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Add line breaks to format strings.

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Addresses https://github.com/jensengroup/propka-3.1/issues/44#issuecomment-634233970
This commit is contained in:
Nathan Baker
2020-05-27 08:01:30 -07:00
parent bcccd89ca4
commit 2305615fbe
1 changed files with 7 additions and 9 deletions
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16
propka/atom.py
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@@ -9,17 +9,18 @@ from . import hybrid36
PKA_FMT = "{:6.2f}"
INPUT_LINE_FMT = (
"{type:6s}{r.numb:>5d} {atom_label} {r.res_name}{r.chain_id:>2s}"
"{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{group:>6s}{pka:>6s} ")
"{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{group:>6s}{pka:>6s} \n")
PDB_LINE_FMT1 = (
"{type:6s}{r.numb:>5d} {atom_label} {r.res_name}{r.chain_id:>2s}"
"{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{r.occ:>6s}{r.beta:>6s}")
"{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{r.occ:>6s}"
"{r.beta:>6s}\n")
MOL2_LINE_FMT = (
"{id:<4d} {atom_label:4s} "
"{r.x:>10.4f} {r.y:>10.4f} {r.z:>10.4f} "
"{r.sybyl_type:>6s} {r.res_num:>6d} {r.res_name:>10s} 0.0000")
"{r.sybyl_type:>6s} {r.res_num:>6d} {r.res_name:>10s} 0.0000\n")
PDB_LINE_FMT2 = (
"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}"
"{x:>12.3f}{y:>8.3f}{z:>8.3f}{occ:>6.2f}{beta:>6.2f}\n"
)
@@ -267,7 +268,6 @@ class Atom(object):
type=self.type.upper(), r=self,
atom_label=propka.lib.make_tidy_atom_label(self.name, self.element),
group=group, pka=model_pka)
str_ += "\n"
return str_
def make_conect_line(self):
@@ -342,7 +342,6 @@ class Atom(object):
str_ = PDB_LINE_FMT1.format(
type=self.type.upper(), r=self,
atom_label=propka.lib.make_tidy_atom_label(self.name, self.element))
str_ += "\n"
return str_
def make_mol2_line(self, id_):
@@ -358,11 +357,11 @@ class Atom(object):
str_ = MOL2_LINE_FMT.format(
id=id_, r=self,
atom_label=propka.lib.make_tidy_atom_label(self.name, self.element))
str_ += "\n"
return str_
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):
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
@@ -397,7 +396,6 @@ class Atom(object):
x=x, y=y, z=z, occ=occ, beta=beta,
atom_label=propka.lib.make_tidy_atom_label(name, self.element)
)
str_ += '\n'
return str_
def get_tidy_label(self):