AA.hh File Reference

#include <ostream>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::chemical

Enumerations
enum	core::chemical::AA {   core::chemical::aa_ala = 1, core::chemical::aa_cys, core::chemical::aa_asp, core::chemical::aa_glu,   core::chemical::aa_phe, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile,   core::chemical::aa_lys, core::chemical::aa_leu, core::chemical::aa_met, core::chemical::aa_asn,   core::chemical::aa_pro, core::chemical::aa_gln, core::chemical::aa_arg, core::chemical::aa_ser,   core::chemical::aa_thr, core::chemical::aa_val, core::chemical::aa_trp, core::chemical::aa_tyr,   core::chemical::num_canonical_aas = aa_tyr, core::chemical::na_ade, core::chemical::first_DNA_aa = na_ade, core::chemical::na_cyt,   core::chemical::na_gua, core::chemical::na_thy, core::chemical::last_DNA_aa = na_thy, core::chemical::na_rgu,   core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_ura, core::chemical::aa_dal,   core::chemical::first_D_aa = aa_dal, core::chemical::aa_dcs, core::chemical::aa_das, core::chemical::aa_dgu,   core::chemical::aa_dph, core::chemical::aa_dhi, core::chemical::aa_dil, core::chemical::aa_dly,   core::chemical::aa_dle, core::chemical::aa_dme, core::chemical::aa_dan, core::chemical::aa_dpr,   core::chemical::aa_dgn, core::chemical::aa_dar, core::chemical::aa_dse, core::chemical::aa_dth,   core::chemical::aa_dva, core::chemical::aa_dtr, core::chemical::aa_dty, core::chemical::last_D_aa = aa_dty,   core::chemical::aa_b3a, core::chemical::first_beta3_aa = aa_b3a, core::chemical::aa_b3c, core::chemical::aa_b3d,   core::chemical::aa_b3e, core::chemical::aa_b3f, core::chemical::aa_b3g, core::chemical::aa_b3h,   core::chemical::aa_b3i, core::chemical::aa_b3k, core::chemical::aa_b3l, core::chemical::aa_b3m,   core::chemical::aa_b3n, core::chemical::aa_b3p, core::chemical::aa_b3q, core::chemical::aa_b3r,   core::chemical::aa_b3s, core::chemical::aa_b3t, core::chemical::aa_b3v, core::chemical::aa_b3w,   core::chemical::aa_b3y, core::chemical::aa_b3cisACPrC, core::chemical::aa_b3cisACPC, core::chemical::aa_b3cisACHC,   core::chemical::last_beta3_aa = aa_b3cisACHC, core::chemical::aa_h2o, core::chemical::aa_vrt, core::chemical::aa_unp,   core::chemical::aa_unk, core::chemical::num_aa_types = aa_unk }
	enumeration for amino acids and nucleotides types with the total number as num_aa_types More...

Functions
AA	core::chemical::aa_from_name (std::string const &name)
	Give an AA string name, return its enum type. More...
bool	core::chemical::is_canonical_D_aa (AA aa)
	Give an enum type, return true if and only if it is a D-amino acid that is the mirror image of a canonical alpha-L-amino acid. More...
AA	core::chemical::get_L_equivalent (AA aa)
	Given an enum type for a D-amino acid with a canonical side-chain, return the enum type for the corresponding L-amino acid (or aa_unk if the corresponding L-amino acid cannot be determined). More...
AA	core::chemical::get_D_equivalent (AA aa)
	Given an enum type for a L-amino acid with a canonical side-chain, return the enum type for the corresponding D-amino acid (or aa_unk if the corresponding D-amino acid cannot be determined). More...
std::string	core::chemical::name_from_aa (AA aa)
	give a enum type and return the string name More...
char	core::chemical::oneletter_code_from_aa (AA aa)
	give a enum type and return the string name More...
AA	core::chemical::aa_from_oneletter_code (char onelettercode)
	give a 1 letter code and return the string name More...
bool	core::chemical::oneletter_code_specifies_aa (char onelettercode)
std::istream &	core::chemical::operator>> (std::istream &is, AA &aa)
	input operator for AA enum type More...
std::ostream &	core::chemical::operator<< (std::ostream &os, AA const &aa)
	output operator for AA enum type More...

Detailed Description

Author

Phil Bradley