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AlignPoseToInvrotTreeMover small mover that takes an invrot tree |
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| AlignPoseToInvrotTreeMoverAP | |||
| AlignPoseToInvrotTreeMoverCAP | |||
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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 |
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| AllowedSeqposForGeomCstAP | |||
| AllowedSeqposForGeomCstCAP | |||
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CovalentConnectionReplaceInfo /////////////////////////////////////////////////////////////////////////////////////... |
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| CovalentConnectionReplaceInfoAP | |||
| CovalentConnectionReplaceInfoCAP | |||
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CstResInteractions protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:141 |
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| CstResInteractionsAP | |||
| CstResInteractionsCAP | |||
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EnzConstraintIO protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh:66 |
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| EnzConstraintIOAP | |||
| EnzConstraintIOCAP | |||
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EnzConstraintParameters class that holds all the parameters for one specific constraint |
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| EnzConstraintParametersAP | |||
| EnzConstraintParametersCAP | |||
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EnzCstTemplateRes helper class for class EnzConstraintParameters, gathers information from cst input and pdb input |
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| EnzCstTemplateResAP | |||
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EnzCstTemplateResAtoms helper class for EnzCstTemplateRes, holds atom ids corresponding to the residue types in a certain pose |
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| EnzCstTemplateResAtomsAP | |||
| EnzCstTemplateResAtomsCAP | |||
| EnzCstTemplateResCAP | |||
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EnzCstTemplateResCache protocols/toolbox/match_enzdes_util/EnzdesCstCache.hh:180 |
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| EnzCstTemplateResCacheAP | |||
| EnzCstTemplateResCacheCAP | |||
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EnzdesCacheableObserver protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.hh:60 |
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| EnzdesCacheableObserverAP | |||
| EnzdesCacheableObserverCAP | |||
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EnzdesCstCache a simple class to store the pose specific enzdes constraint information in the actual pose |
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| EnzdesCstCacheAP | |||
| EnzdesCstCacheCAP | |||
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EnzdesCstParamCache protocols/toolbox/match_enzdes_util/EnzdesCstCache.hh:105 |
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| EnzdesCstParamCacheAP | |||
| EnzdesCstParamCacheCAP | |||
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EnzdesLoopInfo protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:174 |
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| EnzdesLoopInfoAP | |||
| EnzdesLoopInfoCAP | |||
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EnzdesLoopsFile class to process an enzdes loops file |
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| EnzdesLoopsFileAP | |||
| EnzdesLoopsFileCAP | |||
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EnzdesSeqRecoveryCache protocols/toolbox/match_enzdes_util/EnzdesSeqRecoveryCache.hh:41 |
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| EnzdesSeqRecoveryCacheAP | |||
| EnzdesSeqRecoveryCacheCAP | |||
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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. |
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| ExternalGeomSamplerAP | |||
| ExternalGeomSamplerCAP | |||
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ExternalTransform protocols/toolbox/match_enzdes_util/ExternalGeomSampler.fwd.hh:24 |
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GeomSampleInfo class that stores information of one geometric parameter line of the .cst file i.e. |
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| GeomSampleInfoAP | |||
| GeomSampleInfoCAP | |||
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InvrotCollector @ brief helper class for collecting all different definitions of invrots from a tree |
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| InvrotCollectorAP | |||
| InvrotCollectorCAP | |||
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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 |
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| InvrotTargetAP | |||
| InvrotTargetCAP | |||
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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 |
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| InvrotTreeAP | |||
| InvrotTreeCAP | |||
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InvrotTreeNode protocols/toolbox/match_enzdes_util/InvrotTreeNode.hh:36 |
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| InvrotTreeNodeAP | |||
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InvrotTreeNodeBase abstract base class for an inverse rotamer tree node. |
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| InvrotTreeNodeBaseAP | |||
| InvrotTreeNodeBaseCAP | |||
| InvrotTreeNodeCAP | |||
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LigandConformer protocols/toolbox/match_enzdes_util/LigandConformer.hh:48 |
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| LigandConformerAP | |||
| LigandConformerCAP | |||
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MatchConstraintFileInfo protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.hh:142 |
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| MatchConstraintFileInfoAP | |||
| MatchConstraintFileInfoCAP | |||
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MatchConstraintFileInfoList a simple container class to contain several MatchConstraintFileInfo instances. |
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| MatchConstraintFileInfoListAP | |||
| MatchConstraintFileInfoListCAP | |||
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ResInteractions protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:40 |
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| ResInteractionsAP | |||
| ResInteractionsCAP | |||
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SingleResidueInvrotTarget protocols/toolbox/match_enzdes_util/InvrotTarget.hh:115 |
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| SingleResidueInvrotTargetAP | |||
| SingleResidueInvrotTargetCAP | |||
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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. |
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| SingletonBase_T_core_chemical_ChemicalManager_TAP | |||
| SingletonBase_T_core_chemical_ChemicalManager_TCAP | |||
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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. |
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| TheozymeInvrotTreeAP | |||
| TheozymeInvrotTreeCAP | |||
| __CPP_AlignPoseToInvrotTreeMover__ | |||
| __CPP_CstResInteractions__ | |||
| __CPP_InvrotTreeNodeBase__ | |||
| __CPP_InvrotTreeNode__ | |||
| __CPP_InvrotTree__ | |||
| __CPP_ResInteractions__ | |||
| __CPP_TheozymeInvrotTree__ | |||
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HT_ang_U1D2 = rosetta.protocols.toolbox.match_enzdes_util._pro
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HT_ang_U2D1 = rosetta.protocols.toolbox.match_enzdes_util._pro
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HT_tor_U1D3 = rosetta.protocols.toolbox.match_enzdes_util._pro
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HT_tor_U2D2 = rosetta.protocols.toolbox.match_enzdes_util._pro
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HT_tor_U3D1 = rosetta.protocols.toolbox.match_enzdes_util._pro
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__package__ = None
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n_external_transforms = rosetta.protocols.toolbox.match_enzdes
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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>)
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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])
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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])
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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)
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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})
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get_first_protein_residue( (Pose)pose) -> int :
/////////////////////////////////////////////////////////////////////////////////////////////////////////////
C++ signature :
unsigned long get_first_protein_residue(core::pose::Pose)
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get_last_protein_residue( (Pose)pose) -> int :
/////////////////////////////////////////////////////////////////////////////////////////////////////////////
C++ signature :
unsigned long get_last_protein_residue(core::pose::Pose)
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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)
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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})
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HT_ang_U1D2
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HT_ang_U2D1
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HT_tor_U1D3
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HT_tor_U2D2
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HT_tor_U3D1
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n_external_transforms
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