class Chain:
def __init__(self,
chain_id: str = None,
residues: dict = None,
non_residues: dict = None):
self.chain_id = chain_id
self.residues = residues if residues is not None else {}
self.seq = AASeq(''.join(a.res_type for a in residues.values())) if residues is not None else \
AASeq('', name=chain_id)
self.non_residues = non_residues if non_residues is not None else {}
self.non_residues_seq = AASeq(''.join(a.res_type for a in residues.values()), name=chain_id) if \
non_residues is not None else AASeq('', name=chain_id)
def __repr__(self) -> str:
return "chain %s has %i residues" % (self.chain_id, len(self.residues))
def __getitem__(self, item: int) -> Residue:
try:
return self.residues[item]
except:
return self.non_residues[item]
def __iter__(self):
for k, v in self.residues.items():
yield k, v
def __len__(self):
if self.residues == {}:
return 0
return len(self.residues.keys())
def add_residue(self, residue: Residue) -> None:
if residue.res_type_3 in three_2_one.keys():
self.seq.add_aa(residue.res_type)
self.residues[residue.res_num] = residue
else:
self.non_residues_seq.add_aa(residue.res_type)
self.non_residues[residue.res_num] = residue
def min_distance_chain(self, other: Residue) -> float:
distances = []
for mrid, mres in self:
for orid, ores in other:
distances.append(mres.min_distance_res(ores))
return min(distances)
def keys(self):
return self.residues.keys()
def values(self):
return self.residues.values()
def COM(self) -> XYZ:
"""
:return:the Center Of Mass of the chain as calculated by the averages over Xs, Ys and Zs of all CAs
"""
Xs = []
Ys = []
Zs = []
for res in self.values():
if 'CA' in res.keys():
Xs.append(res['CA'].xyz.x)
Ys.append(res['CA'].xyz.y)
Zs.append(res['CA'].xyz.z)
return XYZ(np.mean(Xs), np.mean(Ys), np.mean(Zs))
def change_chain_name(self, new: str) -> None:
self.chain_id = new
for rid, r in self:
r.change_chain_name(new)
def translate_xyz(self, xyz: XYZ) -> None:
"""
:param xyz: an xyz point
:return: None. translate all chain atoms by xyz
"""
for rid, r in self:
r.translate_xyz(xyz)
class Chain:
def __init__(self, chain_id: str = None, residues: dict = None, non_residues: dict = None):
self.chain_id = chain_id
self.residues = residues if residues is not None else {}
self.seq = AASeq(''.join(a.res_type for a in residues.values())) if residues is not None else \
AASeq('', name=chain_id)
self.non_residues = non_residues if non_residues is not None else {}
self.non_residues_seq = AASeq(''.join(a.res_type for a in residues.values()), name=chain_id) if \
non_residues is not None else AASeq('', name=chain_id)
def __repr__(self) -> str:
return "chain %s has %i residues" % (self.chain_id, len(self.residues))
def __getitem__(self, item: int) -> Residue:
try:
return self.residues[item]
except:
return self.non_residues[item]
def __iter__(self):
for k, v in self.residues.items():
yield k, v
def __len__(self):
if self.residues == {}:
return 0
return len(self.residues.keys())
def add_residue(self, residue: Residue) -> None:
if residue.res_type_3 in three_2_one.keys():
self.seq.add_aa(residue.res_type)
self.residues[residue.res_num] = residue
else:
self.non_residues_seq.add_aa(residue.res_type)
self.non_residues[residue.res_num] = residue
def min_distance_chain(self, other: Residue) -> float:
distances = []
for mrid, mres in self:
for orid, ores in other:
distances.append(mres.min_distance_res(ores))
return min(distances)
def keys(self):
return self.residues.keys()
def values(self):
return self.residues.values()
def COM(self) -> XYZ:
"""
:return:the Center Of Mass of the chain as calculated by the averages over Xs, Ys and Zs of all CAs
"""
Xs = []
Ys = []
Zs = []
for res in self.values():
if 'CA' in res.keys():
Xs.append(res['CA'].xyz.x)
Ys.append(res['CA'].xyz.y)
Zs.append(res['CA'].xyz.z)
return XYZ(np.mean(Xs), np.mean(Ys), np.mean(Zs))
def change_chain_name(self, new: str) -> None:
self.chain_id = new
for rid, r in self:
r.change_chain_name(new)
def translate_xyz(self, xyz: XYZ) -> None:
"""
:param xyz: an xyz point
:return: None. translate all chain atoms by xyz
"""
for rid, r in self:
r.translate_xyz(xyz)
