drrafter_rna Namespace Reference

Functions
def	get_density_per_residue (model, density_map)
def	write_flags_extend_last_round (outfile_basename, output_tag, last_flags, last_round, nstruct, test)
def	write_command_file (command_file_name, flags_file, rosetta_dir, rosetta_ext)
def	setup_next_round (models, last_flags, output_tag, outfile_basename, do_not_recalc_convergence=False, last_round=False, skip_clash_check=False, dens_thr=-1.0, nstruct=0, chunk_res=[], final_round_2=False, map_to_use='', rosetta_dir='', rosetta_ext='', test=False)

Variables
	parser = argparse.ArgumentParser(description="")
	type
	str
	nargs
	required
	True
	help
	int
	default
	action
	False
	float
	args = parser.parse_args()
	models
	nstruct
	last_flags
	output_tag
	outfile_basename
	do_not_recalc_convergence
	last_round
	skip_clash_check
	chunk_res
	dens_thr
	final_round_2
	map_to_use
	rosetta_dir

Function Documentation

get_density_per_residue()

def drrafter_rna.get_density_per_residue	(		model,
			density_map
	)

References float, int, basic::database.open(), and binder.replace().

Referenced by setup_next_round().

setup_next_round()

def drrafter_rna.setup_next_round	(		models,
			last_flags,
			output_tag,
			outfile_basename,
			do_not_recalc_convergence = False,
			last_round = False,
			skip_clash_check = False,
			dens_thr = -1.0,
			nstruct = 0,
			chunk_res = [],
			final_round_2 = False,
			map_to_use = '',
			rosetta_dir = '',
			rosetta_ext = '',
			test = False
	)

References DRRAFTER_util.better_reorder_pdb(), basic::options::OptionKeys::stepwise.enumerate, utility::options::OptionKeys::options.exit, float, get_density_per_residue(), DRRAFTER_util.graph_from_ss(), int, ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, basic::database.open(), DRRAFTER_util.pdbslice(), print(), range, binder.replace(), set(), binder.split(), str, write_command_file(), and write_flags_extend_last_round().

Referenced by auto-DRRAFTER_setup_next_round.figure_out_next_round().

write_command_file()

def drrafter_rna.write_command_file	(		command_file_name,
			flags_file,
			rosetta_dir,
			rosetta_ext
	)

References basic::database.open().

Referenced by setup_next_round().

write_flags_extend_last_round()

def drrafter_rna.write_flags_extend_last_round	(		outfile_basename,
			output_tag,
			last_flags,
			last_round,
			nstruct,
			test
	)

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

Referenced by setup_next_round().

Variable Documentation

action

drrafter_rna.action

args

drrafter_rna.args = parser.parse_args()

chunk_res

drrafter_rna.chunk_res

default

drrafter_rna.default

dens_thr

drrafter_rna.dens_thr

do_not_recalc_convergence

drrafter_rna.do_not_recalc_convergence

False

drrafter_rna.False

final_round_2

drrafter_rna.final_round_2

float

drrafter_rna.float

Referenced by get_density_per_residue(), and setup_next_round().

help

drrafter_rna.help

int

drrafter_rna.int

Referenced by get_density_per_residue(), and setup_next_round().

last_flags

drrafter_rna.last_flags

last_round

drrafter_rna.last_round

map_to_use

drrafter_rna.map_to_use

models

drrafter_rna.models

nargs

drrafter_rna.nargs

nstruct

drrafter_rna.nstruct

outfile_basename

drrafter_rna.outfile_basename

output_tag

drrafter_rna.output_tag

Referenced by MyProtocol.apply(), calculate_distances(), capri_t033_centroid_trim_dock_test(), capri_t033_loop_test(), create_ensemble(), diversify_sam_loop_test(), dna_dr_loop_test(), dna_specificity_test(), dna_stats(), protocols::abinitio::JumpSpecificAbrelax.do_distributed_rerun(), protocols::abinitio::JumpSpecificAbrelax.fold(), main(), minimize_with_constraints(), my_main(), not1_loop_test(), optimize_pose(), run_mc(), sample_rna_dofs_new(), show_residue_residue_clashes(), spec_test(), tf_specificity_test(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), and zf_relax_test().

parser

drrafter_rna.parser = argparse.ArgumentParser(description="")

required

drrafter_rna.required

rosetta_dir

drrafter_rna.rosetta_dir

skip_clash_check

drrafter_rna.skip_clash_check

str

drrafter_rna.str

Referenced by setup_next_round(), and write_flags_extend_last_round().

True

drrafter_rna.True

type

drrafter_rna.type