Deferring

bin/martinize2

@@ -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 (
@@ -118,23 +118,23 @@ def pdb_to_universal(system, delete_unknown=False, force_field=None,
  fudge=bonds_fudge).run_system(canonicalized)
  vermouth.MergeNucleicStrands().run_system(canonicalized)
  if write_graph is not None:
- vermouth.pdb.write_pdb(canonicalized, str(write_graph), omit_charges=True)
- DeferredFileWriter().write()
+ vermouth.pdb.write_pdb(canonicalized, str(write_graph), omit_charges=True,
+  defer_writing=False)
 
  LOGGER.debug('Annotating required mutations and modifications.', type='step')
  vermouth.AnnotateMutMod(modifications, mutations).run_system(canonicalized)
  LOGGER.info('Repairing the graph.', type='step')
  vermouth.RepairGraph(delete_unknown=delete_unknown, include_graph=False).run_system(canonicalized)
  if write_repair is not None:
  vermouth.pdb.write_pdb(canonicalized, str(write_repair),
- omit_charges=True, nan_missing_pos=True)
- DeferredFileWriter().write()
+ omit_charges=True, nan_missing_pos=True, 
+  defer_writing=False)
  LOGGER.info('Dealing with modifications.', type='step')
  vermouth.CanonicalizeModifications().run_system(canonicalized)
  if write_canon is not None:
  vermouth.pdb.write_pdb(canonicalized, str(write_canon),
- omit_charges=True, nan_missing_pos=True)
- DeferredFileWriter().write()
+ omit_charges=True, nan_missing_pos=True,
+  defer_writing=False)
  vermouth.AttachMass(attribute='mass').run_system(canonicalized)
  vermouth.SortMoleculeAtoms().run_system(canonicalized) # was system
  return canonicalized
@@ -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:")
@@ -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(

vermouth/dssp/dssp.py

@@ -22,7 +22,7 @@
 import subprocess
 import tempfile
 
-from ..file_writer import open
+from ..file_writer import deferred_open
 from ..pdb import pdb
 from ..system import System
 from ..processors.processor import Processor
@@ -143,7 +143,7 @@ def read_dssp2(lines):
  return secstructs
 
 
-def run_dssp(system, executable='dssp', savefile=None):
+def run_dssp(system, executable='dssp', savefile=None, defer_writing=True):
  """
  Run DSSP on a system and return the assigned secondary structures.
 
@@ -170,6 +170,8 @@ def run_dssp(system, executable='dssp', savefile=None):
  Where to find the DSSP executable.
  savefile: None or str or pathlib.Path
  If set to a path, the output of DSSP is written in that file.
+ defer_writing: bool
+ Whether to use :meth:`~vermouth.file_writer.DeferredFileWriter.write` for writing data
 
  Returns
  list of str
@@ -216,6 +218,8 @@ def run_dssp(system, executable='dssp', savefile=None):
  LOGGER.debug('DSSP input file written to {}', tmpfile_name)
 
  if savefile is not None:
+ if defer_writing:
+ open = deferred_open
  with open(str(savefile), 'w') as outfile:
  outfile.write(process.stdout)
  return read_dssp2(process.stdout.split('\n'))

vermouth/file_writer.py

@@ -202,4 +202,4 @@ def __del__(self):
  # super().__del__() # object has no __del__
 
 
-open = DeferredFileWriter().open
+deferred_open = DeferredFileWriter().open

vermouth/forcefield.py

@@ -19,7 +19,6 @@
 import itertools
 from glob import glob
 import os
-from .file_writer import open
 from .gmx.rtp import read_rtp
 from .ffinput import read_ff
 from .citation_parser import read_bib

vermouth/gmx/gro.py

@@ -20,7 +20,7 @@
 
 import numpy as np
 
-from ..file_writer import open
+from ..file_writer import deferred_open
 from ..molecule import Molecule
 from ..truncating_formatter import TruncFormatter
 from ..utils import first_alpha
@@ -110,7 +110,7 @@ def read_gro(file_name, exclude=('SOL',), ignh=False):
  return molecule
 
 
-def write_gro(system, file_name, precision=7, title='Martinized!', box=(0, 0, 0)):
+def write_gro(system, file_name, precision=7, title='Martinized!', box=(0, 0, 0), defer_writing=True):
  """
  Write `system` to `file_name`, which will be a GRO96 file.
 
@@ -126,6 +126,8 @@ def write_gro(system, file_name, precision=7, title='Martinized!', box=(0, 0, 0)
  Title for the gro file.
  box: tuple[float]
  Box length and optionally angles.
+ defer_writing: bool
+ Whether to use :meth:`~vermouth.file_writer.DeferredFileWriter.write` for writing data
  """
  formatter = TruncFormatter()
  pos_format_string = '{{:{ntx}.3ft}}'.format(ntx=precision + 1)
@@ -138,6 +140,8 @@ def write_gro(system, file_name, precision=7, title='Martinized!', box=(0, 0, 0)
  vel_format_string = '{{:{ntx}.4ft}}'*3
  vel_format_string = vel_format_string.format(ntx=precision+1)
 
+ if defer_writing:
+ open = deferred_open
  with open(str(file_name), 'w') as out:
  out.write(title + '\n') # Title
  out.write(formatter.format('{}\n', system.num_particles)) # number of atoms

vermouth/map_input.py

@@ -22,7 +22,6 @@
 import itertools
 from pathlib import Path
 
-from .file_writer import open
 from .log_helpers import StyleAdapter, get_logger
 from .map_parser import MappingDirector, Mapping
 

vermouth/map_parser.py

@@ -18,7 +18,6 @@
 from collections import defaultdict
 from functools import partial
 
-from .file_writer import open
 from .ffinput import _tokenize, _parse_atom_attributes
 from .graph_utils import MappingGraphMatcher
 from .log_helpers import StyleAdapter, get_logger

vermouth/pdb/pdb.py

@@ -19,7 +19,7 @@
 import numpy as np
 import networkx as nx
 
-from ..file_writer import open
+from ..file_writer import deferred_open
 from ..molecule import Molecule
 from ..utils import first_alpha, distance, format_atom_string
 from ..parser_utils import LineParser
@@ -552,7 +552,7 @@ def write_pdb_string(system, conect=True, omit_charges=True, nan_missing_pos=Fal
  return '\n'.join(out)
 
 
-def write_pdb(system, path, conect=True, omit_charges=True, nan_missing_pos=False):
+def write_pdb(system, path, conect=True, omit_charges=True, nan_missing_pos=False, defer_writing=True):
  """
  Writes `system` to `path` as a PDB formatted string.
 
@@ -573,10 +573,14 @@ def write_pdb(system, path, conect=True, omit_charges=True, nan_missing_pos=Fals
  with 'nan' as coordinates; this will cause the output file to be
  *invalid* for most uses.
  for most use.
+ defer_writing: bool
+ Whether to use :class:`~vermouth.file_writer.DeferredFileWriter` for writing data
 
  See Also
  --------
  :func:write_pdb_string
  """
+ if defer_writing:
+ open = deferred_open
  with open(path, 'w') as out:
  out.write(write_pdb_string(system, conect, omit_charges, nan_missing_pos))

vermouth/processors/quote.py

@@ -21,7 +21,6 @@
 import os.path
 import random
 
-from ..file_writer import open
 from .processor import Processor
 from .. import DATA_PATH
 from ..log_helpers import StyleAdapter, get_logger