kic_runner Namespace Reference

Classes
class	ParseIterations

Functions
def	setup_hook ()
def	find_rosetta_installation ()

Variables
dictionary	name_abbreviations
list	algorithm_choices
string	default_name = 'sandbox'
string	default_algorithm = 'refactor'
string	default_structure = 'structures/kic/1srp.pdb'
	parser = argparse.ArgumentParser()
	default
	action
	dest
	choices
	ParseIterations
	nargs
	type
	float
	job = scripting.Job()
	arguments = parser.parse_args()
	pdb
	commit
	shell
	job_id
	background
	overwrite
string	loop_path = os.path.splitext(arguments.structure)[0] + '.loop'
	loop
def	rosetta_path = find_rosetta_installation()
	rosetta_subpath = lambda subpath: os.path.join(rosetta_path, subpath)
	command = rosetta_subpath('source/bin/loopmodel')
	database = rosetta_subpath('database')
string	loop_file = os.path.splitext(arguments.structure)[0] + '.loop'
string	remodel = 'perturb_kic'
string	refine = 'refine_kic'

Function Documentation

find_rosetta_installation()

def kic_runner.find_rosetta_installation

(

)

References basic::database.open().

setup_hook()

def kic_runner.setup_hook

(

)

References basic::database.open(), and rosetta_subpath.

Variable Documentation

action

kic_runner.action

algorithm_choices

list kic_runner.algorithm_choices

Initial value:

=  [
        'refactor',
        'refactor-only',
        'balanced',
        'legacy',
        'loopmodel-standard',
        'loopmodel-small-move',
        'loopmodel-hybrid',
        'loopmodel-refactor',
        'loopmodel-master',
]

arguments

kic_runner.arguments = parser.parse_args()

background

kic_runner.background

choices

kic_runner.choices

command

kic_runner.command = rosetta_subpath('source/bin/loopmodel')

commit

kic_runner.commit

database

kic_runner.database = rosetta_subpath('database')

Referenced by acc_store_hbs(), HBondReporter.apply(), cnl_store_hbs(), cnlres_store_hbs(), don_store_hbs(), utility::sql_database::DatabaseSessionManager.get_session_mysql(), utility::sql_database::DatabaseSessionManager.get_session_postgres(), utility::sql_database::DatabaseSessionManager.get_session_sqlite3(), hbonds_to_ptnres(), is_hbond(), make_fragments(), basic::options.process(), run(), and store_hb_counts().

default

kic_runner.default

default_algorithm

kic_runner.default_algorithm = 'refactor'

default_name

string kic_runner.default_name = 'sandbox'

default_structure

string kic_runner.default_structure = 'structures/kic/1srp.pdb'

dest

kic_runner.dest

float

kic_runner.float

job

kic_runner.job = scripting.Job()

job_id

kic_runner.job_id

Referenced by NativeEnsemble.write_job_to_db(), and NativeEnsemble.write_schema_to_db().

loop

kic_runner.loop

loop_file

string kic_runner.loop_file = os.path.splitext(arguments.structure)[0] + '.loop'

Referenced by dna_dr_loop_test(), protocols::abinitio::JumpSpecificAbrelax.do_distributed_rerun(), loop_rebuilding_test(), main(), my_main(), and protocols::abinitio::JumpSpecificAbrelax.setup_fold().

loop_path

string kic_runner.loop_path = os.path.splitext(arguments.structure)[0] + '.loop'

name_abbreviations

dictionary kic_runner.name_abbreviations

Initial value:

=  {
        'sandbox': 'jobs/sandbox',
        'algorithm': 'jobs/{0.algorithm}',
        'pdb': 'jobs/{0.algorithm}/{0.pdb}',
        'commit': 'jobs/{0.pdb}/{0.algorithm}/{0.commit}',
        'cluster': 'jobs/cluster/{0.algorithm}/{0.pdb}/{0.job_id:03d}',
        'small-move': 'jobs/cluster/{0.algorithm}/{0.step_size:05.2f}/{0.pdb}/{0.job_id:03d}',
        'valgrind': 'jobs/valgrind/{0.algorithm}'
}

nargs

kic_runner.nargs

overwrite

kic_runner.overwrite

ParseIterations

kic_runner.ParseIterations

parser

kic_runner.parser = argparse.ArgumentParser()

pdb

kic_runner.pdb

Referenced by mtransferase.apply(), HolesTrainingDataMover.apply(), RosettaHolesMover.apply(), build_asn_motifs(), calculate_hASA_by_type_and_attractiveE(), calculate_hASA_by_type_and_exposure(), calculate_hASA_by_type_and_nbcount(), calculate_hydrophobic_accessible_surface_area(), calculate_percent_hydrophobic_distribution(), calculate_percent_hydrophobic_stats(), calculate_total_hASA_within_distance_avg_values(), calculate_total_hASA_within_distance_avgresiduevalues_allnbs_conditionalonnumnbs(), calculate_total_hASA_within_distance_exact_hASA_values(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs_exposedornot_conditionalonnumnbs(), calculate_total_hASA_within_distance_miniSASAvalues_allnbs_exposedornot_conditionalonnumnbs(), cs_rosetta_rna_pdb(), dna_coupled_rotamer_design_test(), dna_deriv_test(), dna_deriv_test_old(), dna_design_test(), dna_design_test_old(), dna_dr_loop_test(), dna_io_test(), dna_nbr_radii_test(), InterfaceDDGBindJobInputter.fill_jobs(), find_hppatches_distance(), find_hppatches_nb_graph(), fname2pdbcode(), protocols::abinitio::JumpSpecificAbrelax.fold(), get_ddG(), get_sc(), loop_modeling_test(), loop_rebuilding_test(), main(), my_main(), output_packstat(), output_packstat_pdb(), Prepare(), basic::options.process(), process_file_list(), read_ddg_file(), read_fragdata(), read_frags(), repack_minimize_test(), SamplingManager.SamplingManager(), score_pdb(), set_fullatom_flag_test(), PDB_IOBenchmark.setUp(), shear_moves_test(), simple_dna_test(), simple_loop_modeling_test(), simple_opte_test(), simple_rotamer_recovery(), small_moves_test(), test(), test_ddg(), test_gradient(), test_vs_dots(), and tf_specificity_test().

refine

string kic_runner.refine = 'refine_kic'

Referenced by doit_refine(), LoopBuild_main(), main(), and abbinding.set_refine().

remodel

string kic_runner.remodel = 'perturb_kic'

Referenced by graphics_main(), LoopBuild_main(), and main().

rosetta_path

def kic_runner.rosetta_path = find_rosetta_installation()

rosetta_subpath

kic_runner.rosetta_subpath = lambda subpath: os.path.join(rosetta_path, subpath)

Referenced by setup_hook().

shell

kic_runner.shell

Referenced by concave_shell(), and main().

type

kic_runner.type