rosetta.core.pack._core_pack_ API documentation

def create_packer_graph(

...)

create_packer_graph( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (int)total_nodes, (vector1_Real)residue_radii) -> Graph : core/pack/packer_neighbors.hh:49

C++ signature :
    boost::shared_ptr<core::graph::Graph> create_packer_graph(core::pose::Pose,core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,unsigned long,utility::vector1<double, std::allocator<double> >)

create_packer_graph( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task) -> Graph : core/pack/packer_neighbors.hh:40

C++ signature :
    boost::shared_ptr<core::graph::Graph> create_packer_graph(core::pose::Pose,core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>)

def figure_out_repackable_residues(

...)

figure_out_repackable_residues( (Pose)pose, (AtomID_Map_T_bool_T)to_repack, (vector1_bool)repackable) -> bool : return vector of bools with true for each residue that has >=1 atom in to_repack that is not VIRTUAL, ORBS or LPbb

C++ signature : bool figure_out_repackable_residues(core::pose::Pose {lvalue},core::id::AtomID_Map,utility::vector1 > {lvalue})

def find_residue_max_radii(

...)

find_residue_max_radii( (Pose)pose, (PackerTask)task) -> vector1_Real : core/pack/packer_neighbors.hh:55

C++ signature : utility::vector1 > find_residue_max_radii(core::pose::Pose,boost::shared_ptr)

def make_new_symmetric_PackerTask_by_requested_method(

...)

make_new_symmetric_PackerTask_by_requested_method( (Pose)pose, (PackerTask)non_symmetric_task) -> PackerTask : core/pack/make_symmetric_task.hh:40

C++ signature : boost::shared_ptr make_new_symmetric_PackerTask_by_requested_method(core::pose::Pose,boost::shared_ptr)

def make_symmetric_PackerTask_by_truncation(

...)

make_symmetric_PackerTask_by_truncation( (Pose)pose, (PackerTask)task) -> None : core/pack/make_symmetric_task.hh:32

C++ signature : void make_symmetric_PackerTask_by_truncation(core::pose::Pose,boost::shared_ptr)

def min_pack(

...)

min_pack( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task [, (bool)cartesian=False [, (bool)nonideal=False]]) -> None : Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm.

C++ signature : void min_pack(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr [,bool=False [,bool=False]])

def min_pack_optimize(

...)

min_pack_optimize( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (object)rotsets, (object)scminmap, (CPP_MinimizationGraph)mingraph, (object)atc, (MinimizerOptions)min_options, (object)best_state) -> None : core/pack/min_pack.hh:76

C++ signature : void min_pack_optimize(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr,boost::shared_ptr,boost::shared_ptr,boost::shared_ptr,boost::shared_ptr,core::optimization::MinimizerOptions,core::pack::scmin::SidechainStateAssignment {lvalue})

def min_pack_place_opt_rotamers_on_pose(

...)

min_pack_place_opt_rotamers_on_pose( (Pose)pose, (ScoreFunction)sfxn, (object)rotsets, (object)atc, (object)best_state, (float)start_score) -> None : core/pack/min_pack.hh:86

C++ signature : void min_pack_place_opt_rotamers_on_pose(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr,boost::shared_ptr,core::pack::scmin::SidechainStateAssignment,double)

def min_pack_setup(

...)

min_pack_setup( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (bool)cartesian, (bool)nonideal, (object)rotsets, (object)scminmap, (CPP_MinimizationGraph)mingraph, (object)atc, (MinimizerOptions)min_options) -> None : core/pack/min_pack.hh:63

C++ signature : void min_pack_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr,bool,bool,boost::shared_ptr {lvalue},boost::shared_ptr {lvalue},boost::shared_ptr {lvalue},boost::shared_ptr {lvalue},boost::shared_ptr {lvalue})

def off_rotamer_pack(

...)

off_rotamer_pack( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task) -> None : Interface to a version of the packer that uses very little memory and simultaneously is able to go off rotamer and explore more of sidechain conformation space. Quite a bit faster than the min-packer.

C++ signature : void off_rotamer_pack(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr)

def off_rotamer_pack_optimize(

...)

off_rotamer_pack_optimize( (object)rotsets, (object)atc, (object)ig, (object)best_state) -> None : core/pack/min_pack.hh:114

C++ signature : void off_rotamer_pack_optimize(core::pack::rotamer_set::ContinuousRotamerSets,boost::shared_ptr,core::pack::interaction_graph::SimpleInteractionGraph {lvalue},core::pack::scmin::SidechainStateAssignment {lvalue})

def off_rotamer_pack_setup(

...)

off_rotamer_pack_setup( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (object)rotsets, (object)atc, (object)ig) -> None : core/pack/min_pack.hh:106

C++ signature : void off_rotamer_pack_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr,boost::shared_ptr {lvalue},boost::shared_ptr {lvalue},boost::shared_ptr {lvalue})

def off_rotamer_pack_update_pose(

...)

off_rotamer_pack_update_pose( (Pose)pose, (object)rotsets, (object)atc, (object)best_state) -> None : core/pack/min_pack.hh:122

C++ signature : void off_rotamer_pack_update_pose(core::pose::Pose {lvalue},core::pack::rotamer_set::ContinuousRotamerSets,boost::shared_ptr,core::pack::scmin::SidechainStateAssignment)

def optimizeH(

...)

optimizeH( (Pose)pose, (ScoreFunction)sfxn) -> None : This function will optimize the placement of all movable hydrogen atoms. This includes the hydroxyl hydrogens as well as the HIS protonation state. If the -flip_HNQ flag is on the command line, then it will also consider the flip states of histadine, asparagine and glutamine, (nearly) as described by Word et al. 1999.

C++ signature : void optimizeH(core::pose::Pose {lvalue},core::scoring::ScoreFunction)

def optimize_H_and_notify(

...)

optimize_H_and_notify( (Pose)pose, (AtomID_Map_T_bool_T)missing) -> None : Call optimizeH and tell the user what chi angles have changed

C++ signature : void optimize_H_and_notify(core::pose::Pose {lvalue},core::id::AtomID_Map)

def pack_missing_sidechains(

...)

pack_missing_sidechains( (Pose)pose, (AtomID_Map_T_bool_T)missing) -> None : This function runs rotamer trials on residues missing sidechain density (as described by the AtomID_Mask)

C++ signature : void pack_missing_sidechains(core::pose::Pose {lvalue},core::id::AtomID_Map)

def pack_rotamers(

...)

pack_rotamers( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task) -> None : core/pack/pack_rotamers.hh:53

C++ signature : void pack_rotamers(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr)

def pack_rotamers_loop(

...)

pack_rotamers_loop( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (int)nloop) -> None : core/pack/pack_rotamers.hh:80

C++ signature :
    void pack_rotamers_loop(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,unsigned long)

pack_rotamers_loop( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (int)nloop, (vector1_pair_Real_string)results, (vector1_PoseOP)pose_list) -> None : core/pack/pack_rotamers.hh:72

C++ signature :
    void pack_rotamers_loop(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,unsigned long,utility::vector1<std::pair<double, std::string>, std::allocator<std::pair<double, std::string> > > {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > {lvalue})

pack_rotamers_loop( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (int)nloop, (vector1_pair_Real_string)results) -> None : core/pack/pack_rotamers.hh:62

C++ signature :
    void pack_rotamers_loop(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,unsigned long,utility::vector1<std::pair<double, std::string>, std::allocator<std::pair<double, std::string> > > {lvalue})

def pack_rotamers_run(

...)

pack_rotamers_run( (Pose)pose, (PackerTask)task, (object)rotsets, (object)ig, (vector0_T_int_std_allocator_T_int_T__T)rot_to_pack, (object)bestrotamer_at_seqpos, (float)bestenergy) -> None : Run simulated annealing and return the best rotamer assignment found. This function does not modify the input pose.

C++ signature :
    void pack_rotamers_run(core::pose::Pose,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::FixbbRotamerSets const>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase>,utility::vector0<int, std::allocator<int> >,ObjexxFCL::FArray1D<int> {lvalue},float {lvalue})

pack_rotamers_run( (Pose)pose, (PackerTask)task, (object)rotsets, (object)ig, (vector0_T_int_std_allocator_T_int_T__T)rot_to_pack) -> float : Run simulated annealing, return the energy of the best rotamer assignment found, and place the best rotamers onto the input pose.

C++ signature :
    double pack_rotamers_run(core::pose::Pose {lvalue},boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::FixbbRotamerSets const>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase>,utility::vector0<int, std::allocator<int> >)

def pack_rotamers_setup(

...)

pack_rotamers_setup( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (object)rotsets) -> object : core/pack/pack_rotamers.hh:98

C++ signature :
    boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase> pack_rotamers_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::RotamerSets>)

pack_rotamers_setup( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (object)rotsets, (object)ig) -> None : core/pack/pack_rotamers.hh:89

C++ signature :
    void pack_rotamers_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::RotamerSets>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase> {lvalue})

def pack_scorefxn_pose_handshake(

...)

pack_scorefxn_pose_handshake( (Pose)pose, (ScoreFunction)scfxn) -> None : core/pack/packer_neighbors.hh:61

C++ signature : void pack_scorefxn_pose_handshake(core::pose::Pose {lvalue},core::scoring::ScoreFunction)

def reinitialize_mingraph_neighborhood_for_residue(

...)

reinitialize_mingraph_neighborhood_for_residue( (Pose)pose, (ScoreFunction)scorefxn, (object)bgres, (object)scminmap, (Residue)rsd, (MinimizationGraph)mingraph) -> None : core/pack/rtmin.hh:80

C++ signature : void reinitialize_mingraph_neighborhood_for_residue(core::pose::Pose {lvalue},core::scoring::ScoreFunction,utility::vector1, std::allocator > >,core::pack::scmin::SCMinMinimizerMap,core::conformation::Residue,core::scoring::MinimizationGraph {lvalue})

def repackable_residues(

...)

repackable_residues( (PackerTask)the_task) -> vector1_Size : core/pack/rotamer_trials.hh:35

C++ signature : utility::vector1 > repackable_residues(core::pack::task::PackerTask)

def rotamer_trials(

...)

rotamer_trials( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)input_task) -> None : core/pack/rotamer_trials.hh:43

C++ signature : void rotamer_trials(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr)

def setup_IG_res_res_weights(

...)

setup_IG_res_res_weights( (Pose)pose, (PackerTask)task, (object)rotsets, (object)ig) -> None : core/pack/pack_rotamers.hh:106

C++ signature : void setup_IG_res_res_weights(core::pose::Pose,boost::shared_ptr,boost::shared_ptr,boost::shared_ptr)

def symmetric_pack_rotamers(

...)

symmetric_pack_rotamers( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task) -> None : core/pack/pack_rotamers.hh:138

C++ signature : void symmetric_pack_rotamers(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr)

def symmetric_pack_rotamers_run(

...)

symmetric_pack_rotamers_run( (Pose)pose, (PackerTask)task, (object)rotsets, (object)ig, (vector0_T_int_std_allocator_T_int_T__T)rot_to_pack) -> float : core/pack/pack_rotamers.hh:165

C++ signature : double symmetric_pack_rotamers_run(core::pose::Pose {lvalue},boost::shared_ptr,boost::shared_ptr,boost::shared_ptr,utility::vector0 >)

def symmetric_pack_rotamers_setup(

...)

symmetric_pack_rotamers_setup( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (object)rotsets) -> object : core/pack/pack_rotamers.hh:156

C++ signature :
    boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase> symmetric_pack_rotamers_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::symmetry::SymmetricRotamerSets>)

symmetric_pack_rotamers_setup( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (object)rotsets, (object)ig) -> None : core/pack/pack_rotamers.hh:147

C++ signature :
    void symmetric_pack_rotamers_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::symmetry::SymmetricRotamerSets>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase> {lvalue})

def symmetric_rotamer_trials(

...)

symmetric_rotamer_trials( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)input_task) -> None : core/pack/rotamer_trials.hh:50

C++ signature : void symmetric_rotamer_trials(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr)

class RTMin

core/pack/rtmin.hh:40

Ancestors (in MRO)

RTMin
Boost.Python.instance
__builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature :
    void __init__(_object*)

init( (object)arg1, (RTMin)) -> None : core/pack/rtmin.hh:40

C++ signature :
    void __init__(_object*,core::pack::RTMin)

init( (object)arg1, (bool)minimize_ligand_chis, (bool)minimize_ligand_jumps) -> None : core/pack/rtmin.hh:48

C++ signature :
    void __init__(_object*,bool,bool)

def rtmin(

...)

rtmin( (RTMin)arg1, (Pose)pose, (ScoreFunction)sfxn, (PackerTask)input_task) -> None : core/pack/rtmin.hh:61

C++ signature : void rtmin(core::pack::RTMin {lvalue},core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr)

def set_cartesian(

...)

set_cartesian( (RTMin)arg1, (bool)cartesian_in) -> None : core/pack/rtmin.hh:54

C++ signature : void set_cartesian(core::pack::RTMin {lvalue},bool)

def set_nonideal(

...)

set_nonideal( (RTMin)arg1, (bool)nonideal_in) -> None : core/pack/rtmin.hh:53

C++ signature : void set_nonideal(core::pack::RTMin {lvalue},bool)

class RTMinAP

Ancestors (in MRO)

RTMinAP
Boost.Python.instance
__builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (RTMinAP)arg1) -> RTMin :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class RTMinCAP

Ancestors (in MRO)

RTMinCAP
Boost.Python.instance
__builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (RTMinCAP)arg1) -> RTMin :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

Index

Functions

Classes

rosetta.core.pack._core_pack_ module

Functions

Classes

Ancestors (in MRO)

Methods

Ancestors (in MRO)

Methods

Ancestors (in MRO)

Methods