def _parse_pdb(pdb: Path):
struct = read_pdb(str(pdb))
r_work = None
r_free = None
bonds = None
angles = None
#
# look for 'REMARK Final:' remark line
# which specifies r-work, r-free, bonds and angles values
#
for rem in struct.raw_remarks:
match = REM_FINAL_RE.match(rem)
if match is None:
continue
# remark line found, get our values and end the loop
r_work, r_free, bonds, angles = match.groups()
break
# remove all spaces from the space group specification,
# e.g. 'P 1 21 1' becomes 'P1211'
spacegroup = "".join(struct.spacegroup_hm.split(" "))
return (
spacegroup,
struct.resolution,
r_work,
r_free,
bonds,
angles,
struct.cell,
)
def _parse_pdb(pdb: Path):
struct = read_pdb(str(pdb))
r_work = None
r_free = None
bonds = None
angles = None
for rem in struct.raw_remarks:
if rem.startswith(R_WORK_LINE):
r_work = _cut_prefix_strip(R_WORK_LINE, rem)
if rem.startswith(R_FREE_LINE):
r_free = _cut_prefix_strip(R_FREE_LINE, rem)
if rem.startswith(BONDS_LINE):
bonds = _cut_prefix_strip(BONDS_LINE, rem)
bonds = bonds.split(";")[1].strip()
if rem.startswith(ANGLES_LINE):
angles = _cut_prefix_strip(ANGLES_LINE, rem)
angles = angles.split(";")[1].strip()
# remove all spaces from the space group specification,
# e.g. 'P 1 21 1' becomes 'P1211'
spacegroup = "".join(struct.spacegroup_hm.split(" "))
return (
spacegroup,
struct.resolution,
r_work,
r_free,
bonds,
angles,
struct.cell,
)
def find_water_chains(file):
'''
Find which chain(s) contain only water molecules
:param file: A pdb file name.
:return: A list of chains that contain water
'''
structure = gemmi.read_pdb(file)
old = [x.name for x in structure[0]]
structure.remove_waters()
structure.remove_empty_chains()
new = [x.name for x in structure[0]]
return list(set(old) - set(new))
def get_chain_center(chain_name, file):
'''
Calculate the center of mass for a particular chain within a particular pdb file
:param chain_name: Name of the chain
:param file: Filepath of pdb file.
:return: The center of mass of the specified chain.
'''
structure = gemmi.read_pdb(file)[0]
names = [x.name for x in structure]
for i in names:
if i == chain_name:
continue
else:
structure.remove_chain(i)
return structure.calculate_center_of_mass()
def __init__(self, pdb):
self.pdb = gemmi.read_pdb(pdb)