Setting nproc in the class attribute now

bin/martinize2

@@ -44,6 +44,8 @@ from vermouth.map_input import (
  combine_mappings
 )
 
+from vermouth.processors.processor import Processor
+
 # TODO Since vermouth's __init__.py does some logging (KDTree), this may or may
 # not work as intended. Investigation required.
 
@@ -95,7 +97,7 @@ def read_system(path, ignore_resnames=(), ignh=None, modelidx=None):
 
 def pdb_to_universal(system, delete_unknown=False, force_field=None,
  bonds_from_name=True, bonds_from_dist=True, bonds_fudge=1,
- write_graph=None, write_repair=None, write_canon=None, nproc=1):
+ write_graph=None, write_repair=None, write_canon=None):
  """
  Convert a system read from the PDB to a clean canonical atomistic system.
  """
@@ -106,7 +108,7 @@ def pdb_to_universal(system, delete_unknown=False, force_field=None,
  LOGGER.info('Guessing the bonds.', type='step')
  vermouth.MakeBonds(allow_name=bonds_from_name,
  allow_dist=bonds_from_dist,
- fudge=bonds_fudge, nproc=nproc).run_system(canonicalized)
+ 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)
@@ -402,6 +404,9 @@ def entry():
  'multiple times.', default=0)
 
  args = parser.parse_args()
+
+ Processor.nproc = args.nproc
+
  if args.elastic and args.govs_includes:
  parser.error('A rubber band elastic network and GoMartini are not '
  'compatible. The -elastic and -govs-include flags cannot '
@@ -496,8 +501,7 @@ def entry():
  bonds_fudge=args.bonds_fudge,
  write_graph=args.write_graph,
  write_repair=args.write_repair,
- write_canon=args.write_canon,
- nproc=args.nproc
+ write_canon=args.write_canon
  )
 
  LOGGER.info('Read input.', type='step')

vermouth/processors/make_bonds.py

@@ -277,11 +277,10 @@ def make_bonds(molecule, allow_name=True, allow_dist=True, fudge=1.0):
 
 
 class MakeBonds(Processor):
- def __init__(self, allow_name=True, allow_dist=True, fudge=1, nproc=1):
+ def __init__(self, allow_name=True, allow_dist=True, fudge=1):
  self.allow_name = allow_name
  self.allow_dist = allow_dist
  self.fudge = fudge
- self.nproc = nproc
 
  def run_system(self, system):
  if not system.molecules:
@@ -293,7 +292,7 @@ def run_system(self, system):
  for mol_idx, molecule in enumerate(system.molecules):
  nx.set_node_attributes(molecule, mol_idx, 'mol_idx')
  # If using multiple processors, run the system normally
- if hasattr(self, 'nproc') and self.nproc > 1:
+ if self.nproc > 1:
  super().run_system(system)
  # If not using multiple processors, compose molecules into one
  else: