|
| | ProtectedConformation (ProtectedConformation const &src) |
| |
| | ProtectedConformation (EnvironmentCAP, core::conformation::Conformation const &) |
| |
| | ~ProtectedConformation () override |
| |
| EnvironmentCAP | environment () const |
| |
| void | env_destruction () |
| |
| bool | is_protected () const override |
| |
| core::conformation::ResidueOP | match_variants (core::Size seqpos, core::conformation::Residue const &in_rsd) const |
| |
| SequenceAnnotationCOP | resolver () const |
| |
| SequenceAnnotationCOP | annotations () const |
| |
| core::conformation::ConformationOP | clone () const override |
| | clone the conformation More...
|
| |
| Conformation & | operator= (Conformation const &src) override |
| | equals operator More...
|
| |
| void | set_torsion (TorsionID const &id, core::Real const setting) override |
| | Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump. More...
|
| |
| void | set_jump (AtomID const &, core::kinematics::Jump const &) override |
| | set a jump More...
|
| |
| void | set_jump (int const, core::kinematics::Jump const &) override |
| | Sets the jump <jump_number> to <new_jump> More...
|
| |
| void | set_secstruct (core::Size const seqpos, char const setting) override |
| | Sets the secondary structure of the position <seqpos> to <setting> More...
|
| |
| void | replace_residue (core::Size const seqpos, core::conformation::Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) override |
| | function to replace a residue based on superposition on the specified input atom pairs More...
|
| |
| void | replace_residue (core::Size const seqpos, core::conformation::Residue const &new_rsd, bool const orient_backbone) override |
| | replace residue More...
|
| |
| void | set_stub_transform (core::id::StubID const &stub_id1, core::id::StubID const &stub_id2, core::kinematics::RT const &target_rt) override |
| | Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms. More...
|
| |
| void | set_dof (DOF_ID const &id, core::Real const setting) override |
| | Sets the AtomTree degree of freedom (DOF) <id> to <setting> More...
|
| |
| void | set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, core::Real const setting, bool const quiet=false) override |
| | Sets the torsion angle defined by <atom[1-4]> to <setting> More...
|
| |
| void | set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, core::Real const setting) override |
| | Sets the bond angle defined by <atom[1-3]> to <setting> More...
|
| |
| void | set_bond_length (AtomID const &atom1, AtomID const &atom2, core::Real const setting) override |
| | Sets the cond length between <atom1> and <atom2> to <setting> More...
|
| |
| void | insert_fragment (core::id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz) override |
| |
| void | fold_tree (FoldTree const &) override |
| | Sets the FoldTree to <fold_tree_in> More...
|
| |
| void | chain_endings (utility::vector1< core::Size > const &) override |
| | Sets the list of (chain number) chain endings. More...
|
| |
| void | insert_chain_ending (core::Size const) override |
| | Marks <seqpos> as the end of a new (chain number) chain. More...
|
| |
| void | delete_chain_ending (core::Size const) override |
| | Deletes <seqpos> from the list of (chain number) chain endings. More...
|
| |
| void | reset_chain_endings () override |
| | Resets chain data so that the Conformation is marked as a single (chain number) chain. More...
|
| |
| void | chains_from_termini () override |
| | Rederive the (chain number) chains from the termini/polymer status. More...
|
| |
| void | append_residue_by_jump (core::conformation::Residue const &, core::Size const, std::string const &="", std::string const &="", bool const _=false) override |
| | Append a new residue by a jump. More...
|
| |
| void | append_polymer_residue_after_seqpos (core::conformation::Residue const &, core::Size const, bool const) override |
| | glues to seqpos and perhaps also seqpos+1 More...
|
| |
| void | safely_append_polymer_residue_after_seqpos (core::conformation::Residue const &, core::Size const, bool const) override |
| | glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary More...
|
| |
| void | prepend_polymer_residue_before_seqpos (core::conformation::Residue const &, core::Size const, bool const) override |
| | glues to seqpos and perhaps also seqpos-1 More...
|
| |
| void | safely_prepend_polymer_residue_before_seqpos (core::conformation::Residue const &, core::Size const, bool const) override |
| | glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary More...
|
| |
| void | delete_polymer_residue (core::Size const) override |
| | Delete polymer residue at the given sequence position. More...
|
| |
| void | delete_residue_slow (core::Size const) override |
| | Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More...
|
| |
| void | delete_residue_range_slow (core::Size const range_begin, core::Size const range_end) override |
| | Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More...
|
| |
| void | declare_chemical_bond (core::Size const, std::string const &, core::Size const, std::string const &) override |
| | Declare that a chemical bond exists between two residues. More...
|
| |
| void | insert_conformation_by_jump (Conformation const &, core::Size const, core::Size const, core::Size const, core::Size const, std::string const &="", std::string const &="") override |
| | Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump. More...
|
| |
| void | rebuild_polymer_bond_dependent_atoms (core::Size const) override |
| | Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1. More...
|
| |
| void | insert_ideal_geometry_at_polymer_bond (core::Size const seqpos) override |
| |
| void | insert_ideal_geometry_at_residue_connection (core::Size const pos1, core::Size const connid1) override |
| |
| void | set_polymeric_connection (core::Size, core::Size) override |
| | identify polymeric connections More...
|
| |
| void | fix_disulfides (utility::vector1< std::pair< core::Size, core::Size > > const &) override |
| | Assigns disulfide bonds based on a pre-determined list. More...
|
| |
| void | set_xyz (AtomID const &id, core::PointPosition const &position) override |
| |
| void | batch_set_xyz (utility::vector1< AtomID > const &id, utility::vector1< core::PointPosition > const &position) override |
| |
| void | reset_move_data () override |
| | forget all the structure modifications More...
|
| |
| void | clear () |
| |
| void | fill_missing_atoms (core::id::AtomID_Mask missing) override |
| |
| bool | same_type_as_me (Conformation const &other, bool const recurse) const override |
| | determine the type of the ConformationOP More...
|
| |
| iterator | begin () noexcept |
| |
| const_iterator | begin () const noexcept |
| |
| iterator | end () noexcept |
| |
| const_iterator | end () const noexcept |
| |
| | Conformation () |
| | constructor More...
|
| |
| | ~Conformation () override |
| | default destructor More...
|
| |
| | Conformation (Conformation const &src) |
| | copy constructor More...
|
| |
| virtual void | detached_copy (Conformation const &src) |
| | copy the other conformation into this, but make sure that the two share no possibly-non-bitwise-const data nor do they refer to each other (as the AtomTree does with its topological observer system). More...
|
| |
| void | clear () |
| | clear data More...
|
| |
| ConformationCOP | get_self_ptr () const |
| | self pointers More...
|
| |
| ConformationOP | get_self_ptr () |
| |
| ConformationCAP | get_self_weak_ptr () const |
| |
| ConformationAP | get_self_weak_ptr () |
| |
| void | debug_residue_torsions (bool verbose=false) const |
| | debugging More...
|
| |
| void | show_residue_connections () const |
| | Show residue connections for debugging purposes. More...
|
| |
| void | show_residue_connections (std::ostream &os) const |
| | Show residue connections for debugging purposes. More...
|
| |
| bool | sequence_matches (Conformation const &other) const |
| | do the names of all residues in this and src match? More...
|
| |
| Size | size () const |
| | Returns the number of residues in the Conformation. More...
|
| |
| bool | empty () const |
| | Returns true if this conformation does not have any residues. More...
|
| |
| core::chemical::ResidueTypeSetCOP | residue_type_set_for_conf (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const |
| | Return the appropriate ResidueTypeSet for the Conformation If mode is INVALID_t (the default), then return the typeset for the majority mode of the Conformation. Note: This may be a GlobalResidueTypeSet, if the Conformation doesn't have a specific PoseResidueTypeSet. More...
|
| |
| core::chemical::PoseResidueTypeSetOP | modifiable_residue_type_set_for_conf (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const |
| | Return a clone of the Conformation-specific PoseResidueTypeSet (note this is const) Modifications to this RTS won't be seen in the Conformation unless you pass it back in with reset_residue_type_set_for_conf() Should always return a non-null pointer: will create a new PoseResidueTypeSet if the Conformation doesn't have it already. More...
|
| |
| void | reset_residue_type_set_for_conf (core::chemical::PoseResidueTypeSetCOP new_set, core::chemical::TypeSetMode mode=core::chemical::INVALID_t) |
| | Reset the Conformation-specific PoseResidueTypeSet for the appropriate mode to the given RTS. (If the given mode is INVALID_t (the recommended default) the mode will be auto-determined from the RTS.) More...
|
| |
| core::chemical::TypeSetMode | residue_typeset_mode (bool majority=true) const |
| | What mode of ResidueTypeSet is this Conformation made of? If majority is true, it will be the mode of the ResidueTypes for most residues in the pose. If majority is false, core::chemical::MIXED_t will be returned for conformations with ResidueTypes of multiple modes. More...
|
| |
| bool | is_fullatom () const |
| | convenience test for residue_type_set mode More...
|
| |
| bool | is_centroid () const |
| | convenience test for residue_type_set mode More...
|
| |
| bool | is_mixed_mode () const |
| | convenience test for residue_type_set mode More...
|
| |
| bool | is_membrane () const |
| | convenience test for if the conformation contains information for a membrane protein More...
|
| |
| bool | contains_carbohydrate_residues () const |
| | Return true if this conformation contains any carbohydrate residues. More...
|
| |
| void | contains_carbohydrate_residues (bool setting) |
| | Set whether this conformation contains any carbohydrate residues. More...
|
| |
| Size | chain_end (Size chain) const |
| | Returns the position number of the last residue in chain number <chain> More...
|
| |
| Size | chain_begin (Size chain) const |
| | Returns the position number of the first residue in chain number <chain> More...
|
| |
| Size | num_chains () const |
| | Returns the number of chains. More...
|
| |
| utility::vector1< Size > const & | chain_endings () const |
| | Returns the list of (chain number) chain endings. More...
|
| |
| char | secstruct (Size seqpos) const |
| | Returns the secondary structure the position <seqpos> More...
|
| |
| void | set_membrane_info (membrane::MembraneInfoOP mem_info) |
| | Setup a Membrane Info object in Conformation - pos & topology. More...
|
| |
| membrane::MembraneInfoOP | membrane_info () |
| | Returns the const MembraneInfo object in conformation. More...
|
| |
| membrane::MembraneInfoOP | membrane_info () const |
| | Returns the const MembraneInfo object in conformation. More...
|
| |
| void | update_membrane_position (Vector center, Vector normal) |
| | Update Normal, Center in the Membrane. More...
|
| |
| void | check_valid_membrane () const |
| | Check that a new membrane position is valid. More...
|
| |
| carbohydrates::GlycanTreeSetCOP | glycan_tree_set () const |
| | Get the glycan tree set. Nullptr if not present. More...
|
| |
| void | setup_glycan_trees () |
| | Setup glycan trees and attach length observer. More...
|
| |
| void | clear_glycan_trees () |
| | Safely detaches any tree observers and clears it to null. More...
|
| |
| virtual FoldTree const & | fold_tree () const |
| | Returns the conformation's FoldTree. More...
|
| |
| AtomTree const & | atom_tree () const |
| | Returns the conformation's AtomTree. More...
|
| |
| chemical::AA const & | aa (Size seqpos) const |
| | Returns the AA enum for position <seqpos> More...
|
| |
| std::string | annotated_sequence (bool show_all_variants) const |
| | Returns the variant-tagged string representing the residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]. More...
|
| |
| Residue const & | residue (Size seqpos) const |
| | access one of the residues More...
|
| |
| basic::datacache::BasicDataCache const & | residue_data (Size seqpos) const |
| | Read access to the datacache array stored inside a Residue object. Also accessible to the user by calling residue( seqpos ).data_ptr() directly. More...
|
| |
| basic::datacache::BasicDataCache & | residue_data (Size seqpos) |
| | Write access to the datacache array stored inside a Residue object. Although the Conformation very deliberately does not grant users write access to the whole of its Residue objects, it will grant users access to the Residue objects data cache. So while the coordinates and dihedrals of the Residue will not be changable e.g. during the setup-for-scoring phase, data derived from those coordinates and dihedrals and which ends up living in the Residue will be changable. More...
|
| |
| ResidueCOP | residue_cop (Size seqpos) const |
| | access one of the residues, using COP More...
|
| |
| chemical::ResidueType const & | residue_type (Size seqpos) const |
| | access one of the residue's types – avoids coord/torsion update More...
|
| |
| chemical::ResidueTypeCOP | residue_type_ptr (Size seqpos) const |
| | access one of the residue's types as a COP – avoids coord/torsion update More...
|
| |
| ResidueCOPs | const_residues () const |
| | Inefficient – constructs copy of residues_. More...
|
| |
| virtual void | append_residues (utility::vector1< conformation::ResidueOP > const &residues, utility::vector1< core::Size > const &jump_connection) |
| | Function for building poses Append all the residues to the Conformation. If the corresponding jump connection is zero, attach by polymeric connection to the previous residue. More...
|
| |
| void | insert_residue_by_jump (Residue const &new_rsd_in, Size seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false) |
| | Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) More...
|
| |
| void | insert_residue_by_bond (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false) |
| | Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) More...
|
| |
| void | append_residue_by_bond (conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool const start_new_chain=false, bool const lookup_bond_length=false) |
| | Append a new residue by a bond. More...
|
| |
| virtual utility::vector1< bool > | get_residue_mask () const |
| | returns a mask of residues to be used in scoring More...
|
| |
| virtual Real | get_residue_weight (core::Size, core::Size) const |
| | returns a residue-pair weight More...
|
| |
| void | detect_bonds () |
| |
| void | detect_pseudobonds () |
| |
| virtual void | sever_chemical_bond (Size seqpos1, Size res1_resconn_index, Size seqpos2, Size res2_resconn_index) |
| | Sever the chemical bond between two residues by stating that the connections for those residues are "incomplete" (i.e. in a state where these residues are not ready to be scored). More...
|
| |
| void | rebuild_polymer_bond_dependent_atoms_this_residue_only (Size const seqpos) |
| | Rebuilds the atoms that are dependent on polymer bonds for the specified residue only. More...
|
| |
| void | rebuild_residue_connection_dependent_atoms (Size seqpos, Size connid) |
| |
| AtomID | inter_residue_connection_partner (Size seqpos, int connection_index) const |
| | This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to. More...
|
| |
| AtomID | resolve_partial_atom_id (PartialAtomID const &partial_id) const |
| | Resolve a partial atom ID into an AtomID that is specific for this Conformation. More...
|
| |
| bool | is_bonded (core::id::AtomID const &atomid1, core::id::AtomID const &atomid2, bool virt=false, bool skip_canonical_and_solvent=false) const |
| | Returns a boolean for two atomIDs to be bonded. More...
|
| |
| utility::vector1< core::id::AtomID > | bonded_neighbor_all_res (core::id::AtomID const &atomid, bool virt=false, bool skip_canonical_and_solvent=false, bool intra_res=true, bool inter_res=true) const |
| | Get all atoms bonded to another. More...
|
| |
| bool | atom_is_backbone_norefold (Size pos, Size atomno) const |
| | returns true if atom is part of backbone. More...
|
| |
| kinematics::RT | get_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2) const |
| | get the transform between two stubs More...
|
| |
| void | set_jump_atom_stub_id (id::StubID const &id) |
| |
| kinematics::Stub | stub_from_id (id::StubID const &id) const |
| |
| kinematics::Stub | upstream_jump_stub (int jump_number) const |
| | The upstream and downstream Stubs are the coordinate frames between which this jump is transforming. More...
|
| |
| kinematics::Stub | downstream_jump_stub (int jump_number) const |
| | The upstream and downstream Stubs are the coordinate frames between which this jump is transforming. More...
|
| |
| void | set_noncanonical_connection (Size res_id_lower, Size lr_conn_id, Size res_id_upper, Size ur_conn_id) |
| | Create an arbitrary covalent connection between two residues. More...
|
| |
| void | update_polymeric_connection (Size lower_seqpos, bool update_connection_dep_atoms=false) |
| | Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini. If update_connection_dep_atoms is true, positions of atoms dependent on the polymer connection are updated. More...
|
| |
| virtual void | update_noncanonical_connection (Size lower_seqpos, Size lr_conn_id, Size upper_seqpos, Size ur_conn_id) |
| | Update the connection status between the lower_seqpos residue's lr_conn_id connection ID and the upper_seqpos residue's ur_conn_id connection ID. More...
|
| |
| virtual void | detect_disulfides (utility::vector1< std::pair< Size, Size > > const &disulfs) |
| | Detect existing disulfides from the protein structure, using the provided pairs as a starting point. More...
|
| |
| void | detect_disulfides () |
| | Detect existing disulfides from the protein structure. More...
|
| |
| virtual bool | add_disulfide_bond (core::Size res1, core::Size res2) |
| | Attempt to add a disulfide bond between the two residues. Returns true on success and false on failure. More...
|
| |
| void | create_new_parameters_set () |
| | Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object. More...
|
| |
| void | add_parameters_set (ParametersSetOP newset) |
| | Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object. More...
|
| |
| core::Size | n_parameters_sets () const |
| | Get the number of parameters sets defined for this Conformation. More...
|
| |
| void | clear_parameters_set_list () |
| | Delete the list of ParametersSetOP objects. More...
|
| |
| ParametersSetOP | parameters_set (core::Size const index) |
| | Access one of the ParametersSets objects linked to this Conformation. More...
|
| |
| ParametersSetCOP | parameters_set (core::Size const index) const |
| | Const access to one of the ParametersSets objects linked to this Conformation. More...
|
| |
| void | copy_segment (Size size, Conformation const &src, Size begin, Size src_begin) |
| | copy a stretch of coordinates/torsions from another Conformation More...
|
| |
| Real | dof (DOF_ID const &id) const |
| | Returns the AtomTree degree of freedom (DOF) <id> More...
|
| |
| Real | torsion (TorsionID const &id) const |
| | Return the torsion angle OR rigid-body offset for <id> More...
|
| |
| Real | torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const |
| | Returns the torsion angle defined by <atom[1-4]> in Radians. More...
|
| |
| Real | bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const |
| | Returns the bond angle defined by <atom[1-3]> through the AtomTree. More...
|
| |
| Real | bond_length (AtomID const &atom1, AtomID const &atom2) const |
| | Returns the bond length between <atom1> and <atom2> through the AtomTree. More...
|
| |
| core::Vector | bond_orientation (AtomID const &atom1, AtomID const &atom2) const |
| | Return the normalized vector of the bond between these two atoms. More...
|
| |
| core::Vector | bond_orientation (core::id::TorsionID const torsion) const |
| | Return the normalized vector of the bond about which this torsion angle twists. More...
|
| |
| const Jump & | jump (int jump_number) const |
| | Returns the Jump with jump number <jump_number> More...
|
| |
| const Jump & | jump (AtomID const &id) const |
| | access a jump More...
|
| |
| PointPosition const & | xyz (AtomID const &id) const |
| | access xyz coordinates of an atom More...
|
| |
| virtual void | set_xyz (AtomID const &id, PointPosition const &position) |
| |
| virtual void | batch_set_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > const &position) |
| |
| virtual void | batch_get_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const |
| |
| virtual void | apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > const &R, Vector const &v) |
| |
| void | update_actcoords () |
| |
| void | update_actcoord (Size resid) |
| |
| void | update_orbital_coords (Residue &rsd) const |
| |
| void | update_orbital_coords (Size resid) |
| |
| id::DOF_ID | dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3, id::AtomID const &id4) const |
| | Get the DOF_ID corresponding to the torsion angle defined by these four atoms. More...
|
| |
| id::DOF_ID | dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3) const |
| | Get the DOF_ID corresponding to the bond angle defined by these three atoms. More...
|
| |
| id::DOF_ID | dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2) const |
| | Get the DOF_ID corresponding to the bond distance defined by these two atoms. More...
|
| |
| id::DOF_ID | dof_id_from_atom_ids (utility::vector1< id::AtomID > const &ids) const |
| | Get the DOF_ID defined by these atoms. More...
|
| |
| DOF_ID | dof_id_from_torsion_id (TorsionID const &id) const |
| | Get the DOF_ID corresponding to this TorsionID. More...
|
| |
| id::AtomID | jump_atom_id (int jump_number) const |
| |
| bool | get_torsion_angle_atom_ids (TorsionID const &tor_id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const |
| | get four atoms which defined this torsion More...
|
| |
| bool | get_jump_atom_ids (core::Size jump_number, AtomID &upstream_id, AtomID &downstream_id) const |
| | get two atoms connect by jump More...
|
| |
| bool | atoms_are_bonded (AtomID const &id1, AtomID const &id2) const |
| | Helper method to determine whether two atoms have a chemical bond linking them. More...
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| |
| void | update_domain_map (DomainMap &domain_map) const |
| | Generate a domain_map from the current dof/xyz moved data. More...
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| |
| bool | structure_moved () const |
| | has the structure moved since the last call to reset_move_data or reset_structure_moved More...
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| |
| void | reset_structure_moved () const |
| | reset the structure_moved_ bool More...
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| |
| void | align_virtual_atoms_in_carbohydrate_residue (uint const sequence_position) |
| | Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of this conformation. More...
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| |
| template<typename MemFn , typename Ptr > |
| utility::signals::Link | attach_connection_obs (MemFn fn, Ptr ptr) const |
| | attach ConnectionEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| bool | detach_connection_obs (MemFn fn, Ptr ptr) const |
| | detach ConnectionEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| utility::signals::Link | attach_general_obs (MemFn fn, Ptr ptr) const |
| | attach GeneralEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| bool | detach_general_obs (MemFn fn, Ptr ptr) const |
| | detach GeneralEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| utility::signals::Link | attach_identity_obs (MemFn fn, Ptr ptr) const |
| | attach IdentityEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| bool | detach_identity_obs (MemFn fn, Ptr ptr) const |
| | detach IdentityEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| utility::signals::Link | attach_length_obs (MemFn fn, Ptr ptr) const |
| | attach LengthEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| bool | detach_length_obs (MemFn fn, Ptr ptr) const |
| | detach LengthEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| utility::signals::Link | attach_xyz_obs (MemFn fn, Ptr ptr) const |
| | attach XYZEvent observer function More...
|
| |
| template<typename MemFn , typename Ptr > |
| bool | detach_xyz_obs (MemFn fn, Ptr ptr) const |
| | detach XYZEvent observer function More...
|
| |
| void | clear_observers () |
| | clear all observers More...
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| |
| void | receive_observers_from (Conformation const &src) |
| | fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation More...
|
| |
| void | debug_pause (bool flag) const |
| | wait for stdin after sending a GeneralEvent signal More...
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| |
| bool | debug_pause () const |
| | waiting for stdin after sending a GeneralEvent signal? More...
|
| |
| void | buffer_signals () |
| | block signals from being sent and buffer them to be sent after unblocking More...
|
| |
| void | block_signals () |
| | block signals from being sent More...
|
| |
| void | unblock_signals () |
| | allow signals to be sent More...
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| |
| bool | buffering_signals () const |
| | are signals being blocked and buffered? More...
|
| |
| bool | blocking_signals () const |
| | are signals being blocked? More...
|
| |
| bool | backbone_torsion_angle_atoms (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const |
| | get four backbone atoms which define this backbone torsion More...
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| |
Public Member Functions inherited from core::conformation::Conformation