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Replace complex old-style format with new format strings.

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This commit is contained in:
Nathan Baker
2020-05-27 08:19:36 -07:00
parent 2305615fbe
commit 557ab19312
1 changed files with 9 additions and 9 deletions
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16
propka/atom.py
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@@ -20,8 +20,10 @@ MOL2_LINE_FMT = (
"{r.sybyl_type:>6s} {r.res_num:>6d} {r.res_name:>10s} 0.0000\n") "{r.sybyl_type:>6s} {r.res_num:>6d} {r.res_name:>10s} 0.0000\n")
PDB_LINE_FMT2 = ( PDB_LINE_FMT2 = (
"ATOM {numb:>6d} {atom_label} {res_name}{chain_id:>2s}{res_num:>4d}" "ATOM {numb:>6d} {atom_label} {res_name}{chain_id:>2s}{res_num:>4d}"
"{x:>12.3f}{y:>8.3f}{z:>8.3f}{occ:>6.2f}{beta:>6.2f}\n" "{x:>12.3f}{y:>8.3f}{z:>8.3f}{occ:>6.2f}{beta:>6.2f}\n")
) STR_FMT = (
"{r.numb:>5d}-{r.name:>4s} {r.res_num:>5d}-{r.res_name:>3s} "
"({r.chain_id:1s}) [{r.x:>8.3f} {r.y:>8.3f} {r.z:>8.3f}] {r.element:s}")
class Atom(object): class Atom(object):
@@ -152,9 +154,9 @@ class Atom(object):
array of bonded atoms. array of bonded atoms.
""" """
res = [] res = []
for ba in self.bonded_atoms: for bond_atom in self.bonded_atoms:
if ba.element == element: if bond_atom.element == element:
res.append(ba) res.append(bond_atom)
return res return res
def get_bonded_heavy_atoms(self): def get_bonded_heavy_atoms(self):
@@ -409,9 +411,7 @@ 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' % ( return STR_FMT.format(r=self)
self.numb, self.name, self.res_num, self.res_name, self.chain_id,
self.x, self.y, 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