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NPDHBondInteractionGraph.hh File Reference

Interaction graph which implements a non-PD score that optimizes against surface hydrophobic patches. Computational Protein Design with Explicit Consideration of Surface Hydrophobic Patches. R. Jacak, A. Leaver-Fay, and B. Kuhlman. Proteins. 2012 Mar;80(3):825-38. More...

#include <core/pack/interaction_graph/NPDHBondInteractionGraph.fwd.hh>
#include <core/pack/interaction_graph/AdditionalBackgroundNodesInteractionGraph.hh>
#include <core/pack/interaction_graph/InteractionGraphBase.hh>
#include <core/pack/interaction_graph/LinearMemoryInteractionGraph.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/NPDHBondSet.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/constants.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/graph/Graph.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray1.io.hh>
#include <ObjexxFCL/format.hh>
#include <vector>

Classes

class  core::pack::interaction_graph::NPDHBondNode< V, E, G >
 Defines a FirstClass node which will keep track of the hydrogen bonds coming in to the residue and the hydrogen bond score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
 
class  core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >
 Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable. More...
 
class  core::pack::interaction_graph::NPDHBondEdge< V, E, G >
 Defines a NPDHBond Edge which connects two first-class NPDHBond Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...
 
class  core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >
 Defines an edge between a FirstClass (NPDHBondNode) and a background node (NPDHBondBackgroundNode) More...
 
class  core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
 Defines the interaction graph that will keep track of changes to the hpatch score. More...
 
struct  core::pack::interaction_graph::NPDHBond
 
class  core::pack::interaction_graph::NPDHBondNode< V, E, G >
 Defines a FirstClass node which will keep track of the hydrogen bonds coming in to the residue and the hydrogen bond score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
 
class  core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >
 Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable. More...
 
class  core::pack::interaction_graph::NPDHBondEdge< V, E, G >
 Defines a NPDHBond Edge which connects two first-class NPDHBond Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...
 
class  core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >
 Defines an edge between a FirstClass (NPDHBondNode) and a background node (NPDHBondBackgroundNode) More...
 
class  core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
 Defines the interaction graph that will keep track of changes to the hpatch score. More...
 

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::pack
 
 core::pack::interaction_graph
 

Functions

static basic::Tracer core::pack::interaction_graph::TR ("core.pack.npd_hbond_ig")
 
void core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds (conformation::Residue const &res, utility::vector1< utility::vector1< NPDHBondOP > > const &atom_hbonds,utility::vector1< Real > &tmp_energies,utility::vector1< Real > &temp_weights)
 Compute the don_wt_alt_s and the acc_wt_alt_s from the perspective of the input residue given the (complete) arrays of NPDHBondOPs for each atom. More...
 
template<typename V , typename E , typename G >
void core::pack::interaction_graph::create_hbonds_one_way (scoring::hbonds::HBondDatabase const &database, scoring::hbonds::HBondOptions const &hbondoptions, scoring::hbonds::HBondSet const &hbset, NPDHBondInteractionGraph< V, E, G > &ig, utility::vector1< char > &hbonding_to_res, conformation::Residue const &acc_res, utility::vector1< NPDHBondOP > &acc_hbonds, utility::vector1< utility::vector1< NPDHBondOP > > &acc_atom_hbonds, conformation::Residue const &don_res, utility::vector1< NPDHBondOP > &don_hbonds, utility::vector1< utility::vector1< NPDHBondOP > > &don_atom_hbonds)
 

Detailed Description

Interaction graph which implements a non-PD score that optimizes against surface hydrophobic patches. Computational Protein Design with Explicit Consideration of Surface Hydrophobic Patches. R. Jacak, A. Leaver-Fay, and B. Kuhlman. Proteins. 2012 Mar;80(3):825-38.

Author
Ron Jacak (ron.j.nosp@m.acak.nosp@m.@gmai.nosp@m.l.co.nosp@m.m)
Andrew Leaver-Fay