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Rosetta
3.8
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Rosetta
3.8
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A single case of a patch, eg proline Nterminus is a case of NtermProteinFull. More...
#include <Patch.hh>
Public Member Functions | |
| ~PatchCase () override | |
| Automatically generated virtual destructor for class deriving directly from ReferenceCount. More... | |
| bool | applies_to (ResidueType const &rsd) const |
| whether the PatchCase is applicable to this ResidueType? More... | |
| virtual ResidueTypeOP | apply (ResidueType const &rsd_in, bool const instantiate=true) const |
| returns patched residue, 0 if patch failed More... | |
| void | add_operation (PatchOperationOP operation) |
| add one more operation in this PatchCase More... | |
| ResidueTypeSelector & | selector () |
| to which ResidueTypes this PatchCase applies to? More... | |
| void | set_selector (ResidueTypeSelector const &selector) |
| utility::vector1< std::string > | adds_atoms () const |
| returns list of added atom names, useful for identifying patches that go with PDB residues More... | |
| utility::vector1< std::string > | deletes_atoms () const |
| returns list of deleted atom names, useful for identifying patches that go with PDB residues More... | |
| utility::vector1< std::string > | adds_properties () const |
| returns list of added property names, useful for identifying patches that go with PDB residues More... | |
| utility::vector1< std::string > | deletes_properties () const |
| returns list of deleted property names, useful for identifying patches that go with PDB residues More... | |
| utility::vector1< std::string > | deletes_variants () const |
| returns list of deleted variant names, useful for identifying patches that go with PDB residues More... | |
| std::string | generates_new_name3 () const |
| returns new name3, if changed More... | |
| std::string | generates_interchangeability_group () const |
| returns interchangeability group, if set. More... | |
| bool | may_change_aa () const |
| returns list of new interchangeability_group, useful for identifying patches that go with PDB residues More... | |
Private Attributes | |
| ResidueTypeSelector | selector_ |
| to which ResidueTypes this PatchCase applies to? More... | |
| utility::vector1 < PatchOperationOP > | operations_ |
| operations to done in this PatchCase More... | |
A single case of a patch, eg proline Nterminus is a case of NtermProteinFull.
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overridedefault |
Automatically generated virtual destructor for class deriving directly from ReferenceCount.
Auto-generated virtual destructor
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inline |
add one more operation in this PatchCase
References operations_.
Referenced by core::chemical::apply_adducts_to_residue().
| utility::vector1< std::string > core::chemical::PatchCase::adds_atoms | ( | ) | const |
returns list of added atom names, useful for identifying patches that go with PDB residues
Go through patch operations in this PatchCase, and compile list of any atom names that are added.
References operations_.
| utility::vector1< std::string > core::chemical::PatchCase::adds_properties | ( | ) | const |
returns list of added property names, useful for identifying patches that go with PDB residues
Go through patch operations in this PatchCase, and compile list of any property names that are added.
References operations_.
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inline |
whether the PatchCase is applicable to this ResidueType?
References selector_.
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virtual |
returns patched residue, 0 if patch failed
First clone the base ResidueType. Then patching for this case is done by applying all the operations. finalize() is called after the VariantTypes and name are set by Patch::apply().
References core::chemical::ResidueType::clone(), operations_, and core::chemical::ResidueType::placeholder_clone().
Referenced by core::chemical::apply_adducts_to_residue().
| utility::vector1< std::string > core::chemical::PatchCase::deletes_atoms | ( | ) | const |
returns list of deleted atom names, useful for identifying patches that go with PDB residues
Go through patch operations in this PatchCase, and compile list of any atom names that are deleted.
References operations_.
| utility::vector1< std::string > core::chemical::PatchCase::deletes_properties | ( | ) | const |
returns list of deleted property names, useful for identifying patches that go with PDB residues
Go through patch operations in this PatchCase, and compile list of any property names that are deleted.
References operations_.
| utility::vector1< std::string > core::chemical::PatchCase::deletes_variants | ( | ) | const |
returns list of deleted variant names, useful for identifying patches that go with PDB residues
Go through patch operations in this PatchCase, and compile list of any property names that are deleted.
References operations_.
| std::string core::chemical::PatchCase::generates_interchangeability_group | ( | ) | const |
returns interchangeability group, if set.
returns list of new interchangeability_group, useful for identifying patches that go with PDB residues
References operations_.
| std::string core::chemical::PatchCase::generates_new_name3 | ( | ) | const |
returns new name3, if changed
returns list of new name3, useful for identifying patches that go with PDB residues
References operations_.
| bool core::chemical::PatchCase::may_change_aa | ( | ) | const |
returns list of new interchangeability_group, useful for identifying patches that go with PDB residues
References operations_.
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inline |
to which ResidueTypes this PatchCase applies to?
References selector_.
Referenced by set_selector().
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inline |
References selector(), and selector_.
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private |
operations to done in this PatchCase
Referenced by add_operation(), adds_atoms(), adds_properties(), apply(), deletes_atoms(), deletes_properties(), deletes_variants(), generates_interchangeability_group(), generates_new_name3(), and may_change_aa().
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private |
to which ResidueTypes this PatchCase applies to?
Referenced by applies_to(), selector(), and set_selector().
1.8.7