util.hh File Reference

Utility code for the simple_cycpep_predict app and its MPI version. More...

#include <protocols/cyclic_peptide_predict/HierarchicalHybridJD_JobResultsSummary.fwd.hh>
#include <core/types.hh>
#include <utility/VirtualBase.hh>
#include <utility/vector1.hh>
#include <cstdio>
#include <string>
#include <map>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::cyclic_peptide_predict

Enumerations
enum	protocols::cyclic_peptide_predict::HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE { protocols::cyclic_peptide_predict::SORT_BY_ENERGIES =1, protocols::cyclic_peptide_predict::SORT_BY_RMSD, protocols::cyclic_peptide_predict::SORT_BY_HBONDS, protocols::cyclic_peptide_predict::SORT_BY_CIS_PEPTIDE_BONDS }

Functions
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. More...
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. More...
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. More...
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. More...
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. More...

Detailed Description

Utility code for the simple_cycpep_predict app and its MPI version.

This application predicts structures of simple backbone-cyclized peptides made of alpha-, beta-, or gamma-amino acids (of any chirality) using generalized kinematic closure (GenKIC) for cyclization, and enforcing user-defined requiresments for numbers of mainchain hydrogen bonds. This version uses MPI for cross-communication with parallel processes.

Author

Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu)