35 #ifndef OPENMS_CHEMISTRY_AAINDEX_H 
   36 #define OPENMS_CHEMISTRY_AAINDEX_H 
   77       if (aa == 
'A' || aa == 
'G' || aa == 
'F' || aa == 
'I' || aa == 
'M' || aa == 
'L' || aa == 
'P' || aa == 
'V')
 
   90       if (aa == 
'D' || aa == 
'E')
 
  103       if (aa == 
'K' || aa == 
'R' || aa == 
'H' || aa == 
'W')
 
  116       if (aa == 
'S' || aa == 
'T' || aa == 
'Y' || aa == 
'H' || aa == 
'C' || aa == 
'N' || aa == 
'Q' || aa == 
'W')
 
 1397       for (
Size i = 0; i <= seq.
size(); i++)
 
 1402           Residue leftchar = seq[i - 1];
 
 1407         if (i == seq.
size())
 
 1416         DoubleReal contrib = exp((GBleft_(left) + GBdeltaright_(right)) / (R * T));
 
 1417         if (i > 0 && i < seq.
size())
 
 1419           contrib += exp(GBsidechain_(right) / (R * T));
 
 1424       return R * T * log(k_app) / log(2.0);
 
static DoubleReal polar(char aa)
Returns if the residue is polar (1.0 or 0.0) 
Definition: AAIndex.h:114
A more convenient string class. 
Definition: String.h:56
static DoubleReal getNADH010106(char aa)
Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-...
Definition: AAIndex.h:390
const String & getOneLetterCode() const 
returns the name as one letter code 
static DoubleReal getWILM950102(char aa)
Hydrophobicity coefficient in RP-HPLC, C8 with 0.1TFA/MeCN/H2O (Wilce et al. 1995) ...
Definition: AAIndex.h:639
static DoubleReal getFINA770101(char aa)
Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977) 
Definition: AAIndex.h:1138
Representation of a peptide/protein sequence. 
Definition: AASequence.h:84
Representation of a residue. 
Definition: Residue.h:64
static DoubleReal getVASM830103(char aa)
Relative population of conformational state E (Vasquez et al., 1983) 
Definition: AAIndex.h:263
static DoubleReal GBleft_(char aa)
Calculates part of the gas-phase basicity. 
Definition: AAIndex.h:1554
static DoubleReal aliphatic(char aa)
Returns if the residue is aliphatic (1.0 or 0.0) 
Definition: AAIndex.h:75
static DoubleReal basic(char aa)
Returns if the residue is basic (1.0 or 0.0) 
Definition: AAIndex.h:101
static DoubleReal GBdeltaright_(char aa)
Calculates part of the gas-phase basicity. 
Definition: AAIndex.h:1678
static DoubleReal getKHAG800101(char aa)
The Kerr-constant increments (Khanarian-Moore, 1980) 
Definition: AAIndex.h:139
static DoubleReal GBsidechain_(char aa)
Calculates part of the gas-phase basicity. 
Definition: AAIndex.h:1436
static DoubleReal getOOBM850104(char aa)
Optimized average non-bonded energy per atom (Oobatake et al., 1985) 
Definition: AAIndex.h:886
static DoubleReal getFAUJ880111(char aa)
Positive charge (Fauchere et al., 1988) 
Definition: AAIndex.h:1011
static DoubleReal calculateGB(const AASequence &seq, DoubleReal T=500.0)
Calculates an estimated gas-phase basicity for an amino acid sequence at a given temperature. 
Definition: AAIndex.h:1381
Invalid value exception. 
Definition: Exception.h:336
static DoubleReal getARGP820102(char aa)
Signal sequence helical potential (Argos et al., 1982) 
Definition: AAIndex.h:1262
Size size() const 
returns the number of residues 
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
static DoubleReal acidic(char aa)
Returns if the residue is acidic (1.0 or 0.0) 
Definition: AAIndex.h:88
static DoubleReal getROBB760107(char aa)
Information measure for extended without H-bond (Robson-Suzuki, 1976) 
Definition: AAIndex.h:762
static DoubleReal getNADH010107(char aa)
Hydropathy scale based on self-information values in the two-state model (50% accessibility) (Naderi-...
Definition: AAIndex.h:514
const double GAS_CONSTANT
Representation of selected AAIndex properties. 
Definition: AAIndex.h:70