"""
Functions to work with CIF files.
"""
from tabulate import tabulate
_bond_order_map = {
1: "SING",
2: "DOUB",
3: "TRIP",
}
"""
Bond order mappings to strings
"""
_rev_bond_order_map = {
"SING": 1,
"DOUB": 2,
"TRIP": 3,
}
"""
Reverse bond order mappings to strings
"""
_categories = (
"comp_id",
"atom_id_1",
"atom_id_2",
"label_atom_id_1",
"label_atom_id_2",
"value_order",
"pdbx_ordinal",
)
"""
The categories of the bond table
"""
[docs]
def write_bond_table(mol, filename, fmt_header: str = "_bond"):
"""
Write a bond table to a CIF file.
Parameters
----------
mol : bam.Molecule
The molecule to generate the connectivity for.
filename : str
The filename to write the CIF file to.
fmt_header : str, optional
The format string to use for the header of the table, by default "_bond"
"""
with open(filename, "r") as f:
c = f.read()
with open(filename, "w") as f:
f.write(c + "\n")
f.write(make_bond_table(mol, fmt_header))
[docs]
def make_bond_table(mol, fmt_header: str = "_bond"):
"""
Generate a table of bond information for a molecule.
Parameters
----------
mol : bam.Molecule
The molecule to generate the connectivity for.
fmt_header : str, optional
The format string to use for the header of the table, by default "_bond"
Returns
-------
table : str
The table of bond information.
"""
lines = make_bond_lines(mol)
table = tabulate(lines, tablefmt="plain")
header = make_header(fmt_header)
return header + table + "\n# #\n"
[docs]
def make_bond_lines(mol):
"""
Generate a list of lines for a CIF file that describe the connectivity
of the molecule.
Parameters
----------
mol : bam.Molecule
The molecule to generate the connectivity for.
Returns
-------
lines : list
A list of lines that describe the connectivity of the molecule.
"""
# bond_counts = {}
# for bond in mol.bonds:
# if bond not in bond_counts:
# bond_counts[bond] = 1
# else:
# bond_counts[bond] += 1
lines = []
comp_id = mol.id
for bdx, bond in enumerate(mol.get_bonds()):
atom_a = bond[0]
atom_b = bond[1]
order = _bond_order_map[bond.order]
lines.append(
(
comp_id,
atom_a.serial_number,
atom_b.serial_number,
atom_a.id,
atom_b.id,
order,
bdx + 1,
)
)
return lines
[docs]
def parse_bond_table(filename, fmt_header: str = "_bond"):
"""
Parse the bond table from a BuildAMol generated CIF file.
"""
bonds = {}
at_bonds_table = False
starter = fmt_header + "." + _categories[-1] # the last header line
with open(filename, "r") as f:
for line in f:
if line.startswith(starter):
at_bonds_table = True
continue
if not at_bonds_table:
continue
if line[0] == "#":
continue
line = line.strip().split()
if len(line) == 0:
break
a, b, order = int(line[1]), int(line[2]), line[-2]
order = _rev_bond_order_map[order]
bonds.setdefault((a, b), 0)
bonds[(a, b)] += order
return [(a, b, order) for (a, b), order in bonds.items()]
if __name__ == "__main__":
from buildamol import molecule
mol = molecule("GLC")
print(make_bond_table(mol, fmt_header="_bond"))
