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Rosetta
2016.11
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A container of Residues and the kinematics to manage them. More...
#include <Conformation.hh>
Public Member Functions | |
Conformation () | |
constructor More... | |
virtual | ~Conformation () |
default destructor More... | |
Conformation (Conformation const &src) | |
copy constructor More... | |
virtual Conformation & | operator= (Conformation const &src) |
equals operator 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... | |
virtual ConformationOP | clone () const |
clone the conformation 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... | |
virtual bool | same_type_as_me (Conformation const &other, bool recurse=true) const |
determine the type of the ConformationOP 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... | |
bool | is_residue_typeset (std::string tag) const |
convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) More... | |
bool | is_fullatom () const |
convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) More... | |
bool | is_centroid () const |
convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) 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> More... | |
Size | chain_begin (Size chain) const |
Returns the position number of the first residue in <chain> More... | |
Size | num_chains () const |
Returns the number of chains. More... | |
utility::vector1< Size > const & | chain_endings () const |
Returns the list of chain endings. More... | |
void | chain_endings (utility::vector1< Size > const &endings) |
Sets the list of chain endings. More... | |
void | insert_chain_ending (Size seqpos) |
Marks <seqpos> as the end of a new chain. More... | |
void | delete_chain_ending (Size seqpos) |
Deletes <seqpos> from the list of chain endings. More... | |
void | reset_chain_endings () |
Resets chain data so that the Conformation is marked as a single chain. More... | |
void | chains_from_termini () |
Rederive the chains from the termini/polymer status. More... | |
char | secstruct (Size seqpos) const |
Returns the secondary structure the position <seqpos> More... | |
virtual void | set_secstruct (Size seqpos, char setting) |
Sets the secondary structure of the position <seqpos> to <setting> 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... | |
virtual FoldTree const & | fold_tree () const |
Returns the conformation's FoldTree. More... | |
virtual void | fold_tree (FoldTree const &fold_tree_in) |
Sets the FoldTree to <fold_tree_in> 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... | |
ResidueOP | residue_op (Size seqpos) |
Access one of the residues, using OP. 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... | |
ResidueCOPs | const_residues () const |
Inefficient – constructs copy of residues_. More... | |
virtual void | append_residue_by_jump (conformation::Residue const &new_rsd, Size anchor_residue, std::string const &anchor_atom="", std::string const &root_atom="", bool start_new_chain=false) |
Append a new residue by a jump. 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 seqpos, Size anchor_pos, bool build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool 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 build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool start_new_chain=false, bool lookup_bond_length=false) |
Append a new residue by a bond. More... | |
void | append_polymer_residue_after_seqpos (Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) |
glues to seqpos and perhaps also seqpos+1 More... | |
void | safely_append_polymer_residue_after_seqpos (Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) |
glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary More... | |
void | prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) |
glues to seqpos and perhaps also seqpos-1 More... | |
void | safely_prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) |
glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary More... | |
virtual void | replace_residue (Size seqpos, Residue const &new_rsd, bool orient_backbone) |
replace residue More... | |
virtual void | replace_residue (Size seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) |
function to replace a residue based on superposition on the specified input atom pairs More... | |
void | delete_polymer_residue (Size seqpos) |
Delete polymer residue at the given sequence position. More... | |
void | delete_residue_slow (Size seqpos) |
Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More... | |
void | delete_residue_range_slow (Size range_begin, Size range_end) |
Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. 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 | declare_chemical_bond (Size seqpos1, std::string const &atom_name1, Size seqpos2, std::string const &atom_name2) |
Declare that a chemical bond exists between two residues. More... | |
void | rebuild_polymer_bond_dependent_atoms_this_residue_only (Size seqpos) |
Rebuilds the atoms that are depenent on polymer bonds for the specified residue only. More... | |
void | rebuild_polymer_bond_dependent_atoms (Size seqpos) |
Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1. 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... | |
utility::vector1 < core::id::AtomID > | bonded_neighbor_all_res (core::id::AtomID atomid, bool virt=false) const |
get all atoms bonded to another More... | |
void | fill_missing_atoms (id::AtomID_Mask missing) |
bool | atom_is_backbone_norefold (Size pos, Size atomno) const |
returns true if atom is part of backbone. More... | |
void | set_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt) |
Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms. 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_polymeric_connection (Size res_id_lower, Size res_id_upper) |
identify polymeric connections 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... | |
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< Size > const &disulf_one=utility::vector1< Size >(), utility::vector1< Size > const &disulf_two=utility::vector1< Size >()) |
Detect existing disulfides from the protein structure using suggestions from the FileData (or not!) More... | |
void | fix_disulfides (utility::vector1< std::pair< Size, Size > > disulf_bonds) |
Assigns disulfide bonds based on a pre-determined list. More... | |
virtual void | create_new_parameters_set () |
Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object. More... | |
virtual void | add_parameters_set (ParametersSetOP newset) |
Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object. More... | |
virtual core::Size | n_parameters_sets () const |
Get the number of parameters sets defined for this Conformation. More... | |
virtual void | clear_parameters_set_list () |
Delete the list of ParametersSetOP objects. More... | |
virtual ParametersSetOP | parameters_set (core::Size const index) |
Access one of the ParametersSets objects linked to this Conformation. More... | |
virtual ParametersSetCOP | parameters_set (core::Size const index) const |
Const access to one of the ParametersSets objects linked to this Conformation. More... | |
virtual void | insert_conformation_by_jump (Conformation const &conf, Size insert_seqpos, Size insert_jumppos, Size anchor_pos, Size anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="") |
Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump. More... | |
void | copy_segment (Size size, Conformation const &src, Size begin, Size src_begin) |
copy a stretch of coordinates/torsions from another Conformation More... | |
void | insert_fragment (id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz) |
Real | dof (DOF_ID const &id) const |
Returns the AtomTree degree of freedom (DOF) <id> More... | |
virtual void | set_dof (DOF_ID const &id, Real setting) |
Sets the AtomTree degree of freedom (DOF) <id> to <setting> More... | |
Real | torsion (TorsionID const &id) const |
Return the torsion angle OR rigid-body offset for <id> More... | |
virtual void | set_torsion (TorsionID const &id, Real setting) |
Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump. 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]> More... | |
virtual void | set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real setting, bool quiet=false) |
Sets the torsion angle defined by <atom[1-4]> to <setting> 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... | |
virtual void | set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real setting) |
Sets the bond angle defined by <atom[1-3]> to <setting> More... | |
Real | bond_length (AtomID const &atom1, AtomID const &atom2) const |
Returns the bond length between <atom1> and <atom2> through the AtomTree. More... | |
virtual void | set_bond_length (AtomID const &atom1, AtomID const &atom2, Real setting) |
Sets the cond length between <atom1> and <atom2> to <setting> 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... | |
virtual void | set_jump (int jump_number, Jump const &new_jump) |
Sets the jump <jump_number> to <new_jump> More... | |
virtual void | set_jump (AtomID const &id, Jump const &new_jump) |
set 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 |
void | insert_ideal_geometry_at_polymer_bond (Size seqpos) |
void | insert_ideal_geometry_at_residue_connection (Size pos1, Size connid1) |
void | update_actcoords () |
void | update_actcoord (Size resid) |
void | update_orbital_coords (Residue &rsd) const |
void | update_orbital_coords (Size resid) |
DOF_ID | dof_id_from_torsion_id (TorsionID const &id) const |
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... | |
void | update_domain_map (DomainMap &domain_map) const |
Generate a domain_map from the current dof/xyz moved data. More... | |
bool | structure_moved () const |
has the structure moved since the last call to reset_move_data or reset_structure_moved More... | |
void | reset_structure_moved () const |
reset the structure_moved_ bool More... | |
void | reset_move_data () |
forget all the structure modifications More... | |
virtual void | push_passport (core::environment::DofPassportCOP) |
virtual core::environment::DofPassportCOP | pop_passport () |
virtual bool | has_passport () const |
virtual bool | is_protected () const |
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... | |
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... | |
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... | |
bool | buffering_signals () const |
are signals being blocked and buffered? More... | |
bool | blocking_signals () const |
are signals being blocked? More... | |
Protected Member Functions | |
Residue const & | const_residue_ (Size seqpos) const |
Returns a constant residue reference without triggering coordinate/torsion update. More... | |
void | force_update_residue_torsions () const |
Force updating of residue torsions. More... | |
void | force_update_residue_coordinates () const |
Force updating of residue coordinates. More... | |
Private Member Functions | |
Residue & | residue_ (Size seqpos) |
Returns a non-constant residue reference without triggering coordinate/torsion update. More... | |
void | update_sequence_numbering (Size new_size, utility::vector1< Size > const &old2new) |
remap *_moved arrays, sequence numbering in the residues_ arrays, etc, after insertion or deletion of rsds More... | |
void | rebuild_polymer_bond_dependent_atoms (Size seqpos, int upper_lower) |
rebuild atoms in residue seqpos dependent on either the lower (-1) or upper(1) polymer residue More... | |
void | insert_polymer_residue (Residue const &new_rsd_in, Size seqpos, bool join_lower, bool join_upper) |
void | append_residue (Residue const &new_rsd_in, bool attach_by_jump, std::string const &root_atom, id::NamedAtomID anchor_id, bool start_new_chain) |
Now a private method public interface: append_residue_by_bond or append_residue_by_jump. More... | |
void | residues_replace (Size seqpos, Residue const &new_rsd) |
wrap direct access to the Residues container More... | |
void | residues_insert (Size seqpos, Residue const &new_rsd, bool use_lower_chain=false, bool new_chain=false) |
void | residues_append (Residue const &new_rsd, bool start_new_chain, bool by_jump=false, std::string const &root_atom="", id::NamedAtomID anchor_id=id::BOGUS_NAMED_ATOM_ID) |
void | residues_delete (Size seqpos) |
void | setup_atom_tree () |
(re-)builds the AtomTree using the FoldTree and the Residues More... | |
Real | atom_tree_torsion (TorsionID const &tor_id) const |
access a torsion from the atom_tree 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... | |
bool | branch_connection_torsion_angle_atoms (TorsionID const &torsion, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const |
Find the four atoms that define the torsion angle of this branch connection. 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... | |
void | set_xyz_moved (AtomID const &id) |
notify of xyz-change More... | |
void | set_xyz_moved (utility::vector1< AtomID > const &ids) |
notify of mutiple-xyz-change More... | |
void | set_dof_moved (AtomID const &id) |
notify of dof-change More... | |
void | set_dof_moved (DOF_ID const &id) |
notify of dof-change More... | |
void | update_residue_coordinates () const |
Will (if necessary) copy the xyz coordinates from the AtomTree to the Residues being managed. More... | |
void | update_residue_coordinates (Size seqpos, bool fire_signal=true) const |
void | rederive_chain_endings () |
void | rederive_chain_ids () |
void | update_residue_torsions () const |
Will (if necessary) copy the torsion angles (mainchain/chi) from the AtomTree to the Residues being managed. More... | |
void | update_residue_torsions (Size seqpos, bool fire_signal=true) const |
void | add_pseudobond (Size lr, Size lr_connid, Size ur, Size ur_connid, Size nbonds) |
void | in_place_copy (Conformation const &src) |
Optimizing the common case of assigning a conformation to another with the same sequence. More... | |
void | pre_nresidue_change () |
The Conformation must transfer lazily accumulated "moved" data from the AtomTree before changing the number of residues. More... | |
void | notify_connection_obs (ConnectionEvent const &e) const |
notify ConnectionEvent observers More... | |
void | notify_general_obs (GeneralEvent const &e) const |
notify GeneralEvent observers More... | |
void | notify_identity_obs (IdentityEvent const &e, bool fire_general=true) const |
notify IdentityEvent observers More... | |
void | notify_length_obs (LengthEvent const &e, bool fire_general=true) const |
notify LengthEvent observers More... | |
void | notify_xyz_obs (XYZEvent const &e, bool fire_general=true) const |
notify XYZEvent observers More... | |
Private Attributes | |
ResidueOPs | residues_ |
container of Residues More... | |
utility::vector1< Size > | chain_endings_ |
chain number for each position More... | |
membrane::MembraneInfoOP | membrane_info_ |
Membrane Info object. More... | |
FoldTreeOP | fold_tree_ |
fold tree for the kinematics More... | |
AtomTreeOP | atom_tree_ |
atom tree for the kinematics More... | |
utility::vector1< ParametersSetOP > | parameters_set_ |
Parameter sets for parametric conformation generation. More... | |
bool | contains_carbohydrate_residues_ |
bool | residue_coordinates_need_updating_ |
do we need to update the coordinates in the Residues? More... | |
bool | residue_torsions_need_updating_ |
do we need to update the torsion angles in the Residues? More... | |
AtomID_Mask | dof_moved_ |
book-keeping array for energy evaluations More... | |
AtomID_Mask | xyz_moved_ |
book-keeping array for energy evaluations More... | |
bool | structure_moved_ |
has the structure moved since the last call to reset_move_data? More... | |
utility::vector1< char > | secstruct_ |
utility::signals::BufferedSignalHub < void, ConnectionEvent > | connection_obs_hub_ |
ConnectionEvent observers. More... | |
utility::signals::PausableSignalHub < void, GeneralEvent > | general_obs_hub_ |
GeneralEvent observers. More... | |
utility::signals::BufferedSignalHub < void, IdentityEvent > | identity_obs_hub_ |
IdentityEvent observers. More... | |
utility::signals::BufferedSignalHub < void, LengthEvent > | length_obs_hub_ |
LengthEvent observers. More... | |
utility::signals::BufferedSignalHub < void, XYZEvent > | xyz_obs_hub_ |
LengthEvent observers. More... | |
A container of Residues and the kinematics to manage them.
typedef core::conformation::signals::ConnectionEvent core::conformation::Conformation::ConnectionEvent |
typedef std::map< id::StubID, kinematics::RT > core::conformation::Conformation::FragRT |
typedef std::map< id::AtomID, Vector > core::conformation::Conformation::FragXYZ |
typedef core::conformation::parametric::ParametersOP core::conformation::Conformation::ParametersCOP |
typedef core::conformation::parametric::ParametersSet core::conformation::Conformation::ParametersSet |
typedef core::conformation::parametric::ParametersSetCOP core::conformation::Conformation::ParametersSetCOP |
typedef core::conformation::parametric::ParametersSetOP core::conformation::Conformation::ParametersSetOP |
core::conformation::Conformation::Conformation | ( | ) |
constructor
References atom_tree_.
Referenced by clone().
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default destructor
core::conformation::Conformation::Conformation | ( | Conformation const & | src | ) |
copy constructor
References atom_tree_, chain_endings_, contains_carbohydrate_residues_, dof_moved_, fold_tree_, membrane_info_, parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, secstruct_, size(), structure_moved_, and xyz_moved_.
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Returns the AA enum for position <seqpos>
References residues_, and size().
Referenced by core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), and core::conformation::symmetry::SymmetricConformation::recalculate_transforms().
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Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundle::apply(), and insert_conformation_by_jump().
std::string core::conformation::Conformation::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].
References core::chemical::aa_from_oneletter_code(), core::pack::dunbrack::c, core::conformation::Residue::name(), core::conformation::Residue::name1(), core::chemical::name_from_aa(), core::chemical::oneletter_code_specifies_aa(), residue(), and size().
Referenced by fold_tree().
void core::conformation::Conformation::append_polymer_residue_after_seqpos | ( | Residue const & | new_rsd, |
Size | seqpos, | ||
bool | build_ideal_geometry | ||
) |
glues to seqpos and perhaps also seqpos+1
Fires a LengthEvent::RESIDUE_PREPEND signal at seqpos + 1 due to insert_polymer_residue() call.
References core::conformation::Residue::clone(), dof_moved_, fold_tree_, insert_polymer_residue(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect(), core::conformation::Residue::natoms(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), residue_(), residue_coordinates_need_updating_, size(), core::id::AtomID_Map< T >::size(), update_residue_coordinates(), core::conformation::Residue::upper_connect(), and xyz_moved_.
Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), and safely_append_polymer_residue_after_seqpos().
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Now a private method public interface: append_residue_by_bond or append_residue_by_jump.
add a residue into residues_ container, update its seqpos, chainid as well fold tree and atoms. private now – this is our internal routine with everything determined ahead of time root_atomno and anchor_id.atomno() may not be filled in yet Fires a LengthEvent::RESIDUE_APPEND signal.
References core::id::NamedAtomID::atom(), core::conformation::Residue::atom_index(), atom_tree_, const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::name(), notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, residue_torsions_need_updating_, residues_, residues_append(), core::id::NamedAtomID::rsd(), setup_atom_tree(), size(), and core::conformation::TR().
Referenced by append_residue_by_bond(), and append_residue_by_jump().
void core::conformation::Conformation::append_residue_by_bond | ( | conformation::Residue const & | new_rsd, |
bool | build_ideal_geometry = false , |
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int | residue_connection_index = 0 , |
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Size | anchor_pos = 0 , |
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int | anchor_residue_connection_index = 0 , |
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bool | start_new_chain = false , |
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bool | lookup_bond_length = false |
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) |
Append a new residue by a bond.
The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues. Otherwise the incoming coordinates of new_rsd are preserved. Fires a LengthEvent::RESIDUE_APPEND signal.
References append_residue(), core::conformation::atom_id_to_named_atom_id(), core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::chemical::ResidueConnection::atomno(), core::id::BOGUS_NAMED_ATOM_ID, core::conformation::Residue::clone(), core::conformation::Residue::is_polymer(), core::conformation::Residue::lower_connect(), core::conformation::Residue::lower_connect_atom(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::name(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), residue_(), core::conformation::Residue::residue_connection(), residue_coordinates_need_updating_, residues_, size(), core::conformation::Residue::type(), update_residue_coordinates(), core::conformation::Residue::upper_connect(), core::conformation::Residue::upper_connect_atom(), and core::chemical::ResidueType::upper_connect_id().
Referenced by protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), and core::conformation::is_ideal_position().
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Append a new residue by a jump.
add a residue into residues_ container, update its seqpos, chainid as well fold tree and atoms. Fires a LengthEvent::RESIDUE_APPEND signal.
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References append_residue(), core::id::BOGUS_NAMED_ATOM_ID, pre_nresidue_change(), and size().
Referenced by protocols::environment::EnvClaimBroker::add_virtual_residues(), protocols::comparative_modeling::ExtraThreadingMover::apply(), and core::conformation::symmetry::setup_symmetric_conformation().
returns true if atom is part of backbone.
There is a version of this in Residue.hh. The problem with that function is that accessing a residue in the pose triggers a refold which is really slow. We do not need a correctly folded residue to makethis check
References residues_.
Referenced by core::conformation::symmetry::guess_torsion_type_of_dof_id().
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Returns the conformation's AtomTree.
References atom_tree_.
Referenced by protocols::simple_filters::JumpEvaluator::apply(), protocols::environment::collect_dofs(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), and protocols::environment::claims::XYZClaim::yield_elements().
access a torsion from the atom_tree
used when we want to copy torsions from the atomtree to the residues used when updating the torsion angles stashed in the Residues other torsion access calls look inside the residues since this will be faster than getting from the atomtree, at least in the current implementation of this routine
References atom_tree_, core::id::AtomID::atomno(), atoms_are_bonded(), const_residue_(), dof_id_from_torsion_id(), get_torsion_angle_atom_ids(), core::id::JUMP, core::id::AtomID::rsd(), core::id::TorsionID::type(), and xyz().
Referenced by debug_residue_torsions(), and update_residue_torsions().
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Helper method to determine whether two atoms have a chemical bond linking them.
Helper function to determine whether two atoms have a chemical bond linking them.
Intended for internal use, but there's really no reason not to make this a public method. This works for atoms within the same residue or in different residues.
References core::id::AtomID::atomno(), const_residue_(), and core::id::AtomID::rsd().
Referenced by atom_tree_torsion().
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attach ConnectionEvent observer function
fn | pointer to observer's unary member function with signature void( ConnectionEvent const & ) |
ptr | RAW pointer to observer object |
References connection_obs_hub_.
Referenced by core::pose::PDBInfo::attach_to().
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attach GeneralEvent observer function
fn | pointer to observer's unary member function with signature void( GeneralEvent const & ) |
ptr | RAW pointer to observer object |
References general_obs_hub_.
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attach IdentityEvent observer function
fn | pointer to observer's unary member function with signature void( IdentityEvent const & ) |
ptr | RAW pointer to observer object |
References identity_obs_hub_.
Referenced by core::pose::PDBInfo::attach_to().
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attach LengthEvent observer function
fn | pointer to observer's unary member function with signature void( LengthEvent const & ) |
ptr | RAW pointer to observer object |
References length_obs_hub_.
Referenced by protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::attach_impl(), core::pose::datacache::LengthEventCollector::attach_impl(), core::pose::datacache::SpecialSegmentsObserver::attach_impl(), protocols::forge::build::BuildInstruction::attach_to(), and core::pose::PDBInfo::attach_to().
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attach XYZEvent observer function
fn | pointer to observer's unary member function with signature void( XYZEvent const & ) |
ptr | RAW pointer to observer object |
References xyz_obs_hub_.
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get four backbone atoms which define this backbone torsion
References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::chemical::C_METHYLAMIDATION, core::conformation::Residue::chain(), chain_begin(), chain_end(), core::conformation::Residue::connection_incomplete(), const_residue_(), core::chemical::CTERM_CONNECT, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::FIVE_PRIME_PHOSPHATE, fold_tree_, core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::icoor(), core::conformation::Residue::is_carbohydrate(), core::chemical::ResidueType::lower_connect_id(), core::conformation::Residue::mainchain_atom(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsions(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::chemical::NTERM_CONNECT, core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), residues_, core::id::AtomID::rsd(), core::conformation::Residue::seqpos(), core::chemical::THREE_PRIME_PHOSPHATE, torsion(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by get_torsion_angle_atom_ids().
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References xyz().
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Reimplemented in core::conformation::symmetry::SymmetricConformation.
References atom_tree_, residues_, and set_xyz_moved().
Referenced by core::conformation::symmetry::SymmetricConformation::batch_set_xyz(), and core::conformation::UltraLightResidue::update_conformation().
void core::conformation::Conformation::block_signals | ( | ) |
block signals from being sent
References general_obs_hub_, identity_obs_hub_, length_obs_hub_, and xyz_obs_hub_.
bool core::conformation::Conformation::blocking_signals | ( | ) | const |
are signals being blocked?
References general_obs_hub_.
Real core::conformation::Conformation::bond_angle | ( | AtomID const & | atom1, |
AtomID const & | atom2, | ||
AtomID const & | atom3 | ||
) | const |
Returns the bond angle defined by <atom[1-3]> through the AtomTree.
References atom_tree_.
Referenced by protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), and core::fragment::BBTorsionAndAnglesSRFD::steal().
Real core::conformation::Conformation::bond_length | ( | AtomID const & | atom1, |
AtomID const & | atom2 | ||
) | const |
Returns the bond length between <atom1> and <atom2> through the AtomTree.
References atom_tree_.
Referenced by protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record().
utility::vector1< id::AtomID > core::conformation::Conformation::bonded_neighbor_all_res | ( | core::id::AtomID | atomid, |
bool | virt = false |
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) | const |
get all atoms bonded to another
virtual atoms are excluded by default
References core::conformation::Residue::actual_residue_connection(), core::id::AtomID::atomno(), core::conformation::Residue::bonded_neighbor(), core::conformation::Residue::connection_incomplete(), core::conformation::Residue::is_virtual(), core::conformation::Residue::n_possible_residue_connections(), residue(), core::conformation::Residue::residue_connect_atom_index(), and core::id::AtomID::rsd().
Referenced by protocols::branch_angle::branching_atomid1(), protocols::branch_angle::branching_atomids2(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), and protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry().
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Find the four atoms that define the torsion angle of this branch connection.
This method figures out which four atoms define the torsion angle about the given branch connection point and sets the four AtomIDs passed to it.
<torsion> | the TorsionID for this branch connection, which must have the BRANCH TorsionType |
<id1> | through <id2>: AtomID variables that will be filled with the found atoms |
References core::id::BRANCH, core::conformation::Residue::connect_atom(), core::conformation::Residue::first_adjacent_heavy_atom(), core::conformation::Residue::is_branch_point(), core::conformation::Residue::n_non_polymeric_residue_connections(), core::conformation::Residue::n_polymeric_residue_connections(), core::conformation::Residue::residue_connection_partner(), residues_, core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), core::conformation::TR(), and core::id::TorsionID::type().
Referenced by get_torsion_angle_atom_ids().
void core::conformation::Conformation::buffer_signals | ( | ) |
block signals from being sent and buffer them to be sent after unblocking
References general_obs_hub_, identity_obs_hub_, length_obs_hub_, and xyz_obs_hub_.
bool core::conformation::Conformation::buffering_signals | ( | ) | const |
are signals being blocked and buffered?
References general_obs_hub_.
Returns the position number of the first residue in <chain>
References chain_endings_.
Referenced by protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::ligand_docking::append_ligand_RMSD(), protocols::simple_moves::AddJobPairData::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::qsar::qsarMover::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::MinimizeLigand::apply(), protocols::ligand_docking::RandomConformers::apply(), protocols::ligand_docking::TetherLigand::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::simple_moves::CyclizationMover::apply(), protocols::toolbox::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::toolbox::task_operations::PreventChainFromRepackingOperation::apply(), protocols::toolbox::task_operations::RestrictChainToRepackingOperation::apply(), protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::HeavyAtomFilter::apply(), protocols::ligand_docking::MolarMassFilter::apply(), protocols::ligand_docking::MolecularMassFilter::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::toolbox::task_operations::RestrictToTerminiOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::denovo_design::connection::BridgeChains::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::ligand_docking::Translate::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::ligand_docking::Transform::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::fldsgn::CircularPermutation::apply(), backbone_torsion_angle_atoms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::protein_interface_design::filters::HbondsToAtomFilter::compute(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::floppy_tail::create_extra_output(), protocols::simple_moves::CutChainMover::create_subpose(), protocols::seeded_abinitio::define_movemap_chains(), protocols::analysis::PeptideDeriverFilter::derive_peptide(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), protocols::ligand_docking::InterfaceBuilder::find_interface_residues(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::select::util::find_neighbors_within_CB_cutoff(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::rosetta_scripts::foreach_movemap_tag(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::conformation::symmetry::get_chain2range(), core::pose::get_chain_from_chain_id(), core::pose::get_chain_residues(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), core::pose::get_hash_from_chain(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::get_psi_from_rsd(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), protocols::loops::loopfinder(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), MinimizeInterface(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::protein_interface_design::movers::TopologyBrokerMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::rigid::RollMover::parse_my_tag(), protocols::ligand_docking::Rotate::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::contact_map::ContactMap::parse_region_string(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::analysis::PeptideDeriverFilter::push_chain_residue_indices(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::features::ScreeningFeatures::report_features(), protocols::features::ResidueGridScoresFeatures::report_features(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), protocols::ligand_docking::Rotate::rotate_ligand(), core::select::residue_selector::ChainSelector::select_chain_by_index(), protocols::ligand_docking::MoveMapBuilder::set_all_chi(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), protocols::antibody::AntibodyInfo::setup_FrameWorkInfo(), protocols::simple_moves::CyclizationMover::setup_minimizer(), protocols::ncbb::setup_pert_foldtree(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::seeded_abinitio::SwapSegment::swap_chain(), protocols::protein_interface_design::PatchdockReader::transform_pose(), update_residue_torsions(), and protocols::fldsgn::CircularPermutation::which_chain().
Returns the position number of the last residue in <chain>
References chain_endings_, and size().
Referenced by protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::ligand_docking::append_ligand_RMSD(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::RandomConformers::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::MinimizeLigand::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::simple_moves::CyclizationMover::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::ligand_docking::MolecularMassFilter::apply(), protocols::ligand_docking::MolarMassFilter::apply(), protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::HeavyAtomFilter::apply(), protocols::toolbox::task_operations::PreventChainFromRepackingOperation::apply(), protocols::toolbox::task_operations::RestrictChainToRepackingOperation::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::toolbox::task_operations::RestrictToTerminiOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::denovo_design::connection::BridgeChains::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::fldsgn::CircularPermutation::apply(), backbone_torsion_angle_atoms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::ligand_docking::Rotate::create_random_rotations(), protocols::simple_moves::CutChainMover::create_subpose(), protocols::seeded_abinitio::define_movemap_chains(), protocols::analysis::PeptideDeriverFilter::derive_peptide(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), protocols::ligand_docking::InterfaceBuilder::find_interface_residues(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::select::util::find_neighbors_within_CB_cutoff(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::simple_moves::CutChainMover::foldTree(), protocols::rosetta_scripts::foreach_movemap_tag(), core::conformation::symmetry::get_chain2range(), core::pose::get_chain_residues(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), core::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), core::pose::get_hash_from_chain(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::get_omg_from_rsd(), core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::get_phi_from_rsd(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), insert_conformation_by_jump(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), protocols::loops::loopfinder(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), MinimizeInterface(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::protein_interface_design::movers::TopologyBrokerMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::rigid::RollMover::parse_my_tag(), protocols::ligand_docking::Rotate::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::contact_map::ContactMap::parse_region_string(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::analysis::PeptideDeriverFilter::push_chain_residue_indices(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::features::ScreeningFeatures::report_features(), protocols::features::ResidueGridScoresFeatures::report_features(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::select::residue_selector::ChainSelector::select_chain_by_index(), protocols::ligand_docking::MoveMapBuilder::set_all_chi(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), protocols::docking::setup_foldtree(), protocols::antibody::AntibodyInfo::setup_FrameWorkInfo(), protocols::simple_moves::CyclizationMover::setup_minimizer(), protocols::ncbb::setup_pert_foldtree(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::seeded_abinitio::SwapSegment::swap_chain(), protocols::protein_interface_design::PatchdockReader::transform_pose(), update_residue_torsions(), and protocols::fldsgn::CircularPermutation::which_chain().
utility::vector1< Size > const & core::conformation::Conformation::chain_endings | ( | ) | const |
Returns the list of chain endings.
References chain_endings_.
Referenced by protocols::denovo_design::components::StructureData::check_chain_beginnings(), protocols::denovo_design::components::StructureData::check_chain_endings(), protocols::denovo_design::components::StructureData::create_from_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), protocols::denovo_design::components::StructureData::infer_from_pose(), protocols::features::PoseConformationFeatures::load_chain_endings(), protocols::forge::build::SegmentRebuild::modify_impl(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::features::LoopAnchorFeatures::report_features(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::sewing::Assembly::to_multichain_pose(), and protocols::surface_docking::SurfaceDockingProtocol::valid_surface_pose().
void core::conformation::Conformation::chain_endings | ( | utility::vector1< Size > const & | endings | ) |
Sets the list of chain endings.
References chain_endings_, rederive_chain_ids(), and size().
void core::conformation::Conformation::chains_from_termini | ( | ) |
Rederive the chains from the termini/polymer status.
References chain_endings_, rederive_chain_ids(), residues_, and size().
void core::conformation::Conformation::check_valid_membrane | ( | ) | const |
Check that a new membrane position is valid.
Given a new membrane normal/center pair, check that the newly constructed stub represents an orthogonal coordinate frame
References downstream_jump_stub(), jump(), and membrane_info_.
Referenced by update_membrane_position().
void core::conformation::Conformation::clear | ( | ) |
clear data
References atom_tree_, chain_endings_, core::id::AtomID_Map< T >::clear(), dof_moved_, fold_tree_, parameters_set_, pre_nresidue_change(), residues_, and xyz_moved_.
Referenced by operator=(), protocols::stepwise::modeler::slice(), core::conformation::symmetry::MirrorSymmetricConformation::~MirrorSymmetricConformation(), and core::conformation::symmetry::SymmetricConformation::~SymmetricConformation().
void core::conformation::Conformation::clear_observers | ( | ) |
clear all observers
References connection_obs_hub_, core::conformation::signals::ConnectionEvent::DISCONNECT, general_obs_hub_, identity_obs_hub_, length_obs_hub_, notify_connection_obs(), and xyz_obs_hub_.
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Delete the list of ParametersSetOP objects.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundle::apply().
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clone the conformation
make a copy of this conformation( allocate actual memory for it )
Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References Conformation().
Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), and core::conformation::symmetry::setup_symmetric_conformation().
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Returns a constant residue reference without triggering coordinate/torsion update.
Use with care. Useful inside torsion/coordinate setters where we want chemical info about a given residue but don't want to trigger the coordinate/torsion updates that go along with a call to residue(seqpos).
References residues_, and size().
Referenced by atom_tree_torsion(), atoms_are_bonded(), backbone_torsion_angle_atoms(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), get_torsion_angle_atom_ids(), and jump_atom_id().
ResidueCOPs core::conformation::Conformation::const_residues | ( | ) | const |
Inefficient – constructs copy of residues_.
References residues_, and size().
Referenced by append_residue(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), replace_residue(), and setup_atom_tree().
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Return true if this conformation contains any carbohydrate residues.
References contains_carbohydrate_residues_.
Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::import_pose::build_pose_as_is2(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::pose::carbohydrates::glycosylate_pose(), and core::pose::make_pose_from_saccharide_sequence().
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Set whether this conformation contains any carbohydrate residues.
References contains_carbohydrate_residues_.
void core::conformation::Conformation::copy_segment | ( | Size | size, |
Conformation const & | src, | ||
Size | begin, | ||
Size | src_begin | ||
) |
copy a stretch of coordinates/torsions from another Conformation
copy a stretch of coordinates/torsions from another pose Fires IdentityEvent signals as residues are replaced.
References replace_residue(), residue(), and size().
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Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose().
void core::conformation::Conformation::debug_pause | ( | bool | flag | ) | const |
wait for stdin after sending a GeneralEvent signal
References general_obs_hub_.
bool core::conformation::Conformation::debug_pause | ( | ) | const |
waiting for stdin after sending a GeneralEvent signal?
References general_obs_hub_.
void core::conformation::Conformation::debug_residue_torsions | ( | bool | verbose = false | ) | const |
debugging
check that the residue torsions are in sync with the residue coords and atomtree coords
References protocols::comparative_modeling::features::A, atom_tree_, atom_tree_torsion(), core::id::AtomID::atomno(), core::id::BB, core::id::CHI, core::conformation::Residue::chi(), core::chemical::element::F, fold_tree_, get_torsion_angle_atom_ids(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::nchi(), core::io::raw_data::precision(), residue(), core::id::AtomID::rsd(), size(), torsion(), update_residue_coordinates(), update_residue_torsions(), and xyz().
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Declare that a chemical bond exists between two residues.
Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.
References core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_partner(), residue_torsions_need_updating_, residues_, and update_residue_torsions().
Referenced by core::util::add_covalent_linkage(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::indel::IndelOptimizationMover::apply(), core::pose::correctly_add_cutpoint_variants(), protocols::relax::cyclize_pose(), core::conformation::symmetry::SymmetricConformation::declare_chemical_bond(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::protein_interface_design::movers::DisulfideMover::form_disulfide(), core::conformation::form_disulfide(), protocols::grafting::insert_pose_into_pose(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent().
void core::conformation::Conformation::delete_chain_ending | ( | Size | seqpos | ) |
Deletes <seqpos> from the list of chain endings.
References chain_endings_, and rederive_chain_ids().
Referenced by protocols::forge::build::SegmentRebuild::modify_impl().
void core::conformation::Conformation::delete_polymer_residue | ( | Size | seqpos | ) |
Delete polymer residue at the given sequence position.
delete a polymer residues Fires a LengthEvent::RESIDUE_DELETE signal.
References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), and size().
Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply().
void core::conformation::Conformation::delete_residue_range_slow | ( | Size | range_begin, |
Size | range_end | ||
) |
Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.
Like above but only one call to setup_atom_tree Fires a LengthEvent::RESIDUE_DELETE signal.
References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), setup_atom_tree(), and size().
Referenced by protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::moves::StructureRestrictor::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::environment::Environment::remove_nonpermenant_features(), and protocols::hybridization::HybridizeFoldtreeDynamic::reset().
void core::conformation::Conformation::delete_residue_slow | ( | Size | seqpos | ) |
Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.
Delete a residue from the Conformation the slow way – triggers a rebuild of the atomtree Fires a LengthEvent::RESIDUE_DELETE signal.
LOGIC: uses fold_tree.delete_seqpos to handle shifting the topology around if necessary, then calls setup_atom_tree
References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), setup_atom_tree(), and size().
Referenced by protocols::simple_moves::VirtualRootMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::loops::apply_sequence_mapping(), protocols::sic_dock::auto_trim_floppy_termini(), protocols::simple_filters::MutationsFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::grafting::delete_overhang_residues(), protocols::relax::delete_virtual_residues(), protocols::features::ReportToDB::initialize_pose(), protocols::match::MatcherMover::process_pose(), core::pose::remove_ligand_canonical_residues(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), core::pose::remove_nonprotein_residues(), protocols::hybridization::remove_residues(), core::pose::remove_virtual_residues(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::nonlocal::StarTreeBuilder::tear_down(), protocols::star::StarAbinitio::tear_down_kinematics(), protocols::sewing::Model::trim_db_pose(), and protocols::features::ModelFeatures::trim_pose().
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detach ConnectionEvent observer function
fn | pointer to observer's unary member function with signature void( ConnectionEvent const & ) |
ptr | RAW pointer to observer object |
References connection_obs_hub_.
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detach GeneralEvent observer function
fn | pointer to observer's unary member function with signature void( GeneralEvent const & ) |
ptr | RAW pointer to observer object |
References general_obs_hub_.
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detach IdentityEvent observer function
fn | pointer to observer's unary member function with signature void( IdentityEvent const & ) |
ptr | RAW pointer to observer object |
References identity_obs_hub_.
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detach LengthEvent observer function
fn | pointer to observer's unary member function with signature void( LengthEvent const & ) |
ptr | RAW pointer to observer object |
References length_obs_hub_.
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detach XYZEvent observer function
fn | pointer to observer's unary member function with signature void( XYZEvent const & ) |
ptr | RAW pointer to observer object |
References xyz_obs_hub_.
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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).
Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References atom_tree_.
Referenced by core::conformation::symmetry::SymmetricConformation::detached_copy().
void core::conformation::Conformation::detect_bonds | ( | ) |
References core::conformation::Residue::atom(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::atoms(), core::chemical::AtomICoor::build(), core::conformation::Residue::connection_distance(), core::conformation::Residue::connection_incomplete(), core::chemical::AtomICoor::d(), core::conformation::Residue::has_incomplete_connection(), core::chemical::ResidueConnection::icoor(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::n_residue_connections_for_atom(), core::conformation::Residue::name(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), residue(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::residue_connection(), residues_, size(), core::conformation::TR(), core::conformation::Residue::type(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().
Referenced by protocols::simple_moves::PeptideStapleMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), core::pose::symmetry::make_symmetric_pose(), protocols::frag_picker::FragmentCandidate::output_silent(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::simple_moves::CyclizationMover::setup_connections(), and protocols::topology_broker::TopologyBroker::switch_to_fullatom().
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Detect existing disulfides from the protein structure using suggestions from the FileData (or not!)
For full atom confomations, looks at SG-SG distance. If the SG-SG are about 2.02 A apart, calls it a disulfide bond. For centroid and other conformations, the less accurate CB-CB distance is used instead. In this case a CB-CB distance of 3.72 A is optimal.
Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::atoms(), core::conformation::change_cys_state(), core::chemical::DISULFIDE, core::chemical::FA_STANDARD, core::conformation::find_neighbors(), core::chemical::ResidueType::get_disulfide_atom_name(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_disulfide_bonded(), core::chemical::ResidueType::is_sidechain_thiol(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_type(), residues_, size(), core::conformation::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().
Referenced by protocols::simple_moves::AddChainMover::add_new_chain(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::hybridization::MRMover::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::cryst::MakeLayerMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::analysis::InterfaceAnalyzerMover::apply_const(), protocols::environment::EnvClaimBroker::broker_dofs(), protocols::stepwise::setup::cleanup(), protocols::grafting::delete_region(), protocols::loop_modeling::utilities::PrepareForFullatom::do_apply(), core::pose::symmetry::extract_asymmetric_unit(), protocols::abinitio::AbrelaxApplication::fold(), protocols::simple_moves::CutChainMover::foldTree(), core::pose::initialize_disulfide_bonds(), core::pose::symmetry::make_symmetric_pose(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::analysis::PeptideDeriverFilter::prepare_pose(), protocols::sic_dock::read_biounit(), protocols::grafting::replace_region(), protocols::forge::methods::restore_residues(), protocols::grafting::return_region(), protocols::simple_moves::AddChainMover::swap_chain(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and protocols::protein_interface_design::PatchdockReader::transform_pose().
void core::conformation::Conformation::detect_pseudobonds | ( | ) |
References core::conformation::Residue::actual_residue_connection(), add_pseudobond(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::is_coarse(), core::chemical::ResidueType::n_possible_residue_connections(), core::conformation::Residue::path_distance(), core::chemical::ResConnID::resid(), residue(), residue_(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), size(), core::conformation::TR(), and core::conformation::Residue::type().
Referenced by protocols::simple_moves::DeleteChainsMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().
Returns the AtomTree degree of freedom (DOF) <id>
References atom_tree_.
Referenced by protocols::environment::collect_dofs(), core::conformation::symmetry::MirrorSymmetricConformation::set_dof(), and core::conformation::symmetry::SymmetricConformation::set_dof().
id::DOF_ID core::conformation::Conformation::dof_id_from_torsion_id | ( | TorsionID const & | id | ) | const |
References atom_tree_, core::id::BOGUS_DOF_ID, core::id::get_rb_type(), get_torsion_angle_atom_ids(), core::id::JUMP, jump_atom_id(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), and core::id::TorsionID::type().
Referenced by atom_tree_torsion(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), protocols::environment::claims::TorsionClaim::insert_dof_element(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), protocols::environment::ProtectedConformation::set_secstruct(), protocols::environment::ProtectedConformation::set_torsion(), set_torsion(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), and torsion().
kinematics::Stub core::conformation::Conformation::downstream_jump_stub | ( | int | jump_number | ) | const |
The upstream and downstream Stubs are the coordinate frames between which this jump is transforming.
References atom_tree_, and jump_atom_id().
Referenced by protocols::ligand_docking::RigidSearchMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::simple_moves::UniformRotationMover::apply(), protocols::simple_moves::UniformTranslationMover::apply(), protocols::enzdes::PredesignPerturbMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTiltMover::apply(), check_valid_membrane(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), and protocols::environment::CoMTrackerCM::update_tracking_residue().
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Returns true if this conformation does not have any residues.
References residues_.
void core::conformation::Conformation::fill_missing_atoms | ( | id::AtomID_Mask | missing | ) |
References core::kinematics::AtomTree::atom(), core::chemical::ICoorAtomID::atom_id(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::build_atom_ideal(), core::conformation::build_residue_tree(), core::id::D, core::chemical::AtomICoor::d(), core::chemical::AtomICoor::depends_on_residue_connection(), core::kinematics::AtomTree::dof(), core::conformation::Residue::icoor(), core::kinematics::tree::Atom::input_stub_atom1_id(), core::kinematics::tree::Atom::input_stub_atom2_id(), core::kinematics::tree::Atom::input_stub_atom3_id(), core::chemical::ICoorAtomID::is_connect(), core::chemical::AtomType::is_heavyatom(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::id::PHI, core::chemical::AtomICoor::phi(), residue_(), set_xyz(), size(), core::kinematics::Stub::spherical(), core::chemical::AtomICoor::stub_atom(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), core::id::THETA, core::chemical::AtomICoor::theta(), core::conformation::TR(), core::conformation::Residue::type(), update_residue_coordinates(), core::conformation::Residue::xyz(), and xyz().
Referenced by protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftOneMover::apply(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().
void core::conformation::Conformation::fix_disulfides | ( | utility::vector1< std::pair< Size, Size > > | disulf_bonds | ) |
Assigns disulfide bonds based on a pre-determined list.
References core::conformation::Residue::atom_index(), core::conformation::change_cys_state(), core::chemical::DISULFIDE, core::chemical::ResidueType::get_disulfide_atom_name(), residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), residues_, size(), core::conformation::TR(), and core::conformation::Residue::type().
Referenced by protocols::simple_moves::ForceDisulfidesMover::apply(), protocols::hybridization::MRMover::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), core::pose::initialize_disulfide_bonds(), core::io::raw_data::DisulfideFile::read_in_and_set_disulfides(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and core::pose::full_model_info::update_disulfides_from_full_model_info().
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Returns the conformation's FoldTree.
Reimplemented in core::conformation::symmetry::SymmetricConformation.
References fold_tree_.
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(), protocols::environment::EnvClaimBroker::broker_fold_tree(), core::conformation::symmetry::SymmetryInfo::dependent_dofs(), core::conformation::symmetry::SymmetryInfo::dof_is_independent(), core::conformation::Residue::fill_missing_atoms(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::pose::symmetry::find_symmetric_basejump_anchor(), core::conformation::symmetry::SymmetricConformation::fold_tree(), protocols::topology_broker::FoldandDockClaimer::generate_claims(), protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(), protocols::topology_broker::FibrilModelingClaimer::generate_claims(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight(), core::conformation::idealize_position(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::is_ideal_position(), protocols::membrane::is_membrane_fixed(), protocols::membrane::is_membrane_moveable_by_itself(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::conformation::symmetry::process_residue_request(), protocols::environment::EnvClaimBroker::render_fold_tree(), protocols::fibril::reorient_extended_fibril(), protocols::simple_filters::AlaScan::report(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), protocols::environment::ClientMover::sandboxed_copy(), core::conformation::symmetry::set_asymm_unit_fold_tree(), core::conformation::symmetry::set_fold_tree_from_symm_data(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::setup_symmetric_conformation(), core::conformation::symmetry::symmetrize_fold_tree(), core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree(), core::conformation::symmetry::MirrorSymmetricConformation::update_njumps_nres(), and protocols::environment::claims::VirtResClaim::yield_elements().
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Sets the FoldTree to <fold_tree_in>
setup atom tree as well from the fold tree
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References annotated_sequence(), core::kinematics::FoldTree::nres(), setup_atom_tree(), size(), core::conformation::TR(), and update_residue_coordinates().
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Force updating of residue coordinates.
Needed by derived classes (particularly MirrorSymmetricConformation).
References residue_coordinates_need_updating_, and update_residue_coordinates().
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Force updating of residue torsions.
Needed by derived classes (particularly MirrorSymmetricConformation).
References residue_torsions_need_updating_, and update_residue_torsions().
bool core::conformation::Conformation::get_jump_atom_ids | ( | core::Size | jump_number, |
AtomID & | upstream_id, | ||
AtomID & | downstream_id | ||
) | const |
get two atoms connect by jump
References atom_tree_, and jump_atom_id().
Referenced by protocols::toolbox::AtomLevelDomainMap::get_jump().
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returns a mask of residues to be used in scoring
Returns a mask of residues over which scoring is restricted. Only these residues will be used in constructing the neighbor list.
Reimplemented in core::conformation::symmetry::SymmetricConformation.
References residues_.
Referenced by core::scoring::NeighborList::setup().
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returns a residue-pair weight
Returns a weight to be used when scoring this residue.
Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
Referenced by core::scoring::NeighborList::setup().
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self pointers
Referenced by core::conformation::upper_is_symm_equivalent_of_lower().
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Referenced by core::pose::PDBInfo::attach_to().
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kinematics::RT core::conformation::Conformation::get_stub_transform | ( | id::StubID const & | stub_id1, |
id::StubID const & | stub_id2 | ||
) | const |
get the transform between two stubs
References atom_tree_.
Referenced by protocols::forge::build::ConnectRight::extract_rt(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), and core::fragment::DownJumpSRFD::steal().
bool core::conformation::Conformation::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
References core::id::AtomID::atomno(), backbone_torsion_angle_atoms(), core::id::BB, core::id::BRANCH, branch_connection_torsion_angle_atoms(), core::id::CHI, core::conformation::Residue::chi_atoms(), const_residue_(), core::id::JUMP, core::id::NU, core::conformation::Residue::nu_atoms(), core::id::AtomID::rsd(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), torsion(), core::conformation::TR(), and core::id::TorsionID::type().
Referenced by protocols::ncbb::oop::OopCreatorMover::apply(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), atom_tree_torsion(), core::optimization::cartesian_collect_torsional_deriv(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), debug_residue_torsions(), dof_id_from_torsion_id(), protocols::toolbox::AtomLevelDomainMap::get(), core::pose::rna::RNA_IdealCoord::is_torsion_exists(), core::pose::rna::is_torsion_valid(), protocols::stepwise::modeler::rna::print_torsion_info(), core::pose::rna::print_torsion_info(), set_torsion(), and update_residue_torsions().
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Reimplemented in protocols::environment::ProtectedConformation.
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Optimizing the common case of assigning a conformation to another with the same sequence.
References atom_tree_, chain_endings_, dof_moved_, fold_tree_, parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, secstruct_, size(), structure_moved_, and xyz_moved_.
Referenced by operator=().
void core::conformation::Conformation::insert_chain_ending | ( | Size | seqpos | ) |
Marks <seqpos> as the end of a new chain.
References chain_endings_, rederive_chain_ids(), and size().
Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::simple_moves::ChainSplitMover::apply(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::pose::create_subpose(), core::fragment::make_pose_from_frags(), core::io::serialization::read_binary(), and protocols::fldsgn::CircularPermutation::split_chains().
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Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump.
Insert one conformation into another. Some tricky issues: (1) residue connections: assume all residue connections within conf carry over, after renumbering residues positions (2) jump numbers: see FoldTree::insert_fold_tree_by_jump (3) chains: chain endings are inserted before insert_seqpos, and after insert_seqpos+conf.size()-1 ie. at the beginning and ending of the inserted conformation; all internal chain endings from conf are used (4) atom_tree: setup_atom_tree is called to rebuild from scratch using the fold_tree
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References add_parameters_set(), chain_end(), chain_endings_, core::id::AtomID_Map< T >::clear(), core::conformation::Residue::clone(), dof_moved_, fold_tree(), fold_tree_, n_parameters_sets(), notify_length_obs(), num_chains(), parameters_set(), pre_nresidue_change(), rederive_chain_ids(), residue(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, residue_op(), residue_torsions_need_updating_, residues_, core::id::AtomID_Map< T >::resize(), secstruct_, setup_atom_tree(), size(), update_sequence_numbering(), and xyz_moved_.
Referenced by core::pose::Pose::append_pose_by_jump(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), protocols::motif_grafting::movers::MotifGraftMover::join_two_poses_by_jump(), and core::conformation::symmetry::setup_symmetric_conformation().
void core::conformation::Conformation::insert_fragment | ( | id::StubID const & | instub_id, |
FragRT const & | outstub_transforms, | ||
FragXYZ const & | frag_xyz | ||
) |
References atom_tree_, and set_dof_moved().
void core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond | ( | Size | seqpos | ) |
Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS – NOT EVEN OMEGA IF IT'S A PROTEIN
References core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::mainchain_atom(), core::chemical::ResidueType::mainchain_atoms(), rebuild_polymer_bond_dependent_atoms(), residue_type(), set_bond_angle(), set_bond_length(), and core::chemical::ResidueType::upper_connect().
Referenced by protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::grafting::idealize_combined_pose(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), and protocols::forge::remodel::RemodelLoopMover::repeat_propagation().
void core::conformation::Conformation::insert_ideal_geometry_at_residue_connection | ( | Size | pos1, |
Size | connid1 | ||
) |
Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS – NOT EVEN OMEGA IF IT'S A PROTEIN
References rebuild_residue_connection_dependent_atoms(), residues_, set_bond_angle(), and set_bond_length().
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insert a polymer residue Fires a LengthEvent::RESIDUE_PREPEND signal.
References atom_tree_, const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), notify_length_obs(), pre_nresidue_change(), residue_(), core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_insert(), and size().
Referenced by append_polymer_residue_after_seqpos(), and prepend_polymer_residue_before_seqpos().
void core::conformation::Conformation::insert_residue_by_bond | ( | Residue const & | new_rsd_in, |
Size | seqpos, | ||
Size | anchor_pos, | ||
bool | build_ideal_geometry = false , |
||
std::string const & | anchor_atom = "" , |
||
std::string const & | root_atom = "" , |
||
bool | new_chain = false , |
||
bool | 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() )
insert a residue by bond Fires a LengthEvent::RESIDUE_PREPEND signal.
References core::chemical::ResidueType::atom_index(), atom_tree_, core::conformation::Residue::clone(), const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), notify_length_obs(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), residue_(), core::conformation::Residue::residue_connection(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_coordinates_need_updating_, core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_, residues_insert(), core::conformation::Residue::seqpos(), size(), core::conformation::Residue::type(), and update_residue_coordinates().
void core::conformation::Conformation::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() )
insert a residue by jump Fires a LengthEvent::RESIDUE_PREPEND signal.
References atom_tree_, const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), notify_length_obs(), pre_nresidue_change(), residue_(), core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_insert(), core::conformation::Residue::seqpos(), and size().
Referenced by protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), and core::conformation::symmetry::SymmetricConformation::append_residue_by_jump().
id::AtomID core::conformation::Conformation::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.
References core::chemical::ResidueConnection::atomno(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_partner(), and residues_.
Referenced by core::chemical::ICoorAtomID::atom_id().
bool core::conformation::Conformation::is_centroid | ( | ) | const |
convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos )
References core::chemical::CENTROID, and is_residue_typeset().
Referenced by protocols::environment::EnvClaimBroker::broker_dofs().
bool core::conformation::Conformation::is_fullatom | ( | ) | const |
convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos )
References core::chemical::FA_STANDARD, and is_residue_typeset().
Referenced by core::conformation::form_disulfide().
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convenience test for if the conformation contains information for a membrane protein
References membrane_info_.
Referenced by core::select::residue_selector::MembraneResidueSelector::apply(), core::select::residue_selector::ByMembraneDepthSelector::apply(), core::select::residue_selector::TMSpanSelector::apply(), protocols::membrane::SetMembranePositionMover::apply(), protocols::membrane::RandomPositionRotationMover::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::membrane::visualize::VisualizeEmbeddingMover::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::relax::membrane::MPFastRelaxMover::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::membrane::visualize::VisualizeMembraneMover::apply(), protocols::symmetric_docking::membrane::MPSymDockMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::membrane::TranslationMover::apply(), protocols::membrane::RandomPositionTranslationMover::apply(), protocols::membrane::SetMembraneNormalMover::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::membrane::SetMembraneCenterMover::apply(), protocols::membrane::RotationMover::apply(), protocols::moves::PyMolMover::apply(), protocols::membrane::TranslationRotationMover::apply(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts(), protocols::membrane::create_membrane_foldtree_anchor_com(), protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom(), protocols::membrane::create_membrane_foldtree_anchor_tmcom(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::membrane::create_specific_membrane_foldtree(), protocols::relax::FastRelax::do_minimize(), core::scoring::hbonds::fill_hbond_set(), protocols::relax::RangeRelaxMover::finalize_setup(), core::scoring::membrane::MPLipoEnergy::finalize_total_energy(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), protocols::membrane::is_membrane_fixed(), protocols::membrane::is_membrane_moveable_by_itself(), protocols::membrane::mem_all_atom_rmsd_no_super(), protocols::membrane::mem_all_atom_rmsd_with_super(), protocols::membrane::mem_bb_rmsd_no_super(), protocols::membrane::mem_bb_rmsd_with_super(), core::pose::operator<<(), core::scoring::membrane::MPCbetaEnergy::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::membrane::MPEnvEnergy::residue_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), protocols::moves::PyMolMover::send_membrane_planes(), protocols::membrane::setup_foldtree_from_anchors(), protocols::membrane::setup_foldtree_pose_com(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), and core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy().
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inlinevirtual |
Reimplemented in protocols::environment::ProtectedConformation.
Referenced by protocols::abinitio::abscript::FragmentCM::apply(), and protocols::environment::DofUnlock::~DofUnlock().
bool core::conformation::Conformation::is_residue_typeset | ( | std::string | tag | ) | const |
convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos )
References residue_type(), core::chemical::ResidueType::residue_type_set(), size(), and core::conformation::TR().
Referenced by is_centroid(), and is_fullatom().
Conformation::Jump const & core::conformation::Conformation::jump | ( | int | jump_number | ) | const |
Returns the Jump with jump number <jump_number>
References atom_tree_, and jump_atom_id().
Referenced by check_valid_membrane(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree().
Conformation::Jump const & core::conformation::Conformation::jump | ( | AtomID const & | id | ) | const |
access a jump
References atom_tree_.
id::AtomID core::conformation::Conformation::jump_atom_id | ( | int | jump_number | ) | const |
References const_residue_(), core::kinematics::dir_jump, fold_tree_, core::conformation::get_root_atomno(), and residues_.
Referenced by dof_id_from_torsion_id(), downstream_jump_stub(), get_jump_atom_ids(), jump(), protocols::environment::ProtectedConformation::set_jump(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::SymmetricConformation::set_jump(), set_jump(), upstream_jump_stub(), protocols::environment::claims::JumpClaim::yield_elements(), and protocols::environment::claims::VirtResClaim::yield_elements().
membrane::MembraneInfoOP core::conformation::Conformation::membrane_info | ( | ) |
Returns the const MembraneInfo object in conformation.
Returns the MembraneInfo object in conformation.
Membrane Info contains information describing location of the membrane virtual residue in the pose sequence, membrane spanning region definitions and lipid exposure/burial data
References membrane_info_.
Referenced by core::select::residue_selector::MembraneResidueSelector::apply(), core::select::residue_selector::TMSpanSelector::apply(), protocols::membrane::benchmark::SampleTiltAngles::apply(), protocols::membrane::RandomPositionRotationMover::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::membrane::visualize::VisualizeEmbeddingMover::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::relax::membrane::MPFastRelaxMover::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::membrane::SpinAroundPartnerMover::apply(), protocols::membrane::TiltMover::apply(), protocols::membrane::FlipMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::membrane::AddMembraneMover::apply(), protocols::membrane::TranslationMover::apply(), protocols::membrane::RandomPositionTranslationMover::apply(), protocols::docking::membrane::MPDockingMover::apply(), protocols::membrane::SetMembraneCenterMover::apply(), protocols::membrane::RotationMover::apply(), protocols::membrane::TranslationRotationMover::apply(), core::scoring::membrane::FaMPEnvSmoothEnergy::calc_energy(), protocols::membrane::calc_helix_axis(), protocols::membrane::calc_helix_tilt_angle(), protocols::membrane::chain_tm_com(), core::select::residue_selector::TMSpanSelector::check_valid_tm_selection(), protocols::membrane::compute_embeddings_by_chain(), protocols::membrane::compute_structure_based_embedding(), protocols::membrane::create_membrane_docking_foldtree_from_partners(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::membrane::create_membrane_multi_partner_foldtree_anchor_tmcom(), protocols::membrane::create_specific_membrane_foldtree(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::docking::membrane::MPFindInterfaceMover::finalize_setup(), core::scoring::membrane::MPLipoEnergy::finalize_total_energy(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::scoring::membrane::FaMPSolvEnergy::init(), protocols::membrane::is_membrane_fixed(), protocols::membrane::is_membrane_moveable_by_itself(), protocols::membrane::mem_all_atom_rmsd_no_super(), protocols::membrane::mem_all_atom_rmsd_with_super(), protocols::membrane::mem_bb_rmsd_no_super(), protocols::membrane::mem_bb_rmsd_with_super(), protocols::membrane::membrane_axis(), core::pose::operator<<(), protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_center(), protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_normal(), protocols::membrane::pose_tilt_angle_and_center_distance(), protocols::membrane::pose_tm_com(), protocols::symmetric_docking::membrane::MPSymDockMover::position_membrane_at_topology_com(), protocols::membrane::reorder_membrane_foldtree(), core::scoring::membrane::MPCbetaEnergy::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::membrane::MPEnvEnergy::residue_energy(), core::select::residue_selector::ByMembraneDepthSelector::residue_within_depth(), protocols::membrane::rsd_closest_to_chain_com(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), protocols::relax::membrane::MPFastRelaxMover::show_protocol(), protocols::membrane::split_topology_by_jump(), protocols::membrane::split_topology_by_jump_noshift(), and protocols::membrane::update_partner_embeddings().
membrane::MembraneInfoOP core::conformation::Conformation::membrane_info | ( | ) | const |
Returns the const MembraneInfo object in conformation.
Returns a Membrane Info Object in the conformation.
Membrane Info contains information describing location of the membrane virtual residue in the pose sequence, membrane spanning region definitions and lipid exposure/burial data
Membrane Info contains information regarding membrane residues, foldtree modifications, fullatom vs. centroid embedding parameters for scoring and the spanning topology/lipids accessibility data
References membrane_info_.
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inlinevirtual |
Get the number of parameters sets defined for this Conformation.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose(), protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info(), and insert_conformation_by_jump().
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notify ConnectionEvent observers
work in progress void insert_chemical_chainbreak_between_polymer_residues( Size const lower_seqpos ) { ResidueOP lower_rsd( residues_[ lower_seqpos ] );
the type of the desired variant residue ResidueTypeSet const & rsd_set( lower_rsd->residue_type_set() );
ResidueType const & new_lower_rsd_type ( rsd_set.get_residue_type_with_variant_removed( lower_rsd.type(), UPPER_TERMINUS ) ); ResidueOP new_lower_rsd( ResidueFactory::create_residue( new_lower_rsd_type ) ); }
References connection_obs_hub_.
Referenced by clear_observers(), and receive_observers_from().
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notify GeneralEvent observers
References general_obs_hub_.
Referenced by notify_identity_obs(), notify_length_obs(), and notify_xyz_obs().
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notify IdentityEvent observers
e | the event |
fire_general | fire a GeneralEvent afterwards? default true |
References identity_obs_hub_, and notify_general_obs().
Referenced by operator=(), and replace_residue().
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notify LengthEvent observers
e | the event |
fire_general | fire a GeneralEvent afterwards? default true |
References length_obs_hub_, and notify_general_obs().
Referenced by append_residue(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), and operator=().
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notify XYZEvent observers
e | the event |
fire_general | fire a GeneralEvent afterwards? default true |
References notify_general_obs(), and xyz_obs_hub_.
Referenced by operator=(), update_residue_coordinates(), and update_residue_torsions().
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Returns the number of chains.
References chain_endings_.
Referenced by protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::simple_moves::CyclizationMover::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::toolbox::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::toolbox::task_operations::RestrictChainToRepackingOperation::apply(), protocols::toolbox::task_operations::PreventChainFromRepackingOperation::apply(), protocols::toolbox::task_operations::RestrictToTerminiOperation::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::denovo_design::connection::BridgeChains::apply(), protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation::apply(), protocols::enzdes::LigInterfaceEnergyFilter::apply(), protocols::analysis::InterfaceAnalyzerMover::apply_const(), protocols::analysis::PeptideDeriverMarkdownStreamOutputter::begin_structure(), protocols::simple_moves::GenericMonteCarloMover::boltzmann(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::RmsdSimpleFilter::compute(), protocols::protein_interface_design::filters::SSamountFilter::compute(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::indexed_structure_store::filters::FragmentLookupFilter::compute(), protocols::simple_filters::SSMotifFinder::compute_jump(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), core::pose::conf2pdb_chain(), core::pose::conf2pdb_chain_default_map(), protocols::floppy_tail::create_extra_output(), protocols::denovo_design::connection::BridgeChains::create_remodel_mover(), protocols::seeded_abinitio::define_movemap_chains(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::motif_grafting::movers::MotifGraftMover::generate_scaffold_matches(), protocols::features::InterfaceFeatures::get_all_pose_chains(), core::conformation::symmetry::get_chain2range(), core::pose::get_chain_ids_from_chain(), protocols::analysis::PeptideDeriverFilter::get_chain_indices(), core::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::get_omg_from_rsd(), core::pose::has_chain(), protocols::antibody::AntibodyInfo::identify_antibody(), protocols::denovo_design::components::StructureData::infer_from_pose(), insert_conformation_by_jump(), protocols::forge::build::SegmentRebuild::modify_impl(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::protein_interface_design::movers::TopologyBrokerMover::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::simple_moves::SwitchChainOrderMover::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::rigid::RollMover::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::analysis::PeptideDeriverFilter::prepare_pose(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), core::io::external::PsiPredInterface::run_psipred(), protocols::pmut_scan::AlterSpecDisruptionDriver::score(), core::select::residue_selector::ChainSelector::select_chain_by_index(), protocols::ligand_docking::MoveMapBuilder::set_all_chi(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::analysis::InterfaceAnalyzerMover::setup_for_dock_chains(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), and protocols::fldsgn::CircularPermutation::which_chain().
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equals operator
If lengths & sequence of source and target are different, will fire a LengthEvent::INVALIDATE signal and then an IdentityEvent::INVALIDATE signal.
Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References atom_tree_, chain_endings_, clear(), contains_carbohydrate_residues_, dof_moved_, fold_tree_, in_place_copy(), core::conformation::signals::LengthEvent::INVALIDATE, core::conformation::signals::IdentityEvent::INVALIDATE, membrane_info_, notify_identity_obs(), notify_length_obs(), notify_xyz_obs(), parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, secstruct_, sequence_matches(), size(), structure_moved_, and xyz_moved_.
Referenced by protocols::environment::ProtectedConformation::operator=().
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Access one of the ParametersSets objects linked to this Conformation.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose(), protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info(), and insert_conformation_by_jump().
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Const access to one of the ParametersSets objects linked to this Conformation.
References parameters_set_.
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Reimplemented in protocols::environment::ProtectedConformation.
Referenced by protocols::environment::DofUnlock::~DofUnlock().
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The Conformation must transfer lazily accumulated "moved" data from the AtomTree before changing the number of residues.
Copy any un-registered coordinate or DOF changes into the existing residues. For now, the AtomTree only tracks which Residues need external coordinate changes, and not internal coordinate changes. When internal coordinates go out-of-date in the atom tree, the "update_internal_coordinates" recursion begins at the root. Moreover, the Conformation updates internal coordinates for all residues when it updates. However, when this changes and the AtomTree starts tracking which residues need to have their internal coordinates updated, then it will be necessary to add a call to update_residue_torsions() here.
References update_residue_coordinates().
Referenced by append_polymer_residue_after_seqpos(), append_residue(), append_residue_by_bond(), append_residue_by_jump(), clear(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), prepend_polymer_residue_before_seqpos(), and safely_append_polymer_residue_after_seqpos().
void core::conformation::Conformation::prepend_polymer_residue_before_seqpos | ( | Residue const & | new_rsd, |
Size | seqpos, | ||
bool | build_ideal_geometry | ||
) |
glues to seqpos and perhaps also seqpos-1
Fires a LengthEvent::RESIDUE_PREPEND signal.
References core::conformation::Residue::clone(), dof_moved_, fold_tree_, insert_polymer_residue(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect(), core::conformation::Residue::natoms(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), residue_(), residue_coordinates_need_updating_, size(), core::id::AtomID_Map< T >::size(), update_residue_coordinates(), core::conformation::Residue::upper_connect(), and xyz_moved_.
Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), and safely_prepend_polymer_residue_before_seqpos().
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Reimplemented in protocols::environment::ProtectedConformation.
Referenced by protocols::environment::DofUnlock::DofUnlock().
void core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms | ( | Size | seqpos | ) |
Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1.
rebuilds the atoms that are dependent on the bond between seqpos and seqpos+1 for their torsion offset
Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms_this_residue_only(), and update_polymeric_connection().
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rebuild atoms in residue seqpos dependent on either the lower (-1) or upper(1) polymer residue
References core::conformation::Residue::atom_name(), core::chemical::AtomICoor::build(), core::chemical::AtomICoor::depends_on_polymer_lower(), core::chemical::AtomICoor::depends_on_polymer_upper(), core::conformation::Residue::icoor(), core::conformation::Residue::natoms(), residue_(), set_xyz(), and update_residue_coordinates().
void core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms_this_residue_only | ( | Size | seqpos | ) |
Rebuilds the atoms that are depenent on polymer bonds for the specified residue only.
References rebuild_polymer_bond_dependent_atoms().
Referenced by protocols::cyclic_peptide::DeclareBond::apply(), and protocols::relax::fixH().
void core::conformation::Conformation::rebuild_residue_connection_dependent_atoms | ( | Size | seqpos, |
Size | connid | ||
) |
References core::chemical::AtomICoor::build(), core::chemical::AtomICoor::depends_on_residue_connection(), core::conformation::Residue::icoor(), core::conformation::Residue::natoms(), residue_(), set_xyz(), and update_residue_coordinates().
Referenced by insert_ideal_geometry_at_residue_connection(), protocols::simple_moves::CyclizationMover::minimize_rebuild(), and protocols::simple_moves::CyclizationMover::setup_connections().
void core::conformation::Conformation::receive_observers_from | ( | Conformation const & | src | ) |
fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation
src | Take observers from this source Conformation. |
References notify_connection_obs(), and core::conformation::signals::ConnectionEvent::TRANSFER.
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References chain_endings_, residues_, and size().
Referenced by residues_append(), residues_delete(), and residues_insert().
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References chain_endings_, residues_, and size().
Referenced by chain_endings(), chains_from_termini(), delete_chain_ending(), insert_chain_ending(), insert_conformation_by_jump(), reset_chain_endings(), residues_append(), and residues_delete().
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replace residue
replace a residue Fires an IdentityEvent signal.
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, const_residues(), fold_tree_, notify_identity_obs(), core::conformation::replace_residue_in_atom_tree(), core::conformation::signals::IdentityEvent::RESIDUE, residue_torsions_need_updating_, residues_, and residues_replace().
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), core::conformation::change_cys_state(), copy_segment(), core::conformation::form_disulfide_helper(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), core::conformation::idealize_position(), protocols::denovo_design::rebuild_missing_atoms(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), protocols::grafting::replace_region(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::symmetry::SymmetricConformation::replace_residue(), and replace_residue().
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function to replace a residue based on superposition on the specified input atom pairs
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References core::conformation::Residue::orient_onto_residue(), replace_residue(), and residues_.
void core::conformation::Conformation::reset_chain_endings | ( | ) |
Resets chain data so that the Conformation is marked as a single chain.
References chain_endings_, and rederive_chain_ids().
Referenced by protocols::domain_assembly::AssembleLinkerMover::apply(), and protocols::fldsgn::CircularPermutation::apply().
void core::conformation::Conformation::reset_move_data | ( | ) |
forget all the structure modifications
called after domain map information is transferred to the Energies class
References dof_moved_, core::id::AtomID_Map< T >::fill_with(), structure_moved_, and xyz_moved_.
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reset the structure_moved_ bool
References structure_moved_.
access one of the residues
update coordinates and torsions for this and all other residues before allowing read access
References residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, size(), update_residue_coordinates(), and update_residue_torsions().
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::conformation::add_variant_type_to_conformation_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::environment::EnvClaimBroker::add_virtual_residues(), core::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::annotated_atom_graph_from_conformation(), annotated_sequence(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), protocols::simple_filters::atom_distance(), core::conformation::atom_graph_from_conformation(), core::conformation::membrane::MembraneInfo::atom_z_position(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), bonded_neighbor_all_res(), core::conformation::break_disulfide(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), core::conformation::change_cys_state(), protocols::environment::collect_dofs(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::simple_filters::SSMotifFinder::compute_jump(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), protocols::star::copy_residues(), copy_segment(), debug_residue_torsions(), core::conformation::symmetry::SymmetricConformation::declare_chemical_bond(), detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), detect_disulfides(), detect_pseudobonds(), core::scoring::constraints::AtomPairConstraint::dist(), core::conformation::disulfide_bonds(), protocols::environment::dof_id_to_string(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::viewer::dump_residue_kinemage(), protocols::viewer::dump_structure_kinemage(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception(), protocols::environment::find_implied_cut(), protocols::pockets::PocketGrid::findExemplars(), fix_disulfides(), core::conformation::form_disulfide(), core::conformation::form_disulfide_helper(), core::pack::task::residue_selector::ClashBasedRepackShellSelector::get_clashing_positions(), core::conformation::get_disulf_partner(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::pose::get_hash_excluding_chain(), core::pose::get_hash_from_chain(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::pose::get_sha1_hash_excluding_chain(), core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), protocols::pockets::PocketGrid::getRelaxResidues(), core::conformation::idealize_position(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::membrane::AddMembraneMover::initialize_membrane_residue(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::is_disulfide_bond(), core::conformation::is_ideal_position(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), core::conformation::membrane::MembraneInfo::membrane_center(), core::conformation::membrane::MembraneInfo::membrane_normal(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), protocols::pockets::PocketGrid::move_pose_to_standard_orie(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), protocols::pockets::PocketConstraint::PocketConstraint(), core::conformation::print_atom(), protocols::viewer::print_node(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bin(), core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bins(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::conformation::symmetry::recenter(), core::conformation::remove_variant_type_from_conformation_residue(), core::pose::remove_variant_type_from_pose_residue(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), protocols::simple_filters::res_res_min_distance(), protocols::simple_filters::res_rmsd(), protocols::protein_interface_design::filters::res_rmsd(), core::scoring::func::ConformationXYZ::residue(), core::conformation::symmetry::residue_center_of_mass(), core::conformation::residue_point_graph_from_conformation(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::conformation::symmetry::return_nearest_residue(), protocols::pockets::PlaidFingerprint::rmsd(), protocols::environment::ClientMover::sandboxed_copy(), core::pose::symmetry::sealed_symmetric_fold_tree(), sequence_matches(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::pockets::PocketConstraint::set_target_res(), protocols::pockets::PocketConstraint::set_target_res_pdb(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::topology_broker::SymmetryClaimer::symmetry_duplicate(), protocols::simple_filters::RelativePoseFilter::thread_seq(), torsion(), core::conformation::symmetry::MirrorSymmetricConformation::update_residue_identities(), core::conformation::ConformationKinWriter::write_coords(), and protocols::environment::claims::XYZClaim::yield_elements().
Returns a non-constant residue reference without triggering coordinate/torsion update.
Use with care. Useful inside torsion/coordinate setters where we want chemical info about a given residue but don't want to trigger the coordinate/torsion updates that go along with a call to residue(seqpos).
References residues_, and size().
Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), detect_pseudobonds(), fill_missing_atoms(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), and set_polymeric_connection().
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access one of the residues, using COP
References residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, size(), update_residue_coordinates(), and update_residue_torsions().
Access one of the residues, using OP.
Non-const access.
References residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, size(), update_residue_coordinates(), and update_residue_torsions().
Referenced by protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose(), insert_conformation_by_jump(), and core::conformation::parametric::ParametersSet::update_residue_links().
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access one of the residue's types – avoids coord/torsion update
References residues_, and size().
Referenced by core::pose::add_variant_type_to_pose_residue(), core::conformation::annotated_atom_graph_from_conformation(), protocols::simple_moves::AddJobPairData::apply(), core::conformation::atom_graph_from_conformation(), core::chemical::ICoorAtomID::atom_id(), core::conformation::symmetry::calculate_inverting_virtuals(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), detect_disulfides(), core::conformation::form_disulfide(), core::conformation::form_disulfide_helper(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), insert_ideal_geometry_at_polymer_bond(), is_residue_typeset(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), protocols::viewer::print_node(), core::conformation::symmetry::recenter(), core::pose::remove_variant_type_from_pose_residue(), protocols::fibril::reorient_extended_fibril(), and core::chemical::ICoorAtomID::xyz().
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PRIVATE: wrap direct access to the Residues container for appending
References core::id::NamedAtomID::atom(), core::id::BOGUS_NAMED_ATOM_ID, core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::natoms(), rederive_chain_endings(), rederive_chain_ids(), residues_, core::id::AtomID_Map< T >::resize(), core::id::NamedAtomID::rsd(), secstruct_, structure_moved_, core::conformation::TR(), update_noncanonical_connection(), update_polymeric_connection(), and xyz_moved_.
Referenced by append_residue().
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PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays and updating of sequence numbers
References rederive_chain_endings(), rederive_chain_ids(), residues_, secstruct_, update_polymeric_connection(), and update_sequence_numbering().
Referenced by delete_polymer_residue(), delete_residue_range_slow(), and delete_residue_slow().
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PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays and updating of sequence numbers
References core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::name(), core::conformation::Residue::natoms(), rederive_chain_endings(), residues_, secstruct_, structure_moved_, update_polymeric_connection(), update_sequence_numbering(), and xyz_moved_.
Referenced by insert_polymer_residue(), insert_residue_by_bond(), and insert_residue_by_jump().
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wrap direct access to the Residues container
PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays
References core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::natoms(), residues_, structure_moved_, and xyz_moved_.
Referenced by replace_residue().
void core::conformation::Conformation::safely_append_polymer_residue_after_seqpos | ( | Residue const & | new_rsd, |
Size | seqpos, | ||
bool | build_ideal_geometry | ||
) |
glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary
References append_polymer_residue_after_seqpos(), pre_nresidue_change(), and core::conformation::remove_upper_terminus_type_from_conformation_residue().
Referenced by protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::loops::apply_sequence_mapping(), protocols::forge::methods::grow_right_r(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), and protocols::ub_e2c::ubi_e2c_modeler::restore_cter().
void core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos | ( | Residue const & | new_rsd, |
Size | seqpos, | ||
bool | build_ideal_geometry | ||
) |
glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary
Fires a LengthEvent::RESIDUE_PREPEND signal.
References prepend_polymer_residue_before_seqpos(), and core::conformation::remove_lower_terminus_type_from_conformation_residue().
Referenced by protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::loops::apply_sequence_mapping(), and protocols::forge::methods::grow_left_r().
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determine the type of the ConformationOP
Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References same_type_as_me().
Referenced by core::import_pose::pose_from_file(), core::conformation::symmetry::MirrorSymmetricConformation::same_type_as_me(), core::conformation::symmetry::SymmetricConformation::same_type_as_me(), same_type_as_me(), and protocols::environment::ProtectedConformation::same_type_as_me().
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Returns the secondary structure the position <seqpos>
References secstruct_.
Referenced by protocols::loophash::LoopHashDiversifier::apply(), protocols::LoopRebuild::fast_ccd_close_loops(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::membrane::get_secstruct(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), and core::scoring::methods::CenPairEnergy::residue_pair_energy().
bool core::conformation::Conformation::sequence_matches | ( | Conformation const & | other | ) | const |
do the names of all residues in this and src match?
Am I composed of the same sequence of ResidueType objects as other? DANGER! Fails, unexpectedly, if a histidine pair has a different tautomerization. tex, 9/12/08 The above comment points out that this method isn't a clearly defined idea, because there are many ways that someone could imagine comparing the a sequence, including:
References core::conformation::Residue::chain(), core::conformation::Residue::connections_match(), residue(), size(), and core::conformation::Residue::type().
Referenced by operator=(), protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same(), and protocols::matdes::MatDesGreedyOptMutationMover::pose_coords_are_same().
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Sets the bond angle defined by <atom[1-3]> to <setting>
Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, and set_dof_moved().
Referenced by core::fragment::BBTorsionAndAnglesSRFD::apply(), protocols::helical_bundle::copy_helix_bondangles(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), insert_ideal_geometry_at_residue_connection(), core::conformation::insert_ideal_mainchain_bonds(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), and protocols::generalized_kinematic_closure::set_loop_pose().
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Sets the cond length between <atom1> and <atom2> to <setting>
Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, and set_dof_moved().
Referenced by protocols::helical_bundle::copy_helix_bondlengths(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), insert_ideal_geometry_at_residue_connection(), core::conformation::insert_ideal_mainchain_bonds(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), and protocols::generalized_kinematic_closure::set_loop_pose().
Sets the AtomTree degree of freedom (DOF) <id> to <setting>
Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References atom_tree_, residue_torsions_need_updating_, and set_dof_moved().
Referenced by protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), core::conformation::symmetry::MirrorSymmetricConformation::set_dof(), and core::conformation::symmetry::SymmetricConformation::set_dof().
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notify of dof-change
References dof_moved_, residue_coordinates_need_updating_, and structure_moved_.
Referenced by insert_fragment(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_stub_transform(), set_torsion(), and set_torsion_angle().
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notify of dof-change
References dof_moved_, residue_coordinates_need_updating_, and structure_moved_.
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Sets the jump <jump_number> to <new_jump>
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, jump_atom_id(), core::kinematics::Jump::ortho_check(), and set_dof_moved().
Referenced by protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::environment::ProtectedConformation::set_jump(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::SymmetricConformation::set_jump(), and core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree().
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set a jump
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, core::kinematics::Jump::ortho_check(), and set_dof_moved().
void core::conformation::Conformation::set_jump_atom_stub_id | ( | id::StubID const & | id | ) |
References atom_tree_.
void core::conformation::Conformation::set_membrane_info | ( | membrane::MembraneInfoOP | mem_info | ) |
Setup a Membrane Info object in Conformation - pos & topology.
Rosetta Membrane Framework /// Core data for interacting with membrane proteins in Rosetta /// /// Authors: ///
Add a MembraneInfo object - describes the position of the membrane virtual residue, information on membrane spanning regions, lipid exposure/burial of residues in the pose, and fullatom steepness and thickness parameters. At construction, specify membrane position and list of spanning topology objects by chain.
Add a MembraneInfo object - describes the position of the membrane virtual residue, information on membrane spanning regions, lipid exposure/burial of residues in the pose, and fullatom steepness and thickness parameters. At construction, specify membrane position and list of spanning topology objects by chain.
References membrane_info_.
Referenced by protocols::membrane::AddMembraneMover::apply().
void core::conformation::Conformation::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.
References residues_.
Referenced by protocols::cyclic_peptide::DeclareBond::apply(), and update_noncanonical_connection().
void core::conformation::Conformation::set_polymeric_connection | ( | Size | res_id_lower, |
Size | res_id_upper | ||
) |
identify polymeric connections
The lower residue connects to the upper residue through its upper_connect connection The upper residue connects to the lower residue through its lower_connect connection
References residue_(), and residues_.
Referenced by update_polymeric_connection().
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Sets the secondary structure of the position <seqpos> to <setting>
Sets secondary structure character of a sequence position. Will resize the secondary structure array if the requested sequence position is larger than the length of the array.
Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.
References secstruct_.
Referenced by protocols::environment::ProtectedConformation::set_secstruct(), and core::conformation::symmetry::SymmetricConformation::set_secstruct().
void core::conformation::Conformation::set_stub_transform | ( | id::StubID const & | stub_id1, |
id::StubID const & | stub_id2, | ||
kinematics::RT const & | target_rt | ||
) |
Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms.
References atom_tree_, and set_dof_moved().
Referenced by core::fragment::DownJumpSRFD::apply(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::forge::build::ConnectRight::modify_impl(), protocols::jumping::MembraneJump::rt_templates(), protocols::jumping::PairingLibrary::set_tmh_jump(), and core::pose::swap_transform().
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Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump.
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, core::id::BB, core::id::BRANCH, core::id::CHI, dof_id_from_torsion_id(), get_torsion_angle_atom_ids(), core::id::JUMP, core::id::NU, residues_, core::id::TorsionID::rsd(), set_dof_moved(), core::id::TorsionID::torsion(), core::conformation::TR(), core::id::TorsionID::type(), and core::id::DOF_ID::valid().
Referenced by protocols::simple_moves::RandomOmegaFlipMover::apply(), protocols::simple_moves::RandomTorsionMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::helical_bundle::copy_helix_dihedrals(), protocols::environment::ProtectedConformation::set_torsion(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion(), and core::conformation::symmetry::SymmetricConformation::set_torsion().
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Sets the torsion angle defined by <atom[1-4]> to <setting>
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, residue_torsions_need_updating_, set_dof_moved(), and core::conformation::TR().
Referenced by protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::frags::TorsionFragment::insert(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::pose::carbohydrates::set_glycosidic_torsion(), protocols::generalized_kinematic_closure::set_loop_pose(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion_angle(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), and protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_().
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Reimplemented in core::conformation::symmetry::SymmetricConformation.
References atom_tree_, residues_, and set_xyz_moved().
Referenced by core::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), fill_missing_atoms(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), core::conformation::symmetry::recenter(), protocols::fibril::reorient_extended_fibril(), protocols::generalized_kinematic_closure::set_loop_pose(), and core::conformation::symmetry::SymmetricConformation::set_xyz().
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notify of xyz-change
References residue_torsions_need_updating_, structure_moved_, and xyz_moved_.
Referenced by batch_set_xyz(), and set_xyz().
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notify of mutiple-xyz-change
References residue_torsions_need_updating_, structure_moved_, and xyz_moved_.
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(re-)builds the AtomTree using the FoldTree and the Residues
References atom_tree_, core::conformation::build_tree(), const_residues(), fold_tree_, residue_coordinates_need_updating_, residue_torsions_need_updating_, and update_residue_torsions().
Referenced by append_residue(), delete_residue_range_slow(), delete_residue_slow(), fold_tree(), and insert_conformation_by_jump().
void core::conformation::Conformation::show_residue_connections | ( | ) | const |
Show residue connections for debugging purposes.
References core::conformation::TR().
Referenced by core::conformation::operator<<().
void core::conformation::Conformation::show_residue_connections | ( | std::ostream & | os | ) | const |
Show residue connections for debugging purposes.
References core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::conformation::Residue::n_non_polymeric_residue_connections(), core::conformation::Residue::n_polymeric_residue_connections(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name(), core::chemical::ResConnID::resid(), core::conformation::Residue::residue_connect_atom_index(), residues_, and size().
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Returns the number of residues in the Conformation.
References residues_.
Referenced by aa(), protocols::environment::EnvClaimBroker::add_virtual_residues(), core::conformation::annotated_atom_graph_from_conformation(), annotated_sequence(), append_polymer_residue_after_seqpos(), append_residue(), append_residue_by_bond(), append_residue_by_jump(), core::conformation::atom_graph_from_conformation(), protocols::idealize::basic_idealize(), core::conformation::break_disulfide(), protocols::environment::EnvClaimBroker::broker_fold_tree(), chain_end(), chain_endings(), chains_from_termini(), protocols::environment::collect_dofs(), Conformation(), const_residue_(), const_residues(), copy_segment(), debug_residue_torsions(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), detect_disulfides(), detect_pseudobonds(), core::conformation::disulfide_bonds(), protocols::viewer::dump_residue_kinemage(), protocols::viewer::dump_structure_kinemage(), core::scoring::disulfides::FullatomDisulfideEnergy::ensure_lrenergy_container_is_up_to_date(), fill_missing_atoms(), core::conformation::Residue::fill_missing_atoms(), protocols::environment::find_implied_cut(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), fix_disulfides(), fold_tree(), core::conformation::get_disulf_partner(), core::conformation::idealize_position(), in_place_copy(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), insert_chain_ending(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), core::conformation::is_ideal_position(), is_residue_typeset(), core::conformation::signals::LengthEvent::LengthEvent(), core::pose::symmetry::make_symmetric_movemap(), operator=(), core::conformation::Residue::orient_onto_residue_peptoid(), prepend_polymer_residue_before_seqpos(), core::conformation::symmetry::process_residue_request(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::conformation::symmetry::recenter(), rederive_chain_endings(), rederive_chain_ids(), protocols::fibril::reorient_extended_fibril(), residue(), residue_(), residue_cop(), residue_op(), core::conformation::residue_point_graph_from_conformation(), residue_type(), sequence_matches(), core::conformation::symmetry::set_fold_tree_from_symm_data(), core::conformation::symmetry::setup_symmetric_conformation(), show_residue_connections(), protocols::environment::Environment::start(), core::conformation::symmetry::symmetrize_fold_tree(), update_actcoords(), update_domain_map(), update_noncanonical_connection(), update_polymeric_connection(), core::conformation::parametric::ParametersSet::update_residue_links(), update_residue_torsions(), update_sequence_numbering(), core::conformation::ConformationKinWriter::write_coords(), and core::chemical::ICoorAtomID::xyz().
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has the structure moved since the last call to reset_move_data or reset_structure_moved
References structure_moved_.
Referenced by protocols::qsar::qsarMover::apply(), core::pack::create_packer_graph(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::TaskOperationFeatures::report_features(), protocols::features::HBondFeatures::report_features(), and protocols::features::PairFeatures::report_residue_pairs().
kinematics::Stub core::conformation::Conformation::stub_from_id | ( | id::StubID const & | id | ) | const |
References atom_tree_.
Return the torsion angle OR rigid-body offset for <id>
References atom_tree_, core::id::BB, core::id::BRANCH, core::id::CHI, dof_id_from_torsion_id(), core::id::JUMP, core::id::NU, residue(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), and core::id::TorsionID::type().
Referenced by protocols::simple_moves::RandomOmegaFlipMover::apply(), protocols::simple_moves::RandomTorsionMover::apply(), backbone_torsion_angle_atoms(), protocols::helical_bundle::copy_helix_dihedrals(), debug_residue_torsions(), get_torsion_angle_atom_ids(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion(), and core::conformation::symmetry::SymmetricConformation::set_torsion().
Real core::conformation::Conformation::torsion_angle | ( | AtomID const & | atom1, |
AtomID const & | atom2, | ||
AtomID const & | atom3, | ||
AtomID const & | atom4 | ||
) | const |
Returns the torsion angle defined by <atom[1-4]>
References atom_tree_.
Referenced by protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::simple_moves::a3b_hbs::A3BHbsRandomSmallMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_delta_torsion_selector(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::pose::carbohydrates::get_glycosidic_torsion(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), and protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_().
void core::conformation::Conformation::unblock_signals | ( | ) |
allow signals to be sent
If unblocking after buffering, buffered/held signals will be sent.
References general_obs_hub_, identity_obs_hub_, length_obs_hub_, and xyz_obs_hub_.
void core::conformation::Conformation::update_domain_map | ( | DomainMap & | domain_map | ) | const |
Generate a domain_map from the current dof/xyz moved data.
References atom_tree_, dof_moved_, size(), and xyz_moved_.
Referenced by protocols::farna::movers::RNA_LoopCloser::passes_fast_scan().
Update Normal, Center in the Membrane.
Sets the center and normal coordinates to the appropriate parameters and checks for a valid stub prior to returning.
References core::conformation::membrane::center, check_valid_membrane(), membrane_info_, core::conformation::membrane::normal, and residues_.
Referenced by protocols::membrane::SetMembranePositionMover::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::membrane::SetMembraneNormalMover::apply(), protocols::membrane::SetMembraneCenterMover::apply(), and protocols::membrane::membrane_normal_to_length_15().
void core::conformation::Conformation::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.
References set_noncanonical_connection(), and size().
Referenced by core::pose::add_variant_type_to_pose_residue(), core::pose::remove_variant_type_from_pose_residue(), and residues_append().
void core::conformation::Conformation::update_orbital_coords | ( | Residue & | rsd | ) | const |
void core::conformation::Conformation::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.
References core::chemical::C_METHYLAMIDATION, core::conformation::Residue::chain(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), core::chemical::N_ACETYLATION, rebuild_polymer_bond_dependent_atoms(), residues_, set_polymeric_connection(), and size().
Referenced by protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::relax::cyclize_pose(), protocols::metal_interface::MatchGrafter::graft(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), residues_append(), residues_delete(), and residues_insert().
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Will (if necessary) copy the xyz coordinates from the AtomTree to the Residues being managed.
The AtomTree is responsible for tracking the set of residues whose coordinates need updating, and informs the Conformation object of these residues. The Conformation only updates coordinates for this subset of residues.
References atom_tree_, notify_xyz_obs(), and residue_coordinates_need_updating_.
Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), debug_residue_torsions(), fill_missing_atoms(), fold_tree(), force_update_residue_coordinates(), insert_residue_by_bond(), pre_nresidue_change(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), residue(), residue_cop(), and residue_op().
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Will (if necessary) copy the torsion angles (mainchain/chi) from the AtomTree to the Residues being managed.
References notify_xyz_obs(), residue_torsions_need_updating_, residues_, and size().
Referenced by debug_residue_torsions(), declare_chemical_bond(), force_update_residue_torsions(), residue(), residue_cop(), residue_op(), and setup_atom_tree().
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References core::chemical::ACETYLATED_NTERMINUS_VARIANT, atom_tree_torsion(), core::id::AtomID::atomno(), core::id::BB, core::conformation::Residue::chain(), chain_begin(), chain_end(), core::chemical::rna::CHI, core::id::CHI, core::conformation::Residue::chi(), core::chemical::CTERM_CONNECT, get_torsion_angle_atom_ids(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::mainchain_torsions(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::conformation::Residue::n_nus(), core::conformation::Residue::nchi(), notify_xyz_obs(), core::chemical::NTERM_CONNECT, core::id::NU, core::conformation::Residue::nus(), residues_, core::id::AtomID::rsd(), and update_orbital_coords().
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remap *_moved arrays, sequence numbering in the residues_ arrays, etc, after insertion or deletion of rsds
private need to update:
References dof_moved_, residues_, size(), core::id::AtomID_Map< T >::update_sequence_numbering(), and xyz_moved_.
Referenced by insert_conformation_by_jump(), residues_delete(), and residues_insert().
kinematics::Stub core::conformation::Conformation::upstream_jump_stub | ( | int | jump_number | ) | const |
The upstream and downstream Stubs are the coordinate frames between which this jump is transforming.
References atom_tree_, and jump_atom_id().
Referenced by protocols::protein_interface_design::movers::SpinMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::nonlocal::HelixRotate::apply(), protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::simple_moves::UniformRotationMover::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::membrane::TranslationMover::apply(), protocols::simple_moves::UniformTranslationMover::apply(), protocols::membrane::RotationMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTiltMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::toolbox::apply_superposition_transform_to_jump(), core::scoring::DockingScoreFunction::operator()(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::farna::MultipleDomainMover::slide_back_to_origin(), protocols::farna::MultipleDomainMover::try_to_slide_into_contact(), and protocols::environment::CoMTrackerCM::update_tracking_residue().
PointPosition const & core::conformation::Conformation::xyz | ( | AtomID const & | id | ) | const |
access xyz coordinates of an atom
References atom_tree_.
Referenced by core::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), atom_tree_torsion(), batch_get_xyz(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), debug_residue_torsions(), core::conformation::symmetry::SymmetricConformation::declare_chemical_bond(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), fill_missing_atoms(), core::pose::get_hash_excluding_chain(), core::pose::get_hash_from_chain(), core::pose::get_sha1_hash_excluding_chain(), core::scoring::func::ConformationXYZ::operator()(), core::conformation::symmetry::recenter(), protocols::fibril::reorient_extended_fibril(), core::scoring::constraints::DistancePairConstraint::score(), core::scoring::constraints::DihedralPairConstraint::score(), core::scoring::constraints::DihedralConstraint::score(), and core::chemical::ICoorAtomID::xyz().
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atom tree for the kinematics
Referenced by append_residue(), atom_tree(), atom_tree_torsion(), batch_set_xyz(), bond_angle(), bond_length(), clear(), Conformation(), debug_residue_torsions(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), detached_copy(), dof(), dof_id_from_torsion_id(), downstream_jump_stub(), get_jump_atom_ids(), get_stub_transform(), in_place_copy(), insert_fragment(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), jump(), operator=(), replace_residue(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_jump_atom_stub_id(), set_stub_transform(), set_torsion(), set_torsion_angle(), set_xyz(), setup_atom_tree(), stub_from_id(), torsion(), torsion_angle(), update_domain_map(), update_residue_coordinates(), upstream_jump_stub(), and xyz().
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chain number for each position
conformation is in charge of making sure that the Residue chain ID's and the chain_endings_ vector stay in sync.
Referenced by chain_begin(), chain_end(), chain_endings(), chains_from_termini(), clear(), Conformation(), delete_chain_ending(), in_place_copy(), insert_chain_ending(), insert_conformation_by_jump(), num_chains(), operator=(), rederive_chain_endings(), rederive_chain_ids(), and reset_chain_endings().
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ConnectionEvent observers.
Referenced by attach_connection_obs(), clear_observers(), detach_connection_obs(), and notify_connection_obs().
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Referenced by Conformation(), contains_carbohydrate_residues(), and operator=().
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book-keeping array for energy evaluations
store which DOF's have changed since the last call to reset_move_data note that we are not currently differentiating dof's from the same atom
Referenced by append_polymer_residue_after_seqpos(), clear(), Conformation(), in_place_copy(), insert_conformation_by_jump(), operator=(), prepend_polymer_residue_before_seqpos(), reset_move_data(), residues_append(), residues_insert(), residues_replace(), set_dof_moved(), update_domain_map(), and update_sequence_numbering().
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fold tree for the kinematics
Referenced by append_polymer_residue_after_seqpos(), append_residue(), backbone_torsion_angle_atoms(), clear(), Conformation(), debug_residue_torsions(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), fold_tree(), in_place_copy(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), jump_atom_id(), operator=(), prepend_polymer_residue_before_seqpos(), replace_residue(), and setup_atom_tree().
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GeneralEvent observers.
Referenced by attach_general_obs(), block_signals(), blocking_signals(), buffer_signals(), buffering_signals(), clear_observers(), debug_pause(), detach_general_obs(), notify_general_obs(), and unblock_signals().
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IdentityEvent observers.
Referenced by attach_identity_obs(), block_signals(), buffer_signals(), clear_observers(), detach_identity_obs(), notify_identity_obs(), and unblock_signals().
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LengthEvent observers.
Referenced by attach_length_obs(), block_signals(), buffer_signals(), clear_observers(), detach_length_obs(), notify_length_obs(), and unblock_signals().
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Membrane Info object.
Referenced by check_valid_membrane(), Conformation(), is_membrane(), membrane_info(), operator=(), set_membrane_info(), and update_membrane_position().
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Parameter sets for parametric conformation generation.
This is a list of pointers to parameter set objects. The list is empty by default; the list only contains anything if the conformation has parametrically-generated bits. Each ParametersSet is intended to describe an assemblage of secondary structure (e.g. a helical bundle); each Parameters object in a ParametersSet is intended to describe a single piece of (likely contiguous) structure (e.g. a single helix in a helical bundle).
Referenced by add_parameters_set(), clear(), clear_parameters_set_list(), Conformation(), create_new_parameters_set(), in_place_copy(), n_parameters_sets(), operator=(), and parameters_set().
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do we need to update the coordinates in the Residues?
Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), Conformation(), force_update_residue_coordinates(), in_place_copy(), insert_residue_by_bond(), operator=(), prepend_polymer_residue_before_seqpos(), residue(), residue_cop(), residue_op(), set_dof_moved(), setup_atom_tree(), and update_residue_coordinates().
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do we need to update the torsion angles in the Residues?
Referenced by append_residue(), Conformation(), declare_chemical_bond(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), force_update_residue_torsions(), in_place_copy(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), operator=(), replace_residue(), residue(), residue_cop(), residue_op(), set_dof(), set_torsion_angle(), set_xyz_moved(), setup_atom_tree(), and update_residue_torsions().
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container of Residues
Referenced by aa(), add_pseudobond(), append_residue(), append_residue_by_bond(), atom_is_backbone_norefold(), backbone_torsion_angle_atoms(), batch_set_xyz(), branch_connection_torsion_angle_atoms(), chains_from_termini(), clear(), Conformation(), const_residue_(), const_residues(), declare_chemical_bond(), detect_bonds(), detect_disulfides(), empty(), fix_disulfides(), get_residue_mask(), in_place_copy(), insert_conformation_by_jump(), insert_ideal_geometry_at_residue_connection(), insert_residue_by_bond(), inter_residue_connection_partner(), jump_atom_id(), operator=(), rederive_chain_endings(), rederive_chain_ids(), replace_residue(), residue(), residue_(), residue_cop(), residue_op(), residue_type(), residues_append(), residues_delete(), residues_insert(), residues_replace(), set_noncanonical_connection(), set_polymeric_connection(), set_torsion(), set_xyz(), show_residue_connections(), size(), update_actcoord(), update_actcoords(), update_membrane_position(), update_orbital_coords(), update_polymeric_connection(), update_residue_coordinates(), update_residue_torsions(), and update_sequence_numbering().
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has the structure moved since the last call to reset_move_data?
Referenced by Conformation(), in_place_copy(), operator=(), reset_move_data(), reset_structure_moved(), residues_append(), residues_insert(), residues_replace(), set_dof_moved(), set_xyz_moved(), and structure_moved().
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book-keeping array for energy evaluations
store which xyz's have changed since the last call to reset_move_data
Referenced by append_polymer_residue_after_seqpos(), clear(), Conformation(), in_place_copy(), insert_conformation_by_jump(), operator=(), prepend_polymer_residue_before_seqpos(), reset_move_data(), residues_append(), residues_insert(), residues_replace(), set_xyz_moved(), update_domain_map(), and update_sequence_numbering().
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LengthEvent observers.
Referenced by attach_xyz_obs(), block_signals(), buffer_signals(), clear_observers(), detach_xyz_obs(), notify_xyz_obs(), and unblock_signals().