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AlignPoseToInvrotTreeMover small mover that takes an invrot tree |
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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 |
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AllowedSeqposForGeomCstAP | |||
AllowedSeqposForGeomCstCAP | |||
CovalentConnectionReplaceInfo /////////////////////////////////////////////////////////////////////////////////////... |
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CovalentConnectionReplaceInfoAP | |||
CovalentConnectionReplaceInfoCAP | |||
CstResInteractions protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:141 |
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CstResInteractionsAP | |||
CstResInteractionsCAP | |||
EnzConstraintIO protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh:66 |
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EnzConstraintIOAP | |||
EnzConstraintIOCAP | |||
EnzConstraintParameters class that holds all the parameters for one specific constraint |
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EnzConstraintParametersAP | |||
EnzConstraintParametersCAP | |||
EnzCstTemplateRes helper class for class EnzConstraintParameters, gathers information from cst input and pdb input |
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EnzCstTemplateResAP | |||
EnzCstTemplateResAtoms helper class for EnzCstTemplateRes, holds atom ids corresponding to the residue types in a certain pose |
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EnzCstTemplateResAtomsAP | |||
EnzCstTemplateResAtomsCAP | |||
EnzCstTemplateResCAP | |||
EnzCstTemplateResCache protocols/toolbox/match_enzdes_util/EnzdesCstCache.hh:180 |
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EnzCstTemplateResCacheAP | |||
EnzCstTemplateResCacheCAP | |||
EnzdesCacheableObserver protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.hh:60 |
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EnzdesCacheableObserverAP | |||
EnzdesCacheableObserverCAP | |||
EnzdesCstCache a simple class to store the pose specific enzdes constraint information in the actual pose |
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EnzdesCstCacheAP | |||
EnzdesCstCacheCAP | |||
EnzdesCstParamCache protocols/toolbox/match_enzdes_util/EnzdesCstCache.hh:105 |
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EnzdesCstParamCacheAP | |||
EnzdesCstParamCacheCAP | |||
EnzdesLoopInfo protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:174 |
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EnzdesLoopInfoAP | |||
EnzdesLoopInfoCAP | |||
EnzdesLoopsFile class to process an enzdes loops file |
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EnzdesLoopsFileAP | |||
EnzdesLoopsFileCAP | |||
EnzdesSeqRecoveryCache protocols/toolbox/match_enzdes_util/EnzdesSeqRecoveryCache.hh:41 |
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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. |
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ExternalGeomSamplerAP | |||
ExternalGeomSamplerCAP | |||
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 | |||
InvrotCollector @ brief helper class for collecting all different definitions of invrots from a tree |
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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 |
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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 |
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InvrotTreeAP | |||
InvrotTreeCAP | |||
InvrotTreeNode protocols/toolbox/match_enzdes_util/InvrotTreeNode.hh:36 |
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InvrotTreeNodeAP | |||
InvrotTreeNodeBase abstract base class for an inverse rotamer tree node. |
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InvrotTreeNodeBaseAP | |||
InvrotTreeNodeBaseCAP | |||
InvrotTreeNodeCAP | |||
LigandConformer protocols/toolbox/match_enzdes_util/LigandConformer.hh:48 |
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LigandConformerAP | |||
LigandConformerCAP | |||
MatchConstraintFileInfo protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.hh:142 |
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MatchConstraintFileInfoAP | |||
MatchConstraintFileInfoCAP | |||
MatchConstraintFileInfoList a simple container class to contain several MatchConstraintFileInfo instances. |
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MatchConstraintFileInfoListAP | |||
MatchConstraintFileInfoListCAP | |||
ResInteractions protocols/toolbox/match_enzdes_util/EnzdesLoopsFile.hh:40 |
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ResInteractionsAP | |||
ResInteractionsCAP | |||
SingleResidueInvrotTarget protocols/toolbox/match_enzdes_util/InvrotTarget.hh:115 |
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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. |
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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. |
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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>) |
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( (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( (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( (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( (Pose)pose) -> int : ///////////////////////////////////////////////////////////////////////////////////////////////////////////// C++ signature : unsigned long get_first_protein_residue(core::pose::Pose) |
get_last_protein_residue( (Pose)pose) -> int : ///////////////////////////////////////////////////////////////////////////////////////////////////////////// C++ signature : unsigned long get_last_protein_residue(core::pose::Pose) |
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( (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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