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Functions | Variables
DRRAFTER_util Namespace Reference

Functions

def get_helix_stems
 
def graph_from_ss
 
def find_pairs
 
def residue_graph_from_ss
 
def pdbslice
 
def matches
 
def make_tag
 
def make_tag_with_dashes
 
def parse_tag
 
def get_sequences
 
def read_pdb
 
def read_pdb_with_segid
 
def better_reorder_pdb
 
def rna_helix
 
def get_resnum_chain
 
def renumber_pdb
 
def get_ints
 
def easy_cat
 
def cat_outfiles
 
def extract_lowscore_decoys
 

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

def DRRAFTER_util.better_reorder_pdb (   pdb)
def DRRAFTER_util.cat_outfiles (   outfiles,
  output_file 
)

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

Referenced by easy_cat().

def DRRAFTER_util.easy_cat (   outfile)
def DRRAFTER_util.extract_lowscore_decoys (   silent_file,
  NSTRUCT,
  rosetta_directory,
  rosetta_extension,
  test = False 
)
def DRRAFTER_util.find_pairs (   secstruct,
  helix_chars = [['(',' 
)
def DRRAFTER_util.get_helix_stems (   secstruct)
def DRRAFTER_util.get_ints (   int_string,
  value 
)
def DRRAFTER_util.get_resnum_chain (   input_string,
  resnums,
  chains,
  segids 
)
def DRRAFTER_util.get_sequences (   pdbname,
  removechain = 0 
)
def DRRAFTER_util.graph_from_ss (   ss_init,
  add_closing_pair = True 
)
def DRRAFTER_util.make_tag (   int_vector)

Referenced by prepare_threaded_model().

def DRRAFTER_util.make_tag_with_dashes (   int_vector,
  char_vector = 0 
)
def DRRAFTER_util.matches (   res,
  chain,
  match_res,
  match_chain 
)
def DRRAFTER_util.parse_tag (   tag,
  alpha_sort = False 
)
def DRRAFTER_util.pdbslice (   pdbfile,
  subset_or_excise,
  segment_residues,
  prefix 
)
def DRRAFTER_util.read_pdb (   filename)
def DRRAFTER_util.read_pdb_with_segid (   filename)
def DRRAFTER_util.renumber_pdb (   pdbnames,
  new_numbers,
  chains = [],
  segids = [],
  retain_atom_num = 0 
)
def DRRAFTER_util.residue_graph_from_ss (   ss)
def DRRAFTER_util.rna_helix (   seq,
  resnum,
  output_pdb,
  rosetta_directory,
  rosetta_extension,
  test = False 
)

Variable Documentation

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' }
dictionary DRRAFTER_util.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  }