|
| 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::aa_b2a
,
core::chemical::first_beta2_aa = aa_b2a
, core::chemical::last_beta2_aa = aa_b2a
, 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...
|
| |
|
| 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...
|
| |
| std::string | core::chemical::full_name_from_aa (AA aa) |
| | give the canonical "full" ResidueType name for given AA 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...
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| |
