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
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]
elif not multires_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(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()
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:
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:
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):
for res in struct:
Mol2File.write(res, dest, mol3)
return
elif isinstance(struct, Structure) and len(struct.residues) > 1:
for res in ResidueTemplateContainer.from_structure(struct):
Mol2File.write(res, dest, mol3)
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
if not struct.name:
name = struct[0].name
else:
name = struct.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' % name)
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('%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()