disulfides.hh File Reference

Some utility functions for dealing with disulfides. More...

#include <core/pose/Pose.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/Stub.hh>
#include <basic/Tracer.hh>
#include <core/pose/disulfide_util.hh>
#include <core/conformation/util.hh>
#include <core/chemical/VariantType.hh>

Functions
Real	residue_distance (pose::Pose const &pose, Size residueA_pos, string atomA, Size residueB_pos, string atomB)
	Determines the distance between two residues. More...
Real	CA_distance (pose::Pose const &pose, Size posA, Size posB)
Real	CB_distance (pose::Pose const &pose, Size posA, Size posB)
bool	reasonable_disulfide_orientation (pose::Pose const &pose, Size residueA_pos, Size residueB_pos)
	Decides whether a disulfide bond could exist between two residues based on backbone orientation. More...
bool	possible_disulfide (pose::Pose const &pose, Size residueA_pos, Size residueB_pos)
	Detect whether a disulfide bond could exist. More...
bool	actual_disulfide (pose::Pose const &pose, Size residueA_pos, Size residueB_pos)
	Detect 'actual' disulfide bonds. More...
void	find_disulfides (pose::Pose const &pose, vector1< pair< Size, Size > > &disulfides)
bool	same_secondary_structure (pose::Pose const &pose, Size resA_pos, Size resB_pos)
	Determines whether two residues are on the same secondary structure element. More...

Variables
static basic::Tracer	TR_apps_pilot_blivens_disulfides_hh ("apps.pilot.blivens.disulfides")

Detailed Description

Some utility functions for dealing with disulfides.

Note

These were written before I know all the tricks of mini some have been supersceded by core functions.

Author

Spencer Bliven blive.nosp@m.ns@u.nosp@m..wash.nosp@m.ingt.nosp@m.on.ed.nosp@m.u

Date

Created October 2008

Function Documentation

actual_disulfide()

bool actual_disulfide	(	pose::Pose const &	pose,
		Size	residueA_pos,
		Size	residueB_pos
	)

Detect 'actual' disulfide bonds.

Since disulfide bonds are generally not annotated, we define a disulfide to exist between a pair of residues if 1) They are both cysteines 2) They are bonded (which is marked by conformer.detect_disulfides)

References beta_nonlocal::pose.

Referenced by main(), and PairScore::score().

CA_distance()

Real CA_distance	(	pose::Pose const &	pose,
		Size	posA,
		Size	posB
	)

References beta_nonlocal::pose, and residue_distance().

Referenced by reasonable_disulfide_orientation().

CB_distance()

Real CB_distance	(	pose::Pose const &	pose,
		Size	posA,
		Size	posB
	)

References beta_nonlocal::pose, and residue_distance().

find_disulfides()

void find_disulfides	(	pose::Pose const &	pose,
		vector1< pair< Size, Size > > &	disulfides
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, utility::io::oc::cerr, detail::fill(), create_a3b_hbs::ii, basic::Tracer::Info, beta_nonlocal::jj, beta_nonlocal::pose, TR_apps_pilot_blivens_disulfides_hh, and utility_exit.

Referenced by main().

possible_disulfide()

bool possible_disulfide	(	pose::Pose const &	pose,
		Size	residueA_pos,
		Size	residueB_pos
	)

Detect whether a disulfide bond could exist.

References beta_nonlocal::pose, and reasonable_disulfide_orientation().

Referenced by main().

reasonable_disulfide_orientation()

bool reasonable_disulfide_orientation	(	pose::Pose const &	pose,
		Size	residueA_pos,
		Size	residueB_pos
	)

Decides whether a disulfide bond could exist between two residues based on backbone orientation.

Looks at the backbone distance and orientation between two residues. Returns whether this backbone would be a reasonable place to put a disulfide bond.

Current criteria used:

1. Distance between CA-CA possible enhancements:

• CB distance
• general orientation (pointing towards one another)
• ramachandra plot orientation
• other sidechains which need to be repacked/mutated

References CA_distance(), beta_nonlocal::pose, and create_a3b_hbs::r.

Referenced by possible_disulfide().

residue_distance()

Real residue_distance	(	pose::Pose const &	pose,
		Size	residueA_pos,
		string	atomA,
		Size	residueB_pos,
		string	atomB
	)

Determines the distance between two residues.

Parameters

atom	The atom to measure from within each residue, eg "CA"

Returns

-1 on error (for instance, CB distance of Gly)

References a, compute_difference::b, and beta_nonlocal::pose.

Referenced by CA_distance(), and CB_distance().

same_secondary_structure()

bool same_secondary_structure	(	pose::Pose const &	pose,
		Size	resA_pos,
		Size	resB_pos
	)

Determines whether two residues are on the same secondary structure element.

Before running the correct secondary structure must be assigned to each residue.

Algorithm

Walk from one residue to the next, stopping if you cross a ss border. O(longest ss element).

References extract_by_sidechain_sasa_score::l, beta_nonlocal::pose, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::u.

Referenced by PairScore::score().

Variable Documentation

TR_apps_pilot_blivens_disulfides_hh

basic::Tracer TR_apps_pilot_blivens_disulfides_hh("apps.pilot.blivens.disulfides") ( "apps.pilot.blivens.disulfides"  )

static

Referenced by find_disulfides().