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Clean up line breaks.

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For https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
2020-05-25 16:42:09 -07:00
parent 75cdf0ea04
commit 4408b23448
1 changed files with 32 additions and 23 deletions
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55
propka/atom.py
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@@ -8,12 +8,12 @@ from . import hybrid36
class Atom(object): class Atom(object):
"""Atom class - contains all atom information found in the PDB file""" """Atom class - contains all atom information found in the PDB file"""
def __init__(self, line=None, verbose=False): def __init__(self, line=None, _=False):
"""Initialize Atom object. """Initialize Atom object.
Args: Args:
line: Line from a PDB file to set properties of atom. line: Line from a PDB file to set properties of atom.
verbose: TODO - this does not appear to be used. Can we remove it? _: TODO - this does not appear to be used. Can we remove it?
""" """
self.occ = None self.occ = None
self.numb = None self.numb = None
@@ -48,7 +48,8 @@ class Atom(object):
self.num_pi_elec_conj_2_3_bonds = 0 self.num_pi_elec_conj_2_3_bonds = 0
self.groups_extracted = 0 self.groups_extracted = 0
self.set_properties(line) self.set_properties(line)
self.residue_label = "%-3s%4d%2s" % (self.name, self.res_num, self.chain_id) self.residue_label = "%-3s%4d%2s" % (
self.name, self.res_num, self.chain_id)
# ligand atom types # ligand atom types
self.sybyl_type = '' self.sybyl_type = ''
@@ -101,7 +102,8 @@ class Atom(object):
if len(self.name) == 4: if len(self.name) == 4:
self.element = self.element[0] self.element = self.element[0]
if len(self.element) == 2: if len(self.element) == 2:
self.element = '%1s%1s' % (self.element[0], self.element[1].lower()) self.element = '%1s%1s' % (
self.element[0], self.element[1].lower())
def set_group_type(self, type_): def set_group_type(self, type_):
"""Set group type of atom. """Set group type of atom.
@@ -156,12 +158,14 @@ class Atom(object):
if ba == other_atom: if ba == other_atom:
return True return True
if max_bonds > cur_bond: if max_bonds > cur_bond:
if ba.is_atom_within_bond_distance(other_atom, max_bonds, cur_bond+1): if ba.is_atom_within_bond_distance(other_atom, max_bonds,
cur_bond+1):
return True return True
return False return False
def set_property(self, numb=None, name=None, res_name=None, chain_id=None, def set_property(self, numb=None, name=None, res_name=None, chain_id=None,
res_num=None, x=None, y=None, z=None, occ=None, beta=None): res_num=None, x=None, y=None, z=None, occ=None,
beta=None):
"""Set properties of the atom object. """Set properties of the atom object.
Args: Args:
@@ -225,7 +229,8 @@ class Atom(object):
"""PDB line for this atom. """PDB line for this atom.
TODO - Could be @property method/attribute TODO - Could be @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line, and make_pdb_line2 TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
Returns: Returns:
String with PDB-format line. String with PDB-format line.
@@ -239,11 +244,12 @@ class Atom(object):
if self.group.titratable: if self.group.titratable:
model_pka = '%6.2f'%self.group.model_pka model_pka = '%6.2f'%self.group.model_pka
str_ = "%-6s%5d %s " % (self.type.upper(), self.numb, str_ = "%-6s%5d %s " % (
propka.lib.make_tidy_atom_label(self.name, self.element)) self.type.upper(), self.numb,
str_ += "%s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (self.res_name, self.chain_id, propka.lib.make_tidy_atom_label(self.name, self.element))
self.res_num, self.x, self.y, str_ += "%s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (
self.z, group, model_pka) self.res_name, self.chain_id, self.res_num, self.x, self.y,
self.z, group, model_pka)
return str_ return str_
def make_conect_line(self): def make_conect_line(self):
@@ -294,7 +300,9 @@ class Atom(object):
group_attr = getattr(propka.group, group_attr) group_attr = getattr(propka.group, group_attr)
self.group = group_attr(self) self.group = group_attr(self)
except: except:
raise Exception('%s in input_file is not recognized as a group' % self.occ) # TODO - be more specific with expection handling here
str_ = '%s in input_file is not recognized as a group' % self.occ
raise Exception(str_)
# set the model pKa value # set the model pKa value
if self.beta != '-': if self.beta != '-':
self.group.model_pka = float(self.beta) self.group.model_pka = float(self.beta)
@@ -307,7 +315,8 @@ class Atom(object):
"""Create PDB line. """Create PDB line.
TODO - this could/should be a @property method/attribute TODO - this could/should be a @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line, and make_pdb_line2 TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
Returns: Returns:
String with PDB line. String with PDB line.
@@ -330,11 +339,11 @@ class Atom(object):
Returns: Returns:
String with MOL2 line. String with MOL2 line.
""" """
str_ = "%-4d %-4s " % (id_, propka.lib.make_tidy_atom_label(self.name, str_ = "%-4d %-4s " % (
self.element)) id_, propka.lib.make_tidy_atom_label(self.name, self.element))
str_ += "%10.4f %10.4f %10.4f " % (self.x, self.y, self.z) str_ += "%10.4f %10.4f %10.4f " % (self.x, self.y, self.z)
str_ += "%6s %6d %10s %10.4f\n" % (self.sybyl_type.replace('-', ''), str_ += "%6s %6d %10s %10.4f\n" % (
self.res_num, self.res_name, 0.0) self.sybyl_type.replace('-', ''), self.res_num, self.res_name, 0.0)
return str_ return str_
def make_pdb_line2(self, numb=None, name=None, res_name=None, chain_id=None, def make_pdb_line2(self, numb=None, name=None, res_name=None, chain_id=None,
@@ -342,7 +351,8 @@ class Atom(object):
"""Create a PDB line. """Create a PDB line.
TODO - this could/should be a @property method/attribute TODO - this could/should be a @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line, and make_pdb_line2 TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
Returns: Returns:
String with PDB line. String with PDB line.
@@ -392,10 +402,9 @@ class Atom(object):
def __str__(self): def __str__(self):
"""Return an undefined-format string version of this atom.""" """Return an undefined-format string version of this atom."""
return '%5d-%4s %5d-%3s (%1s) [%8.3f %8.3f %8.3f] %s' % (self.numb, self.name, return '%5d-%4s %5d-%3s (%1s) [%8.3f %8.3f %8.3f] %s' % (
self.res_num, self.res_name, self.numb, self.name, self.res_num, self.res_name, self.chain_id,
self.chain_id, self.x, self.y, self.x, self.y, self.z, self.element)
self.z, self.element)
def set_residue(self, residue): def set_residue(self, residue):
""" Makes a reference to the parent residue """ Makes a reference to the parent residue