DRRAFTER Namespace Reference

Functions
def	pdbslice
def	matches
def	make_tag
def	make_tag_with_dashes
def	parse_tag
def	get_sequences
def	read_pdb
def	get_coord_csts
def	find_pairs
def	find_pairs_dict
def	parse_fasta
def	parse_secstruct
def	get_near_residues
def	setup_job
def	get_n_cycles
def	write_flags_file
def	estimate_error

Variables
list	protein_one_letter
dictionary	hetatm_map = { '5BU':' U', ' MG':' MG', 'OMC':' C', '5MC':' C', 'CCC':' C', ' DC':' C', 'CBR':' C', 'CBV':' C', 'CB2':' C', '2MG':' G', 'H2U':'H2U', 'PSU':'PSU', '5MU':' U', 'OMG':' G', '7MG':' G', '1MG':' G', 'GTP':' G', 'AMP':' A', ' YG':' G', '1MA':' A', 'M2G':' G', 'YYG':' G', ' DG':' G', 'G46':' G', ' IC':' IC',' IG':' IG', 'ZMP':'ZMP' }
dictionary	longer_names
tuple	parser = argparse.ArgumentParser( description="DRRAFTER: De novo RNP modeling in Real-space through Assembly of Fragments Together with Experimental density in Rosetta" )
string	help = 'fasta file for the full structure'
string	type = ""
string	default = ""
string	nargs = '+'
string	action = 'store_true'
tuple	args = parser.parse_args()

Function Documentation

def DRRAFTER.estimate_error

(

args

)

References utility::options::OptionKeys::options.exit, get_sequences(), and ObjexxFCL.len().

def DRRAFTER.find_pairs	(		secstruct,
			helix_chars = ['(','
	)

References ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, and basic::options::OptionKeys::relax::range.range.

Referenced by find_pairs_dict().

def DRRAFTER.find_pairs_dict	(		secstruct,
			helix_chars = ['(','
	)

References find_pairs().

Referenced by setup_job().

def DRRAFTER.get_coord_csts	(		ref_pdb,
			dist,
			exclude_resi = []
	)

References utility::options::OptionKeys::options.exit, basic::database.open(), basic::options::OptionKeys::relax::range.range, and binder.replace().

Referenced by setup_job().

def DRRAFTER.get_n_cycles

(

remodel_residues

)

References ObjexxFCL.len(), min(), and parse_tag().

Referenced by write_flags_file().

def DRRAFTER.get_near_residues	(		struct,
			resnums,
			chains,
			dist_cutoff
	)

References ObjexxFCL.len(), basic::options::OptionKeys::relax::range.range, and read_pdb().

Referenced by setup_job().

def DRRAFTER.get_sequences	(		pdbname,
			removechain = 0
	)

References ObjexxFCL.len(), basic::database.open(), and binder.replace().

Referenced by estimate_error(), and setup_job().

def DRRAFTER.make_tag

(

int_vector

)

Referenced by prepare_threaded_model().

def DRRAFTER.make_tag_with_dashes	(		int_vector,
			char_vector = 0
	)

References ObjexxFCL.len(), and basic::options::OptionKeys::relax::range.range.

Referenced by mutant_modeler.figure_out_WT_seq(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), prepare_threaded_model(), and setup_job().

def DRRAFTER.matches	(		res,
			chain,
			match_res,
			match_chain
	)

References ObjexxFCL.len(), and basic::options::OptionKeys::relax::range.range.

Referenced by MPDomainAssembly.apply(), and pdbslice().

def DRRAFTER.parse_fasta

(

fasta

)

References utility::options::OptionKeys::options.exit, ObjexxFCL.len(), basic::database.open(), and parse_tag().

Referenced by setup_job().

def DRRAFTER.parse_secstruct

(

secstruct_file

)

References basic::database.open().

Referenced by setup_job().

def DRRAFTER.parse_tag	(		tag,
			alpha_sort = False
	)

References ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, and basic::options::OptionKeys::in::file.zip.

Referenced by get_n_cycles(), parse_fasta(), pdbslice(), and setup_job().

def DRRAFTER.pdbslice	(		pdbfile,
			subset_or_excise,
			segment_residues,
			prefix
	)

References utility::options::OptionKeys::options.exit, ObjexxFCL.len(), matches(), basic::database.open(), and parse_tag().

Referenced by calc_rms_test(), setup_job(), and write_base_pair_step_to_silent_struct().

def DRRAFTER.read_pdb

(

filename

)

References ObjexxFCL.len(), and basic::database.open().

Referenced by combine_pdbs.combine_pdbs(), mutant_modeler.figure_out_WT_seq(), and get_near_residues().

def DRRAFTER.setup_job

(

args

)

References basic::options::OptionKeys::stepwise.enumerate, utility::options::OptionKeys::options.exit, find_pairs_dict(), get_coord_csts(), get_near_residues(), get_sequences(), ObjexxFCL.len(), make_tag_with_dashes(), basic::database.open(), parse_fasta(), parse_secstruct(), parse_tag(), pdbslice(), basic::options::OptionKeys::relax::range.range, and write_flags_file().

def DRRAFTER.write_flags_file	(		args,
			helix_chunks,
			use_init_structs,
			input_structs_for_dash_s
	)

References get_n_cycles(), ObjexxFCL.len(), and basic::database.open().

Referenced by setup_job().

Variable Documentation

string DRRAFTER.action = 'store_true'

Referenced by add_rosetta_options_15().

tuple DRRAFTER.args = parser.parse_args()

Referenced by utility::graph::LowMemGraph< _Node, _Edge >.add_edge(), binder.bind_constructor(), binder.bind_function(), binder.bind_member_functions_for_call_back(), fmt::internal::FormatterBase.FormatterBase(), fmt::BasicFormatter< CharType, ArgFormatter >.get_arg(), utility::tag.handle_xml_error(), utility::tag.handle_xml_warning(), utility::graph::LowMemGraph< _Node, _Edge >.internal_create_new_edge(), numeric::expression_parser::ExpressionCreator.visit(), and fmt::BasicWriter< Char >.write().

string DRRAFTER.default = ""

string DRRAFTER.help = 'fasta file for the full structure'

Referenced by utility::options::OptionCollection.add_built_in_options(), and utility::options::OptionCollection.load().

dictionary DRRAFTER.hetatm_map = { '5BU':' U', ' MG':' MG', 'OMC':' C', '5MC':' C', 'CCC':' C', ' DC':' C', 'CBR':' C', 'CBV':' C', 'CB2':' C', '2MG':' G', 'H2U':'H2U', 'PSU':'PSU', '5MU':' U', 'OMG':' G', '7MG':' G', '1MG':' G', 'GTP':' G', 'AMP':' A', ' YG':' G', '1MA':' A', 'M2G':' G', 'YYG':' G', ' DG':' G', 'G46':' G', ' IC':' IC',' IG':' IG', 'ZMP':'ZMP' }

dictionary DRRAFTER.longer_names

Initial value:

= {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D',
              'CYS': 'C', 'GLU': 'E', 'GLN': 'Q', 'GLY': 'G',
              'HIS': 'H', 'ILE': 'I', 'LEU': 'L', 'LYS': 'K',
              'MET': 'M', 'PHE': 'F', 'PRO': 'P', 'SER': 'S',
              'THR': 'T', 'TRP': 'W', 'TYR': 'Y', 'VAL': 'V',
              ' rA': 'a', ' rC': 'c', ' rG': 'g', ' rU': 'u',
              '  A': 'a', '  C': 'c', '  G': 'g', '  U': 'u',
              ' MG': 'Z[MG]',' IC':'c[ICY]',' IG':'g[IGU]',
              'ROS': 'Z[ROS]','HOH':'w[HOH]', 'H2U': 'X[H2U]',
              'PSU': 'X[PSU]', '5MU': 'X[5MU]', 'FME': 'X[FME]',
        'U33': 'X[U33]', '  I': 'X[INO]', 'BRU': 'X[5BU]',
              }

string DRRAFTER.nargs = '+'

tuple DRRAFTER.parser = argparse.ArgumentParser( description="DRRAFTER: De novo RNP modeling in Real-space through Assembly of Fragments Together with Experimental density in Rosetta" )

list DRRAFTER.protein_one_letter

Initial value:

= ['A', 'R', 'N', 'D', 'C', 
  'E', 'Q', 'G', 'H', 'I', 'L', 'K', 'M', 
  'F', 'P','S', 'T', 'W', 'Y', 'V']

string DRRAFTER.type = ""

Referenced by pyrosetta.distributed.utility.pickle.__cereal_setstate__(), basic::datacache::DataMap.add(), basic::datacache::ConstDataMap.add(), binder.add_relevant_include_for_decl(), add_rosetta_options_9(), test.T850_SubClassing.My_New_Mover.apply(), utility::json_spirit::Value_impl< Config >.check_type(), pyrosetta.defineEnergyMethodCreator(), utility.from_string(), basic::datacache::HierarchicalDataMap.get(), GlycanClashCheckMover.get_name(), DockGlycansProtocol.get_name(), basic::datacache::HierarchicalDataMap.get_or_null(), utility::json_spirit::Value_impl< Config >.get_real(), basic::datacache.get_set_from_datamap(), options_class.Option.getDoxygenRow(), options_class.Option.getMarkdownRow(), options_class.Option.getOptionCC(), options_class.Option.getWikiTableRow(), harvest_scores(), pyrosetta.distributed.viewer.core.init(), GlycanClashCheckMover.init(), DockGlycansProtocol.init(), utility::json_spirit::Value_impl< Config >.is_null(), LigandRepackMinimizeProtocol.LigandRepackMinimizeProtocol(), main(), fmt::internal.make_type(), fmt::internal::MakeArg< Formatter >.MakeArg(), name2elt(), pyrosetta.bindings.energies.nonzero_weights_dtype(), utility::json_spirit::Value_impl< Config >.operator==(), basic::datacache::DataMap.operator[](), basic::datacache::ConstDataMap.operator[](), fmt::ArgList.operator[](), options_class.Option_Group(), utility::xsd_util.output_all_tag_options(), numeric.read_tensor_from_file(), binder::Context.request_bindings(), ScoreFragmentSetMover.run(), FragmentAssemblyMover.run(), basic::datacache::HierarchicalDataMap.set(), binder.simplify_std_class_name(), utility.string_split(), rosetta_binders.stringstream_add_on_binder(), erraser_util.subprocess_call(), erraser_util.subprocess_out(), pyrosetta.distributed.packed_pose.core.to_dict(), pyrosetta.distributed.packed_pose.core.to_packed(), pyrosetta.distributed.packed_pose.core.to_pose(), fmt::ArgList.type(), options_class.wrapCStrig(), fmt::BasicWriter< Char >.write_double(), and numeric.write_tensor_to_file().