toolbox.mutants Namespace Reference

Functions
def	mutate_residue
def	pose_from_sequence
def	random_sequence
def	compare_mutants__
def	compare_sequences
def	compare_hbonds

Variables
string	protein_letters = 'ACDEFGHIKLMNPQRSTVWY'
list	nucleic_letters = ['A[ADE]','G[GUA]','C[CYT]','T[THY]']

Function Documentation

def toolbox.mutants.compare_hbonds	(		pose1,
			pose2,
			Ethresh = .5,
			display = False
	)

Definition at line 174 of file mutants.py.

References ObjexxFCL.abs(), toolbox.get_hbonds(), ObjexxFCL.len(), ObjexxFCL.ljust(), name, src.PyMolLink.PyMOL_Mover, and numeric::crick_equations.xyz().

def toolbox.mutants.compare_mutants__	(		pose1,
			pose2
	)

Definition at line 158 of file mutants.py.

def toolbox.mutants.compare_sequences	(		seq1,
			seq2
	)

Definition at line 166 of file mutants.py.

References ObjexxFCL.len().

def toolbox.mutants.mutate_residue	(		pose,
			mutant_position,
			mutant_aa,
			pack_radius = 0.0,
			pack_scorefxn = ''
	)

Replaces the residue at  <mutant_position>  in  <pose>  with  <mutant_aa>
    and repack any residues within  <pack_radius>  Angstroms of the mutating
    residue's center (nbr_atom) using  <pack_scorefxn>
note: <mutant_aa>  is the single letter name for the desired ResidueType

example:
    mutate_residue(pose,30,A)
See also:
    Pose
    PackRotamersMover
    MutateResidue
    pose_from_sequence

Definition at line 34 of file mutants.py.

References src.standard_packer_task().

def toolbox.mutants.pose_from_sequence	(		seq,
			res_type = 'fa_standard',
			name = '',
			chain_id = 'A'
	)

Returns a pose generated from amino acid single letters in  <seq>  using
the  <res_type>  ResidueType, the new pose's PDBInfo is named  <name>
and all residues have chain ID  <chain_id>

example:
    pose=pose_from_sequence('LIGAND')
See also:
    Pose
    make_pose_from_sequence
    pose_from_pdb
    pose_from_rcsb

Definition at line 108 of file mutants.py.

References name.

def toolbox.mutants.random_sequence	(		length = 1,
			letters = protein_letters
	)

Definition at line 152 of file mutants.py.

References extract_scores_and_constraints.join, and ObjexxFCL.len().

Variable Documentation

list toolbox.mutants.nucleic_letters = ['A[ADE]','G[GUA]','C[CYT]','T[THY]']

Definition at line 149 of file mutants.py.

string toolbox.mutants.protein_letters = 'ACDEFGHIKLMNPQRSTVWY'

Definition at line 148 of file mutants.py.