
if isinstance(atoms, Atom):
atoms = Selection(atoms.getAtomGroup(), [atoms.getIndex()],
atoms.getACSIndex(),
'index ' + str(atoms.getIndex()))
n_atoms = atoms.numAtoms()
atomnames = atoms.getNames()
if atomnames is None:
raise RuntimeError('atom names are not set')
for i, an in enumerate(atomnames):
lenan = len(an)
if lenan < 4:
atomnames[i] = ' ' + an
elif lenan > 4:
atomnames[i] = an[:4]
s_or_u = np.array(['a']).dtype.char
resnames = atoms._getResnames()
if resnames is None:
resnames = ['UNK'] * n_atoms
resnums = atoms._getResnums()
if resnums is None:
resnums = np.ones(n_atoms, int)
chainids = atoms._getChids()
if chainids is None:
chainids = np.zeros(n_atoms, s_or_u + '1')
charges = atoms._getCharges()
if charges is None:
charges = np.zeros(n_atoms, float)
radii = atoms._getRadii()
if radii is None:
radii = np.zeros(n_atoms, float)
icodes = atoms._getIcodes()
if icodes is None:
icodes = np.zeros(n_atoms, s_or_u + '1')
hetero = ['ATOM'] * n_atoms
heteroflags = atoms._getFlags('hetatm')
if heteroflags is None:
heteroflags = atoms._getFlags('hetero')
if heteroflags is not None:
hetero = np.array(hetero, s_or_u + '6')
hetero[heteroflags] = 'HETATM'
altlocs = atoms._getAltlocs()
if altlocs is None:
altlocs = np.zeros(n_atoms, s_or_u + '1')
format = ('{0:6s} {1:5d} {2:4s} {3:1s}' +
'{4:4s} {5:1s} {6:4d} {7:1s} ' +
'{8:8.3f} {9:8.3f} {10:8.3f}' + '{11:8.4f} {12:7.4f}\n').format
coords = atoms._getCoords()
write = stream.write
for i, xyz in enumerate(coords):
write(
format(hetero[i], i + 1,
atomnames[i], altlocs[i], resnames[i], chainids[i],
int(resnums[i]), icodes[i], xyz[0], xyz[1], xyz[2],
charges[i], radii[i]))
def writePQRStream(stream, atoms, **kwargs):
if isinstance(atoms, Atom):
atoms = Selection(atoms.getAtomGroup(), [atoms.getIndex()],
atoms.getACSIndex(),
'index ' + str(atoms.getIndex()))
n_atoms = atoms.numAtoms()
atomnames = atoms.getNames()
if atomnames is None:
raise RuntimeError('atom names are not set')
for i, an in enumerate(atomnames):
lenan = len(an)
if lenan < 4:
atomnames[i] = ' ' + an
elif lenan > 4:
atomnames[i] = an[:4]
s_or_u = np.array(['a']).dtype.char
resnames = atoms._getResnames()
if resnames is None:
resnames = ['UNK'] * n_atoms
resnums = atoms._getResnums()
if resnums is None:
resnums = np.ones(n_atoms, int)
chainids = atoms._getChids()
if chainids is None:
chainids = np.zeros(n_atoms, s_or_u + '1')
charges = atoms._getCharges()
if charges is None:
charges = np.zeros(n_atoms, float)
radii = atoms._getRadii()
if radii is None:
radii = np.zeros(n_atoms, float)
icodes = atoms._getIcodes()
if icodes is None:
icodes = np.zeros(n_atoms, s_or_u + '1')
hetero = ['ATOM'] * n_atoms
heteroflags = atoms._getFlags('hetatm')
if heteroflags is None:
heteroflags = atoms._getFlags('hetero')
if heteroflags is not None:
hetero = np.array(hetero, s_or_u + '6')
hetero[heteroflags] = 'HETATM'
altlocs = atoms._getAltlocs()
if altlocs is None:
altlocs = np.zeros(n_atoms, s_or_u + '1')
format = ('{0:6s} {1:5d} {2:4s} {3:1s}' +
'{4:4s} {5:1s} {6:4d} {7:1s} ' +
'{8:8.3f} {9:8.3f} {10:8.3f}' +
'{11:8.4f} {12:7.4f}\n').format
coords = atoms._getCoords()
write = stream.write
for i, xyz in enumerate(coords):
write(format(hetero[i], i+1, atomnames[i], altlocs[i],
resnames[i], chainids[i], int(resnums[i]),
icodes[i], xyz[0], xyz[1], xyz[2], charges[i], radii[i]))
def writePQR(filename, atoms):
"""Write *atoms* in PQR format to a file with name *filename*. Only
current coordinate set is written. Returns *filename* upon success. If
*filename* ends with :file:`.gz`, a compressed file will be written."""
if not isinstance(atoms, Atomic):
raise TypeError('atoms does not have a valid type')
if isinstance(atoms, Atom):
atoms = Selection(atoms.getAtomGroup(), [atoms.getIndex()],
atoms.getACSIndex(),
'index ' + str(atoms.getIndex()))
stream = openFile(filename, 'w')
n_atoms = atoms.numAtoms()
atomnames = atoms.getNames()
if atomnames is None:
raise RuntimeError('atom names are not set')
for i, an in enumerate(atomnames):
lenan = len(an)
if lenan < 4:
atomnames[i] = ' ' + an
elif lenan > 4:
atomnames[i] = an[:4]
s_or_u = np.array(['a']).dtype.char
resnames = atoms._getResnames()
if resnames is None:
resnames = ['UNK'] * n_atoms
resnums = atoms._getResnums()
if resnums is None:
resnums = np.ones(n_atoms, int)
chainids = atoms._getChids()
if chainids is None:
chainids = np.zeros(n_atoms, s_or_u + '1')
charges = atoms._getCharges()
if charges is None:
charges = np.zeros(n_atoms, float)
radii = atoms._getRadii()
if radii is None:
radii = np.zeros(n_atoms, float)
icodes = atoms._getIcodes()
if icodes is None:
icodes = np.zeros(n_atoms, s_or_u + '1')
hetero = ['ATOM'] * n_atoms
heteroflags = atoms._getFlags('hetatm')
if heteroflags is None:
heteroflags = atoms._getFlags('hetero')
if heteroflags is not None:
hetero = np.array(hetero, s_or_u + '6')
hetero[heteroflags] = 'HETATM'
altlocs = atoms._getAltlocs()
if altlocs is None:
altlocs = np.zeros(n_atoms, s_or_u + '1')
format = ('{0:6s}{1:5d} {2:4s}{3:1s}' + '{4:4s}{5:1s}{6:4d}{7:1s} ' +
'{8:8.3f}{9:8.3f}{10:8.3f}' + '{11:8.4f}{12:7.4f}\n').format
coords = atoms._getCoords()
write = stream.write
for i, xyz in enumerate(coords):
write(
format(hetero[i], i + 1,
atomnames[i], altlocs[i], resnames[i], chainids[i],
int(resnums[i]), icodes[i], xyz[0], xyz[1], xyz[2],
charges[i], radii[i]))
write('TER\nEND')
stream.close()
return filename
def writePQR(filename, atoms):
"""Write *atoms* in PQR format to a file with name *filename*. Only
current coordinate set is written. Returns *filename* upon success. If
*filename* ends with :file:`.gz`, a compressed file will be written."""
if not isinstance(atoms, Atomic):
raise TypeError("atoms does not have a valid type")
if isinstance(atoms, Atom):
atoms = Selection(
atoms.getAtomGroup(), [atoms.getIndex()], atoms.getACSIndex(), "index " + str(atoms.getIndex())
)
stream = openFile(filename, "w")
n_atoms = atoms.numAtoms()
atomnames = atoms.getNames()
if atomnames is None:
raise RuntimeError("atom names are not set")
for i, an in enumerate(atomnames):
lenan = len(an)
if lenan < 4:
atomnames[i] = " " + an
elif lenan > 4:
atomnames[i] = an[:4]
resnames = atoms._getResnames()
if resnames is None:
resnames = ["UNK"] * n_atoms
resnums = atoms._getResnums()
if resnums is None:
resnums = np.ones(n_atoms, int)
chainids = atoms._getChids()
if chainids is None:
chainids = np.zeros(n_atoms, "|S1")
charges = atoms._getCharges()
if charges is None:
charges = np.zeros(n_atoms, float)
radii = atoms._getRadii()
if radii is None:
radii = np.zeros(n_atoms, float)
icodes = atoms._getIcodes()
if icodes is None:
icodes = np.zeros(n_atoms, "|S1")
hetero = ["ATOM"] * n_atoms
heteroflags = atoms._getHeteros()
if heteroflags is not None:
hetero = np.array(hetero, "|S6")
hetero[heteroflags] = "HETATM"
altlocs = atoms._getAltlocs()
if altlocs is None:
altlocs = np.zeros(n_atoms, "|S1")
format = (
"{0:6s}{1:5d} {2:4s}{3:1s}"
+ "{4:4s}{5:1s}{6:4d}{7:1s} "
+ "{8:8.3f}{9:8.3f}{10:8.3f}"
+ "{11:8.4f}{12:7.4f}\n"
).format
coords = atoms._getCoords()
write = stream.write
for i, xyz in enumerate(coords):
write(
format(
hetero[i],
i + 1,
atomnames[i],
altlocs[i],
resnames[i],
chainids[i],
int(resnums[i]),
icodes[i],
xyz[0],
xyz[1],
xyz[2],
charges[i],
radii[i],
)
)
write("TER\nEND")
stream.close()
return filename
def writePQR(filename, atoms):
"""Write *atoms* in PQR format to a file with name *filename*. Only
current coordinate set is written. Returns *filename* upon success. If
*filename* ends with :file:`.gz`, a compressed file will be written."""
if not isinstance(atoms, Atomic):
raise TypeError('atoms does not have a valid type')
if isinstance(atoms, Atom):
atoms = Selection(atoms.getAtomGroup(), [atoms.getIndex()],
atoms.getACSIndex(),
'index ' + str(atoms.getIndex()))
stream = openFile(filename, 'w')
n_atoms = atoms.numAtoms()
atomnames = atoms.getNames()
if atomnames is None:
raise RuntimeError('atom names are not set')
for i, an in enumerate(atomnames):
lenan = len(an)
if lenan < 4:
atomnames[i] = ' ' + an
elif lenan > 4:
atomnames[i] = an[:4]
s_or_u = np.array(['a']).dtype.char
resnames = atoms._getResnames()
if resnames is None:
resnames = ['UNK'] * n_atoms
resnums = atoms._getResnums()
if resnums is None:
resnums = np.ones(n_atoms, int)
chainids = atoms._getChids()
if chainids is None:
chainids = np.zeros(n_atoms, s_or_u + '1')
charges = atoms._getCharges()
if charges is None:
charges = np.zeros(n_atoms, float)
radii = atoms._getRadii()
if radii is None:
radii = np.zeros(n_atoms, float)
icodes = atoms._getIcodes()
if icodes is None:
icodes = np.zeros(n_atoms, s_or_u + '1')
hetero = ['ATOM'] * n_atoms
heteroflags = atoms._getFlags('hetatm')
if heteroflags is None:
heteroflags = atoms._getFlags('hetero')
if heteroflags is not None:
hetero = np.array(hetero, s_or_u + '6')
hetero[heteroflags] = 'HETATM'
altlocs = atoms._getAltlocs()
if altlocs is None:
altlocs = np.zeros(n_atoms, s_or_u + '1')
format = ('{0:6s}{1:5d} {2:4s}{3:1s}' +
'{4:4s}{5:1s}{6:4d}{7:1s} ' +
'{8:8.3f}{9:8.3f}{10:8.3f}' +
'{11:8.4f}{12:7.4f}\n').format
coords = atoms._getCoords()
write = stream.write
for i, xyz in enumerate(coords):
write(format(hetero[i], i+1, atomnames[i], altlocs[i],
resnames[i], chainids[i], int(resnums[i]),
icodes[i], xyz[0], xyz[1], xyz[2], charges[i], radii[i]))
write('TER\nEND')
stream.close()
return filename