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Deferring #394

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merged 3 commits into from
Dec 7, 2021
Merged

Deferring #394

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0e25a52
Renamed open from file_writer to deferred_open, made deferred_writing…
Tsjerk Dec 3, 2021
be3ec45
Updated file_write call in martinize2
Tsjerk Dec 6, 2021
558b6c2
Simplified PDB writing in martinize2
Tsjerk Dec 6, 2021
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Updated file_write call in martinize2
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@Tsjerk
Tsjerk committed Dec 6, 2021
commit be3ec4561fc4fbf11c518df9df76c81c9f368420
6 changes: 3 additions & 3 deletions bin/martinize2
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ import sys

import vermouth
import vermouth.forcefield
from vermouth.file_writer import open, DeferredFileWriter
from vermouth.file_writer import deferred_open, DeferredFileWriter
from vermouth import DATA_PATH
from vermouth.dssp import dssp
from vermouth.dssp.dssp import (
Expand Down Expand Up @@ -191,7 +191,7 @@ def write_gmx_topology(system, top_path, defines=(), header=()):
# A given moltype can appear more than once in the sequence of
# molecules, without being uninterupted by other moltypes. Even in
# that case, we want to write the ITP only once.
with open('{}.itp'.format(moltype), 'w') as outfile:
with deferred_open('{}.itp'.format(moltype), 'w') as outfile:
# here we format and merge all citations
header[-1] = header[-1]+"\n"
header.append("Pleas cite the following papers:")
Expand Down Expand Up @@ -232,7 +232,7 @@ def write_gmx_topology(system, top_path, defines=(), header=()):
define_string = '\n'.join(
'#define {}'.format(define) for define in defines
)
with open(str(top_path), 'w') as outfile:
with deferred_open(str(top_path), 'w') as outfile:
outfile.write(
textwrap.dedent(
template.format(
Expand Down