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OpenMS
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76 if (aa ==
'A' || aa ==
'G' || aa ==
'F' || aa ==
'I' || aa ==
'M' || aa ==
'L' || aa ==
'P' || aa ==
'V')
89 if (aa ==
'D' || aa ==
'E')
102 if (aa ==
'K' || aa ==
'R' || aa ==
'H' || aa ==
'W')
115 if (aa ==
'S' || aa ==
'T' || aa ==
'Y' || aa ==
'H' || aa ==
'C' || aa ==
'N' || aa ==
'Q' || aa ==
'W')
996 for (
Size i = 0; i <= seq.
size(); i++)
1001 Residue leftchar = seq[i - 1];
1006 if (i == seq.
size())
1015 double contrib = exp((GBleft_(left) + GBdeltaright_(right)) / (
R * T));
1016 if (i > 0 && i < seq.
size())
1018 contrib += exp(GBsidechain_(right) / (
R * T));
1023 return R * T * log(k_app) / log(2.0);
static double getARGP820102(char aa)
Signal sequence helical potential (Argos et al., 1982)
Definition: AAIndex.h:901
static double calculateGB(const AASequence &seq, double T=500.0)
Calculates an estimated gas-phase basicity for an amino acid sequence at a given temperature.
Definition: AAIndex.h:980
static double getROBB760107(char aa)
Information measure for extended without H-bond (Robson-Suzuki, 1976)
Definition: AAIndex.h:561
static double basic(char aa)
Returns if the residue is basic (1.0 or 0.0)
Definition: AAIndex.h:100
Invalid value exception.
Definition: Exception.h:335
static double getNADH010106(char aa)
Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-...
Definition: AAIndex.h:309
A more convenient string class.
Definition: String.h:58
const String & getOneLetterCode() const
returns the name as one letter code (String of size 1)
static double GBleft_(char aa)
Calculates part of the gas-phase basicity.
Definition: AAIndex.h:1111
static double getFAUJ880111(char aa)
Positive charge (Fauchere et al., 1988)
Definition: AAIndex.h:730
static double GBdeltaright_(char aa)
Calculates part of the gas-phase basicity.
Definition: AAIndex.h:1191
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static double getFINA770101(char aa)
Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977)
Definition: AAIndex.h:817
static double getNADH010107(char aa)
Hydropathy scale based on self-information values in the two-state model (50% accessibility) (Naderi-...
Definition: AAIndex.h:393
static double getVASM830103(char aa)
Relative population of conformational state E (Vasquez et al., 1983)
Definition: AAIndex.h:222
static double acidic(char aa)
Returns if the residue is acidic (1.0 or 0.0)
Definition: AAIndex.h:87
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Representation of a residue.
Definition: Residue.h:61
static double GBsidechain_(char aa)
Calculates part of the gas-phase basicity.
Definition: AAIndex.h:1035
static double getOOBM850104(char aa)
Optimized average non-bonded energy per atom (Oobatake et al., 1985)
Definition: AAIndex.h:645
Size size() const
returns the number of residues
static double getKHAG800101(char aa)
The Kerr-constant increments (Khanarian-Moore, 1980)
Definition: AAIndex.h:138
static double aliphatic(char aa)
Returns if the residue is aliphatic (1.0 or 0.0)
Definition: AAIndex.h:74
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
static double getWILM950102(char aa)
Hydrophobicity coefficient in RP-HPLC, C8 with 0.1TFA/MeCN/H2O (Wilce et al. 1995)
Definition: AAIndex.h:478
Representation of selected AAIndex properties.
Definition: AAIndex.h:69
const double GAS_CONSTANT
static double polar(char aa)
Returns if the residue is polar (1.0 or 0.0)
Definition: AAIndex.h:113