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

EnzymeDataSet

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

ConsensusSequenceType

enum core::enzymes::ConsensusSequenceType

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

Enumerator
AA
NA
SACCHARIDE

Function Documentation

get_3_letter_codes_from_NA_consensus_sequence()

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().

get_3_letter_codes_from_peptide_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().

get_AA_3_letter_codes_or_punctuation_from_1_letter_code_at_position()

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
	)

References core::chemical::aa_from_oneletter_code(), and core::chemical::name_from_aa().

Referenced by get_3_letter_codes_from_peptide_consensus_sequence().

get_codes_from_saccharide_consensus_sequence()

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().

read_enzyme_data_from_file()

EnzymeData core::enzymes::read_enzyme_data_from_file

(

std::string const &

filename

)

References AA, core::enzymes::EnzymeData::atom_to_modify, core::enzymes::EnzymeData::consensus_sequence, core::enzymes::EnzymeData::cs_resnum, core::enzymes::EnzymeData::cs_type, core::enzymes::EnzymeData::efficiency, protocols::abinitio::filename(), NA, SACCHARIDE, core::enzymes::EnzymeData::second_substrates_or_byproducts, and TR().

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