toolbox Namespace Reference

Namespaces
	adjust_library_path
	cleaning
	extract_coords_pose
	generate_resfile
	load_ligand
	make_rna_rosetta_ready
	mutants
	rcsb
	structural_alignment

Functions
def	mutate_residue
def	restrict_non_nbrs_from_repacking
def	generate_resfile_from_pose
def	generate_resfile_from_pdb
def	cleanATOM
def	cleanCRYS
def	load_from_rcsb
def	pose_from_rcsb
def	get_secstruct
def	get_hbonds

Function Documentation

def toolbox.cleanATOM	(		pdb_file,
			edit = -4
	)

Writes a PDB file from <pdb_file> with all lines not beginning with
ATOM removed tp <pdb_file>.clean.pdb.

Note: the second argument, <edit>, is for PDB files not ending in .pdb.

Example:
    cleanATOM("1YY9.pdb")
See also:
    Pose
    Pose.dump_pdb
    pose_from_file
    pose_from_rcsb
    cleanCRYS

References basic::database.open().

Referenced by toolbox.rcsb.pose_from_rcsb(), and pose_from_rcsb().

def toolbox.cleanCRYS	(		pdb_file,
			olig = 2
	)

Removes redundant crystal contacts and isolates a monomer by writing a PDB
file for a monomer of <pdb_file>, if it is an <olig>-mer, to
<pdb_file>.mono.

Note: This is by simple sequence comparison.

Example:
    cleanCRYS("1YY8.pdb", 2)
See also:
    Pose
    Pose.dump_pdb
    pose_from_file
    pose_from_rcsb
    cleanATOM

References basic::options::OptionKeys::relax::range.range, round(), and sum().

Referenced by toolbox.rcsb.pose_from_rcsb(), and pose_from_rcsb().

def toolbox.generate_resfile_from_pdb	(		pdbfilename,
			resfilename,
			input_sc = True
	)

Writes a resfile for PDB file <pdbfilename> named <resfilename>,
optionally allowing input side chains to be used in packing.

Example:
    generate_resfile_from_pdb("1YY8.pdb", "1YY8.resfile")
See also:
    Pose
    PackRotamersMover
    TaskFactory

References generate_resfile_from_pose().

def toolbox.generate_resfile_from_pose	(		pose,
			resfilename,
			input_sc = True
	)

Writes a resfile for <pose> named <resfilename>, optionally allowing
input side chains to be used in packing.

Example:
    generate_resfile_from_pose(pose, "1YY8.resfile")
See also:
    Pose
    PackRotamersMover
    TaskFactory

References basic::options::OptionKeys::run.chain, basic::database.open(), basic::options::OptionKeys::relax::range.range, and ObjexxFCL.rjust().

Referenced by generate_resfile_from_pdb().

def toolbox.get_hbonds

(

pose

)

Returns an HBondSet of the hydrogen bonding in <pose>.

Note: More info can be found in rosetta.core.scoring.hbonds.

Example:
    hbset = get_hbonds(pose)
    hbset.show()
    hbset.hbond(1).acc_res()
See also:
    Pose
    Energies
    HBondSet
    ScoreFunction
    create_score_function

Referenced by toolbox.mutants.compare_hbonds().

def toolbox.get_secstruct	(		pose,
			output = True,
			space = 8,
			page = 80
	)

Predicts the secondary structure of <pose>, loading this data into
the pose's secstruct information and printing the prediction to screen.

<output> determines if the information is printed to the screen or not;
<space> and <page> determine formatting.

Example:
    get_secstruct(pose)
See also:
    Pose
    Pose.secstruct
    Pose.sequence
    pose_from_file
    pose_from_sequence
    pose_from_rcsb

References ObjexxFCL.len(), ObjexxFCL.ljust(), and basic::options::OptionKeys::relax::range.range.

Referenced by spanfile_for_each_chain(), and spanfile_from_pdb().

def toolbox.load_from_rcsb	(		pdb_code,
			pdb_filename = None
	)

Writes PDB data for RCSB data for <pdb_code> into <pdb_filename>. If not
specified, outputs file to <pdb_code>.pdb.

Example:
    load_from_rcsb("1YY8")
See also:
    Pose
    pose_from_file
    pose_from_rcsb
    pose_from_sequence
    cleanATOM
    cleanCRYS

References basic::database.open().

Referenced by pose_from_rcsb().

def toolbox.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

References basic::options::OptionKeys::relax::range.range, and restrict_non_nbrs_from_repacking().

def toolbox.pose_from_rcsb	(		pdb_code,
			ATOM = True,
			CRYS = False
	)

Returns a pose for RCSB PDB <pdb_code>, also writes this data to
<pdb_code>.pdb, and optionally calls cleanATOM and/or cleanCRYS

example:
    pose = pose_from_rcsb("1YY8")
See also:
    Pose
    pose_from_file
    pose_from_sequence
    load_from_rcsb
    cleanATOM
    cleanCRYS

References cleanATOM(), cleanCRYS(), and load_from_rcsb().

def toolbox.restrict_non_nbrs_from_repacking	(		pose,
			res,
			task,
			pack_radius
	)

Evan's nbr detection in a function.  Should go in C++

References basic::options::OptionKeys::packing.prevent_repacking, basic::options::OptionKeys::relax::range.range, and basic::options::OptionKeys::in::file.xyz.

Referenced by app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignProtocols.design_residue(), mutate_residue(), and app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignProtocols.pack_residue().