repic.commands.run_ilp

Apply integer linear programming (ILP) optimizer (either Gurobi or SciPy supported) to identify best subset of k-sized cliques (consensus particles) in a globally optimal manner

Attributes

use_gurobi	Gurobi integer linear programming optimizer flag
use_gurobi	Gurobi integer linear programming optimizer flag
name	module name (used by argparse subparser)
parser	argparse parse_args() object

Functions

add_arguments(parser)	Adds argparse command line arguments for run_ilp.py
plot_particle_weights(args, weights, num_mrc, out_dir)	Creates Matplotlib line plot of the expected number of particles per micrograph vs. clique weights
main(args)	Applies integer linear programming optimizer to output of get_cliques.py (clique weights, constraint matrix, linear constraints, etc.) and identifies the globally optimal subset of cliques

Module Contents

repic.commands.run_ilp.use_gurobi = False

Gurobi integer linear programming optimizer flag

Type:

bool

repic.commands.run_ilp.use_gurobi = True

Gurobi integer linear programming optimizer flag

Type:

bool

repic.commands.run_ilp.name = 'run_ilp'

module name (used by argparse subparser)

Type:

str

repic.commands.run_ilp.add_arguments(parser)

Adds argparse command line arguments for run_ilp.py

Parameters:

parser (object) – argparse parse_args() object

Returns:

None

repic.commands.run_ilp.plot_particle_weights(args, weights, num_mrc, out_dir)

Creates Matplotlib line plot of the expected number of particles per micrograph vs. clique weights

Parameters:

• args (obj) – argparse command line argument object

• weights (list) – list of consensus particle weights

• num_mrc (int) – number of micrographs analyzed

• out_dir (str) – dirpath to output directory

Returns:

None

repic.commands.run_ilp.main(args)

Applies integer linear programming optimizer to output of get_cliques.py (clique weights, constraint matrix, linear constraints, etc.) and identifies the globally optimal subset of cliques

Parameters:

args (obj) – argparse command line argument object

repic.commands.run_ilp.parser

argparse parse_args() object

Type:

obj