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Rosetta
2020.50
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Parameters class, used to store sets of parameters for parametric backbone generation. More...
#include <Parameters.hh>
Public Member Functions | |
Parameters () | |
constructors More... | |
Parameters (Parameters const &src) | |
Copy constructor. More... | |
~Parameters () override | |
virtual ParametersOP | clone () const |
Copy this residue( allocate actual memory for it ) More... | |
ParametersCOP | get_self_ptr () const |
self pointers More... | |
ParametersOP | get_self_ptr () |
ParametersCAP | get_self_weak_ptr () const |
ParametersAP | get_self_weak_ptr () |
void | add_residue (core::conformation::ResidueCOP residue) |
Add a residue to the list of residues that these parameters describe. More... | |
core::conformation::ResidueCOP | residue (core::Size const index) const |
Get an owning pointer to a residue in the list of residues that these parameters describe. More... | |
core::conformation::ResidueCOP | first_residue () const |
Get a const owning pointer to the first residue in the list of residues that these parameters describe. More... | |
core::conformation::ResidueCOP | last_residue () const |
Get a const owning pointer to the last residue in the list of residues that these parameters describe. More... | |
core::Size | first_residue_index () const |
Get the index of the first residue. More... | |
core::Size | last_residue_index () const |
Get the index of the last residue. More... | |
core::Size | n_residue () const |
Returns the number (count) of residues that these parameters describe. More... | |
void | reset_residue_list () |
Clears the list of residues that these parameters describe. More... | |
void | reset_sampling_and_perturbing_info () const |
Clears the sampling and perturbing information in the individual parameters. More... | |
void | set_residue (core::Size const index, core::conformation::ResidueCOP existing_residue) |
Assign an element in the residue list to be an owning pointer to an existing residue. More... | |
core::Size | num_parameters () const |
Get the number of parameters stored in this Parameters object. More... | |
void | add_parameter (ParameterOP parameter) |
Add a parameter. More... | |
ParameterOP | parameter_op (core::Size const index) const |
Access a parameter, by index. More... | |
ParameterCOP | parameter_cop (core::Size const index) const |
Access a parameter, by index. More... | |
void | replace_parameter_via_clone (core::Size const param_index, ParameterCOP new_parameter, bool const reset_sampling_copying_perturbing=true) |
Replace one of the contained parameter objects with a copy of an input parameter object. More... | |
Private Attributes | |
utility::vector1 < core::conformation::ResidueCOP > | residue_list_ |
A list of the residues in this conformation that are described by the parameters in this Parameters object. More... | |
utility::vector1< ParameterOP > | parameter_list_ |
A list of the parameters that describe these residues. More... | |
Parameters class, used to store sets of parameters for parametric backbone generation.
core::conformation::parametric::Parameters::Parameters | ( | ) |
constructors
Constructor.
core::conformation::parametric::Parameters::Parameters | ( | Parameters const & | src | ) |
Copy constructor.
Deep-copies the residue list and the parameters list.
References parameter_list_, and residue_list_.
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overridedefault |
void core::conformation::parametric::Parameters::add_parameter | ( | ParameterOP | parameter | ) |
Add a parameter.
Does NOT clone the parameter, but stores the OP directly.
References parameter_list_.
void core::conformation::parametric::Parameters::add_residue | ( | core::conformation::ResidueCOP | residue | ) |
Add a residue to the list of residues that these parameters describe.
References residue_list_.
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virtual |
Copy this residue( allocate actual memory for it )
make a copy of this residue( allocate actual memory for it )
Reimplemented in protocols::helical_bundle::parameters::BundleParameters.
core::conformation::ResidueCOP core::conformation::parametric::Parameters::first_residue | ( | ) | const |
Get a const owning pointer to the first residue in the list of residues that these parameters describe.
Note that this might not be the first residue in linear sequence, if the residues were put in in non- sequential order or the residue numbering has changed.
References residue_list_.
core::Size core::conformation::parametric::Parameters::first_residue_index | ( | ) | const |
Get the index of the first residue.
MUST BE REWRITTEN when the OP issue is resolved.
References residue_list_.
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inline |
self pointers
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inline |
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inline |
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inline |
core::conformation::ResidueCOP core::conformation::parametric::Parameters::last_residue | ( | ) | const |
Get a const owning pointer to the last residue in the list of residues that these parameters describe.
Note that this might not be the last residue in linear sequence, if the residues were put in in non- sequential order or the residue numbering has changed.
References residue_list_.
core::Size core::conformation::parametric::Parameters::last_residue_index | ( | ) | const |
Get the index of the last residue.
MUST BE REWRITTEN when the OP issue is resolved.
References residue_list_.
core::Size core::conformation::parametric::Parameters::n_residue | ( | ) | const |
Returns the number (count) of residues that these parameters describe.
References residue_list_.
core::Size core::conformation::parametric::Parameters::num_parameters | ( | ) | const |
Get the number of parameters stored in this Parameters object.
References parameter_list_.
ParameterCOP core::conformation::parametric::Parameters::parameter_cop | ( | core::Size const | index | ) | const |
Access a parameter, by index.
Const access.
References parameter_list_.
Referenced by protocols::helical_bundle::parameters::BundleParameters::get_pdb_remark().
ParameterOP core::conformation::parametric::Parameters::parameter_op | ( | core::Size const | index | ) | const |
void core::conformation::parametric::Parameters::replace_parameter_via_clone | ( | core::Size const | param_index, |
ParameterCOP | new_parameter, | ||
bool const | reset_sampling_copying_perturbing = true |
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Replace one of the contained parameter objects with a copy of an input parameter object.
If reset_sampling_copying_perturbing is true, then the sampling, copying, and perturbing information of the copied parameter object are all reset. True by default.
References parameter_list_.
void core::conformation::parametric::Parameters::reset_residue_list | ( | ) |
Clears the list of residues that these parameters describe.
References residue_list_.
void core::conformation::parametric::Parameters::reset_sampling_and_perturbing_info | ( | ) | const |
Clears the sampling and perturbing information in the individual parameters.
References parameter_list_.
core::conformation::ResidueCOP core::conformation::parametric::Parameters::residue | ( | core::Size const | index | ) | const |
Get an owning pointer to a residue in the list of residues that these parameters describe.
References residue_list_.
void core::conformation::parametric::Parameters::set_residue | ( | core::Size const | index, |
core::conformation::ResidueCOP | existing_residue | ||
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Assign an element in the residue list to be an owning pointer to an existing residue.
References residue_list_.
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private |
A list of the parameters that describe these residues.
Referenced by add_parameter(), num_parameters(), parameter_cop(), parameter_op(), Parameters(), replace_parameter_via_clone(), and reset_sampling_and_perturbing_info().
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private |
A list of the residues in this conformation that are described by the parameters in this Parameters object.
This is a list of owning pointers so that the residue indices don't mess things up. (That is, as residue indices change, these should still point to the proper residues).
Referenced by add_residue(), first_residue(), first_residue_index(), last_residue(), last_residue_index(), n_residue(), Parameters(), reset_residue_list(), residue(), and set_residue().