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Namespaces | Enumerations | Functions
AA.hh File Reference
#include <iosfwd>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::chemical
 

Enumerations

enum  core::chemical::AA {
  core::chemical::aa_none = 0, core::chemical::aa_ala = 1, core::chemical::first_l_aa = aa_ala, 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_b3cisACPC,
  core::chemical::aa_b3transACPC, core::chemical::aa_b3cisACHC, core::chemical::last_beta3_aa = aa_b3cisACHC, core::chemical::na_lra,
  core::chemical::na_lrc, core::chemical::na_lrg, core::chemical::na_lur, core::chemical::ou3_ala,
  core::chemical::first_oligourea = ou3_ala, core::chemical::ou3_cys, core::chemical::ou3_asp, core::chemical::ou3_glu,
  core::chemical::ou3_phe, core::chemical::ou3_gly, core::chemical::ou3_his, core::chemical::ou3_ile,
  core::chemical::ou3_lys, core::chemical::ou3_leu, core::chemical::ou3_met, core::chemical::ou3_asn,
  core::chemical::ou3_pro, core::chemical::ou3_gln, core::chemical::ou3_arg, core::chemical::ou3_ser,
  core::chemical::ou3_thr, core::chemical::ou3_val, core::chemical::ou3_trp, core::chemical::ou3_tyr,
  core::chemical::ou3_aib, core::chemical::last_oligourea = ou3_aib, 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 3-letter code, return its enum type. More...
 
AA core::chemical::aa_from_one_or_three (std::string const &name)
 
bool core::chemical::is_canonical_D_aa (AA const 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...
 
bool core::chemical::is_canonical_L_aa_excluding_gly (AA const aa)
 Give an enum type, return true if and only if it is an L-amino acid of a canonical type. More...
 
bool core::chemical::is_canonical_L_aa_or_gly (AA const aa)
 Given an enum type, return true if and only if it is a canonical L-amino acid. Rocco approves. More...
 
bool core::chemical::is_canonical_beta3_aa (AA const aa)
 Given an enum type, return true if and only if it is a canonical beta-amino acid. More...
 
bool core::chemical::is_aa_name_unknown (std::string const &name)
 Given aa three letter string, return true if it is an unknown aa. More...
 
AA core::chemical::get_L_equivalent (AA const 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 const 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