src Namespace Reference

Namespaces
namespace	protocols
Classes
class	PyJobDistributor
class	PySocketClient
class	PyMOL_Mover
class	PyMOL_Observer
Functions
def	add_extend
def	new_vector1_init
def	replace_init
def	Vector1
def	generate_nonstandard_residue_set
def	standard_task_factory
def	standard_packer_task
def	add_extra_options
def	generate_resfile_from_pose
	TOOLBOX these methods are useful in PyRosetta and intended to demonstrate proper syntax for various common activities for those interested, Rosetta hag a Surface Area calculator and a Radius of Gyration calculator, they are EnergyMethods sa and rg respectively, create an empty ScoreFunction and use ScoreFunction.set_weight to use these calculations other common geometry calculators are CA_rmsd and all_atom_rmsd.
def	generate_resfile_from_pdb
def	mutate_residue
def	cleanATOM
def	cleanCRYS
def	pose_from_sequence
def	load_from_rcsb
def	pose_from_rcsb
def	get_secstruct
def	get_hbonds
def	init
def	version
Variables
tuple	PlatformBits = platform.architecture()
dictionary	X11Colors

---

Function Documentation

def src::add_extend

(

vectype

)

def src::add_extra_options

(

)

def src::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>, if for PDB files not ending in .pdb

example:
    cleanATOM('1YY9.pdb')
See also:
    Pose
    Pose.dump_pdb
    pose_from_pdb
    pose_from_rcsb
    cleanCRYS

def src::cleanCRYS	(		pdb_file,
			olig = 2
	)

Writes a PDB file for a monomer of  <pdb_file>  if it is a  <olig>-mer
to  <pdb_file>.mono
note: this is a simple sequence comparison

example:
    cleanCRYS('1YY8.pdb',2)
See also:
    Pose
    Pose.dump_pdb
    pose_from_pdb
    pose_from_rcsb
    cleanATOM

def src::generate_nonstandard_residue_set

(

params_list

)

def src::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

def src::generate_resfile_from_pose	(		pose,
			resfilename,
			input_sc = True
	)

TOOLBOX these methods are useful in PyRosetta and intended to demonstrate proper syntax for various common activities for those interested, Rosetta hag a Surface Area calculator and a Radius of Gyration calculator, they are EnergyMethods sa and rg respectively, create an empty ScoreFunction and use ScoreFunction.set_weight to use these calculations other common geometry calculators are CA_rmsd and all_atom_rmsd.

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

def src::get_hbonds

(

pose

)

Returns a HBondSet of the hydrogen bonding in  <pose>
note: more info in rosetta.core.scoring.hbonds

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

def src::get_secstruct	(		pose,
			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

example:
    get_secstruct(pose)
See also:
    Pose
    Pose.secstruct
    Pose.sequence
    pose_from_pdb
    pose_from_sequence
    pose_from_rcsb

def src::init

(

args

)

Referenced by utility::io::mpi_stream::basic_mpi_ostreambase< Elem, Tr, ElemA, ByteT, ByteAT >::basic_mpi_ostreambase(), zlib_stream::basic_zip_istreambase< Elem, Tr, ElemA, ByteT, ByteAT >::basic_zip_istreambase(), zlib_stream::basic_zip_ostreambase< Elem, Tr, ElemA, ByteT, ByteAT >::basic_zip_ostreambase(), core_init_from_string(), ObjexxFCL::Fstring::Fstring(), main(), basic::prof_show(), wrap__numeric__by_hand(), and wrap_vector1().

def src::load_from_rcsb

(

pdb_code

)

Writes PDB data for RCSB data for  <pdb_code>  into the file  <pdb_code>.pdb

example:
    load_from_rcsb('1YY8')
See also:
    Pose
    pose_from_pdb
    pose_from_rcsb
    pose_from_sequence
    cleanATOM
    cleanCRYS

def src::mutate_residue	(		pose,
			resid,
			new_res
	)

Replaces the residue at  <resid>  in  <pose>  with  <new_res>
note: <new_res>  is the single letter name for the desired ResidueType

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

def src::new_vector1_init	(		self,
			arg1 = None,
			arg2 = False
	)

def src::pose_from_rcsb	(		pdb_code,
			ATOM = True,
			CRYS = True
	)

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

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

def src::pose_from_sequence	(		seq,
			res_type = 'fa_standard'
	)

Returns a pose generated from amino acid single letters in  <seq>  using
the  <res_type>  ResidueType

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

def src::replace_init	(		cls,
			init
	)

def src::standard_packer_task

(

pose

)

def src::standard_task_factory

(

)

def src::Vector1

(

l

)

Create Vector1 object deducing type from the given list

def src::version

(

)

---

Variable Documentation

tuple src::PlatformBits = platform.architecture()

dictionary src::X11Colors