def parsePSF(filename, title=None, ag=None):
"""Returns an :class:`.AtomGroup` instance storing data parsed from X-PLOR
format PSF file *filename*. Atom and bond information is parsed from the
file. If *title* is not given, *filename* will be set as the title of the
:class:`.AtomGroup` instance. An :class:`.AtomGroup` instance may be
provided as *ag* argument. When provided, *ag* must have the same number
of atoms in the same order as the file. Data from PSF file will be added
to the *ag*. This may overwrite present data if it overlaps with PSF file
content.
This function now includes the angles, dihedrals, and impropers sections
as well as donors, acceptors and crossterms!"""
if ag is not None:
if not isinstance(ag, AtomGroup):
raise TypeError('ag must be an AtomGroup instance')
psf = openFile(filename, 'rb')
line = psf.readline()
while line:
line = line.strip()
if line.endswith(b'!NATOM'):
n_atoms = int(line.split(b'!')[0])
break
line = psf.readline()
if title is None:
title = os.path.splitext(os.path.split(filename)[1])[0]
else:
title = str(title)
if ag is None:
ag = AtomGroup(title)
else:
if n_atoms != ag.numAtoms():
raise ValueError('ag and PSF file must have same number of atoms')
serials = zeros(n_atoms, ATOMIC_FIELDS['serial'].dtype)
segnames = zeros(n_atoms, ATOMIC_FIELDS['segment'].dtype)
resnums = zeros(n_atoms, ATOMIC_FIELDS['resnum'].dtype)
resnames = zeros(n_atoms, ATOMIC_FIELDS['resname'].dtype)
atomnames = zeros(n_atoms, ATOMIC_FIELDS['name'].dtype)
atomtypes = zeros(n_atoms, ATOMIC_FIELDS['type'].dtype)
charges = zeros(n_atoms, ATOMIC_FIELDS['charge'].dtype)
masses = zeros(n_atoms, ATOMIC_FIELDS['mass'].dtype)
n = 0
n_bonds = 0
for line in psf:
if line.strip() == b'':
continue
if b'!NBOND:' in line.upper():
items = line.split()
n_bonds = int(items[0])
break
if n + 1 > n_atoms:
continue
if len(line) <= 71:
serials[n] = line[:8]
segnames[n] = line[9:13].strip()
resnums[n] = line[14:19]
resnames[n] = line[19:23].strip()
atomnames[n] = line[24:28].strip()
atomtypes[n] = line[29:35].strip()
charges[n] = line[35:44]
masses[n] = line[50:60]
else:
items = line.split()
serials[n] = items[0]
segnames[n] = items[1]
resnums[n] = items[2]
resnames[n] = items[3]
atomnames[n] = items[4]
atomtypes[n] = items[5]
charges[n] = items[6]
masses[n] = items[7]
n += 1
if n < n_atoms:
raise IOError(
'number of lines in PSF atoms block is less than the number of '
'atoms')
n_angles = 0
lines = []
for i, line in enumerate(psf):
if line.strip() == b'':
continue
if b'!NTHETA' in line:
items = line.split()
n_angles = int(items[0])
break
lines.append(line.decode(encoding='UTF-8'))
lines = ''.join(lines)
b_array = fromstring(lines, count=n_bonds * 2, dtype=int, sep=' ')
if len(b_array) != n_bonds * 2:
raise IOError('number of bonds expected and parsed do not match')
n_dihedrals = 0
lines = []
for i, line in enumerate(psf):
if line.strip() == b'':
continue
if b'!NPHI' in line:
items = line.split()
n_dihedrals = int(items[0])
break
lines.append(line.decode(encoding='UTF-8'))
lines = ''.join(lines)
a_array = fromstring(lines, count=n_angles * 3, dtype=int, sep=' ')
if len(a_array) != n_angles * 3:
raise IOError('number of angles expected and parsed do not match')
n_impropers = 0
lines = []
for i, line in enumerate(psf):
if line.strip() == b'':
continue
if b'!NIMPHI' in line:
items = line.split()
n_impropers = int(items[0])
break
lines.append(line.decode(encoding='UTF-8'))
lines = ''.join(lines)
d_array = fromstring(lines, count=n_dihedrals * 4, dtype=int, sep=' ')
if len(d_array) != n_dihedrals * 4:
raise IOError('number of dihedrals expected and parsed do not match')
n_donors = 0
lines = []
for i, line in enumerate(psf):
if line.strip() == b'':
continue
if b'!NDON' in line:
items = line.split()
n_donors = int(items[0])
break
lines.append(line.decode(encoding='UTF-8'))
lines = ''.join(lines)
i_array = fromstring(lines, count=n_impropers * 4, dtype=int, sep=' ')
if len(i_array) != n_impropers * 4:
raise IOError('number of impropers expected and parsed do not match')
n_acceptors = 0
lines = []
for i, line in enumerate(psf):
if line.strip() == b'':
continue
if b'!NACC' in line:
items = line.split()
n_acceptors = int(items[0])
break
lines.append(line.decode(encoding='UTF-8'))
lines = ''.join(lines)
do_array = fromstring(lines, count=n_donors * 2, dtype=int, sep=' ')
if len(do_array) != n_donors * 2:
raise IOError('number of donors expected and parsed do not match')
n_exclusions = 0
lines = []
for i, line in enumerate(psf):
if line.strip() == b'':
continue
if b'!NNB' in line:
items = line.split()
n_exclusions = int(items[0])
break
lines.append(line.decode(encoding='UTF-8'))
lines = ''.join(lines)
ac_array = fromstring(lines, count=n_acceptors * 2, dtype=int, sep=' ')
if len(ac_array) != n_acceptors * 2:
raise IOError('number of acceptors expected and parsed do not match')
lines = []
for i, line in enumerate(psf):
if line.strip() == b'':
continue
if b'!' in line:
break
lines.append(line.decode(encoding='UTF-8'))
lines = ''.join(lines)
nbe_array = fromstring(lines, count=n_exclusions * 2, dtype=int, sep=' ')
if len(nbe_array) != n_exclusions * 2:
raise IOError(
'number of nonbonded exclusions expected and parsed do not match')
n_crossterms = 0
for i, line in enumerate(psf):
if b'!NCRTERM' in line:
items = line.split()
n_crossterms = int(items[0])
break
lines = []
for i, line in enumerate(psf):
lines.append(line.decode(encoding='UTF-8'))
lines = ''.join(lines)
c_array = fromstring(lines, count=n_crossterms * 4, dtype=int, sep=' ')
if len(c_array) != n_crossterms * 4:
raise IOError('number of crossterms expected and parsed do not match')
psf.close()
ag.setSerials(serials)
ag.setSegnames(segnames)
ag.setResnums(resnums)
ag.setResnames(resnames)
ag.setNames(atomnames)
ag.setTypes(atomtypes)
ag.setCharges(charges)
ag.setMasses(masses)
if n_bonds > 0:
b_array = add(b_array, -1, b_array)
ag.setBonds(b_array.reshape((n_bonds, 2)))
if n_angles > 0:
a_array = add(a_array, -1, a_array)
ag.setAngles(a_array.reshape((n_angles, 3)))
if n_dihedrals > 0:
d_array = add(d_array, -1, d_array)
ag.setDihedrals(d_array.reshape((n_dihedrals, 4)))
if n_impropers > 0:
i_array = add(i_array, -1, i_array)
ag.setImpropers(i_array.reshape((n_impropers, 4)))
if n_donors > 0:
do_array = add(do_array, -1, do_array)
ag.setDonors(do_array.reshape((n_donors, 2)))
if n_acceptors > 0:
ac_array = add(ac_array, -1, ac_array)
ag.setAcceptors(ac_array.reshape((n_acceptors, 2)))
if n_exclusions > 0:
nbe_array = add(nbe_array, -1, nbe_array)
ag.setNBExclusions(nbe_array.reshape((n_exclusions, 2)))
if n_crossterms > 0:
c_array = add(c_array, -1, c_array)
ag.setCrossterms(c_array.reshape((n_crossterms, 4)))
return ag
def parsePSF(filename, title=None, ag=None):
"""Return an :class:`.AtomGroup` instance storing data parsed from X-PLOR
format PSF file *filename*. Atom and bond information is parsed from the
file. If *title* is not given, *filename* will be set as the title of the
:class:`.AtomGroup` instance. An :class:`.AtomGroup` instance may be
provided as *ag* argument. When provided, *ag* must have the same number
of atoms in the same order as the file. Data from PSF file will be added
to the *ag*. This may overwrite present data if it overlaps with PSF file
content. Note that this function does not evaluate angles, dihedrals, and
impropers sections."""
if ag is not None:
if not isinstance(ag, AtomGroup):
raise TypeError('ag must be an AtomGroup instance')
psf = openFile(filename, 'rb')
line = psf.readline()
i_line = 1
while line:
line = line.strip()
if line.endswith('!NATOM'):
n_atoms = int(line.split('!')[0])
break
line = psf.readline()
i_line += 1
if title is None:
title = os.path.splitext(os.path.split(filename)[1])[0]
else:
title = str(title)
if ag is None:
ag = AtomGroup(title)
else:
if n_atoms != ag.numAtoms():
raise ValueError('ag and PSF file must have same number of atoms')
serials = zeros(n_atoms, ATOMIC_FIELDS['serial'].dtype)
segnames = zeros(n_atoms, ATOMIC_FIELDS['segment'].dtype)
resnums = zeros(n_atoms, ATOMIC_FIELDS['resnum'].dtype)
resnames = zeros(n_atoms, ATOMIC_FIELDS['resname'].dtype)
atomnames = zeros(n_atoms, ATOMIC_FIELDS['name'].dtype)
atomtypes = zeros(n_atoms, ATOMIC_FIELDS['type'].dtype)
charges = zeros(n_atoms, ATOMIC_FIELDS['charge'].dtype)
masses = zeros(n_atoms, ATOMIC_FIELDS['mass'].dtype)
lines = psf.readlines(71 * (n_atoms + 5))
if len(lines) < n_atoms:
raise IOError('number of lines in PSF is less than the number of '
'atoms')
for i, line in enumerate(lines):
if i == n_atoms:
break
i_line += 1
if len(line) <= 71:
serials[i] = line[:8]
segnames[i] = line[9:13].strip()
resnums[i] = line[14:19]
resnames[i] = line[19:23].strip()
atomnames[i] = line[24:28].strip()
atomtypes[i] = line[29:35].strip()
charges[i] = line[35:44]
masses[i] = line[50:60]
else:
items = line.split()
serials[i] = items[0]
segnames[i] = items[1]
resnums[i] = items[2]
resnames[i] = items[3]
atomnames[i] = items[4]
atomtypes[i] = items[5]
charges[i] = items[6]
masses[i] = items[7]
i = n_atoms
while 1:
line = lines[i].split()
if len(line) >= 2 and line[1] == '!NBOND:':
n_bonds = int(line[0])
break
i += 1
lines = ''.join(lines[i + 1:]) + psf.read(n_bonds / 4 * 71)
array = fromstring(lines, count=n_bonds * 2, dtype=int, sep=' ')
if len(array) != n_bonds * 2:
raise IOError('number of bonds expected and parsed do not match')
psf.close()
ag.setSerials(serials)
ag.setSegnames(segnames)
ag.setResnums(resnums)
ag.setResnames(resnames)
ag.setNames(atomnames)
ag.setTypes(atomtypes)
ag.setCharges(charges)
ag.setMasses(masses)
array = add(array, -1, array)
ag.setBonds(array.reshape((n_bonds, 2)))
return ag
def parsePSF(filename, title=None, ag=None):
"""Return an :class:`.AtomGroup` instance storing data parsed from X-PLOR
format PSF file *filename*. Atom and bond information is parsed from the
file. If *title* is not given, *filename* will be set as the title of the
:class:`.AtomGroup` instance. An :class:`.AtomGroup` instance may be
provided as *ag* argument. When provided, *ag* must have the same number
of atoms in the same order as the file. Data from PSF file will be added
to the *ag*. This may overwrite present data if it overlaps with PSF file
content. Note that this function does not evaluate angles, dihedrals, and
impropers sections."""
if ag is not None:
if not isinstance(ag, AtomGroup):
raise TypeError('ag must be an AtomGroup instance')
psf = openFile(filename, 'rb')
line = psf.readline()
i_line = 1
while line:
line = line.strip()
if line.endswith('!NATOM'):
n_atoms = int(line.split('!')[0])
break
line = psf.readline()
i_line += 1
if title is None:
title = os.path.splitext(os.path.split(filename)[1])[0]
else:
title = str(title)
if ag is None:
ag = AtomGroup(title)
else:
if n_atoms != ag.numAtoms():
raise ValueError('ag and PSF file must have same number of atoms')
serials = zeros(n_atoms, ATOMIC_FIELDS['serial'].dtype)
segnames = zeros(n_atoms, ATOMIC_FIELDS['segment'].dtype)
resnums = zeros(n_atoms, ATOMIC_FIELDS['resnum'].dtype)
resnames = zeros(n_atoms, ATOMIC_FIELDS['resname'].dtype)
atomnames = zeros(n_atoms, ATOMIC_FIELDS['name'].dtype)
atomtypes = zeros(n_atoms, ATOMIC_FIELDS['type'].dtype)
charges = zeros(n_atoms, ATOMIC_FIELDS['charge'].dtype)
masses = zeros(n_atoms, ATOMIC_FIELDS['mass'].dtype)
lines = psf.readlines(71 * (n_atoms + 5))
if len(lines) < n_atoms:
raise IOError('number of lines in PSF is less than the number of '
'atoms')
for i, line in enumerate(lines):
if i == n_atoms:
break
i_line += 1
if len(line) <= 71:
serials[i] = line[:8]
segnames[i] = line[9:13].strip()
resnums[i] = line[14:19]
resnames[i] = line[19:23].strip()
atomnames[i] = line[24:28].strip()
atomtypes[i] = line[29:35].strip()
charges[i] = line[35:44]
masses[i] = line[50:60]
else:
items = line.split()
serials[i] = items[0]
segnames[i] = items[1]
resnums[i] = items[2]
resnames[i] = items[3]
atomnames[i] = items[4]
atomtypes[i] = items[5]
charges[i] = items[6]
masses[i] = items[7]
i = n_atoms
while 1:
line = lines[i].split()
if len(line) >= 2 and line[1] == '!NBOND:':
n_bonds = int(line[0])
break
i += 1
lines = ''.join(lines[i+1:]) + psf.read(n_bonds/4 * 71)
array = fromstring(lines, count=n_bonds*2, dtype=int, sep=' ')
if len(array) != n_bonds*2:
raise IOError('number of bonds expected and parsed do not match')
psf.close()
ag.setSerials(serials)
ag.setSegnames(segnames)
ag.setResnums(resnums)
ag.setResnames(resnames)
ag.setNames(atomnames)
ag.setTypes(atomtypes)
ag.setCharges(charges)
ag.setMasses(masses)
array = add(array, -1, array)
ag.setBonds(array.reshape((n_bonds, 2)))
return ag
def parsePSF(filename, title=None, ag=None):
"""Returns an :class:`.AtomGroup` instance storing data parsed from X-PLOR
format PSF file *filename*. Atom and bond information is parsed from the
file. If *title* is not given, *filename* will be set as the title of the
:class:`.AtomGroup` instance. An :class:`.AtomGroup` instance may be
provided as *ag* argument. When provided, *ag* must have the same number
of atoms in the same order as the file. Data from PSF file will be added
to the *ag*. This may overwrite present data if it overlaps with PSF file
content. Note that this function does not evaluate angles, dihedrals, and
impropers sections."""
if ag is not None:
if not isinstance(ag, AtomGroup):
raise TypeError("ag must be an AtomGroup instance")
psf = openFile(filename, "rb")
line = psf.readline()
i_line = 1
while line:
line = line.strip()
if line.endswith(b"!NATOM"):
n_atoms = int(line.split(b"!")[0])
break
line = psf.readline()
i_line += 1
if title is None:
title = os.path.splitext(os.path.split(filename)[1])[0]
else:
title = str(title)
if ag is None:
ag = AtomGroup(title)
else:
if n_atoms != ag.numAtoms():
raise ValueError("ag and PSF file must have same number of atoms")
serials = zeros(n_atoms, ATOMIC_FIELDS["serial"].dtype)
segnames = zeros(n_atoms, ATOMIC_FIELDS["segment"].dtype)
resnums = zeros(n_atoms, ATOMIC_FIELDS["resnum"].dtype)
resnames = zeros(n_atoms, ATOMIC_FIELDS["resname"].dtype)
atomnames = zeros(n_atoms, ATOMIC_FIELDS["name"].dtype)
atomtypes = zeros(n_atoms, ATOMIC_FIELDS["type"].dtype)
charges = zeros(n_atoms, ATOMIC_FIELDS["charge"].dtype)
masses = zeros(n_atoms, ATOMIC_FIELDS["mass"].dtype)
# lines = psf.readlines(71 * (n_atoms + 5))
n = 0
n_bonds = 0
for i, line in enumerate(psf):
if line.strip() == b"":
continue
if b"!NBOND:" in line.upper():
items = line.split()
n_bonds = int(items[0])
break
if n + 1 > n_atoms:
continue
if len(line) <= 71:
serials[n] = line[:8]
segnames[n] = line[9:13].strip()
resnums[n] = line[14:19]
resnames[n] = line[19:23].strip()
atomnames[n] = line[24:28].strip()
atomtypes[n] = line[29:35].strip()
charges[n] = line[35:44]
masses[n] = line[50:60]
else:
items = line.split()
serials[n] = items[0]
segnames[n] = items[1]
resnums[n] = items[2]
resnames[n] = items[3]
atomnames[n] = items[4]
atomtypes[n] = items[5]
charges[n] = items[6]
masses[n] = items[7]
n += 1
if n < n_atoms:
raise IOError("number of lines in PSF is less than the number of " "atoms")
# i = n_atoms
# while 1:
# line = lines[i].split()
# if len(line) >= 2 and line[1] == '!NBOND:':
# n_bonds = int(line[0])
# break
# i += 1
# lines = ''.join(lines[i+1:]) + psf.read(n_bonds/4 * 71)
lines = []
for i, line in enumerate(psf):
if line.strip() == b"":
continue
if b"!" in line:
break
lines.append(line.decode(encoding="UTF-8"))
lines = "".join(lines)
array = fromstring(lines, count=n_bonds * 2, dtype=int, sep=" ")
if len(array) != n_bonds * 2:
raise IOError("number of bonds expected and parsed do not match")
psf.close()
ag.setSerials(serials)
ag.setSegnames(segnames)
ag.setResnums(resnums)
ag.setResnames(resnames)
ag.setNames(atomnames)
ag.setTypes(atomtypes)
ag.setCharges(charges)
ag.setMasses(masses)
array = add(array, -1, array)
ag.setBonds(array.reshape((n_bonds, 2)))
return ag