core::io::raw_data::DisulfideFile Class Reference

Parses and stores a disulfide file. More...

#include <DisulfideFile.hh>

Classes
struct	ResNum
	represents a residue of either pdb or rosetta numbering. More...

Public Types
enum	NumberingSystem { pdb_num , rosetta_num , unknown_num }
	distinguish between PDB numbering and internal Rosetta numbering More...

Public Member Functions
	DisulfideFile (std::string filename)
std::string const &	filename () const
	Accessor for the filename. More...
void	disulfides (utility::vector1< std::pair< core::Size, core::Size > > &disulfides) const
	Get a list of disulfide bonds declared in the file. More...
void	disulfides (utility::vector1< std::pair< core::Size, core::Size > > &disulfides, core::pose::Pose const &pose) const
	Get a list of disulfide bonds declared in the file (renumbered to rosetta numbering if necessary) More...
void	read_in_and_set_disulfides (core::pose::Pose &pose)
	Get a list of disulfide bonds declared in the file (renumbered to rosetta numbering if necessary) also manually set the disulfides in the conformation of the provided pose (this is a necessary workaround for dealing with multiple disulfide specification files in PyRosetta. More...

Private Member Functions
void	parse_disulf_file () const
	helper function to read in the file More...
core::Size	resnum_to_rosetta_num (core::pose::Pose const &pose, ResNum const &resnum) const
	convert a ResNum struct into a normal rosetta residue num More...

Private Attributes
const std::string	filename_
bool	up_to_date_
utility::vector1< std::pair< ResNum, ResNum > >	disulfides_

Detailed Description

Parses and stores a disulfide file.

Initiallizing a DisulfideFile is a lightweight operation. The heavy lifting occurs the first time disulfides() is called. This parses the file and caches the resulting pairs of residues. Subsequent calls to disulfides() are fast since they don't reparse the file but merely reinterpret the results in terms of the specified.

File Format

The disulfide file format is pretty flexible. It looks for three kinds of lines:

• '12 42' Lines with two integers are interpreted as a disulfide bond, indexed by internal rosetta residue number, i.e. the 12th and 42nd residues from the start of the pose.
• '12A 42A' If a single character is appended to the numbers, DisulfideFile assumes that these refer to the pdb number and chain, i.e. the residues of chain A numbered 12 and 42 in the pdb.
• 'SSBOND 1 CYS A 12 CYS A 42' The PDB format for disulfide bond annotations.

All lines not matching these criteria are silently ignored. This implies that whole pdb files can usually be used unaltered as disulfide files, since the SSBOND entries are extracted and all else is ignored.

Question from rhiju, 2014 – I don't see handling of '12A' or SSBOND cases in DisulfideFile.cc – is someone going to check that in?

Member Enumeration Documentation

NumberingSystem

enum core::io::raw_data::DisulfideFile::NumberingSystem

distinguish between PDB numbering and internal Rosetta numbering

unknown_num should be avoided, as one of the other types can generally be infered from the existance of a chain specifier.

Enumerator
pdb_num
rosetta_num
unknown_num

Constructor & Destructor Documentation

DisulfideFile()

core::io::raw_data::DisulfideFile::DisulfideFile ( std::string  filename )

inline

Member Function Documentation

disulfides() [1/2]

void core::io::raw_data::DisulfideFile::disulfides

(

utility::vector1< std::pair< core::Size, core::Size > > &

disulfides

)

const

Get a list of disulfide bonds declared in the file.

Referenced by protocols::frag_picker::CS2ndShift::also_check_fix_disulf(), protocols::topology_broker::TopologyBroker::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), core::pose::initialize_disulfide_bonds(), protocols::frag_picker::scores::MakeDisulfideDistance::make(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), protocols::abinitio::AbrelaxApplication::setup_fold(), and protocols::topology_broker::TopologyBroker::switch_to_fullatom().

disulfides() [2/2]

void core::io::raw_data::DisulfideFile::disulfides	(	utility::vector1< std::pair< core::Size, core::Size > > &	disulfides,
		core::pose::Pose const &	pose
	)		const

Get a list of disulfide bonds declared in the file (renumbered to rosetta numbering if necessary)

filename()

std::string const& core::io::raw_data::DisulfideFile::filename ( ) const

inline

Accessor for the filename.

References filename_.

parse_disulf_file()

void core::io::raw_data::DisulfideFile::parse_disulf_file ( ) const

private

helper function to read in the file

Parses residue numbers out of a disulfide file See DisulfideFile for more details on the file format.

References core::io::raw_data::TR(), protocols::hybridization::u, and core::scoring::methods::ws.

read_in_and_set_disulfides()

void core::io::raw_data::DisulfideFile::read_in_and_set_disulfides

(

core::pose::Pose &

pose

)

Get a list of disulfide bonds declared in the file (renumbered to rosetta numbering if necessary) also manually set the disulfides in the conformation of the provided pose (this is a necessary workaround for dealing with multiple disulfide specification files in PyRosetta.

Get a list of disulfide bonds declared in the file and manually set them in the conformation.

The first time this is called it reads the file and caches the resulting pairs of residues. Subsequent calls to disulfides() are fast since they don't reparse the file but merely reinterpret the results in terms of the specified. (this is a necessary workaround for dealing with multiple disulfide specification files in PyRosetta) Because there is no equivalent of std::pair in python this method avoids needing to provide a vector1 of std::pairs as arguments

Parameters

[out]	disulfides	Appends pairs of residues specified by the file to this list
[in]	pose	is used if PDB numbering is used in the disulfide file and is also needed to manually set the disulfides in the conformation

@postcondition For each pair of residues (l,u) in this list, l<u

References core::pose::Pose::conformation(), core::conformation::Conformation::fix_disulfides(), and protocols::hybridization::u.

resnum_to_rosetta_num()

Size core::io::raw_data::DisulfideFile::resnum_to_rosetta_num ( core::pose::Pose const &  pose, ResNum const &  resnum  ) const

private

convert a ResNum struct into a normal rosetta residue num

Convert a ResNum object into the rosetta residue index.

For ResNums with the rosetta_num type, this just return the n field. For pdb_num ResNums the pose's PDBInfo is used to translate to rosetta numbering.

This function exits with an error message if it is unable to do the conversion.

References core::io::raw_data::DisulfideFile::ResNum::chain, core::io::raw_data::DisulfideFile::ResNum::n, core::pose::Pose::pdb_info(), core::io::raw_data::TR(), and core::io::raw_data::DisulfideFile::ResNum::type.

Member Data Documentation

disulfides_

utility::vector1< std::pair<ResNum,ResNum> > core::io::raw_data::DisulfideFile::disulfides_

mutableprivate

filename_

const std::string core::io::raw_data::DisulfideFile::filename_

private

Referenced by filename().

up_to_date_

bool core::io::raw_data::DisulfideFile::up_to_date_

mutableprivate

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The documentation for this class was generated from the following files:

• src/core/io/raw_data/DisulfideFile.hh
• src/core/io/raw_data/DisulfideFile.cc