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Rosetta
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Classes | |
| class | HierarchicalHybridJD_JobResultsSummary |
| A class for summarizing the result of an MPI-mode job run with the SimpleCycpepPredictApplication. More... | |
| class | HierarchicalHybridJD_PNearToArbitraryStateSummary |
| A class for storing the PNear, Keq, and DeltaG_folding values to an arbitrary state that has been sampled. More... | |
| class | HierarchicalHybridJD_ResultsSummaryBase |
| A pure virtual base class for the helper classes used by the HierarchicalHybridJDApplication class for transmitting information up the MPI hierarchy. More... | |
| class | HierarchicalHybridJD_RMSDToBestSummary |
| A small helper class used by the HierarchicalHybridJDApplication class for transmitting RMSD information up the MPI hierarchy. More... | |
| class | HierarchicalHybridJD_SASASummary |
| A class for storing information about solvent-exposed surface area and for transmitting it up the MPI hierarchy. More... | |
| class | PNearCalculator |
| A class to compute P_Near and DG_folding. More... | |
| class | SimpleCycpepPredictApplication |
| Application-level code for simple_cycpep_predict application. More... | |
Enumerations | |
| enum | SCPA_cyclization_type { SCPA_n_to_c_amide_bond = 1 , SCPA_terminal_disulfide , SCPA_thioether_lariat , SCPA_nterm_isopeptide_lariat , SCPA_cterm_isopeptide_lariat , SCPA_sidechain_isopeptide , SCPA_invalid_type , SCPA_number_of_types = SCPA_invalid_type } |
| An enum for the cyclization type. More... | |
| enum | HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE { SORT_BY_ENERGIES =1 , SORT_BY_RMSD , SORT_BY_HBONDS , SORT_BY_CIS_PEPTIDE_BONDS } |
Functions | |
| void | register_with_citation_manager () |
| Registers the simple_cycpep_predict application with the CitationManager. More... | |
| void | sort_jobsummaries_list (utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP > &jobsummaries, HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE const sort_type) |
| Given a list of job summaries, sort these by some criterion (e.g. energies, rmsd, etc.) from lowest to highest. More... | |
| void | mergesort_jobsummaries_list (utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP > &list_to_sort_into, utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP > const &additional_list, HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE const sort_type) |
| Given an existing, sorted list of job summaries and a new, sorted list of job summaries, merge the two lists into a new, sorted list and replace the existing list with the result. More... | |
| void | read_peptide_design_file (std::string const &filename, std::map< core::Size, utility::vector1< std::string > > &allowed_canonicals_by_position, std::map< core::Size, utility::vector1< std::string > > &allowed_noncanonicals_by_position) |
| Given a filename, read and parse the file, returning a list of canonical residues allowed at each position and a list of noncanonicals allowed at each position. More... | |
| bool | is_canonical (std::string const &resname) |
| Given a residue name, return true if this is one of the 20 canonical amino acids, false otherwise. More... | |
| void | read_file_into_string (std::string &output_string, std::string const &filename, bool const from_database) |
| Given an ASCII file name, read the contents into a string. If from_database is true, the read is from the database. More... | |
| typedef utility::pointer::shared_ptr< HierarchicalHybridJD_JobResultsSummary const > protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummaryCOP |
| typedef utility::vector1<HierarchicalHybridJD_JobResultsSummaryCOP> protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummaryCOPs |
| typedef utility::pointer::shared_ptr< HierarchicalHybridJD_JobResultsSummary > protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummaryOP |
| typedef utility::vector1<HierarchicalHybridJD_JobResultsSummaryOP> protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummaryOPs |
| using protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummaryCOP = typedef utility::pointer::shared_ptr< HierarchicalHybridJD_PNearToArbitraryStateSummary const > |
| using protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummaryOP = typedef utility::pointer::shared_ptr< HierarchicalHybridJD_PNearToArbitraryStateSummary > |
| using protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBaseCOP = typedef utility::pointer::shared_ptr< HierarchicalHybridJD_ResultsSummaryBase const > |
| using protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBaseOP = typedef utility::pointer::shared_ptr< HierarchicalHybridJD_ResultsSummaryBase > |
| using protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummaryCOP = typedef utility::pointer::shared_ptr< HierarchicalHybridJD_RMSDToBestSummary const > |
| using protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummaryOP = typedef utility::pointer::shared_ptr< HierarchicalHybridJD_RMSDToBestSummary > |
| using protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummaryCOP = typedef utility::pointer::shared_ptr< HierarchicalHybridJD_SASASummary const > |
| using protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummaryOP = typedef utility::pointer::shared_ptr< HierarchicalHybridJD_SASASummary > |
| using protocols::cyclic_peptide_predict::PNearCalculatorCOP = typedef utility::pointer::shared_ptr< PNearCalculator const > |
| using protocols::cyclic_peptide_predict::PNearCalculatorOP = typedef utility::pointer::shared_ptr< PNearCalculator > |
| typedef utility::pointer::shared_ptr< SimpleCycpepPredictApplication const > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplicationCOP |
| typedef utility::vector1<SimpleCycpepPredictApplicationCOP> protocols::cyclic_peptide_predict::SimpleCycpepPredictApplicationCOPs |
| typedef utility::pointer::shared_ptr< SimpleCycpepPredictApplication > protocols::cyclic_peptide_predict::SimpleCycpepPredictApplicationOP |
| typedef utility::vector1<SimpleCycpepPredictApplicationOP> protocols::cyclic_peptide_predict::SimpleCycpepPredictApplicationOPs |
An enum for the cyclization type.
If additional values are added, please add them to the SimpleCycpepPredictApplication::get_cyclization_name_from_type() function.
| bool protocols::cyclic_peptide_predict::is_canonical | ( | std::string const & | resname | ) |
Given a residue name, return true if this is one of the 20 canonical amino acids, false otherwise.
Referenced by read_peptide_design_file().
| void protocols::cyclic_peptide_predict::mergesort_jobsummaries_list | ( | utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP > & | list_to_sort_into, |
| utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP > const & | additional_list, | ||
| HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE const | sort_type | ||
| ) |
Given an existing, sorted list of job summaries and a new, sorted list of job summaries, merge the two lists into a new, sorted list and replace the existing list with the result.
| [in,out] | list_to_sort_into | This is an existing, sorted list of job summaries, which will have elements added to it. |
| [in] | additional_list | These are the new job summaries (presorted), which will be merged with the existing list. |
| [in] | sort_type | The criterion based on which we're sorting the list. |
References SORT_BY_CIS_PEPTIDE_BONDS, SORT_BY_ENERGIES, SORT_BY_HBONDS, and SORT_BY_RMSD.
| void protocols::cyclic_peptide_predict::read_file_into_string | ( | std::string & | output_string, |
| std::string const & | filename, | ||
| bool const | from_database | ||
| ) |
Given an ASCII file name, read the contents into a string. If from_database is true, the read is from the database.
| [out] | output_string | The string that will be filled with the file contents. Overwritten by this operation. |
| [in] | filename | The name of the file to read. If from_database is true, this is a relative database path. |
| [in] | from_database | If true, the file is assumed to be in the database. If false, the path is relative the execution directory, or is absolute. |
References protocols::abinitio::filename().
Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options().
| void protocols::cyclic_peptide_predict::read_peptide_design_file | ( | std::string const & | filename, |
| std::map< core::Size, utility::vector1< std::string > > & | allowed_canonicals_by_position, | ||
| std::map< core::Size, utility::vector1< std::string > > & | allowed_noncanonicals_by_position | ||
| ) |
Given a filename, read and parse the file, returning a list of canonical residues allowed at each position and a list of noncanonicals allowed at each position.
This does the actual file read. It is NOT THREADSAFE. The file format is a series of lines with the pattern: residue_index residuetype_1_fullname residuetype_2_fullname residuetype_3_fullname ... Anything after a pound sign should be ignored. A line with DEFAULT in place of the resiude index should be interpreted as providing default values, which should be stored as map key 0.
| [in] | filename | The file name from which we'll read. |
| [out] | allowed_canonicals_by_position | A map of [position->vector of strings of full names] listing the allowed canonical residue types at each position. Reset and populated by this function. Key 0 indicates default settings applied anywhere that lacks a map key. |
| [out] | allowed_noncanonicals_by_position | A map of [position->vector of strings of full names] listing the allowed noncanonical residue types at each position. Reset and populated by this function. Key 0 indicates default settings applied anywhere that lacks a map key. |
References protocols::abinitio::filename(), is_canonical(), and protocols::TR().
Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options().
| void protocols::cyclic_peptide_predict::register_with_citation_manager | ( | ) |
Registers the simple_cycpep_predict application with the CitationManager.
Cites Bhardwaj et al. 2016, Hosseinzadeh et al. 2017, Mulligan et al. 2021.
Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::SimpleCycpepPredictApplication().
| void protocols::cyclic_peptide_predict::sort_jobsummaries_list | ( | utility::vector1< HierarchicalHybridJD_JobResultsSummaryOP > & | jobsummaries, |
| HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE const | sort_type | ||
| ) |
Given a list of job summaries, sort these by some criterion (e.g. energies, rmsd, etc.) from lowest to highest.
Uses the quicksort algorithm (recursive).
| [in,out] | jobsummaries | The list of job summaries. At the end of this operation, this is sorted from lowest to highest by the criterion specified. |
| [in] | sort_type | The criterion based on which we're sorting the list. |
References SORT_BY_CIS_PEPTIDE_BONDS, SORT_BY_ENERGIES, SORT_BY_HBONDS, and SORT_BY_RMSD.
1.9.1