The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. More...

Namespaces
	abinitio

	analysis

	anchored_design

	antibody

	antibody_legacy

	backrub

	boinc

	branch_angle

	canonical_sampling
	Algorithms for rigorously sampling native state ensembles. See disclaimer in detailed description.

	cartesian

	checkpoint

	cluster

	coarse_rna

	comparative_modeling

	constraints_additional

	contact_map

	cryst

	cyclic_peptide

	ddg

	ddG

	denovo_design

	design_opt

	dna

	docking

	domain_assembly

	electron_density

	elscripts

	environment

	enzdes

	evaluation

	farna

	features

	fibril

	filters

	fldsgn

	flexpack

	flexpep_docking

	floppy_tail

	flxbb

	forge

	frag_picker

	frags

	generalized_kinematic_closure

	genetic_algorithm

	geometry

	grafting

	helical_bundle

	helix_capper

	hotspot_hashing

	hybridization

	idealize

	indexed_structure_store

	init

	inputter

	interface

	jd2

	jobdist

	jumping

	kinematic_closure
	Implementation of the kinematic closure algorithm for sampling protein backbone conformations.

	kinmatch

	ligand_docking

	loop_build

	loop_modeling
	Framework for loop structure prediction.

	loophash

	loops

	make_rot_lib

	match

	matdes

	md

	medal

	membrane

	metal_interface

	motif_grafting
	...that lives inside of motif_grafting...

	motifs

	moves

	mpi_refinement

	multistate_design

	ncbb

	neighbor

	noesy_assign

	nonlocal

	normalmode

	optimize_weights

	outputter

	pack_daemon

	pb_potential

	pmut_scan

	pockets

	pose_reporters

	pose_selectors

	protein_interface_design

	qsar

	rbsegment_relax

	relax

	rigid

	rosetta_scripts

	rotamer_recovery

	RotamerDump

	rpc

	sasa_scores

	scoring

	seeded_abinitio

	sic_dock

	simple_filters

	simple_moves

	sparta

	ss_prediction

	star

	stepwise

	surface_docking

	symmetric_docking

	toolbox

	topology_broker

	trajectory

	ub_e2c

	unfolded_state_energy_calculator

	viewer

	vip

	wum

	wum2

Classes
class	LoopRebuild
	The loop-rebuild protocol. More...

class	LoopRefine
	class LoopRefine for fullatom loop refinement More...

class	RBSegmentRelaxImpl

Typedefs
typedef utility::pointer::shared_ptr < AntibodyModeler >	AntibodyModelerOP

typedef utility::pointer::shared_ptr < AntibodyModeler const >	AntibodyModelerCOP

typedef utility::pointer::shared_ptr < RBSegmentRelaxImpl >	RBSegmentRelaxImplOP

Functions
void	print_ddgs (std::string ddg_out, std::string label, ddgs delta_e_components, ddgs, double total_ddgs)

void	read_in_mutations (utility::vector1< mutations > &res_to_mut, std::string filename, pose::Pose &pose)

int	ddG_main ()

static thread_local basic::Tracer	TR ("protocols.looprelax_protocols")

void	Tokenize (const std::string &str, utility::vector1< std::string > &tokens, const std::string &delimiters=" ")
	Helper function tokenizes a str. More...

int	RBSegmentRelax_main ()

Detailed Description

The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.

FIX THIS.

Restrict design to residues with electron density correlation above threshold value.

Restrict design to residues matching user-specified SASA criteria in the monomeric, bound, or unbound state.

Compare the sequences between a native and designed protein.

How many salt bridge interactions are there?

Compare the rotamer recovery between a native protein and a list of other proteins.

How many pi-pi interactiosn are there? pi-stacking considered are T-stacking and offset.

How many cation-pi interactions are there?

unit headers

unit headeers

Set of functions from Sparta class that don't actually manipulate any state in the class and have thus been removed.

Problems found during porting:

initialization protocols for symmetrical docking

set of fragments for a certain alignment frame

swaps both BBangles and residue types

swaps both fragment xyz and amino acid

Inserts a Fragment into a Pose, similar to old Rosetta++ main_frag_trial algorithm.

Hold chi- tensor information for the Pseudocontact Shift calculation.

MPI Headers.

STL Headers.

A class to determine the neighborhood of a set of residues.

Implementation of the Neighborhood class.

This is a protocol...

Does translation and rotation of a pose or the membrane.

Declarations and simple accessor/mutator definitions for MatchScoreWriter.

Forward declarations for MatchScoreWriter.

Boost headers.

Numeric headers.

general functions for generating typical kinds of Loops sets.

kinematic closure move

TODO make this a .fwd.

TODO .fwd fails (why?)

Project Headings.

C++ headers.

#include <ObjexxFCL/format.hh> // apl needed?

metric for Gunn moves

Cost computation for Gunn Moves.

ObjexxFCL headers.

Project headers.

Unit Headers.

Utility headers.

class to compute projection of a protein structure to principal component (PCA) eigenvectors ( as defined in file )

Check if the ligand's pocket is stable by removing the ligand, relaxing the structure and calculating rms to the starting structure.

Replace pack_region_ala_pose_ with a PoseOP to remove this header.

stores movable_jumps info for replica docking

This class will create instances of Mover ConformerSwitchMover for the MoverFactory.

very simple–pulls apart non-DNA (i.e. protein and friends) from DNA to facilitate DNA binding score calculation

Where is the ddGMover.fwd.hh include?

Project Headers.

Unit headers.

simple mover for stealing side chains from one pose and sticking them on another pose.

simple mover that applies another Mover, and then recovers the input sidechains from the input Pose.

LoopRelaxThreadingMover.hh.

LoopRelaxMover.hh.

demo program for implementing loop relax + FA relax

stupid test file for visual studio c++

The instance of CheckPointer contained by AbrelaxApplication should be replaced by a CheckPointerOP

Author: Oliver Lange; Oliver Lange Archive class to collect structures such that variances of scores can be computed to determine normalized weights; Oliver Lange (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Date: Wed Oct 20 12:08:31 2007

Detailed:

Author: Nir London; Yuval Sedan (yuval.nosp@m..sed.nosp@m.an@ma.nosp@m.il.h.nosp@m.uji.a.nosp@m.c.il); Orly Marcu (orly..nosp@m.marc.nosp@m.u@mai.nosp@m.l.hu.nosp@m.ji.ac.nosp@m..il)

Date: Jul. 30, 2014

Author: Nir London; Yuval Sedan (yuval.nosp@m..sed.nosp@m.an@ma.nosp@m.il.h.nosp@m.uji.a.nosp@m.c.il)

Date: Jul. 30, 2014

Author: Yuval Sedan (yuval.nosp@m..sed.nosp@m.an@ma.nosp@m.il.h.nosp@m.uji.a.nosp@m.c.il)

Date: Sep. 21, 2014

Author: Mike Tyka; Mike Tyka; Srivatsan Raman; James Thompson; Daniel J. Mandell; James Thompson

C++ headers Utility headers Project headers

Author: Chris King (chris.nosp@m.k1@u.nosp@m.w.edu); ashworth

sets an appropriate fold tree for a non-DNA/DNA interface (including multichain non-DNA and/or DNA) and then simply separates non-DNA chain(s) from the DNA chain(s) with a single translation. More basic than RigidBodyMover (which maybe needs a new base class?)

Author: ashworth; Andrew Leaver-Fay via code_writer.py (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om); Zhe Zhang; Javier Castellanos (javie.nosp@m.rcv@.nosp@m.ue.ed.nosp@m.u); Rhiju Das; Tim jacobs; Tim Jacobs; Sarel Fleishman (sarel.nosp@m.f@uw.nosp@m..edu); Javier Castellanos ( javie.nosp@m.rcv@.nosp@m.uw.ed.nosp@m.u )

Package headers

Package headers Utility headers Numeric headers

Package headers Numeric headers

Package headers Project headers ObjexxFCL headers Utility headers Numeric headers C++ headers

Package headers Project headers

Package headers Project headers C++ headers

Package headers Project headers Utility headers C++ headers TEMP

C++ headers

Package headers CREATE THE .FWD.HH FILE Project headers ObjexxFCL headers

Unit headers

CREATE THE FORWARD DECLARATION FILE
#INCLUDE IT HERE

Package headers ObjexxFCL headers

Package headers Project headers Utility headers

Author: possu; Dominik Gront (dgron.nosp@m.t@ch.nosp@m.em.uw.nosp@m..edu.nosp@m..pl); Oliver Lange ( olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu )

Date: Wed Aug 22 12:08:31 2007

Code duplication alert: TorsionFragment is going to be phased out Please avoid writing any new code using these classes: look in core/fragment/ instead look in /protocols/abinitio/FragmentMover for usage examples

Author: Frank DiMaio

Project headers Utility headers C++ headers

} In this scheme, jobs will be created for all combinations of rpoteins and ligands, and the job will be tagged with "group_name" using a job string/real pair, in the form "input_group_name group_name_a"

Author: Sam DeLuca samue.nosp@m.l.l..nosp@m.deluc.nosp@m.a@va.nosp@m.nderb.nosp@m.ilt..nosp@m.edu; Roland A. Pache, PhD; Kale Kundert; Oliver Lange

this class replaces the frag_close routines in jumping_pairings.cc the short loop is copied into a special purpose pose that just contains the loop-fragment with the hope that things are speeded up... which may or may not be true! only the linear chainbreak score is used.

Author: Daniel J. Mandell (dmand.nosp@m.ell@.nosp@m.itsa..nosp@m.ucsf.nosp@m..edu)

Date: Tues Jan 08 12:08:31 2008

Author: Amelie Stein (ameli.nosp@m.e.st.nosp@m.ein@u.nosp@m.csf..nosp@m.edu), Oct 2012 – next-generation KIC

ObjexxFCL headers

Author: Kyle Barlow (kb@ky.nosp@m.leba.nosp@m.rlow..nosp@m.com)

A class to save and output matcher data, if matches are scored

Author: Kyle Barlow (kb@ky.nosp@m.leba.nosp@m.rlow..nosp@m.com); Jacob Bale (balej.nosp@m.@uw..nosp@m.edu)

Translates along a vector and rotates a pose or membrane around the axis perpendicular to both vectors. Works for both fixed protein/flexible membrane or fixed membrane/flexible protein Takes the jump number as input, default is the membrane jump

Author: JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

This should probably be a pilot app, but the way Rosetta Scripts is set up, it can't be in the pilot apps

Author: Andrea Bazzoli (bazzo.nosp@m.li@k.nosp@m.u.edu)

Utility headers C++ headers

Author: Sarel Fleishman

EVIL EVIL

Author: Luki Goldschmidt (lugo@.nosp@m.uw.e.nosp@m.du)

Where the # total is how many proteins compared. resi_idx = residue index nat_bb_bin = dssp naming for bb pct_bb = fraction matching backbone bins nat_rot1 = chi 1 pct_rot1 = fraction matching chi bins If 999 appears, that means that the amino acid does not have that chi angle

Detailed:

Parameters

return

Remarks

References: JBNMR 2008 41:179-189 schmitz et all will explains the tensor convention used

Christophe Schmitz

Last Modified: June 2009

Detailed:

Parameters

return

Remarks

References: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 ; Yagi H et.al Structure, 2013, 21(6):883-890: JBNMR 2008 41:179-189 schmitz et all will explains the tensor convention used Christophe Schmitz , Kala Bharath Pilla

Last Modified: Mar 2014

Detailed:

Parameters

return

Remarks

References: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 ; Yagi H et.al Structure, 2013, 21(6):883-890,: JBNMR 2008 41:179-189 schmitz et all will explains the tensor convention used

Christophe Schmitz , Kala Bharath Pilla

Last Modified: Mar 2014

Author: Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), March 2011; Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu); Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), September 2011; Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), May 2011

Computes the change in entropy of the denatured state caused by forcing certain disulfide bonds, according to random flight configurational statistics (Gaussian approximation).

See "Analysis and Classification of Disulphide Connectivity in Proteins: The Entropic effect of Cross-Linkage", PM Harrison & MJE Sternberg, J Mol Biol 1994 244, 448-463

Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias Jakob P. Ulmschneider, JCP, VOl 118, 9

Core headers Numeric headers Utility headers C++ Headers

Author: TJ Brunette (tjbru.nosp@m.nett.nosp@m.e@gma.nosp@m.il.c.nosp@m.om); TJ Brunette (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Date: 3/22/10

Author: Ingemar Andre; Oliver Lange (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Date: Wed Oct 20 12:08:31 2007#include <protocols/abinitio/WobbleMover.fwd.hh>

modified for use inside CS-Rosetta by Oliver Lange

Author: Oliver Lange

modified for use inside CS-Rosetta by Oliver Lange

Author: Oliver Lange; James Thompson

project headers

package headers project headers

CatPiCalculator

Detailed:: Not much detailed here. Iterate through the carbons of aromatic rings and compare that to the distance of the polar hydrogens in basic residues...histidine not considered. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP cat_pi_calculator = new protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "cat_pi_metric", cat_pi_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("cat_pi_metric", "cat_pi") Where cat_pi_metric is the name that it is registered under and "cat_pi" is the key, seen below.

Author: Steven Combs

Last Modified: October 22 2010

PiPiCalculator

Detailed:: Not much detailed here. Iterate through the carbons of aromatic rings and compare that to the distance of the aromatic hydrogens. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP pi_pi_calculator = new protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "pi_pi_metric", pi_pi_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("pi_pi_metric", "pi_pi") Where pi_pi_metric is the name that it is registered under and "pi_pi" is the key, seen below.

Author: Steven Combs

Last Modified: October 22 2010

RotamerRecovery

Detailed:: This is an implementation taken from James Thompson. I am not even sure he knows I stole it from him. The main function that is called is the get_rotamer_recovery() function. You can pass this function a native pdb and a list of altered pdbs, or just 1 native and 1 alterd pdb. The rotamer recovery will be output to the screen. Output looks like:
total = 1

resi_idx nat_bb_bin pct_bb nat_rot1 pct_rot1 nat_rot2 pct_rot2 nat_rot3 pct_rot3 nat_rot4 pct_rot4 1 E 1.0000 1 1.0000 2 1.0000 1 1.0000 999 0.0000 2 B 1.0000 2 1.0000 1 1.0000 999 0.0000 999 0.0000 Where the # total is how many proteins compared. resi_idx = residue index nat_bb_bin = dssp naming for bb pct_bb = how many match the bb bins? nat_rot1 = chi 1 pct_rot1 = how many are correct If 999 appears, that means that the amino acid does not have that chi angle

Authors

Author: James Thompson (original author); Steven Combs (moved it to protocols for general use)

Last Modified: October 20 2010

SaltBridgeCalculator

Detailed:: Not much detailed here. Iterate through the oxygens of acidic residues and compare that to the distance of the polar hydrogens in basic residues. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP sb_calculator = new protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "sb_metric", sb_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("sb_metric", "salt_bridge") Where sb_metric is the name that it is registered under and "salt_bridge" is the key, seen below.

Author: Steven Combs

Last Modified: October 22 2010

SequenceComparison

Detailed:: This is an implementation taken from Ron Jacak, Douglas Renfrew, Matt O Mera. The main function that is called is the get_sequence_recovery() function. You can pass this function a list of native pdbs and designed pdbs, or just 1 native and 1 designed pdb. The sequence recovery will be output in a file called sequencerecovery.txt along with a substitution matrix in a file called submatrix.txt

References:: "Native sequences are close to optimal" paper

Authors: Ron Jacak, Douglas Renfrew (renfr.nosp@m.ew@n.nosp@m.yu.ed.nosp@m.u) ( added rotamer recovery, cleanup ) Steven Combs (moved it into a general use class)

Last Modified: October 20 2010

Author: Kale Kundert (kale..nosp@m.kund.nosp@m.ert@u.nosp@m.csf..nosp@m.edu); Patrick Conway; Ken Jung

Typedef Documentation

typedef utility::pointer::shared_ptr< AntibodyModeler const > protocols::AntibodyModelerCOP

typedef utility::pointer::shared_ptr< AntibodyModeler > protocols::AntibodyModelerOP

typedef utility::pointer::shared_ptr< RBSegmentRelaxImpl > protocols::RBSegmentRelaxImplOP

Function Documentation

int protocols::ddG_main ( )

void protocols::print_ddgs	(	std::string	ddg_out,
		std::string	label,
		ddgs	delta_e_components,
		ddgs	,
		double	total_ddgs
	)

References utility::exit(), F, and core::scoring::TR().

Referenced by ddG_main().

int protocols::RBSegmentRelax_main ( )

References protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::go().

void protocols::read_in_mutations	(	utility::vector1< mutations > &	res_to_mut,
		std::string	filename,
		pose::Pose &	pose
	)

References core::chemical::aa_from_oneletter_code(), core::chemical::aa_unk, core::conformation::Residue::name1(), core::pose::Pose::residue(), protocols::analysis::total, core::pose::Pose::total_residue(), and core::scoring::TR().

Referenced by ddG_main().

void protocols::Tokenize	(	const std::string &	str,
		utility::vector1< std::string > &	tokens,
		const std::string &	delimiters = `" "`
	)

Helper function tokenizes a str.

static thread_local basic::Tracer protocols::TR ( "protocols.looprelax_protocols" )

static

Namespaces

Classes

Typedefs

Functions

Detailed Description

total = 1

Typedef Documentation

Function Documentation