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core::enzymes Namespace Reference

Classes

struct  EnzymeData
 A structure for storing reaction information for specific virtual enzymes. More...
 
class  EnzymeManager
 

Typedefs

typedef std::map< std::string,
std::map< std::string,
std::map< std::string,
EnzymeData > > > 
EnzymeDataSet
 A map of enzyme family to maps of species to maps of enzyme names to enzyme data. More...
 

Enumerations

enum  ConsensusSequenceType { AA = 1, NA, SACCHARIDE }
 The type of consensus sequence stored in an instance of EnzymeData. More...
 

Functions

utility::vector1< std::string > get_AA_3_letter_codes_or_punctuation_from_1_letter_code_at_position (std::string const &sequence, uint &char_pos)
 
utility::vector1
< utility::vector1
< std::string > > 
get_3_letter_codes_from_peptide_consensus_sequence (std::string const &sequence)
 Parse a peptide consensus sequence and return a list of AA residue 3-letter codes. More...
 
utility::vector1
< utility::vector1
< std::string > > 
get_3_letter_codes_from_NA_consensus_sequence (std::string const &sequence)
 Parse a nucleic acid consensus sequence and return a list of NA residue 3-letter codes. More...
 
utility::vector1
< utility::vector1
< std::string > > 
get_codes_from_saccharide_consensus_sequence (std::string const &sequence)
 Parse a saccharide consensus sequence and return a list of monosaccharide residue codes. More...
 
EnzymeData read_enzyme_data_from_file (std::string const &filename)
 

Typedef Documentation

typedef std::map< std::string, std::map< std::string, std::map< std::string, EnzymeData > > > core::enzymes::EnzymeDataSet

A map of enzyme family to maps of species to maps of enzyme names to enzyme data.

Enumeration Type Documentation

The type of consensus sequence stored in an instance of EnzymeData.

Enumerator
AA 
NA 
SACCHARIDE 

Function Documentation

utility::vector1< utility::vector1< std::string > > core::enzymes::get_3_letter_codes_from_NA_consensus_sequence ( std::string const &  sequence)

Parse a nucleic acid consensus sequence and return a list of NA residue 3-letter codes.

This parser recognizes the following one-letter codes:

  • A: adenine
  • B: not A
  • C: cytosine
  • D: not C
  • G: guanine
  • H: not G
  • K: G or T/U
  • M: A or C
  • N: A, C, G, or t/U (aNy)
  • R: A or G (puRines)
  • S: G or C ("strong" nucleobases)
  • T: thymine (m5U)
  • U: uracil
  • V: not T/U
  • W: A or T/U ("weak" nucleobases)
  • Y: C or T/U (pYrimidines)
    Note
    A vector of vectors is returned, because each position may have options and not a specific residue.

Referenced by core::enzymes::EnzymeManager::parse_consensus_sequence().

utility::vector1< utility::vector1< std::string > > core::enzymes::get_3_letter_codes_from_peptide_consensus_sequence ( std::string const &  sequence)

Parse a peptide consensus sequence and return a list of AA residue 3-letter codes.

This parser recognizes the IUPAC-approved one-letter codes B, J, O, U, and Z, which code for Asx, Xle, Pyl, Sec, and Glx, respectively. X alone is recognized to be any of the 20 canonical amino acids; X followed by square brackets specifies a single non-canonical amino acid by 3-letter code. For example, X[SEP] specifies phosphoserine. Parentheses are used to specify multiple possible residue types at that site, separated by forward slashes, e.g., A/G) specifies either Ala or Gly at that position. < and > signify a sequon that is at the N-terminus or C-terminus, repsectively, and these characters are skipped by this function and handled instead by EnzymaticMover::set_pose_reactive_sites().

Note
A vector of vectors is returned, because each position may have options and not a specific residue.

References get_AA_3_letter_codes_or_punctuation_from_1_letter_code_at_position().

Referenced by core::enzymes::EnzymeManager::parse_consensus_sequence().

utility::vector1< std::string > core::enzymes::get_AA_3_letter_codes_or_punctuation_from_1_letter_code_at_position ( std::string const &  sequence,
uint &  char_pos 
)
utility::vector1< utility::vector1< std::string > > core::enzymes::get_codes_from_saccharide_consensus_sequence ( std::string const &  )

Parse a saccharide consensus sequence and return a list of monosaccharide residue codes.

Note
A vector of vectors is returned, because each position may have options and not a specific residue.

Referenced by core::enzymes::EnzymeManager::parse_consensus_sequence().

EnzymeData core::enzymes::read_enzyme_data_from_file ( std::string const &  filename)