DRRAFTER_util Namespace Reference

Functions
def	get_helix_stems (secstruct)
def	graph_from_ss (ss_init, add_closing_pair=True)
def	find_pairs (secstruct, helix_chars=[['(',')'],['[',']'],['{','}'], ['<','>']])
def	residue_graph_from_ss (ss)
def	pdbslice (pdbfile, subset_or_excise, segment_residues, prefix)
def	matches (res, chain, match_res, match_chain)
def	make_tag (int_vector)
def	make_tag_with_dashes (int_vector, char_vector=0)
def	parse_tag (tag, alpha_sort=False)
def	get_sequences (pdbname, removechain=0)
def	read_pdb (filename)
def	read_pdb_with_segid (filename)
def	better_reorder_pdb (pdb)
def	rna_helix (seq, resnum, output_pdb, rosetta_directory, rosetta_extension, test=False)
def	get_resnum_chain (input_string, resnums, chains, segids)
def	renumber_pdb (pdbnames, new_numbers, chains=[], segids=[], retain_atom_num=0)
def	get_ints (int_string, value)
def	easy_cat (outfile)
def	cat_outfiles (outfiles, output_file)
def	extract_lowscore_decoys (silent_file, NSTRUCT, rosetta_directory, rosetta_extension, test=False)

Variables
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

Function Documentation

better_reorder_pdb()

def DRRAFTER_util.better_reorder_pdb

(

pdb

)

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

Referenced by auto-DRRAFTER_setup.auto_setup_helices(), and drrafter_rna.setup_next_round().

cat_outfiles()

def DRRAFTER_util.cat_outfiles	(		outfiles,
			output_file
	)

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

Referenced by easy_cat().

easy_cat()

def DRRAFTER_util.easy_cat

(

outfile

)

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

Referenced by auto-DRRAFTER_setup_next_round.get_results().

extract_lowscore_decoys()

def DRRAFTER_util.extract_lowscore_decoys	(		silent_file,
			NSTRUCT,
			rosetta_directory,
			rosetta_extension,
			test = False
	)

References ObjexxFCL.abs(), run_backbone.float, ObjexxFCL.len(), basic::database.open(), print(), binder.replace(), and binder.split().

Referenced by auto-DRRAFTER_setup.auto_setup_helices().

find_pairs()

def DRRAFTER_util.find_pairs	(		secstruct,
			helix_chars = [['(',')'],['[',']'],['{','}'], ['<','>']]
	)

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

Referenced by residue_graph_from_ss().

get_helix_stems()

def DRRAFTER_util.get_helix_stems

(

secstruct

)

References basic::options::OptionKeys::stepwise.enumerate.

Referenced by graph_from_ss().

get_ints()

def DRRAFTER_util.get_ints	(		int_string,
			value
	)

References enumerate_junctions.int, ObjexxFCL.len(), and range.

Referenced by get_resnum_chain().

get_resnum_chain()

def DRRAFTER_util.get_resnum_chain	(		input_string,
			resnums,
			chains,
			segids
	)

References detail.find(), get_ints(), enumerate_junctions.int, ObjexxFCL.len(), and range.

Referenced by finalize_models.finalize(), and rna_helix().

get_sequences()

def DRRAFTER_util.get_sequences	(		pdbname,
			removechain = 0
	)

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

Referenced by DRRAFTER.estimate_error(), and DRRAFTER.setup_job().

graph_from_ss()

def DRRAFTER_util.graph_from_ss	(		ss_init,
			add_closing_pair = True
	)

References basic::options::OptionKeys::stepwise.enumerate, get_helix_stems(), ObjexxFCL.len(), range, set(), binder.split(), utility.startswith(), and str().

Referenced by auto-DRRAFTER_setup.auto_setup_helices(), and drrafter_rna.setup_next_round().

make_tag()

def DRRAFTER_util.make_tag

(

int_vector

)

Referenced by prepare_threaded_model().

make_tag_with_dashes()

def DRRAFTER_util.make_tag_with_dashes	(		int_vector,
			char_vector = 0
	)

References ObjexxFCL.len(), and range.

Referenced by auto-DRRAFTER_setup.auto_setup_helices(), mutant_modeler.figure_out_WT_seq(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), my_main(), prepare_threaded_model(), and DRRAFTER.setup_job().

matches()

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

References ObjexxFCL.len(), and range.

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

parse_tag()

def DRRAFTER_util.parse_tag	(		tag,
			alpha_sort = False
	)

References enumerate_junctions.int, join(), ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, range, str(), and basic::options::OptionKeys::in::file.zip.

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

pdbslice()

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

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

Referenced by DRRAFTER.setup_job(), and drrafter_rna.setup_next_round().

read_pdb()

def DRRAFTER_util.read_pdb

(

filename

)

References run_backbone.float, enumerate_junctions.int, ObjexxFCL.len(), and basic::database.open().

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

read_pdb_with_segid()

def DRRAFTER_util.read_pdb_with_segid

(

filename

)

References run_backbone.float, enumerate_junctions.int, ObjexxFCL.len(), and basic::database.open().

Referenced by better_reorder_pdb().

renumber_pdb()

def DRRAFTER_util.renumber_pdb	(		pdbnames,
			new_numbers,
			chains = [],
			segids = [],
			retain_atom_num = 0
	)

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

Referenced by finalize_models.finalize(), and rna_helix().

residue_graph_from_ss()

def DRRAFTER_util.residue_graph_from_ss

(

ss

)

References find_pairs(), ObjexxFCL.len(), and range.

Referenced by auto-DRRAFTER_setup.auto_setup_helices().

rna_helix()

def DRRAFTER_util.rna_helix	(		seq,
			resnum,
			output_pdb,
			rosetta_directory,
			rosetta_extension,
			test = False
	)

References utility::options::OptionKeys::options.exit, get_resnum_chain(), ObjexxFCL.len(), print(), and renumber_pdb().

Referenced by auto-DRRAFTER_setup.auto_setup_helices().

Variable Documentation

hetatm_map

dictionary DRRAFTER_util.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' }

longer_names

dictionary DRRAFTER_util.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]',
              }