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rosetta.core.environment._core_environment_ module

Classes

class DofPassport

core/environment/DofPassport.hh:49

Ancestors (in MRO)

Methods

def active_dofs(

...)

active_dofs( (DofPassport)arg1) -> object : core/environment/DofPassport.hh:78

C++ signature : std::set, std::allocator > active_dofs(core::environment::DofPassport {lvalue})

def active_jumps(

...)

active_jumps( (DofPassport)arg1) -> vector1_int : core/environment/DofPassport.hh:80

C++ signature : utility::vector1 > active_jumps(core::environment::DofPassport {lvalue})

def add_dof_access(

...)

add_dof_access( (DofPassport)arg1, (DOF_ID)id) -> None : configure passport to allow access to a bond length or angle dof_id id the DOF_ID to allow access to

C++ signature : void add_dof_access(core::environment::DofPassport {lvalue},core::id::DOF_ID)

def begin(

...)

begin( (DofPassport)arg1) -> object : core/environment/DofPassport.hh:66

C++ signature : std::_Rb_tree_const_iterator begin(core::environment::DofPassport {lvalue})

def dof_access(

...)

dof_access( (DofPassport)arg1, (DOF_ID)id) -> bool : core/environment/DofPassport.hh:83

C++ signature :
    bool dof_access(core::environment::DofPassport {lvalue},core::id::DOF_ID)

dof_access( (DofPassport)arg1, (EnvCore), (DOF_ID)id) -> bool : core/environment/DofPassport.hh:86

C++ signature :
    bool dof_access(core::environment::DofPassport {lvalue},core::environment::EnvCore,core::id::DOF_ID)

def end(

...)

end( (DofPassport)arg1) -> object : core/environment/DofPassport.hh:68

C++ signature : std::_Rb_tree_const_iterator end(core::environment::DofPassport {lvalue})

def env_id(

...)

env_id( (DofPassport)arg1) -> int : core/environment/DofPassport.hh:90

C++ signature : unsigned long env_id(core::environment::DofPassport {lvalue})

def has_jump_access(

...)

has_jump_access( (DofPassport)arg1, (int)jump_num) -> bool : core/environment/DofPassport.hh:76

C++ signature : bool has_jump_access(core::environment::DofPassport {lvalue},int)

def mover(

...)

mover( (DofPassport)arg1) -> str : core/environment/DofPassport.hh:88

C++ signature : std::string mover(core::environment::DofPassport {lvalue})

def reference_conformation(

...)

reference_conformation( (DofPassport)arg1) -> Conformation : core/environment/DofPassport.hh:92

C++ signature :
    boost::shared_ptr<core::conformation::Conformation const> reference_conformation(core::environment::DofPassport {lvalue})

reference_conformation( (DofPassport)arg1, (CPP_Conformation)conf) -> None : core/environment/DofPassport.hh:94

C++ signature :
    void reference_conformation(core::environment::DofPassport {lvalue},boost::shared_ptr<core::conformation::Conformation const>)

def render_movemap(

...)

render_movemap( (DofPassport)arg1) -> MoveMap : core/environment/DofPassport.hh:59

C++ signature :
    boost::shared_ptr<core::kinematics::MoveMap> render_movemap(core::environment::DofPassport {lvalue})

render_movemap( (DofPassport)arg1, (MoveMap)) -> None : core/environment/DofPassport.hh:61

C++ signature :
    void render_movemap(core::environment::DofPassport {lvalue},boost::shared_ptr<core::kinematics::MoveMap>)

def revoke_all_access(

...)

revoke_all_access( (DofPassport)arg1) -> None : core/environment/DofPassport.hh:74

C++ signature : void revoke_all_access(core::environment::DofPassport {lvalue})

def show(

...)

show( (DofPassport)arg1, (OStream)) -> None : core/environment/DofPassport.hh:57

C++ signature : void show(core::environment::DofPassport {lvalue},std::ostream {lvalue})

class DofPassportAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (DofPassportAP)arg1) -> DofPassport :

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

class DofPassportCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (DofPassportCAP)arg1) -> DofPassport :

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

class EXCN_Env_Exception

core/environment/EnvExcnBase.hh:35

Ancestors (in MRO)

  • EXCN_Env_Exception
  • rosetta.utility.excn._utility_excn_.EXCN_Msg_Exception
  • rosetta.utility.excn._utility_excn_.EXCN_Exception
  • rosetta.utility.excn._utility_excn_.EXCN_Base
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1, (EnvCoreCAP)env_ap) -> None : core/environment/EnvExcnBase.hh:38

C++ signature :
    void __init__(_object*,boost::weak_ptr<core::environment::EnvCore const>)

init( (object)arg1, (EXCN_Env_Exception)) -> None : core/environment/EnvExcnBase.hh:35

C++ signature :
    void __init__(_object*,core::environment::EXCN_Env_Exception)

def add_msg(

...)

add_msg( (EXCN_Msg_Exception)arg1, (str)str) -> None : utility/excn/Exceptions.hh:66

C++ signature :
    void add_msg(utility::excn::EXCN_Msg_Exception {lvalue},std::string)

add_msg( (EXCN_Msg_Exception)arg1, (str)str) -> None :

C++ signature :
    void add_msg(EXCN_Msg_Exception_exposer_callback {lvalue},std::string)

def msg(

...)

msg( (EXCN_Msg_Exception)arg1) -> str : utility/excn/Exceptions.hh:65

C++ signature :
    std::string msg(utility::excn::EXCN_Msg_Exception {lvalue})

msg( (EXCN_Msg_Exception)arg1) -> str :

C++ signature :
    std::string msg(EXCN_Msg_Exception_exposer_callback {lvalue})

def show(

...)

show( (EXCN_Msg_Exception)arg1, (OStream)) -> None : utility/excn/Exceptions.hh:64

C++ signature :
    void show(utility::excn::EXCN_Msg_Exception {lvalue},std::ostream {lvalue})

show( (EXCN_Msg_Exception)arg1, (OStream)) -> None :

C++ signature :
    void show(EXCN_Msg_Exception_exposer_callback {lvalue},std::ostream {lvalue})

class EXCN_Env_ExceptionAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (EXCN_Env_ExceptionAP)arg1) -> EXCN_Env_Exception :

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

class EXCN_Env_ExceptionCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (EXCN_Env_ExceptionCAP)arg1) -> EXCN_Env_Exception :

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

class EXCN_FTSketchGraph

core/environment/FoldTreeSketch.hh:48

Ancestors (in MRO)

  • EXCN_FTSketchGraph
  • rosetta.utility.excn._utility_excn_.EXCN_Msg_Exception
  • rosetta.utility.excn._utility_excn_.EXCN_Exception
  • rosetta.utility.excn._utility_excn_.EXCN_Base
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1, (int)by, (int)on, (str)action, (str)reason) -> None : core/environment/FoldTreeSketch.hh:52

C++ signature :
    void __init__(_object*,unsigned long,unsigned long,std::string,std::string)

init( (object)arg1, (EXCN_FTSketchGraph)) -> None : core/environment/FoldTreeSketch.hh:48

C++ signature :
    void __init__(_object*,core::environment::EXCN_FTSketchGraph)

init( (object)arg1, (str)message) -> None : core/environment/FoldTreeSketch.hh:54

C++ signature :
    void __init__(_object*,std::string)

def add_msg(

...)

add_msg( (EXCN_Msg_Exception)arg1, (str)str) -> None : utility/excn/Exceptions.hh:66

C++ signature :
    void add_msg(utility::excn::EXCN_Msg_Exception {lvalue},std::string)

add_msg( (EXCN_Msg_Exception)arg1, (str)str) -> None :

C++ signature :
    void add_msg(EXCN_Msg_Exception_exposer_callback {lvalue},std::string)

def msg(

...)

msg( (EXCN_Msg_Exception)arg1) -> str : utility/excn/Exceptions.hh:65

C++ signature :
    std::string msg(utility::excn::EXCN_Msg_Exception {lvalue})

msg( (EXCN_Msg_Exception)arg1) -> str :

C++ signature :
    std::string msg(EXCN_Msg_Exception_exposer_callback {lvalue})

def show(

...)

show( (EXCN_Msg_Exception)arg1, (OStream)) -> None : utility/excn/Exceptions.hh:64

C++ signature :
    void show(utility::excn::EXCN_Msg_Exception {lvalue},std::ostream {lvalue})

show( (EXCN_Msg_Exception)arg1, (OStream)) -> None :

C++ signature :
    void show(EXCN_Msg_Exception_exposer_callback {lvalue},std::ostream {lvalue})

class EXCN_FTSketchGraphAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (EXCN_FTSketchGraphAP)arg1) -> EXCN_FTSketchGraph :

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

class EXCN_FTSketchGraphCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (EXCN_FTSketchGraphCAP)arg1) -> EXCN_FTSketchGraph :

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

class EnvCore

core/environment/EnvCore.hh:36

Ancestors (in MRO)

  • EnvCore
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1, (str)env_name) -> None : core/environment/EnvCore.hh:38

C++ signature :
    void __init__(_object*,std::string)

init( (object)arg1, (EnvCore)) -> None : core/environment/EnvCore.hh:36

C++ signature :
    void __init__(_object*,core::environment::EnvCore)

def id(

...)

id( (EnvCore)arg1) -> int : core/environment/EnvCore.hh:46

C++ signature : unsigned long id(core::environment::EnvCore {lvalue})

def name(

...)

name( (EnvCore)arg1) -> str : core/environment/EnvCore.hh:42

C++ signature : std::string name(core::environment::EnvCore {lvalue})

def superenv(

...)

superenv( (EnvCore)arg1) -> EnvCoreCAP : core/environment/EnvCore.hh:44

C++ signature : boost::weak_ptr superenv(core::environment::EnvCore {lvalue})

class EnvCoreAP

Ancestors (in MRO)

  • EnvCoreAP
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (EnvCoreAP)arg1) -> EnvCore :

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

class EnvCoreCAP

Ancestors (in MRO)

  • EnvCoreCAP
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (EnvCoreCAP)arg1) -> EnvCore :

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

class FoldTreeSketch

core/environment/FoldTreeSketch.hh:57

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature :
    void __init__(_object*)

init( (object)arg1, (int)length) -> None : core/environment/FoldTreeSketch.hh:69

C++ signature :
    void __init__(_object*,unsigned long)

init( (object)arg1, (FoldTree)) -> None : core/environment/FoldTreeSketch.hh:71

C++ signature :
    void __init__(_object*,core::kinematics::FoldTree)

init( (object)arg1, (FoldTreeSketch)) -> None : copy the FoldTreeSketch @warning This is not a full deep copy. It doesn't copy the Node pointers deeply, which means

C++ signature :
    void __init__(_object*,core::environment::FoldTreeSketch)

def append_peptide(

...)

append_peptide( (FoldTreeSketch)arg1, (int)l) -> None : add a new (graph-detached) peptide-bonded strech of length l at the end of the sequence

C++ signature : void append_peptide(core::environment::FoldTreeSketch {lvalue},unsigned long)

def append_residue(

...)

append_residue( (FoldTreeSketch)arg1) -> None : core/environment/FoldTreeSketch.hh:88

C++ signature : void append_residue(core::environment::FoldTreeSketch {lvalue})

def cycle(

...)

cycle( (FoldTreeSketch)arg1 [, (int)start=1]) -> vector1_Size : core/environment/FoldTreeSketch.hh:94

C++ signature : utility::vector1 > cycle(core::environment::FoldTreeSketch {lvalue} [,unsigned long=1])

def has_cut(

...)

has_cut( (FoldTreeSketch)arg1, (int)) -> bool : core/environment/FoldTreeSketch.hh:90

C++ signature : bool has_cut(core::environment::FoldTreeSketch {lvalue},unsigned long)

def has_jump(

...)

has_jump( (FoldTreeSketch)arg1, (int)p1, (int)p2) -> bool : core/environment/FoldTreeSketch.hh:92

C++ signature : bool has_jump(core::environment::FoldTreeSketch {lvalue},unsigned long,unsigned long)

def insert_cut(

...)

insert_cut( (FoldTreeSketch)arg1, (int)l) -> None : insert a cut after position l (i.e. between position l and l+1)

C++ signature :
    void insert_cut(core::environment::FoldTreeSketch {lvalue},unsigned long)

insert_cut( (FoldTreeSketch)arg1, (vector1_Real)bias) -> int : randomly insert a cut using the bias passed in.

C++ signature :
    unsigned long insert_cut(core::environment::FoldTreeSketch {lvalue},utility::vector1<double, std::allocator<double> >)

def insert_jump(

...)

insert_jump( (FoldTreeSketch)arg1, (int)p1, (int)p2) -> None : insert a jump between positions p1 and p2 in the graph

C++ signature : void insert_jump(core::environment::FoldTreeSketch {lvalue},unsigned long,unsigned long)

def nres(

...)

nres( (FoldTreeSketch)arg1) -> int : core/environment/FoldTreeSketch.hh:106

C++ signature : unsigned long nres(core::environment::FoldTreeSketch {lvalue})

def num_cuts(

...)

num_cuts( (FoldTreeSketch)arg1) -> int : core/environment/FoldTreeSketch.hh:110

C++ signature : unsigned long num_cuts(core::environment::FoldTreeSketch {lvalue})

def num_jumps(

...)

num_jumps( (FoldTreeSketch)arg1) -> int : core/environment/FoldTreeSketch.hh:108

C++ signature : unsigned long num_jumps(core::environment::FoldTreeSketch {lvalue})

def remove_cycles(

...)

remove_cycles( (FoldTreeSketch)arg1) -> set_Size : core/environment/FoldTreeSketch.hh:96

C++ signature :
    std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > remove_cycles(core::environment::FoldTreeSketch {lvalue})

remove_cycles( (FoldTreeSketch)arg1, (vector1_Real)bias) -> set_Size : core/environment/FoldTreeSketch.hh:98

C++ signature :
    std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > remove_cycles(core::environment::FoldTreeSketch {lvalue},utility::vector1<double, std::allocator<double> >)

def render(

...)

render( (FoldTreeSketch)arg1) -> FoldTree : wrapper for the other render()

C++ signature :
    boost::shared_ptr<core::kinematics::FoldTree> render(core::environment::FoldTreeSketch {lvalue})

render( (FoldTreeSketch)arg1, (FoldTree)ft) -> None : build this graph into the FoldTree ft. The state of the graph must be valid here.

C++ signature :
    void render(core::environment::FoldTreeSketch {lvalue},core::kinematics::FoldTree {lvalue})

class FoldTreeSketchAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (FoldTreeSketchAP)arg1) -> FoldTreeSketch :

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

class FoldTreeSketchCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (FoldTreeSketchCAP)arg1) -> FoldTreeSketch :

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

class LocalPosition

core/environment/LocalPosition.hh:35

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature :
    void __init__(_object*)

init( (object)arg1, (LocalPosition)) -> None : core/environment/LocalPosition.hh:35

C++ signature :
    void __init__(_object*,core::environment::LocalPosition)

init( (object)arg1, (str)comma_deliniated) -> None : core/environment/LocalPosition.hh:40

C++ signature :
    void __init__(_object*,std::string)

init( (object)arg1, (str), (int)) -> None : core/environment/LocalPosition.hh:42

C++ signature :
    void __init__(_object*,std::string,unsigned long)

def label(

...)

label( (LocalPosition)arg1) -> str : core/environment/LocalPosition.hh:44

C++ signature : std::string label(core::environment::LocalPosition {lvalue})

def position(

...)

position( (LocalPosition)arg1) -> int : core/environment/LocalPosition.hh:46

C++ signature : unsigned long position(core::environment::LocalPosition {lvalue})

class LocalPositionAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (LocalPositionAP)arg1) -> LocalPosition :

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

class LocalPositionCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (LocalPositionCAP)arg1) -> LocalPosition :

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

class SequenceAnnotation

core/environment/SequenceAnnotation.hh:44

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1, (int)length) -> None : core/environment/SequenceAnnotation.hh:51

C++ signature :
    void __init__(_object*,unsigned long)

init( (object)arg1, (SequenceAnnotation)) -> None : core/environment/SequenceAnnotation.hh:44

C++ signature :
    void __init__(_object*,core::environment::SequenceAnnotation)

def add_jump_label(

...)

add_jump_label( (SequenceAnnotation)arg1, (str), (int)) -> None : core/environment/SequenceAnnotation.hh:59

C++ signature : void add_jump_label(core::environment::SequenceAnnotation {lvalue},std::string,unsigned long)

def add_seq_label(

...)

add_seq_label( (SequenceAnnotation)arg1, (str), (std_vector_Size)) -> None : core/environment/SequenceAnnotation.hh:55

C++ signature :
    void add_seq_label(core::environment::SequenceAnnotation {lvalue},std::string,std::vector<unsigned long, std::allocator<unsigned long> >)

add_seq_label( (SequenceAnnotation)arg1, (str), (vector1_Size)) -> None : core/environment/SequenceAnnotation.hh:57

C++ signature :
    void add_seq_label(core::environment::SequenceAnnotation {lvalue},std::string,utility::vector1<unsigned long, std::allocator<unsigned long> >)

def append_seq(

...)

append_seq( (SequenceAnnotation)arg1, (str)label) -> None : append a single residue with the given label to the end of the Annotation

C++ signature : void append_seq(core::environment::SequenceAnnotation {lvalue},std::string)

def has_seq_label(

...)

has_seq_label( (SequenceAnnotation)arg1, (str)) -> bool : core/environment/SequenceAnnotation.hh:81

C++ signature : bool has_seq_label(core::environment::SequenceAnnotation {lvalue},std::string)

def length(

...)

length( (SequenceAnnotation)arg1) -> int : core/environment/SequenceAnnotation.hh:77

C++ signature :
    unsigned long length(core::environment::SequenceAnnotation {lvalue})

length( (SequenceAnnotation)arg1, (str)label) -> int : core/environment/SequenceAnnotation.hh:79

C++ signature :
    unsigned long length(core::environment::SequenceAnnotation {lvalue},std::string)

def resolve_jump(

...)

resolve_jump( (SequenceAnnotation)arg1, (str)label) -> int : core/environment/SequenceAnnotation.hh:75

C++ signature : unsigned long resolve_jump(core::environment::SequenceAnnotation {lvalue},std::string)

def resolve_seq(

...)

resolve_seq( (SequenceAnnotation)arg1, (LocalPosition)) -> int : core/environment/SequenceAnnotation.hh:70

C++ signature :
    unsigned long resolve_seq(core::environment::SequenceAnnotation {lvalue},core::environment::LocalPosition)

resolve_seq( (SequenceAnnotation)arg1, (str)label) -> vector1_Size : core/environment/SequenceAnnotation.hh:73

C++ signature :
    utility::vector1<unsigned long, std::allocator<unsigned long> > resolve_seq(core::environment::SequenceAnnotation {lvalue},std::string)

def rm_seq_label(

...)

rm_seq_label( (SequenceAnnotation)arg1, (str)) -> None : core/environment/SequenceAnnotation.hh:61

C++ signature : void rm_seq_label(core::environment::SequenceAnnotation {lvalue},std::string)

class SequenceAnnotationAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (SequenceAnnotationAP)arg1) -> SequenceAnnotation :

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

class SequenceAnnotationCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (SequenceAnnotationCAP)arg1) -> SequenceAnnotation :

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