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protocols::cyclic_peptide_predict Namespace Reference

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...
 

Typedefs

typedef
utility::pointer::shared_ptr
< HierarchicalHybridJD_JobResultsSummary
HierarchicalHybridJD_JobResultsSummaryOP
 
typedef
utility::pointer::shared_ptr
< HierarchicalHybridJD_JobResultsSummary
const > 
HierarchicalHybridJD_JobResultsSummaryCOP
 
typedef utility::vector1
< HierarchicalHybridJD_JobResultsSummaryOP
HierarchicalHybridJD_JobResultsSummaryOPs
 
typedef utility::vector1
< HierarchicalHybridJD_JobResultsSummaryCOP
HierarchicalHybridJD_JobResultsSummaryCOPs
 
using HierarchicalHybridJD_PNearToArbitraryStateSummaryOP = utility::pointer::shared_ptr< HierarchicalHybridJD_PNearToArbitraryStateSummary >
 
using HierarchicalHybridJD_PNearToArbitraryStateSummaryCOP = utility::pointer::shared_ptr< HierarchicalHybridJD_PNearToArbitraryStateSummary const >
 
using HierarchicalHybridJD_ResultsSummaryBaseOP = utility::pointer::shared_ptr< HierarchicalHybridJD_ResultsSummaryBase >
 
using HierarchicalHybridJD_ResultsSummaryBaseCOP = utility::pointer::shared_ptr< HierarchicalHybridJD_ResultsSummaryBase const >
 
using HierarchicalHybridJD_RMSDToBestSummaryOP = utility::pointer::shared_ptr< HierarchicalHybridJD_RMSDToBestSummary >
 
using HierarchicalHybridJD_RMSDToBestSummaryCOP = utility::pointer::shared_ptr< HierarchicalHybridJD_RMSDToBestSummary const >
 
using HierarchicalHybridJD_SASASummaryOP = utility::pointer::shared_ptr< HierarchicalHybridJD_SASASummary >
 
using HierarchicalHybridJD_SASASummaryCOP = utility::pointer::shared_ptr< HierarchicalHybridJD_SASASummary const >
 
using PNearCalculatorOP = utility::pointer::shared_ptr< PNearCalculator >
 
using PNearCalculatorCOP = utility::pointer::shared_ptr< PNearCalculator const >
 
typedef
utility::pointer::shared_ptr
< SimpleCycpepPredictApplication
SimpleCycpepPredictApplicationOP
 
typedef
utility::pointer::shared_ptr
< SimpleCycpepPredictApplication
const > 
SimpleCycpepPredictApplicationCOP
 
typedef utility::vector1
< SimpleCycpepPredictApplicationOP
SimpleCycpepPredictApplicationOPs
 
typedef utility::vector1
< SimpleCycpepPredictApplicationCOP
SimpleCycpepPredictApplicationCOPs
 

Enumerations

enum  SCPA_cyclization_type {
  SCPA_n_to_c_amide_bond = 1, SCPA_terminal_disulfide, 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 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 Documentation

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 >

Enumeration Type Documentation

Enumerator
SORT_BY_ENERGIES 
SORT_BY_RMSD 
SORT_BY_HBONDS 
SORT_BY_CIS_PEPTIDE_BONDS 

An enum for the cyclization type.

If additional values are added, please add them to the SimpleCycpepPredictApplication::get_cyclization_name_from_type() function.

Enumerator
SCPA_n_to_c_amide_bond 
SCPA_terminal_disulfide 
SCPA_nterm_isopeptide_lariat 
SCPA_cterm_isopeptide_lariat 
SCPA_sidechain_isopeptide 
SCPA_invalid_type 
SCPA_number_of_types 

Function Documentation

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.

Parameters
[in,out]list_to_sort_intoThis is an existing, sorted list of job summaries, which will have elements added to it.
[in]additional_listThese are the new job summaries (presorted), which will be merged with the existing list.
[in]sort_typeThe 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.

Parameters
[out]output_stringThe string that will be filled with the file contents. Overwritten by this operation.
[in]filenameThe name of the file to read. If from_database is true, this is a relative database path.
[in]from_databaseIf true, the file is assumed to be in the database. If false, the path is relative the execution directory, or is absolute.

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.

Parameters
[in]filenameThe file name from which we'll read.
[out]allowed_canonicals_by_positionA 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_positionA 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 is_canonical(), and protocols::TR().

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options().

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).

Parameters
[in,out]jobsummariesThe list of job summaries. At the end of this operation, this is sorted from lowest to highest by the criterion specified.
[in]sort_typeThe 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.