mutant_modeler Namespace Reference

Classes
class	MutantModeler

Functions
def	figure_out_WT_seq (wt_struct)
def	get_ss (seq, T=37)
def	find_pairs (secstruct)
def	list_NC_BPs (bps, seq)
def	list_mutated_BPs (bps, seq)

Variables
list	protein_residues
list	protein_residues_1letter
list	RNA_residues = [' A', ' U', ' C', ' G']
list	RNA_residues_1letter = [ 'a', 'u', 'c', 'g' ]
dictionary	pdb_to_one_letter

Function Documentation

figure_out_WT_seq()

def mutant_modeler.figure_out_WT_seq

(

wt_struct

)

References ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, DRRAFTER_util.make_tag_with_dashes(), max(), min(), basic::database.open(), DRRAFTER_util.read_pdb(), set(), str(), and test.T040_Types.values.

Referenced by mutant_modeler.MutantModeler.__init__().

find_pairs()

def mutant_modeler.find_pairs

(

secstruct

)

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

Referenced by mutant_modeler.MutantModeler.__init__(), and mutant_modeler.MutantModeler.set_wt_RNA_secstruct().

get_ss()

def mutant_modeler.get_ss	(		seq,
			T = 37
	)

References basic::database.open().

list_mutated_BPs()

def mutant_modeler.list_mutated_BPs	(		bps,
			seq
	)

References ObjexxFCL.len(), and range.

list_NC_BPs()

def mutant_modeler.list_NC_BPs	(		bps,
			seq
	)

References ObjexxFCL.len(), and range.

Referenced by mutant_modeler.MutantModeler.get_med_res_command_lines().

Variable Documentation

pdb_to_one_letter

dictionary mutant_modeler.pdb_to_one_letter

Initial value:

=  { '  A': 'a',
      '  U': 'u',
      '  C': 'c',
      '  G': 'g',
      'ALA': 'A',
      'CYS': 'C',
      'ASP': 'D',
      'GLU': 'E',
      'PHE': 'F',
      'GLY': 'G',
      'HIS': 'H',
      'ILE': 'I',
      'LYS': 'K',
      'LEU': 'L',
      'MET': 'M',
      'ASN': 'N',
      'PRO': 'P',
      'GLN': 'Q',
      'ARG': 'R',
      'SER': 'S',
      'THR': 'T',
      'VAL': 'V',
      'TRP': 'W',
      'TYR': 'Y' }

protein_residues

list mutant_modeler.protein_residues

Initial value:

=  ['ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY', 'HIS', 'ILE', 'LYS', 'LEU', 
      'MET', 'ASN', 'PRO', 'GLN', 'ARG', 'SER', 'THR', 'VAL', 'TRP', 'TYR' ]

Referenced by find_neighbors_directional(), get_interface_residues(), CrystDesign.get_interface_residues(), get_neighbor_residues(), CrystDesign.get_neighbor_residues(), and rna_protein_prepack_test().

protein_residues_1letter

list mutant_modeler.protein_residues_1letter

Initial value:

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

RNA_residues

list mutant_modeler.RNA_residues = [' A', ' U', ' C', ' G']

RNA_residues_1letter

list mutant_modeler.RNA_residues_1letter = [ 'a', 'u', 'c', 'g' ]