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Functions | Variables
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)
def DRRAFTER.find_pairs (   secstruct,
  helix_chars = ['(',' 
)
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 = [] 
)
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 
)
def DRRAFTER.get_sequences (   pdbname,
  removechain = 0 
)
def DRRAFTER.make_tag (   int_vector)

Referenced by prepare_threaded_model().

def DRRAFTER.make_tag_with_dashes (   int_vector,
  char_vector = 0 
)
def DRRAFTER.matches (   res,
  chain,
  match_res,
  match_chain 
)
def DRRAFTER.parse_fasta (   fasta)
def DRRAFTER.parse_secstruct (   secstruct_file)

References basic::database.open().

Referenced by setup_job().

def DRRAFTER.parse_tag (   tag,
  alpha_sort = False 
)
def DRRAFTER.pdbslice (   pdbfile,
  subset_or_excise,
  segment_residues,
  prefix 
)
def DRRAFTER.read_pdb (   filename)
def DRRAFTER.setup_job (   args)
def DRRAFTER.write_flags_file (   args,
  helix_chunks,
  use_init_structs,
  input_structs_for_dash_s 
)

Variable Documentation

string DRRAFTER.action = 'store_true'

Referenced by add_rosetta_options_15().

tuple DRRAFTER.args = parser.parse_args()
string DRRAFTER.default = ""
string DRRAFTER.help = 'fasta file for the full structure'
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:
1 = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D',
2  'CYS': 'C', 'GLU': 'E', 'GLN': 'Q', 'GLY': 'G',
3  'HIS': 'H', 'ILE': 'I', 'LEU': 'L', 'LYS': 'K',
4  'MET': 'M', 'PHE': 'F', 'PRO': 'P', 'SER': 'S',
5  'THR': 'T', 'TRP': 'W', 'TYR': 'Y', 'VAL': 'V',
6  ' rA': 'a', ' rC': 'c', ' rG': 'g', ' rU': 'u',
7  ' A': 'a', ' C': 'c', ' G': 'g', ' U': 'u',
8  ' MG': 'Z[MG]',' IC':'c[ICY]',' IG':'g[IGU]',
9  'ROS': 'Z[ROS]','HOH':'w[HOH]', 'H2U': 'X[H2U]',
10  'PSU': 'X[PSU]', '5MU': 'X[5MU]', 'FME': 'X[FME]',
11  'U33': 'X[U33]', ' I': 'X[INO]', 'BRU': 'X[5BU]',
12  }
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:
1 = ['A', 'R', 'N', 'D', 'C',
2  'E', 'Q', 'G', 'H', 'I', 'L', 'K', 'M',
3  '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().