def make_input_line(self):
"""PDB line for this atom.
TODO - Could be @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
Returns:
String with PDB-format line.
"""
group = '-'
model_pka = '-'
if self.group:
group = self.group.type
if self.terminal == 'C-':
group = 'C-' ## circumventing C-/COO parameter unification
if self.group.titratable:
model_pka = PKA_FMT.format(self.group.model_pka)
str_ = INPUT_LINE_FMT.format(type=self.type.upper(),
r=self,
atom_label=make_tidy_atom_label(
self.name, self.element),
group=group,
pka=model_pka)
return str_
def get_tidy_label(self):
"""Returns a 'tidier' atom label for printing the new pdbfile
TODO - this could/should be a @property method/attribute
Returns:
String with label"""
return make_tidy_atom_label(self.name, self.element)
def make_pdb_line2(self,
numb=None,
name=None,
res_name=None,
chain_id=None,
res_num=None,
x=None,
y=None,
z=None,
occ=None,
beta=None):
"""Create a PDB line.
TODO - this could/should be a @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
Returns:
String with PDB line.
"""
if numb is None:
numb = self.numb
if name is None:
name = self.name
if res_name is None:
res_name = self.res_name
if chain_id is None:
chain_id = self.chain_id
if res_num is None:
res_num = self.res_num
if x is None:
x = self.x
if y is None:
y = self.y
if z is None:
z = self.z
if occ is None:
occ = self.occ
if beta is None:
beta = self.beta
str_ = PDB_LINE_FMT2.format(numb=numb,
res_name=res_name,
chain_id=chain_id,
res_num=res_num,
x=x,
y=y,
z=z,
occ=occ,
beta=beta,
atom_label=make_tidy_atom_label(
name, self.element))
return str_
def make_mol2_line(self, id_):
"""Create MOL2 line.
Format: 1 S1 3.6147 2.0531 1.4795 S.3 1 noname -0.1785
TODO - this could/should be a @property method/attribute
Returns:
String with MOL2 line.
"""
str_ = MOL2_LINE_FMT.format(
id=id_, r=self,
atom_label=make_tidy_atom_label(self.name, self.element))
return str_
def make_pdb_line(self):
"""Create PDB line.
TODO - this could/should be a @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
Returns:
String with PDB line.
"""
str_ = PDB_LINE_FMT1.format(
type=self.type.upper(), r=self,
atom_label=make_tidy_atom_label(self.name, self.element))
return str_
