Package rosetta :: Package protocols :: Package toolbox :: Package match_enzdes_util :: Module _protocols_toolbox_match_enzdes_util_
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Module _protocols_toolbox_match_enzdes_util_

Classes [hide private]
  AlignPoseToInvrotTreeMover
small mover that takes an invrot tree
  AlignPoseToInvrotTreeMoverAP
  AlignPoseToInvrotTreeMoverCAP
  AllowedSeqposForGeomCst
a simple helper class that holds a list of what sequence positions each geom cst is allowd to be at not sure about the ideal home of this class yet, the matcher task could use it too
  AllowedSeqposForGeomCstAP
  AllowedSeqposForGeomCstCAP
  CovalentConnectionReplaceInfo
/////////////////////////////////////////////////////////////////////////////////////...
  CovalentConnectionReplaceInfoAP
  CovalentConnectionReplaceInfoCAP
  CstResInteractions
protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:141
  CstResInteractionsAP
  CstResInteractionsCAP
  EnzConstraintIO
protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh:66
  EnzConstraintIOAP
  EnzConstraintIOCAP
  EnzConstraintParameters
class that holds all the parameters for one specific constraint
  EnzConstraintParametersAP
  EnzConstraintParametersCAP
  EnzCstTemplateRes
helper class for class EnzConstraintParameters, gathers information from cst input and pdb input
  EnzCstTemplateResAP
  EnzCstTemplateResAtoms
helper class for EnzCstTemplateRes, holds atom ids corresponding to the residue types in a certain pose
  EnzCstTemplateResAtomsAP
  EnzCstTemplateResAtomsCAP
  EnzCstTemplateResCAP
  EnzCstTemplateResCache
protocols/toolbox/match_enzdes_util/EnzdesCstCache.hh:180
  EnzCstTemplateResCacheAP
  EnzCstTemplateResCacheCAP
  EnzdesCacheableObserver
protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.hh:60
  EnzdesCacheableObserverAP
  EnzdesCacheableObserverCAP
  EnzdesCstCache
a simple class to store the pose specific enzdes constraint information in the actual pose
  EnzdesCstCacheAP
  EnzdesCstCacheCAP
  EnzdesCstParamCache
protocols/toolbox/match_enzdes_util/EnzdesCstCache.hh:105
  EnzdesCstParamCacheAP
  EnzdesCstParamCacheCAP
  EnzdesLoopInfo
protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:174
  EnzdesLoopInfoAP
  EnzdesLoopInfoCAP
  EnzdesLoopsFile
class to process an enzdes loops file
  EnzdesLoopsFileAP
  EnzdesLoopsFileCAP
  EnzdesSeqRecoveryCache
protocols/toolbox/match_enzdes_util/EnzdesSeqRecoveryCache.hh:41
  EnzdesSeqRecoveryCacheAP
  EnzdesSeqRecoveryCacheCAP
  ExternalGeomSampler
The external geom sampler is a class that manages the data necessary to construct the coordinates of the three atoms in the downstream partner.
  ExternalGeomSamplerAP
  ExternalGeomSamplerCAP
  ExternalTransform
protocols/toolbox/match_enzdes_util/ExternalGeomSampler.fwd.hh:24
  GeomSampleInfo
class that stores information of one geometric parameter line of the .cst file i.e.
  GeomSampleInfoAP
  GeomSampleInfoCAP
  InvrotCollector
@ brief helper class for collecting all different definitions of invrots from a tree
  InvrotCollectorAP
  InvrotCollectorCAP
  InvrotTarget
the 'root' target against which the inverse rotamers are built abstract base class to allow for invrots being built against any sort of entity
  InvrotTargetAP
  InvrotTargetCAP
  InvrotTree
abstract base class for the inverse rotamer tree is abstract so that in the future inverse rots could be generated in different ways than throug the enz cst machinery
  InvrotTreeAP
  InvrotTreeCAP
  InvrotTreeNode
protocols/toolbox/match_enzdes_util/InvrotTreeNode.hh:36
  InvrotTreeNodeAP
  InvrotTreeNodeBase
abstract base class for an inverse rotamer tree node.
  InvrotTreeNodeBaseAP
  InvrotTreeNodeBaseCAP
  InvrotTreeNodeCAP
  LigandConformer
protocols/toolbox/match_enzdes_util/LigandConformer.hh:48
  LigandConformerAP
  LigandConformerCAP
  MatchConstraintFileInfo
protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.hh:142
  MatchConstraintFileInfoAP
  MatchConstraintFileInfoCAP
  MatchConstraintFileInfoList
a simple container class to contain several MatchConstraintFileInfo instances.
  MatchConstraintFileInfoListAP
  MatchConstraintFileInfoListCAP
  ResInteractions
protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:40
  ResInteractionsAP
  ResInteractionsCAP
  SingleResidueInvrotTarget
protocols/toolbox/match_enzdes_util/InvrotTarget.hh:115
  SingleResidueInvrotTargetAP
  SingleResidueInvrotTargetCAP
  SingletonBase_T_core_chemical_ChemicalManager_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.
  SingletonBase_T_core_chemical_ChemicalManager_TAP
  SingletonBase_T_core_chemical_ChemicalManager_TCAP
  TheozymeInvrotTree
This class takes an EnzConstraintIO object and generates a 3D model of the theozyme in it, where inverse rotamers are generated for every block in the cstfile.
  TheozymeInvrotTreeAP
  TheozymeInvrotTreeCAP
  __CPP_AlignPoseToInvrotTreeMover__
  __CPP_CstResInteractions__
  __CPP_InvrotTreeNodeBase__
  __CPP_InvrotTreeNode__
  __CPP_InvrotTree__
  __CPP_ResInteractions__
  __CPP_TheozymeInvrotTree__
Functions [hide private]
 
add_relevant_restypes_to_subset(...)
add_relevant_restypes_to_subset( (object)restype_subset, (object)restypes, (ResidueTypeSetCAP)restype_set) -> None : function to go through a list of restypes and reduce them to chemically identical ones based on the same base_name i.e.
 
assemble_remark_line(...)
assemble_remark_line( (str)chainA, (str)resA, (int)seqposA, (str)chainB, (str)resB, (int)seqposB, (int)cst_block [, (int)ex_geom_id=1]) -> str : protocols/toolbox/match_enzdes_util/util_functions.hh:84
 
constrain_pose_res_to_invrots(...)
constrain_pose_res_to_invrots( (object)invrots, (vector1_Size)seqpos, (Pose)pose, (AtomID)fixed_pt [, (__CPP_Func__)constraint_func=0]) -> AmbiguousConstraint : constraints each invrot to the backbone of each seqpos and throws all those constraints into one ambiguous constraint.
 
cst_residue_in_pose(...)
cst_residue_in_pose( (Pose)pose, (int)geomcst, (int)geomcst_template_res) -> Residue : convenience function that returns a residue of the desired cst interaction in case there are no constraints in the pose, returns null pointer
 
get_enzdes_observer(...)
get_enzdes_observer( (Pose)pose) -> EnzdesCacheableObserver : protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.hh:58
 
get_first_protein_residue(...)
get_first_protein_residue( (Pose)pose) -> int : /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
get_last_protein_residue(...)
get_last_protein_residue( (Pose)pose) -> int : /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
replace_residue_keeping_all_atom_positions(...)
replace_residue_keeping_all_atom_positions( (Pose)pose, (Residue)new_res, (int)res_pos) -> None : protocols/toolbox/match_enzdes_util/util_functions.hh:38
 
split_up_remark_line(...)
split_up_remark_line( (str)line, (str)chainA, (str)resA, (int)seqposA, (str)chainB, (str)resB, (int)seqposB, (int)cst_block, (int)ex_geom_id) -> bool : protocols/toolbox/match_enzdes_util/util_functions.hh:98
Variables [hide private]
  HT_ang_U1D2 = rosetta.protocols.toolbox.match_enzdes_util._pro...
  HT_ang_U2D1 = rosetta.protocols.toolbox.match_enzdes_util._pro...
  HT_tor_U1D3 = rosetta.protocols.toolbox.match_enzdes_util._pro...
  HT_tor_U2D2 = rosetta.protocols.toolbox.match_enzdes_util._pro...
  HT_tor_U3D1 = rosetta.protocols.toolbox.match_enzdes_util._pro...
  __package__ = None
  n_external_transforms = rosetta.protocols.toolbox.match_enzdes...
Function Details [hide private]

add_relevant_restypes_to_subset(...)

 

add_relevant_restypes_to_subset( (object)restype_subset, (object)restypes, (ResidueTypeSetCAP)restype_set) -> None :
    function to go through a list of restypes and
    reduce them to chemically identical ones based on the same base_name
    i.e. this function gets rid of the variant redundancy
    

    C++ signature :
        void add_relevant_restypes_to_subset(utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > > {lvalue},utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > >,boost::weak_ptr<core::chemical::ResidueTypeSet const>)

assemble_remark_line(...)

 

assemble_remark_line( (str)chainA, (str)resA, (int)seqposA, (str)chainB, (str)resB, (int)seqposB, (int)cst_block [, (int)ex_geom_id=1]) -> str :
    protocols/toolbox/match_enzdes_util/util_functions.hh:84

    C++ signature :
        std::string assemble_remark_line(std::string,std::string,int,std::string,std::string,int,unsigned long [,unsigned long=1])

constrain_pose_res_to_invrots(...)

 

constrain_pose_res_to_invrots( (object)invrots, (vector1_Size)seqpos, (Pose)pose, (AtomID)fixed_pt [, (__CPP_Func__)constraint_func=0]) -> AmbiguousConstraint :
    constraints each invrot to the
    backbone of each seqpos and throws all
    those constraints into one ambiguous
    constraint.
    

    C++ signature :
        boost::shared_ptr<core::scoring::constraints::AmbiguousConstraint const> constrain_pose_res_to_invrots(std::list<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,utility::vector1<unsigned long, std::allocator<unsigned long> >,core::pose::Pose,core::id::AtomID [,boost::shared_ptr<core::scoring::func::Func>=0])

constrain_pose_res_to_invrots( (object)invrots, (vector1_Size)seqpos, (Pose)pose [, (__CPP_Func__)constraint_func=0]) -> AmbiguousConstraint :
    fowarding function for function below
    

    C++ signature :
        boost::shared_ptr<core::scoring::constraints::AmbiguousConstraint const> constrain_pose_res_to_invrots(std::list<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,utility::vector1<unsigned long, std::allocator<unsigned long> >,core::pose::Pose [,boost::shared_ptr<core::scoring::func::Func>=0])

cst_residue_in_pose(...)

 

cst_residue_in_pose( (Pose)pose, (int)geomcst, (int)geomcst_template_res) -> Residue :
    convenience function that returns a residue
    of the desired cst interaction
    in case there are no constraints in the pose,
    returns null pointer
    

    C++ signature :
        boost::shared_ptr<core::conformation::Residue const> cst_residue_in_pose(core::pose::Pose,unsigned long,unsigned long)

get_enzdes_observer(...)

 

get_enzdes_observer( (Pose)pose) -> EnzdesCacheableObserver :
    protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.hh:58

    C++ signature :
        boost::shared_ptr<protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver const> get_enzdes_observer(core::pose::Pose)

get_enzdes_observer( (Pose)pose) -> EnzdesCacheableObserver :
    convenience function to get a cacheable observer from a pose
    

    C++ signature :
        boost::shared_ptr<protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver> get_enzdes_observer(core::pose::Pose {lvalue})

get_first_protein_residue(...)

 

get_first_protein_residue( (Pose)pose) -> int :
    /////////////////////////////////////////////////////////////////////////////////////////////////////////////
    

    C++ signature :
        unsigned long get_first_protein_residue(core::pose::Pose)

get_last_protein_residue(...)

 

get_last_protein_residue( (Pose)pose) -> int :
    /////////////////////////////////////////////////////////////////////////////////////////////////////////////
    

    C++ signature :
        unsigned long get_last_protein_residue(core::pose::Pose)

replace_residue_keeping_all_atom_positions(...)

 

replace_residue_keeping_all_atom_positions( (Pose)pose, (Residue)new_res, (int)res_pos) -> None :
    protocols/toolbox/match_enzdes_util/util_functions.hh:38

    C++ signature :
        void replace_residue_keeping_all_atom_positions(core::pose::Pose {lvalue},core::conformation::Residue,unsigned long)

split_up_remark_line(...)

 

split_up_remark_line( (str)line, (str)chainA, (str)resA, (int)seqposA, (str)chainB, (str)resB, (int)seqposB, (int)cst_block, (int)ex_geom_id) -> bool :
    protocols/toolbox/match_enzdes_util/util_functions.hh:98

    C++ signature :
        bool split_up_remark_line(std::string,std::string {lvalue},std::string {lvalue},int {lvalue},std::string {lvalue},std::string {lvalue},int {lvalue},unsigned long {lvalue},unsigned long {lvalue})


Variables Details [hide private]

HT_ang_U1D2

Value:
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_e\
nzdes_util_.ExternalTransform.HT_ang_U1D2

HT_ang_U2D1

Value:
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_e\
nzdes_util_.ExternalTransform.HT_ang_U2D1

HT_tor_U1D3

Value:
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_e\
nzdes_util_.ExternalTransform.HT_tor_U1D3

HT_tor_U2D2

Value:
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_e\
nzdes_util_.ExternalTransform.HT_tor_U2D2

HT_tor_U3D1

Value:
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_e\
nzdes_util_.ExternalTransform.HT_tor_U3D1

n_external_transforms

Value:
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_e\
nzdes_util_.ExternalTransform.n_external_transforms