41 #include "../Alphabet/AlphabetTools.h" 42 #include "../AlphabetIndex/GranthamAAPolarityIndex.h" 43 #include "../AlphabetIndex/GranthamAAVolumeIndex.h" 44 #include "../AlphabetIndex/KleinAANetChargeIndex.h" 45 #include "../AlphabetIndex/AAChouFasmanAHelixIndex.h" 46 #include "../AlphabetIndex/AAChouFasmanBSheetIndex.h" 47 #include "../AlphabetIndex/AAChouFasmanTurnIndex.h" 48 #include "../AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h" 49 #include "../AlphabetIndex/AASurfaceIndex.h" 50 #include "../AlphabetIndex/AAMassIndex.h" 51 #include "../AlphabetIndex/AAVolumeIndex.h" 52 #include "../AlphabetIndex/AAChargeIndex.h" 53 #include "../AlphabetIndex/AASEAInf10Index.h" 54 #include "../AlphabetIndex/AASEA1030Index.h" 55 #include "../AlphabetIndex/AASEASup30Index.h" 56 #include "../AlphabetIndex/AAIndex1Entry.h" 58 #include <Bpp/Text/KeyvalTools.h> 59 #include <Bpp/App/ApplicationTools.h> 69 if (description !=
"None")
72 map<string, string> args;
73 KeyvalTools::parseProcedure(description, name, args);
75 ApplicationTools::displayResult(message_, description);
79 throw Exception(
"BppOAlphabetIndex1Format::read. This index is only supported with a protein alphabet.");
80 if (name ==
"GranthamPolarity")
84 else if (name ==
"GranthamVolume")
88 else if (name ==
"KleinCharge")
92 else if (name ==
"ChouFasmanAHelix")
96 else if (name ==
"ChouFasmanBSheet")
100 else if (name ==
"ChouFasmanTurn")
104 else if (name ==
"ChenGuHuangHydrophobicity")
108 else if (name ==
"Surface")
112 else if (name ==
"Mass")
116 else if (name ==
"Volume")
120 else if (name ==
"Charge")
124 else if (name ==
"SEAMedium")
128 else if (name ==
"SEAHigh")
132 else if (name ==
"SEALow")
136 else if (name ==
"User")
138 string aax1FilePath = ApplicationTools::getAFilePath(
"file", args,
true,
true,
"",
false);
139 ifstream aax1File(aax1FilePath.c_str(), ios::in);
146 throw Exception(
"Invalid index1 '" + name +
"'.");
Polarity index used in Grantham (1974).
Turn score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl...
Percentage of amino acids having a Solvent Exposed Area above 30 Angström^2 for each type of amino ac...
B-sheet score for the Chou-Fasman algorithm of secondary structure prediction, according to http://pr...
This alphabet is used to deal NumericAlphabet.
Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html.
Percentage of amino acids having a Solvent Exposed Area below 10 Angström^2 for each type of amino ac...
Charge of each amino acid.
Volume index used in Grantham (1974).
Mass (dalton) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html.
Percentage of amino acids having a Solvent Exposed Area between 10 and 30 Angström^2 for each type of...
One dimensionnal alphabet index interface.
Charge of each amino acid.
A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://pr...
Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 200...
Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html.
Create a AlphabetIndex1 object from an AAIndex2 entry.