def _write_residue(dest, res):
""" Writes a residue to an open file handle
Parameters
----------
dest : file-like
File object to write the residue information to
res : :class:`ResidueTemplate` or :class:`ResidueTemplateContainer`
The residue template (or template container) to write to the file
"""
if isinstance(res, ResidueTemplate):
# Put it into a template container with the same name
tmp = ResidueTemplateContainer(res.name)
tmp.append(res)
res = tmp
dest.write('!entry.%s.unit.atoms table str name str type int typex '
'int resx int flags int seq int elmnt dbl chg\n' %
res.name)
for i, r in enumerate(res):
for atom in r:
dest.write(' "%s" "%s" 0 %d 131072 %d %d %.6f\n' % (atom.name,
atom.type, i+1, atom.idx+1, atom.atomic_number,
atom.charge))
dest.write('!entry.%s.unit.atomspertinfo table str pname str ptype '
'int ptypex int pelmnt dbl pchg\n' % res.name)
for r in res:
for atom in r:
dest.write(' "%s" "%s" 0 -1 0.0\n' % (atom.name, atom.type))
dest.write('!entry.%s.unit.boundbox array dbl\n' % res.name)
if res.box is None:
dest.write((' -1.000000\n' + ' 0.0\n' * 4))
else:
dest.write(' 1.000000\n')
if res.box[3] == res.box[4] == res.box[5]:
dest.write(' %f\n' % res.box[3])
else:
raise ValueError('Cannot write boxes with different angles')
dest.write(' %f\n' % res.box[0])
dest.write(' %f\n' % res.box[1])
dest.write(' %f\n' % res.box[2])
dest.write('!entry.%s.unit.childsequence single int\n %d\n' %
(res.name, len(res)+1))
dest.write('!entry.%s.unit.connect array int\n' % res.name)
if len(res) > 1:
dest.write(' 0\n 0\n')
else:
if res[0].head is not None:
dest.write(' %d\n' % (res[0].head.idx + 1))
else:
dest.write(' 0\n')
if res[0].tail is not None:
dest.write(' %d\n' % (res[0].tail.idx + 1))
else:
dest.write(' 0\n')
dest.write('!entry.%s.unit.connectivity table int atom1x int atom2x '
'int flags\n' % res.name)
for r in res:
for bond in r.bonds:
dest.write(' %d %d 1\n' % (bond.atom1.idx+1, bond.atom2.idx+1))
dest.write('!entry.%s.unit.hierarchy table str abovetype int '
'abovex str belowtype int belowx\n' % res.name)
c = 1
for i, r in enumerate(res):
dest.write(' "U" 0 "R" %d\n' % (i+1))
for atom in r:
dest.write(' "R" %d "A" %d\n' % (i+1, c))
c += 1
dest.write('!entry.%s.unit.name single str\n' % res.name)
dest.write(' "%s"\n' % res.name)
dest.write('!entry.%s.unit.positions table dbl x dbl y dbl z\n' %
res.name)
for r in res:
for atom in r:
dest.write(' %.6g %.6g %.6g\n' % (atom.xx, atom.xy, atom.xz))
dest.write('!entry.%s.unit.residueconnect table int c1x int c2x '
'int c3x int c4x int c5x int c6x\n' % res.name)
for r in res:
# Make the CONECT1 and 0 default to 1 so that the TREE gets set
# correctly by tleap. Not used for anything else...
conn = [1, 1, 0, 0, 0, 0]
if r.head is not None: conn[0] = r.head.idx + 1
if r.tail is not None: conn[1] = r.tail.idx + 1
for i, at in enumerate(r.connections):
conn[i+2] = at.idx + 1
dest.write(' %d %d %d %d %d %d\n' % tuple(conn))
dest.write('!entry.%s.unit.residues table str name int seq int '
'childseq int startatomx str restype int imagingx\n' %
res.name)
c = 1
for i, r in enumerate(res):
if r.type is PROTEIN:
typ = 'p'
elif r.type is NUCLEIC:
typ = 'n'
elif r.type is SOLVENT:
typ='w'
elif r.type is UNKNOWN:
typ='?'
else:
warnings.warn('Unrecognized residue type %r' % r.type,
AmberWarning)
typ = '?'
dest.write(' "%s" %d %d %d "%s" %d\n' % (r.name, i+1, 1+len(r), c,
typ, _imaging_atom(r)))
c += len(r)
dest.write('!entry.%s.unit.residuesPdbSequenceNumber array int\n' %
res.name)
for i, r in enumerate(res):
if len(res) == 1:
dest.write(' 0\n')
else:
dest.write(' %d\n' % (i+1))
dest.write('!entry.%s.unit.solventcap array dbl\n' % res.name)
dest.write(' -1.000000\n' + ' 0.0\n' * 4)
dest.write('!entry.%s.unit.velocities table dbl x dbl y dbl z\n' %
res.name)
for r in res:
for atom in r:
try:
s = ' %g %g %g\n' % (atom.vx, atom.vy, atom.vz)
except AttributeError:
dest.write(' 0.0 0.0 0.0\n')
else:
dest.write(s)
def _parse_residue(fileobj, name):
"""
Parses the residue information out of the OFF file assuming the file
is pointed at the first line of an atoms table section of the OFF file
Parameters
----------
fileobj : file-like
Assumed to be open for read, this file is parsed until the *next*
atom table is read
name : str
The name of the residue being processed right now
"""
container = ResidueTemplateContainer(name)
nres = 1
templ = ResidueTemplate(name)
line = fileobj.readline()
while line[0] != '!':
nam, typ, typx, resx, flags, seq, elmnt, chg = line.split()
nam = _strip_enveloping_quotes(nam)
typ = _strip_enveloping_quotes(typ)
typx = int(typx)
resx = int(resx)
flags = int(flags)
seq = int(seq)
elmnt = int(elmnt)
chg = float(chg)
atom = Atom(atomic_number=elmnt, type=typ, name=nam, charge=chg)
if resx == nres + 1:
container.append(templ)
nres += 1
templ = ResidueTemplate(name)
templ.add_atom(atom)
line = fileobj.readline()
container.append(templ)
if nres > 1:
start_atoms = []
runsum = 0
for res in container:
start_atoms.append(runsum)
runsum += len(res)
# Make sure we get the next section
rematch = AmberOFFLibrary._sec2re.match(line)
if not rematch:
raise RuntimeError('Expected pertinfo table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
if not line:
raise RuntimeError('Unexpected EOF in Amber OFF library')
# Not used, just skip
# TODO sanity check
line = fileobj.readline()
rematch = AmberOFFLibrary._sec3re.match(line)
if not rematch:
raise RuntimeError('Expected boundbox table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
# Only 5 lines
try:
hasbox = float(fileobj.readline().strip())
angle = float(fileobj.readline().strip())
a = float(fileobj.readline().strip())
b = float(fileobj.readline().strip())
c = float(fileobj.readline().strip())
except ValueError:
raise RuntimeError('Error processing boundbox table entries')
else:
if hasbox > 0:
angle *= RAD_TO_DEG
container.box = [a, b, c, angle, angle, angle]
# Get the child sequence entry
line = fileobj.readline()
rematch = AmberOFFLibrary._sec4re.match(line)
if not rematch:
raise RuntimeError('Expected childsequence table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
n = int(fileobj.readline().strip())
if nres + 1 != n:
warnings.warn('Unexpected childsequence (%d); expected %d for '
'residue %s' % (n, nres+1, name), AmberWarning)
elif not isinstance(templ, ResidueTemplate) and n != len(templ) + 1:
raise RuntimeError('child sequence must be 1 greater than the '
'number of residues in the unit')
# Get the CONNECT array to set head and tail
line = fileobj.readline()
rematch = AmberOFFLibrary._sec5re.match(line)
if not rematch:
raise RuntimeError('Expected connect array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
try:
head = int(fileobj.readline().strip())
tail = int(fileobj.readline().strip())
except ValueError:
raise RuntimeError('Error processing connect table entries')
if head > 0 and nres == 1:
templ.head = templ[head-1]
elif head > 0 and nres > 1:
if head < sum([len(r) for r in container]):
raise RuntimeError('HEAD on multi-residue unit not supported')
if tail > 0 and nres == 1:
templ.tail = templ[tail-1]
elif tail > 0 and nres > 1:
if tail < sum([len(r) for r in container]):
warnings.warn('TAIL on multi-residue unit not supported (%s). '
'Ignored...' % name, AmberWarning)
# Get the connectivity array to set bonds
line = fileobj.readline()
rematch = AmberOFFLibrary._sec6re.match(line)
if not rematch:
raise RuntimeError('Expected connectivity table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
i, j, flag = line.split()
line = fileobj.readline()
if nres > 1:
# Find which residue we belong in
i = int(i) - 1
j = int(j) - 1
for ii, idx in enumerate(start_atoms):
if idx > i:
ii -= 1
break
start_idx = start_atoms[ii]
container[ii].add_bond(i-start_idx, j-start_idx)
else:
templ.add_bond(int(i)-1, int(j)-1)
# Get the hierarchy table
rematch = AmberOFFLibrary._sec7re.match(line)
if not rematch:
raise RuntimeError('Expected hierarchy table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
# Skip this section... not used
# TODO turn this into a sanity check
line = fileobj.readline()
# Get the unit name
rematch = AmberOFFLibrary._sec8re.match(line)
if not rematch:
raise RuntimeError('Expected unit name string not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
fileobj.readline() # Skip this... not used
line = fileobj.readline()
# Get the atomic positions
rematch = AmberOFFLibrary._sec9re.match(line)
if not rematch:
raise RuntimeError('Expected unit positions table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for res in container:
for atom in res:
x, y, z = fileobj.readline().split()
atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
line = fileobj.readline()
# Get the residueconnect table
rematch = AmberOFFLibrary._sec10re.match(line)
if not rematch:
raise RuntimeError('Expected unit residueconnect table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
c1,c2,c3,c4,c5,c6 = [int(x) for x in fileobj.readline().split()]
if templ.head is not None and templ.head is not templ[c1-1]:
warnings.warn('HEAD atom is not connect0')
if templ.tail is not None and templ.tail is not templ[c2-1]:
warnings.warn('TAIL atom is not connect1')
for i in (c3, c4, c5, c6):
if i == 0: continue
templ.connections.append(templ[i-1])
# Get the residues table
line = fileobj.readline()
rematch = AmberOFFLibrary._sec11re.match(line)
if not rematch:
raise RuntimeError('Expected unit residues table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
resname, id, next, start, typ, img = fileobj.readline().split()
resname = _strip_enveloping_quotes(resname)
id = int(id)
start = int(start)
next = int(next)
typ = _strip_enveloping_quotes(typ)
img = int(img)
if next - start != len(container[i]):
warnings.warn('residue table predicted %d, not %d atoms for '
'residue %s' % (next-start, len(container[i]),
name), AmberWarning)
if typ == 'p':
container[i].type = PROTEIN
elif typ == 'n':
container[i].type = NUCLEIC
elif typ == 'w':
container[i].type = SOLVENT
elif typ != '?':
warnings.warn('Unknown residue type "%s"' % typ,
AmberWarning)
if nres > 1:
container[i].name = resname
# Get the residues sequence table
line = fileobj.readline()
rematch = AmberOFFLibrary._sec12re.match(line)
if not rematch:
raise RuntimeError('Expected residue sequence number not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
#TODO sanity check
fileobj.readline()
line = fileobj.readline()
# Get the solventcap array
rematch = AmberOFFLibrary._sec13re.match(line)
if not rematch:
raise RuntimeError('Expected unit solventcap array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
# Ignore the solvent cap
fileobj.readline()
fileobj.readline()
fileobj.readline()
fileobj.readline()
fileobj.readline()
# Velocities
line = fileobj.readline()
rematch = AmberOFFLibrary._sec14re.match(line)
if not rematch:
raise RuntimeError('Expected unit solventcap array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for res in container:
for atom in res:
vx, vy, vz = [float(x) for x in fileobj.readline().split()]
atom.vx, atom.vy, atom.vz = vx, vy, vz
if nres > 1:
return container
return templ
def _write_residue(dest, res):
""" Writes a residue to an open file handle
Parameters
----------
dest : file-like
File object to write the residue information to
res : :class:`ResidueTemplate` or :class:`ResidueTemplateContainer`
The residue template (or template container) to write to the file
"""
if isinstance(res, ResidueTemplate):
# Put it into a template container with the same name
tmp = ResidueTemplateContainer(res.name)
tmp.append(res)
res = tmp
dest.write('!entry.%s.unit.atoms table str name str type int typex '
'int resx int flags int seq int elmnt dbl chg\n' %
res.name)
for i, r in enumerate(res):
for atom in r:
dest.write(' "%s" "%s" 0 %d 131072 %d %d %.6f\n' % (atom.name,
atom.type, i+1, atom.idx+1, atom.atomic_number,
atom.charge))
dest.write('!entry.%s.unit.atomspertinfo table str pname str ptype '
'int ptypex int pelmnt dbl pchg\n' % res.name)
for r in res:
for atom in r:
dest.write(' "%s" "%s" 0 -1 0.0\n' % (atom.name, atom.type))
dest.write('!entry.%s.unit.boundbox array dbl\n' % res.name)
if res.box is None:
dest.write((' -1.000000\n' + ' 0.0\n' * 4))
else:
dest.write(' 1.000000\n')
if res.box[3] == res.box[4] == res.box[5]:
dest.write(' %f\n' % res.box[3])
else:
raise RuntimeError('Cannot write boxes with different angles')
dest.write(' %f\n' % res.box[0])
dest.write(' %f\n' % res.box[1])
dest.write(' %f\n' % res.box[2])
dest.write('!entry.%s.unit.childsequence single int\n %d\n' %
(res.name, len(res)+1))
dest.write('!entry.%s.unit.connect array int\n' % res.name)
if len(res) > 1:
dest.write(' 0\n 0\n')
else:
if res[0].head is not None:
dest.write(' %d\n' % (res[0].head.idx + 1))
else:
dest.write(' 0\n')
if res[0].tail is not None:
dest.write(' %d\n' % (res[0].tail.idx + 1))
else:
dest.write(' 0\n')
if any(len(r) > 1 for r in res):
dest.write('!entry.%s.unit.connectivity table int atom1x '
'int atom2x int flags\n' % res.name)
base = 1
for r in res:
for bond in r.bonds:
dest.write(' %d %d 1\n' % (bond.atom1.idx+base,
bond.atom2.idx+base))
base += len(r)
dest.write('!entry.%s.unit.hierarchy table str abovetype int '
'abovex str belowtype int belowx\n' % res.name)
c = 1
for i, r in enumerate(res):
dest.write(' "U" 0 "R" %d\n' % (i+1))
for atom in r:
dest.write(' "R" %d "A" %d\n' % (i+1, c))
c += 1
dest.write('!entry.%s.unit.name single str\n' % res.name)
dest.write(' "%s"\n' % res.name)
dest.write('!entry.%s.unit.positions table dbl x dbl y dbl z\n' %
res.name)
for r in res:
for atom in r:
dest.write(' %.6g %.6g %.6g\n' % (atom.xx, atom.xy, atom.xz))
dest.write('!entry.%s.unit.residueconnect table int c1x int c2x '
'int c3x int c4x int c5x int c6x\n' % res.name)
c = 1
for r in res:
# Make the CONECT1 and 0 default to first and last atom so that the
# TREE gets set correctly by tleap. Not used for anything else...
conn = [c, c+len(r)-1, 0, 0, 0, 0]
if r.head is not None: conn[0] = r.head.idx + 1
if r.tail is not None: conn[1] = r.tail.idx + 1
for i, at in enumerate(r.connections[:4]):
conn[i+2] = at.idx + 1
dest.write(' %d %d %d %d %d %d\n' % tuple(conn))
c += len(r)
dest.write('!entry.%s.unit.residues table str name int seq int '
'childseq int startatomx str restype int imagingx\n' %
res.name)
c = 1
for i, r in enumerate(res):
if r.type is PROTEIN:
typ = 'p'
elif r.type is NUCLEIC:
typ = 'n'
elif r.type is SOLVENT:
typ='w'
elif r.type is UNKNOWN:
typ='?'
else:
warnings.warn('Unrecognized residue type %r' % r.type,
AmberWarning)
typ = '?'
dest.write(' "%s" %d %d %d "%s" %d\n' % (r.name, i+1, 1+len(r), c,
typ, _imaging_atom(r)+c))
c += len(r)
dest.write('!entry.%s.unit.residuesPdbSequenceNumber array int\n' %
res.name)
for i, r in enumerate(res):
if len(res) == 1:
dest.write(' 0\n')
else:
dest.write(' %d\n' % (i+1))
dest.write('!entry.%s.unit.solventcap array dbl\n' % res.name)
dest.write(' -1.000000\n' + ' 0.0\n' * 4)
dest.write('!entry.%s.unit.velocities table dbl x dbl y dbl z\n' %
res.name)
for r in res:
for atom in r:
try:
s = ' %g %g %g\n' % (atom.vx, atom.vy, atom.vz)
except AttributeError:
dest.write(' 0.0 0.0 0.0\n')
else:
dest.write(s)
def _parse_residue(fileobj, name):
"""
Parses the residue information out of the OFF file assuming the file
is pointed at the first line of an atoms table section of the OFF file
Parameters
----------
fileobj : file-like
Assumed to be open for read, this file is parsed until the *next*
atom table is read
name : str
The name of the residue being processed right now
"""
container = ResidueTemplateContainer(name)
nres = 1
templ = ResidueTemplate(name)
line = fileobj.readline()
while line[0] != '!':
nam, typ, typx, resx, flags, seq, elmnt, chg = line.split()
nam = _strip_enveloping_quotes(nam)
typ = _strip_enveloping_quotes(typ)
typx = int(typx)
resx = int(resx)
flags = int(flags)
seq = int(seq)
elmnt = int(elmnt)
chg = float(chg)
atom = Atom(atomic_number=elmnt, type=typ, name=nam, charge=chg)
if resx == nres + 1:
container.append(templ)
nres += 1
templ = ResidueTemplate(name)
templ.add_atom(atom)
line = fileobj.readline()
# Skip blank lines
while line and not line.strip():
line = fileobj.readline()
container.append(templ)
if nres > 1:
start_atoms = []
runsum = 0
for res in container:
start_atoms.append(runsum)
runsum += len(res)
# Make sure we get the next section
rematch = AmberOFFLibrary._sec2re.match(line)
if not rematch:
raise RuntimeError('Expected pertinfo table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
if not line:
raise RuntimeError('Unexpected EOF in Amber OFF library')
# Not used, just skip
# TODO sanity check
line = fileobj.readline()
rematch = AmberOFFLibrary._sec3re.match(line)
if not rematch:
raise RuntimeError('Expected boundbox table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
# Only 5 lines
try:
hasbox = float(fileobj.readline().strip())
angle = float(fileobj.readline().strip())
a = float(fileobj.readline().strip())
b = float(fileobj.readline().strip())
c = float(fileobj.readline().strip())
except ValueError:
raise RuntimeError('Error processing boundbox table entries')
else:
if hasbox > 0:
if angle < 3.15:
# No box is this acute -- must be in radians
angle *= RAD_TO_DEG
container.box = [a, b, c, angle, angle, angle]
# Get the child sequence entry
line = fileobj.readline()
rematch = AmberOFFLibrary._sec4re.match(line)
if not rematch:
raise RuntimeError('Expected childsequence table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
n = int(fileobj.readline().strip())
if nres + 1 != n:
warnings.warn('Unexpected childsequence (%d); expected %d for '
'residue %s' % (n, nres+1, name), AmberWarning)
elif not isinstance(templ, ResidueTemplate) and n != len(templ) + 1:
raise RuntimeError('child sequence must be 1 greater than the '
'number of residues in the unit')
# Get the CONNECT array to set head and tail
line = fileobj.readline()
rematch = AmberOFFLibrary._sec5re.match(line)
if not rematch:
raise RuntimeError('Expected connect array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
try:
head = int(fileobj.readline().strip())
tail = int(fileobj.readline().strip())
except ValueError:
raise RuntimeError('Error processing connect table entries')
if head > 0 and nres == 1:
templ.head = templ[head-1]
elif head > 0 and nres > 1:
if head < sum((len(r) for r in container)):
raise RuntimeError('HEAD on multi-residue unit not supported')
if tail > 0 and nres == 1:
templ.tail = templ[tail-1]
elif tail > 0 and nres > 1:
if tail < sum((len(r) for r in container)):
warnings.warn('TAIL on multi-residue unit not supported (%s). '
'Ignored...' % name, AmberWarning)
# Get the connectivity array to set bonds
line = fileobj.readline()
if len(templ.atoms) > 1:
rematch = AmberOFFLibrary._sec6re.match(line)
if not rematch:
raise RuntimeError('Expected connectivity table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
i, j, flag = line.split()
line = fileobj.readline()
if nres > 1:
# Find which residue we belong in
i = int(i) - 1
j = int(j) - 1
for ii, idx in enumerate(start_atoms):
if idx > i:
ii -= 1
break
start_idx = start_atoms[ii]
container[ii].add_bond(i-start_idx, j-start_idx)
else:
templ.add_bond(int(i)-1, int(j)-1)
# Get the hierarchy table
rematch = AmberOFFLibrary._sec7re.match(line)
if not rematch:
raise RuntimeError('Expected hierarchy table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
# Skip this section... not used
# TODO turn this into a sanity check
line = fileobj.readline()
# Get the unit name
rematch = AmberOFFLibrary._sec8re.match(line)
if not rematch:
raise RuntimeError('Expected unit name string not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
fileobj.readline() # Skip this... not used
line = fileobj.readline()
# Get the atomic positions
rematch = AmberOFFLibrary._sec9re.match(line)
if not rematch:
raise RuntimeError('Expected unit positions table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for res in container:
for atom in res:
x, y, z = fileobj.readline().split()
atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
line = fileobj.readline()
# Get the residueconnect table
rematch = AmberOFFLibrary._sec10re.match(line)
if not rematch:
raise RuntimeError('Expected unit residueconnect table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
c1,c2,c3,c4,c5,c6 = (int(x) for x in fileobj.readline().split())
if (c1 > 0 and templ.head is not None and
templ.head is not templ[c1-1]):
raise RuntimeError('HEAD atom is not connect0')
if (c2 > 0 and templ.tail is not None and
templ.tail is not templ[c2-1]):
raise RuntimeError('TAIL atom is not connect1')
for i in (c3, c4, c5, c6):
if i == 0: continue
templ.connections.append(templ[i-1])
# Get the residues table
line = fileobj.readline()
rematch = AmberOFFLibrary._sec11re.match(line)
if not rematch:
raise RuntimeError('Expected unit residues table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
resname, id, next, start, typ, img = fileobj.readline().split()
resname = _strip_enveloping_quotes(resname)
id = int(id)
start = int(start)
next = int(next)
typ = _strip_enveloping_quotes(typ)
img = int(img)
if next - start != len(container[i]):
warnings.warn('residue table predicted %d, not %d atoms for '
'residue %s' % (next-start, len(container[i]),
name), AmberWarning)
if typ == 'p':
container[i].type = PROTEIN
elif typ == 'n':
container[i].type = NUCLEIC
elif typ == 'w':
container[i].type = SOLVENT
elif typ != '?':
warnings.warn('Unknown residue type "%s"' % typ, AmberWarning)
if nres > 1:
container[i].name = resname
# Get the residues sequence table
line = fileobj.readline()
rematch = AmberOFFLibrary._sec12re.match(line)
if not rematch:
raise RuntimeError('Expected residue sequence number not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
#TODO sanity check
fileobj.readline()
line = fileobj.readline()
# Get the solventcap array
rematch = AmberOFFLibrary._sec13re.match(line)
if not rematch:
raise RuntimeError('Expected unit solventcap array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
# Ignore the solvent cap
fileobj.readline()
fileobj.readline()
fileobj.readline()
fileobj.readline()
fileobj.readline()
# Velocities
line = fileobj.readline()
rematch = AmberOFFLibrary._sec14re.match(line)
if not rematch:
raise RuntimeError('Expected unit solventcap array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for res in container:
for atom in res:
vx, vy, vz = (float(x) for x in fileobj.readline().split())
atom.vx, atom.vy, atom.vz = vx, vy, vz
if nres > 1:
return container
return templ
def parse(filename, structure=False):
""" Parses a mol2 file (or mol3) file
Parameters
----------
filename : str or file-like
Name of the file to parse or file-like object to parse from
structure : bool, optional
If True, the return value is a :class:`Structure` instance. If
False, it is either a :class:`ResidueTemplate` or
:class:`ResidueTemplateContainter` instance, depending on whether
there is one or more than one residue defined in it. Default is
False
Returns
-------
molecule : :class:`Structure`, :class:`ResidueTemplate`, or
:class:`ResidueTemplateContainer`
The molecule defined by this mol2 file
Raises
------
Mol2Error
If the file format is not recognized or non-numeric values are
present where integers or floating point numbers are expected. Also
raises Mol2Error if you try to parse a mol2 file that has multiple
@<MOLECULE> entries with ``structure=True``.
"""
if isinstance(filename, string_types):
f = genopen(filename, 'r')
own_handle = True
else:
f = filename
own_handle = False
rescont = ResidueTemplateContainer()
struct = Structure()
restemp = ResidueTemplate()
mol_info = []
multires_structure = False
try:
section = None
last_residue = None
headtail = 'head'
molecule_number = 0
for line in f:
if line.startswith('#'): continue
if not line.strip() and section is None: continue
if line.startswith('@<TRIPOS>'):
section = line[9:].strip()
if section == 'MOLECULE' and (restemp.atoms or rescont):
if structure:
raise Mol2Error('Cannot convert MOL2 with multiple '
'@<MOLECULE>s to a Structure')
# Set the residue name from the MOL2 title if the
# molecule had only 1 residue and it was given a name in
# the title
if not multires_structure and mol_info[0]:
restemp.name = mol_info[0]
multires_structure = False
rescont.append(restemp)
restemp = ResidueTemplate()
struct = Structure()
last_residue = None
molecule_number += 1
mol_info = []
continue
if section is None:
raise Mol2Error('Bad mol2 file format')
if section == 'MOLECULE':
# Section formatted as follows:
# mol_name
# num_atoms [num_bonds [num_substr [num_feat [num_sets]]]]
# mol_type
# charge_type
# [status_bits]
# [mol_comment]
# TODO: Do something with the name.
if len(mol_info) == 0:
mol_info.append(line.strip())
elif len(mol_info) == 1:
mol_info.append([int(x) for x in line.split()])
elif len(mol_info) == 2:
mol_info.append(line.strip())
elif len(mol_info) == 3:
mol_info.append(line.strip())
# Ignore the rest
continue
if section == 'ATOM':
# Section formatted as follows:
# atom_id -- serial number of atom
# atom_name -- name of the atom
# x -- X-coordinate of the atom
# y -- Y-coordinate of the atom
# z -- Z-coordinate of the atom
# atom_type -- type of the atom
# subst_id -- Residue serial number
# subst_name -- Residue name
# charge -- partial atomic charge
# status_bit -- ignored
words = line.split()
id = int(words[0])
name = words[1]
x = float(words[2])
y = float(words[3])
z = float(words[4])
typ = words[5]
try:
resid = int(words[6])
except IndexError:
resid = 0
try:
resname = words[7]
except IndexError:
resname = 'UNK'
if 'NO_CHARGES' not in mol_info:
try:
charge = float(words[8])
except IndexError:
charge = 0
else:
charge = 0
if last_residue is None:
last_residue = (resid, resname)
restemp.name = resname
atom = Atom(name=name, type=typ, number=id, charge=charge)
atom.xx, atom.xy, atom.xz = x, y, z
struct.add_atom(atom, resname, resid)
if last_residue != (resid, resname):
rescont.append(restemp)
restemp = ResidueTemplate()
restemp.name = resname
last_residue = (resid, resname)
multires_structure = True
try:
restemp.add_atom(copy.copy(atom))
except ValueError:
# Allow mol2 files being parsed as a Structure to have
# duplicate atom names
if not structure:
raise
continue
if section == 'BOND':
# Section formatted as follows:
# bond_id -- serial number of bond (ignored)
# origin_atom_id -- serial number of first atom in bond
# target_atom_id -- serial number of other atom in bond
# bond_type -- string describing bond type (ignored)
# status_bits -- ignored
words = line.split()
int(words[0]) # Bond serial number... redundant and ignored
a1 = int(words[1])
a2 = int(words[2])
atom1 = struct.atoms.find_original_index(a1)
atom2 = struct.atoms.find_original_index(a2)
struct.bonds.append(Bond(atom1, atom2))
# Now add it to our residue container
# See if it's a head/tail connection
if atom1.residue is not atom2.residue:
if atom1.residue.idx == len(rescont):
res1 = restemp
elif atom1.residue.idx < len(rescont):
res1 = rescont[atom1.residue.idx]
assert atom.residue.idx <= len(rescont), 'Bad bond!'
if atom2.residue.idx == len(rescont):
res2 = restemp
elif atom2.residue.idx < len(rescont):
res2 = rescont[atom2.residue.idx]
assert atom.residue.idx <= len(rescont), 'Bad bond!'
assert res1 is not res2, 'BAD identical residues'
idx1 = atom1.idx - atom1.residue[0].idx
idx2 = atom2.idx - atom2.residue[0].idx
if atom1.residue.idx < atom2.residue.idx:
res1.tail = res1[idx1]
res2.head = res2[idx2]
else:
res1.head = res1[idx1]
res2.tail = res2[idx2]
elif not multires_structure:
if not structure:
restemp.add_bond(a1-1, a2-1)
else:
# Same residue, add the bond
offset = atom1.residue[0].idx
if atom1.residue.idx == len(rescont):
res = restemp
else:
res = rescont[atom1.residue.idx]
res.add_bond(atom1.idx-offset, atom2.idx-offset)
continue
if section == 'CRYSIN':
# Section formatted as follows:
# a -- length of first unit cell vector
# b -- length of second unit cell vector
# c -- length of third unit cell vector
# alpha -- angle b/w b and c
# beta -- angle b/w a and c
# gamma -- angle b/w a and b
# space group -- number of space group (ignored)
# space group setting -- ignored
words = line.split()
box = [float(w) for w in words[:6]]
if len(box) != 6:
raise ValueError('%d box dimensions found; needed 6' %
len(box))
struct.box = copy.copy(box)
rescont.box = copy.copy(box)
continue
if section == 'SUBSTRUCTURE':
# Section formatted as follows:
# subst_id -- residue number
# subst_name -- residue name
# root_atom -- first atom of residue
# subst_type -- ignored (usually 'RESIDUE')
# dict_type -- type of substructure (ignored)
# chain -- chain ID of residue
# sub_type -- type of the chain
# inter_bonds -- # of inter-substructure bonds
# status -- ignored
# comment -- ignored
words = line.split()
if not words: continue
id = int(words[0])
resname = words[1]
try:
chain = words[5]
except IndexError:
chain = ''
# Set the chain ID
for res in struct.residues:
if res.number == id and res.name == resname:
res.chain = chain
continue
# MOL3 sections
if section == 'HEADTAIL':
atname, residx = line.split()
residx = int(residx)
if residx in (0, 1) or residx - 1 == len(rescont):
res = restemp
elif residx - 1 < len(rescont):
res = rescont[residx-1]
else:
raise Mol2Error('Residue out of range in head/tail')
for atom in res:
if atom.name == atname:
if headtail == 'head':
res.head = atom
headtail = 'tail'
else:
res.tail = atom
headtail = 'head'
break
else:
if headtail == 'head':
headtail = 'tail'
else:
headtail = 'head'
continue
if section == 'RESIDUECONNECT':
words = line.split()
residx = int(words[0])
if residx - 1 == len(rescont):
res = restemp
elif residx - 1 < len(rescont):
res = rescont[residx-1]
else:
raise Mol2Error('Residue out of range in '
'residueconnect')
for a in words[3:]:
if a == '0': continue
for atom in res:
if atom.name == a:
res.connections.append(atom)
break
else:
raise Mol2Error('Residue connection atom %s not '
'found in residue %d' % (a, residx))
if structure:
return struct
elif len(rescont) > 0:
if not multires_structure and mol_info[0]:
restemp.name = mol_info[0]
rescont.append(restemp)
return rescont
else:
return restemp
except ValueError as e:
raise Mol2Error('String conversion trouble: %s' % e)
finally:
if own_handle: f.close()
def write(struct, dest, mol3=False, split=False):
""" Writes a mol2 file from a structure or residue template
Parameters
----------
struct : :class:`Structure` or :class:`ResidueTemplate` or
:class:`ResidueTemplateContainer`
The input structure to write the mol2 file from
dest : str or file-like obj
Name of the file to write or open file handle to write to
mol3 : bool, optional
If True and ``struct`` is a ResidueTemplate or container, write
HEAD/TAIL sections. Default is False
split : bool, optional
If True and ``struct`` is a ResidueTemplateContainer or a Structure
with multiple residues, each residue is printed in a separate
@<MOLECULE> section that appear sequentially in the output file
"""
own_handle = False
if not hasattr(dest, 'write'):
own_handle = True
dest = genopen(dest, 'w')
if split:
# Write sequentially if it is a multi-residue container or Structure
if isinstance(struct, ResidueTemplateContainer):
try:
for res in struct:
Mol2File.write(res, dest, mol3)
finally:
if own_handle: dest.close()
return
elif isinstance(struct, Structure) and len(struct.residues) > 1:
try:
for res in ResidueTemplateContainer.from_structure(struct):
Mol2File.write(res, dest, mol3)
finally:
if own_handle: dest.close()
return
try:
if isinstance(struct, ResidueTemplateContainer):
natom = sum([len(c) for c in struct])
# To find the number of bonds, we need to total number of bonds
# + the number of bonds that would be formed by "stitching"
# together residues via their head and tail
bonds = []
charges = []
bases = [1 for res in struct]
for i, res in enumerate(struct):
if i < len(struct) - 1:
bases[i+1] = bases[i] + len(res)
for i, res in enumerate(struct):
for bond in res.bonds:
bonds.append((bond.atom1.idx+bases[i],
bond.atom2.idx+bases[i]))
if i < len(struct)-1 and (res.tail is not None and
struct[i+1].head is not None):
bonds.append((res.tail.idx+bases[i],
struct[i+1].head.idx+bases[i+1]))
charges.extend([a.charge for a in res])
residues = struct
name = struct.name or struct[0].name
else:
natom = len(struct.atoms)
bonds = [(b.atom1.idx+1, b.atom2.idx+1) for b in struct.bonds]
if isinstance(struct, ResidueTemplate):
residues = [struct]
name = struct.name
else:
residues = struct.residues
name = struct.residues[0].name
charges = [a.charge for a in struct.atoms]
dest.write('@<TRIPOS>MOLECULE\n')
dest.write('%s\n' % name)
dest.write('%d %d %d 0 1\n' % (natom, len(bonds), len(residues)))
if len(residues) == 1:
dest.write('SMALL\n')
else:
for residue in residues:
if AminoAcidResidue.has(residue.name):
dest.write('PROTEIN\n')
break
if (RNAResidue.has(residue.name) or
DNAResidue.has(residue.name)):
dest.write('NUCLEIC\n')
break
else:
dest.write('BIOPOLYMER\n')
if not any(charges):
dest.write('NO_CHARGES\n')
printchg = False
else:
dest.write('USER_CHARGES\n')
printchg = True
# See if we want to print box info
if hasattr(struct, 'box') and struct.box is not None:
box = struct.box
dest.write('@<TRIPOS>CRYSIN\n')
dest.write('%10.4f %10.4f %10.4f %10.4f %10.4f %10.4f 1 1\n' %
(box[0], box[1], box[2], box[3], box[4], box[5]))
# Now do ATOM section
dest.write('@<TRIPOS>ATOM\n')
j = 1
for i, res in enumerate(residues):
for atom in res:
try:
x = atom.xx
except AttributeError:
x = 0
try:
y = atom.xy
except AttributeError:
y = 0
try:
z = atom.xz
except AttributeError:
z = 0
dest.write('%8d %-8s %10.4f %10.4f %10.4f %-8s %6d %-8s' % (
j, atom.name, x, y, z,
atom.type.strip() or atom.name, i+1, res.name))
if printchg:
dest.write(' %10.6f\n' % atom.charge)
else:
dest.write('\n')
j += 1
dest.write('@<TRIPOS>BOND\n')
for i, bond in enumerate(bonds):
dest.write('%8d %8d %8d 1\n' % (i+1, bond[0], bond[1]))
dest.write('@<TRIPOS>SUBSTRUCTURE\n')
first_atom = 0
for i, res in enumerate(residues):
if not hasattr(res, 'chain') or not res.chain:
chain = '****'
else:
chain = res.chain
intresbonds = 0
if isinstance(res, ResidueTemplate):
if i != len(residues)-1 and (res.tail is not None and
residues[i+1].head is not None):
intresbonds += 1
if i != 0 and (res.head is not None and residues[i-1].tail
is not None):
intresbonds += 1
else:
for atom in res:
for a2 in atom.bond_partners:
if a2.residue is not res:
intresbonds += 1
dest.write('%8d %-8s %8d RESIDUE %4d %-4s ROOT %6d\n' % (i+1,
res.name, first_atom+1, 0, chain[:4], intresbonds))
first_atom += len(res)
if mol3:
dest.write('@<TRIPOS>HEADTAIL\n')
for i, res in enumerate(residues):
if isinstance(res, ResidueTemplate):
if res.head is not None:
dest.write('%s %d\n' % (res.head.name, i+1))
else:
dest.write('0 0\n')
if res.tail is not None:
dest.write('%s %d\n' % (res.tail.name, i+1))
else:
dest.write('0 0\n')
else:
head = tail = None
for atom in res:
for a2 in atom.bond_partners:
if a2.residue.idx == res.idx - 1:
head = atom
if a2.residue.idx == res.idx + 1:
tail = atom
if head is not None:
dest.write('%s %d\n' % (head.name, i+1))
else:
dest.write('0 0\n')
if tail is not None:
dest.write('%s %d\n' % (tail.name, i+1))
else:
dest.write('0 0\n')
dest.write('@<TRIPOS>RESIDUECONNECT\n')
for i, res in enumerate(residues):
if isinstance(res, ResidueTemplate):
con = [res.head, res.tail, None, None, None, None]
for i, a in enumerate(res.connections):
con[i+2] = a
else:
con = [None, None, None, None, None, None]
ncon = 2
for atom in res:
for a2 in atom.bond_partners:
if a2.residue.idx == res.idx - 1:
con[0] = atom
elif a2.residue.idx == res.idx + 1:
con[1] = atom
elif a2.residue.idx != res.idx:
con[ncon] = atom
ncon += 1
dest.write('%d' % (i+1))
for a in con:
if a is not None:
dest.write(' %s' % a.name)
else:
dest.write(' 0')
dest.write('\n')
finally:
if own_handle: dest.close()
