Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Makebonds molecule #234

Closed
wants to merge 11 commits into from
Closed

Makebonds molecule #234

Changes from 1 commit
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
98033ea
Added multiprocessing to run_system method of Processor class
Mar 4, 2020
eeed05f
Fixed checking for the nproc attribute
Mar 4, 2020
bb84d56
Setting nproc in the class attribute now
Mar 4, 2020
08c6a7e
Added a test for multiprocessing
Mar 4, 2020
bdd89da
Changed make_bonds to work on one molecule instead of a system.
Mar 4, 2020
c560cfa
Moved around code in the run_system method of MakeBonds to use the ru…
Mar 4, 2020
1cd34a0
Moved altered make_bonds function to run_molecule method of MakeBonds
Mar 4, 2020
89df257
Added CLI flag "nproc" to optionally enable multiprocessing
Mar 4, 2020
d3d0783
Fixed some mistakes
Mar 4, 2020
9b16c42
Fixed checking for `nproc` here as well
Mar 4, 2020
848ce74
Setting nproc in the class attribute now
Mar 4, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Added CLI flag "nproc" to optionally enable multiprocessing
  • Loading branch information
Matthijs Tadema authored and Matthijs Tadema committed Mar 4, 2020
commit 89df2577701c8f98bf7e32ca59f5d49ea2bc034d
14 changes: 11 additions & 3 deletions bin/martinize2
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ 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):
write_graph=None, write_repair=None, write_canon=None, nproc=1):
"""
Convert a system read from the PDB to a clean canonical atomistic system.
"""
Expand All @@ -106,7 +106,7 @@ 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).run_system(canonicalized)
fudge=bonds_fudge, nproc=nproc).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)
Expand All @@ -121,7 +121,7 @@ def pdb_to_universal(system, delete_unknown=False, force_field=None,
vermouth.pdb.write_pdb(canonicalized, str(write_canon),
omit_charges=True, nan_missing_pos=True)
vermouth.AttachMass(attribute='mass').run_system(canonicalized)
vermouth.SortMoleculeAtoms().run_system(canonicalized) # was system
vermouth.SortMoleculeAtoms().run_system(canonicalized)
return canonicalized


Expand Down Expand Up @@ -376,6 +376,13 @@ def entry():
type=_cys_argument,
default='none', help='Cystein bonds')

exp_group = parser.add_argument_group('Experimental options')
exp_group.add_argument('-nproc', dest='nproc', type=int, default=1,
help='Optionally use multiprocessing to speed'
'up bond creation. Only use when you\'re'
'very sure that your input file is correct.'
'Very likely to break something.')

debug_group = parser.add_argument_group('Debugging options')
debug_group.add_argument('-write-graph', type=Path, default=None,
help='Write the graph as PDB after the MakeBonds step.')
Expand Down Expand Up @@ -490,6 +497,7 @@ def entry():
write_graph=args.write_graph,
write_repair=args.write_repair,
write_canon=args.write_canon,
nproc=args.nproc
)

LOGGER.info('Read input.', type='step')
Expand Down