def id_format(filename):
"""
Identifies the file type as either Amber-format file (like prmtop) or an
old-style topology file.
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is an Amber-style format, False otherwise
"""
f = io.genopen(filename, 'r')
lines = [f.readline().decode() for i in range(5)]
f.close()
if lines[0].startswith('%VERSION'):
return True
# Try old-style format
try:
return AmberFormat().rdparm_old(lines, check=True)
except ValueError:
return False
def id_format(filename):
"""
Identifies the file type as either Amber-format file (like prmtop) or an
old-style topology file.
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is an Amber-style format, False otherwise
"""
f = io.genopen(filename, 'r')
lines = [f.readline().decode() for i in range(5)]
f.close()
if lines[0].startswith('%VERSION'):
return True
# Try old-style format
try:
return AmberFormat().rdparm_old(lines, check=True)
except ValueError:
return False
def id_format(filename):
""" Identifies the file type as an Amber mdcrd file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is an Amber mdcrd file. False otherwise
"""
f = io.genopen(filename, 'r')
lines = [f.readline().decode() for i in xrange(5)]
f.close()
# Next 4 lines, make sure we have %8.3f format
try:
for i in xrange(4):
i += 1
for j in xrange(10):
j8 = j * 8
if lines[i][j8 + 4] != '.': return False
float(lines[i][j8:j8 + 8])
if lines[i][j8 + 7] not in '0123456789':
return False
except (IndexError, ValueError):
return False
# Must be a mdcrd
return True
def id_format(filename):
""" Identifies the file type as an Amber mdcrd file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is an Amber mdcrd file. False otherwise
"""
f = io.genopen(filename, 'r')
lines = [f.readline().decode() for i in xrange(5)]
f.close()
# Next 4 lines, make sure we have %8.3f format
try:
for i in xrange(4):
i += 1
for j in xrange(10):
j8 = j * 8
if lines[i][j8+4] != '.': return False
float(lines[i][j8:j8+8])
if lines[i][j8+7] not in '0123456789':
return False
except (IndexError, ValueError):
return False
# Must be a mdcrd
return True
def id_format(filename):
""" Identifies the file type as a CHARMM coordinate file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is a CHARMM coordinate file
"""
f = io.genopen(filename)
line = f.readline().decode()
try:
while len(line.strip()) == 0: # Skip whitespace, as a precaution
line = f.readline().decode()
intitle = True
while intitle:
line = f.readline().decode()
if len(line.strip()) == 0:
intitle = False
elif line.strip()[0] != '*':
intitle = False
else:
intitle = True
while len(line.strip()) == 0: # Skip whitespace
line = f.readline().decode()
try:
natom = int(line.strip().split()[0])
for row in xrange(min(natom, 3)):
line = f.readline().decode().strip().split()
int(line[0])
int(line[1])
float(line[4])
float(line[5])
float(line[6])
int(line[8])
float(line[9])
except (IndexError, ValueError):
return False
return True
finally:
f.close()
def id_format(filename):
""" Identifies the file type as a CHARMM coordinate file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is a CHARMM coordinate file
"""
f = io.genopen(filename)
line = f.readline().decode()
try:
while len(line.strip()) == 0: # Skip whitespace, as a precaution
line = f.readline().decode()
intitle = True
while intitle:
line = f.readline().decode()
if len(line.strip()) == 0:
intitle = False
elif line.strip()[0] != '*':
intitle = False
else:
intitle = True
while len(line.strip()) == 0: # Skip whitespace
line = f.readline().decode()
try:
natom = int(line.strip().split()[0])
for row in xrange(min(natom, 3)):
line = f.readline().decode().strip().split()
int(line[0])
int(line[1])
float(line[4])
float(line[5])
float(line[6])
int(line[8])
float(line[9])
except (IndexError, ValueError):
return False
return True
finally:
f.close()
def id_format(filename):
""" Identifies the file type as a CHARMM PSF file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is a CHARMM or Xplor-style PSF file
"""
f = genopen(filename, 'r')
line = f.readline().decode()
f.close()
return line.strip().startswith('PSF')
def id_format(filename):
""" Identifies the file type as a CHARMM restart file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is a CHARMM restart file
"""
f = io.genopen(filename)
line = f.readline().decode()
f.close()
return line.startswith('REST')
def id_format(filename):
""" Identifies the file type as a CHARMM restart file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is a CHARMM restart file
"""
f = io.genopen(filename)
line = f.readline().decode()
f.close()
return line.startswith('REST')
def id_format(filename):
""" Identifies the file type as a CHARMM PSF file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is a CHARMM or Xplor-style PSF file
"""
f = genopen(filename, 'r')
line = f.readline().decode()
f.close()
return line.strip().startswith('PSF')
def id_format(filename):
""" Sees if an open file is an OFF library file.
Parameters
----------
filename : str
The name of the file to see if it is an OFF file format
Returns
-------
is_fmt : bool
True if it is recognized as OFF, False otherwise
"""
f = io.genopen(filename, 'r')
try:
if AmberOFFLibrary._headerre.match(f.readline().decode()):
return True
return False
finally:
f.close()
def id_format(filename):
""" Sees if an open file is an OFF library file.
Parameters
----------
filename : str
The name of the file to see if it is an OFF file format
Returns
-------
is_fmt : bool
True if it is recognized as OFF, False otherwise
"""
f = io.genopen(filename, 'r')
try:
if AmberOFFLibrary._headerre.match(f.readline().decode()):
return True
return False
finally:
f.close()
def id_format(filename):
""" Identify the file as a Mol2 (or Mol3) file format or not
Parameters
----------
filename : str
Name of the file to test whether or not it is a mol2 file
Returns
-------
is_fmt : bool
True if it is a mol2 (or mol3) file, False otherwise
"""
f = TextToBinaryFile(genopen(filename, 'r'))
try:
for line in f:
if line.startswith('#'): continue
if not line.strip(): continue
return line.startswith('@<TRIPOS>')
return False
finally:
f.close()
def id_format(filename):
""" Identifies the file type as an Amber restart/inpcrd file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is an Amber restart/inpcrd file. False otherwise
"""
f = io.genopen(filename, 'r')
lines = [f.readline().decode() for i in xrange(5)]
f.close()
# Look for natom
try:
int(lines[1].split()[0])
except (ValueError, IndexError):
return False
# Next 3 lines, make sure we have %12.7f format
try:
for i in xrange(3):
i += 2
for j in xrange(6):
j12 = j * 12
if lines[i][j12+4] != '.': return False
float(lines[i][j12:j12+12])
if lines[i][j12+11] not in '0123456789':
return False
except (IndexError, ValueError):
return False
# Must be a restart...
return True
def id_format(filename):
""" Identifies the file type as an Amber restart/inpcrd file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is an Amber restart/inpcrd file. False otherwise
"""
f = io.genopen(filename, 'r')
lines = [f.readline().decode() for i in xrange(5)]
f.close()
# Look for natom
try:
int(lines[1].split()[0])
except (ValueError, IndexError):
return False
# Next 3 lines, make sure we have %12.7f format
try:
for i in xrange(3):
i += 2
for j in xrange(6):
j12 = j * 12
if lines[i][j12 + 4] != '.': return False
float(lines[i][j12:j12 + 12])
if lines[i][j12 + 11] not in '0123456789':
return False
except (IndexError, ValueError):
return False
# Must be a restart...
return True
def write(struct, dest, vmd=False):
"""
Writes a PSF file from the stored molecule
Parameters
----------
struct : :class:`Structure`
The Structure instance from which the PSF should be written
dest : str or file-like
The place to write the output PSF file. If it has a "write"
attribute, it will be used to print the PSF file. Otherwise, it will
be treated like a string and a file will be opened, printed, then
closed
vmd : bool
If True, it will write out a PSF in the format that VMD prints it in
(i.e., no NUMLP/NUMLPH or MOLNT sections)
Examples
--------
>>> cs = CharmmPsfFile('testfiles/test.psf')
>>> cs.write_psf('testfiles/test2.psf')
"""
# See if this is an extended format
try:
ext = 'EXT' in struct.flags
except AttributeError:
ext = True
own_handle = False
# Index the atoms and residues
if not hasattr(dest, 'write'):
own_handle = True
dest = TextToBinaryFile(genopen(dest, 'w'))
# Assign the formats we need to write with
if ext:
atmfmt1 = ('%10d %-8s %-8i %-8s %-8s %4d %10.6f %13.4f' + 11 * ' ')
atmfmt2 = ('%10d %-8s %-8i %-8s %-8s %-4s %10.6f %13.4f' +
11 * ' ')
intfmt = '%10d' # For pointers
else:
atmfmt1 = ('%8d %-4s %-4i %-4s %-4s %4d %10.6f %13.4f' + 11 * ' ')
atmfmt2 = ('%8d %-4s %-4i %-4s %-4s %-4s %10.6f %13.4f' + 11 * ' ')
intfmt = '%8d' # For pointers
# Now print the header then the title
dest.write('PSF ')
if hasattr(struct, 'flags'):
dest.write(' '.join(struct.flags))
else:
dest.write('EXT') # EXT is always active
dest.write('\n\n')
dest.write(intfmt % len(struct.title) + ' !NTITLE\n')
dest.write('\n'.join(struct.title) + '\n\n')
# Now time for the atoms
dest.write(intfmt % len(struct.atoms) + ' !NATOM\n')
# atmfmt1 is for CHARMM format (i.e., atom types are integers)
# atmfmt is for XPLOR format (i.e., atom types are strings)
for i, atom in enumerate(struct.atoms):
typ = atom.type
if isinstance(atom.type, str):
fmt = atmfmt2
if not atom.type: typ = atom.name
else:
fmt = atmfmt1
if hasattr(atom, 'segid'):
segid = atom.segid
else:
segid = 'SYS'
atmstr = fmt % (i + 1, segid, atom.residue.number,
atom.residue.name, atom.name, typ, atom.charge,
atom.mass)
if hasattr(atom, 'props'):
dest.write(atmstr + ' '.join(atom.props) + '\n')
else:
dest.write('\n')
dest.write('\n')
# Bonds
dest.write(intfmt % len(struct.bonds) + ' !NBOND: bonds\n')
for i, bond in enumerate(struct.bonds):
dest.write((intfmt * 2) % (bond.atom1.idx + 1, bond.atom2.idx + 1))
if i % 4 == 3: # Write 4 bonds per line
dest.write('\n')
# See if we need to terminate
if len(struct.bonds) % 4 != 0 or len(struct.bonds) == 0:
dest.write('\n')
dest.write('\n')
# Angles
dest.write(intfmt % len(struct.angles) + ' !NTHETA: angles\n')
for i, angle in enumerate(struct.angles):
dest.write(
(intfmt * 3) % (angle.atom1.idx + 1, angle.atom2.idx + 1,
angle.atom3.idx + 1))
if i % 3 == 2: # Write 3 angles per line
dest.write('\n')
# See if we need to terminate
if len(struct.angles) % 3 != 0 or len(struct.angles) == 0:
dest.write('\n')
dest.write('\n')
# Dihedrals
dest.write(intfmt % len(struct.dihedrals) + ' !NPHI: dihedrals\n')
for i, dih in enumerate(struct.dihedrals):
dest.write((intfmt * 4) % (dih.atom1.idx + 1, dih.atom2.idx + 1,
dih.atom3.idx + 1, dih.atom4.idx + 1))
if i % 2 == 1: # Write 2 dihedrals per line
dest.write('\n')
# See if we need to terminate
if len(struct.dihedrals) % 2 != 0 or len(struct.dihedrals) == 0:
dest.write('\n')
dest.write('\n')
# Impropers
dest.write(intfmt % len(struct.impropers) + ' !NIMPHI: impropers\n')
for i, imp in enumerate(struct.impropers):
dest.write((intfmt * 4) % (imp.atom1.idx + 1, imp.atom2.idx + 1,
imp.atom3.idx + 1, imp.atom4.idx + 1))
if i % 2 == 1: # Write 2 dihedrals per line
dest.write('\n')
# See if we need to terminate
if len(struct.impropers) % 2 != 0 or len(struct.impropers) == 0:
dest.write('\n')
dest.write('\n')
# Donor section
dest.write(intfmt % len(struct.donors) + ' !NDON: donors\n')
for i, don in enumerate(struct.donors):
dest.write((intfmt * 2) % (don.atom1.idx + 1, don.atom2.idx + 1))
if i % 4 == 3: # 4 donors per line
dest.write('\n')
if len(struct.donors) % 4 != 0 or len(struct.donors) == 0:
dest.write('\n')
dest.write('\n')
# Acceptor section
dest.write(intfmt % len(struct.acceptors) + ' !NACC: acceptors\n')
for i, acc in enumerate(struct.acceptors):
dest.write((intfmt * 2) % (acc.atom1.idx + 1, acc.atom2.idx + 1))
if i % 4 == 3: # 4 donors per line
dest.write('\n')
if len(struct.acceptors) % 4 != 0 or len(struct.acceptors) == 0:
dest.write('\n')
dest.write('\n')
# NNB section ??
dest.write(intfmt % 0 + ' !NNB\n\n')
for i in xrange(len(struct.atoms)):
dest.write(intfmt % 0)
if i % 8 == 7: # Write 8 0's per line
dest.write('\n')
if len(struct.atoms) % 8 != 0: dest.write('\n')
dest.write('\n')
# Group section
dest.write((intfmt * 2) % (len(struct.groups), struct.groups.nst2))
dest.write(' !NGRP NST2\n')
for i, gp in enumerate(struct.groups):
dest.write((intfmt * 3) % (gp.bs, gp.type, gp.move))
if i % 3 == 2: dest.write('\n')
if len(struct.groups) % 3 != 0 or len(struct.groups) == 0:
dest.write('\n')
dest.write('\n')
# The next two sections are never found in VMD prmtops...
if not vmd:
# Molecule section; first set molecularity
set_molecules(struct.atoms)
mollist = [a.marked for a in struct.atoms]
dest.write(intfmt % max(mollist) + ' !MOLNT\n')
for i, atom in enumerate(struct.atoms):
dest.write(intfmt % atom.marked)
if i % 8 == 7: dest.write('\n')
if len(struct.atoms) % 8 != 0: dest.write('\n')
dest.write('\n')
# NUMLP/NUMLPH section
dest.write((intfmt * 2) % (0, 0) + ' !NUMLP NUMLPH\n')
dest.write('\n')
# CMAP section
dest.write(intfmt % len(struct.cmaps) + ' !NCRTERM: cross-terms\n')
for i, cmap in enumerate(struct.cmaps):
dest.write(
(intfmt * 8) %
(cmap.atom1.idx + 1, cmap.atom2.idx + 1, cmap.atom3.idx + 1,
cmap.atom4.idx + 1, cmap.atom2.idx + 1, cmap.atom3.idx + 1,
cmap.atom4.idx + 1, cmap.atom5.idx + 1))
dest.write('\n')
# Done!
# If we opened our own handle, close it
if own_handle:
dest.close()
def write(struct, dest, vmd=False):
"""
Writes a PSF file from the stored molecule
Parameters
----------
struct : :class:`Structure`
The Structure instance from which the PSF should be written
dest : str or file-like
The place to write the output PSF file. If it has a "write"
attribute, it will be used to print the PSF file. Otherwise, it will
be treated like a string and a file will be opened, printed, then
closed
vmd : bool
If True, it will write out a PSF in the format that VMD prints it in
(i.e., no NUMLP/NUMLPH or MOLNT sections)
Examples
--------
>>> cs = CharmmPsfFile('testfiles/test.psf')
>>> cs.write_psf('testfiles/test2.psf')
"""
# See if this is an extended format
try:
ext = 'EXT' in struct.flags
except AttributeError:
ext = True
own_handle = False
# Index the atoms and residues
if not hasattr(dest, 'write'):
own_handle = True
dest = TextToBinaryFile(genopen(dest, 'w'))
# Assign the formats we need to write with
if ext:
atmfmt1 = ('%10d %-8s %-8i %-8s %-8s %4d %10.6f %13.4f' + 11*' ')
atmfmt2 = ('%10d %-8s %-8i %-8s %-8s %-4s %10.6f %13.4f' + 11*' ')
intfmt = '%10d' # For pointers
else:
atmfmt1 = ('%8d %-4s %-4i %-4s %-4s %4d %10.6f %13.4f' + 11*' ')
atmfmt2 = ('%8d %-4s %-4i %-4s %-4s %-4s %10.6f %13.4f' + 11*' ')
intfmt = '%8d' # For pointers
# Now print the header then the title
dest.write('PSF ')
if hasattr(struct, 'flags'):
dest.write(' '.join(struct.flags))
else:
dest.write('EXT') # EXT is always active
dest.write('\n\n')
dest.write(intfmt % len(struct.title) + ' !NTITLE\n')
dest.write('\n'.join(struct.title) + '\n\n')
# Now time for the atoms
dest.write(intfmt % len(struct.atoms) + ' !NATOM\n')
# atmfmt1 is for CHARMM format (i.e., atom types are integers)
# atmfmt is for XPLOR format (i.e., atom types are strings)
for i, atom in enumerate(struct.atoms):
typ = atom.type
if isinstance(atom.type, str):
fmt = atmfmt2
if not atom.type: typ = atom.name
else:
fmt = atmfmt1
if hasattr(atom, 'segid'):
segid = atom.segid
else:
segid = 'SYS'
atmstr = fmt % (i+1, segid, atom.residue.number,
atom.residue.name, atom.name, typ,
atom.charge, atom.mass)
if hasattr(atom, 'props'):
dest.write(atmstr + ' '.join(atom.props) + '\n')
else:
dest.write('\n')
dest.write('\n')
# Bonds
dest.write(intfmt % len(struct.bonds) + ' !NBOND: bonds\n')
for i, bond in enumerate(struct.bonds):
dest.write((intfmt*2) % (bond.atom1.idx+1, bond.atom2.idx+1))
if i % 4 == 3: # Write 4 bonds per line
dest.write('\n')
# See if we need to terminate
if len(struct.bonds) % 4 != 0 or len(struct.bonds) == 0:
dest.write('\n')
dest.write('\n')
# Angles
dest.write(intfmt % len(struct.angles) + ' !NTHETA: angles\n')
for i, angle in enumerate(struct.angles):
dest.write((intfmt*3) % (angle.atom1.idx+1, angle.atom2.idx+1,
angle.atom3.idx+1)
)
if i % 3 == 2: # Write 3 angles per line
dest.write('\n')
# See if we need to terminate
if len(struct.angles) % 3 != 0 or len(struct.angles) == 0:
dest.write('\n')
dest.write('\n')
# Dihedrals
dest.write(intfmt % len(struct.dihedrals) + ' !NPHI: dihedrals\n')
for i, dih in enumerate(struct.dihedrals):
dest.write((intfmt*4) % (dih.atom1.idx+1, dih.atom2.idx+1,
dih.atom3.idx+1, dih.atom4.idx+1)
)
if i % 2 == 1: # Write 2 dihedrals per line
dest.write('\n')
# See if we need to terminate
if len(struct.dihedrals) % 2 != 0 or len(struct.dihedrals) == 0:
dest.write('\n')
dest.write('\n')
# Impropers
dest.write(intfmt % len(struct.impropers) + ' !NIMPHI: impropers\n')
for i, imp in enumerate(struct.impropers):
dest.write((intfmt*4) % (imp.atom1.idx+1, imp.atom2.idx+1,
imp.atom3.idx+1, imp.atom4.idx+1)
)
if i % 2 == 1: # Write 2 dihedrals per line
dest.write('\n')
# See if we need to terminate
if len(struct.impropers) % 2 != 0 or len(struct.impropers) == 0:
dest.write('\n')
dest.write('\n')
# Donor section
dest.write(intfmt % len(struct.donors) + ' !NDON: donors\n')
for i, don in enumerate(struct.donors):
dest.write((intfmt*2) % (don.atom1.idx+1, don.atom2.idx+1))
if i % 4 == 3: # 4 donors per line
dest.write('\n')
if len(struct.donors) % 4 != 0 or len(struct.donors) == 0:
dest.write('\n')
dest.write('\n')
# Acceptor section
dest.write(intfmt % len(struct.acceptors) + ' !NACC: acceptors\n')
for i, acc in enumerate(struct.acceptors):
dest.write((intfmt*2) % (acc.atom1.idx+1, acc.atom2.idx+1))
if i % 4 == 3: # 4 donors per line
dest.write('\n')
if len(struct.acceptors) % 4 != 0 or len(struct.acceptors) == 0:
dest.write('\n')
dest.write('\n')
# NNB section ??
dest.write(intfmt % 0 + ' !NNB\n\n')
for i in xrange(len(struct.atoms)):
dest.write(intfmt % 0)
if i % 8 == 7: # Write 8 0's per line
dest.write('\n')
if len(struct.atoms) % 8 != 0: dest.write('\n')
dest.write('\n')
# Group section
dest.write((intfmt*2) % (len(struct.groups), struct.groups.nst2))
dest.write(' !NGRP NST2\n')
for i, gp in enumerate(struct.groups):
dest.write((intfmt*3) % (gp.bs, gp.type, gp.move))
if i % 3 == 2: dest.write('\n')
if len(struct.groups) % 3 != 0 or len(struct.groups) == 0:
dest.write('\n')
dest.write('\n')
# The next two sections are never found in VMD prmtops...
if not vmd:
# Molecule section; first set molecularity
set_molecules(struct.atoms)
mollist = [a.marked for a in struct.atoms]
dest.write(intfmt % max(mollist) + ' !MOLNT\n')
for i, atom in enumerate(struct.atoms):
dest.write(intfmt % atom.marked)
if i % 8 == 7: dest.write('\n')
if len(struct.atoms) % 8 != 0: dest.write('\n')
dest.write('\n')
# NUMLP/NUMLPH section
dest.write((intfmt*2) % (0, 0) + ' !NUMLP NUMLPH\n')
dest.write('\n')
# CMAP section
dest.write(intfmt % len(struct.cmaps) + ' !NCRTERM: cross-terms\n')
for i, cmap in enumerate(struct.cmaps):
dest.write((intfmt*8) % (cmap.atom1.idx+1, cmap.atom2.idx+1,
cmap.atom3.idx+1, cmap.atom4.idx+1,
cmap.atom2.idx+1, cmap.atom3.idx+1,
cmap.atom4.idx+1, cmap.atom5.idx+1)
)
dest.write('\n')
# Done!
# If we opened our own handle, close it
if own_handle:
dest.close()
def write(struct, dest, mol3=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
"""
own_handle = False
if not hasattr(dest, 'write'):
own_handle = True
dest = TextToBinaryFile(genopen(dest, 'w'))
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
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]
else:
residues = struct.residues
charges = [a.charge for a in struct.atoms]
dest.write('@<TRIPOS>MOLECULE\n')
dest.write('\n')
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
# 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('%d %s %.4f %.4f %.4f %s %d %s' % (j, atom.name,
x, y, z, atom.type, i+1, res.name))
if printchg:
dest.write(' %.4f\n' % atom.charge)
else:
dest.write('\n')
j += 1
dest.write('@<TRIPOS>BOND\n')
for i, bond in enumerate(bonds):
dest.write('%d %d %d 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('%d %s %d RESIDUE %d %s ROOT %d\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()
def parse(filename, structure=False):
""" Parses a mol2 file (or mol3) file
Parameters
----------
filename : str
Name of the file to parse
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
"""
f = TextToBinaryFile(genopen(filename, 'r'))
rescont = ResidueTemplateContainer()
struct = Structure()
restemp = ResidueTemplate()
mol_info = []
try:
section = None
last_residue = None
headtail = 'head'
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()
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]
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
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)
restemp.add_atom(copy.copy(atom))
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]
else:
raise Mol2Error('Bad bonding pattern detected')
if atom2.residue.idx == len(rescont):
res2 = restemp
elif atom1.residue.idx < len(rescont):
res2 = rescont[atom2.residue.idx]
else:
raise Mol2Error('Bad bonding pattern detected')
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]
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(x) for x 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()
id = int(words[0])
resname = words[1]
root_atom = int(words[2])
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 - 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:
atom.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:
rescont.append(restemp)
return rescont
else:
return restemp
except ValueError, e:
raise Mol2Error('String conversion trouble: %s' % e)
