added scripts and files to make AA index work for all drug targets, add header to the aa index output and fetch the aa index headers

scripts/aa_index_scripts/aa_headerNames.txt

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+ALTS910101 The PAM-120 matrix (Altschul, 1991)
+AZAE970101 The single residue substitution matrix from interchanges of spatially neighbouring residues (Azarya-Sprinzak et al., 1997)
+AZAE970102 The substitution matrix derived from spatially conserved motifs (Azarya-Sprinzak et al., 1997)
+BASU010101 Optimization-based potential derived by the modified perceptron criterion
+BENS940101 Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994)
+BENS940102 Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994)
+BENS940103 Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994)
+BENS940104 Genetic code matrix (Benner et al., 1994)
+BETM990101 Modified version of the Miyazawa-Jernigan transfer energy
+BLAJ010101 Matrix built from structural superposition data for identifying potential remote homologues (Blake-Cohen, 2001)
+BONM030101 Quasichemical statistical potential for the antiparallel orientation of interacting side groups
+BONM030102 Quasichemical statistical potential for the intermediate orientation of interacting side groups
+BONM030103 Quasichemical statistical potential for the parallel orientation of interacting side groups
+BONM030104 Distances between centers of interacting side chains in the antiparallel orientation
+BONM030105 Distances between centers of interacting side chains in the intermediate orientation
+BONM030106 Distances between centers of interacting side chains in the parallel orientation
+BRYS930101 Distance-dependent statistical potential (only energies of contacts within 0-5 Angstrooms are included)
+CROG050101 Substitution matrix computed from the Dirichlet Mixture Model (Crooks-Brenner, 2005)
+CSEM940101 Residue replace ability matrix (Cserzo et al., 1994)
+DAYM780301 Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
+DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978)
+DOSZ010101 Amino acid similarity matrix based on the sausage force field (Dosztanyi-Torda, 2001)
+DOSZ010102 Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001)
+DOSZ010103 An amino acid similarity matrix based on the THREADER force field (Dosztanyi-Torda, 2001)
+DOSZ010104 Normalised version of SM_THREADER (Dosztanyi-Torda, 2001)
+FEND850101 Structure-Genetic matrix (Feng et al., 1985)
+FITW660101 Mutation values for the interconversion of amino acid pairs (Fitch, 1966)
+GEOD900101 Hydrophobicity scoring matrix (George et al., 1990)
+GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic enzymes (Gianese et al., 2001)
+GODA950101 Quasichemical statistical potential derived from  buried contacts
+GONG920101 The mutation matrix for initially aligning (Gonnet et al., 1992)
+GRAR740104 Chemical distance (Grantham, 1974)
+HENS920101 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992)
+HENS920102 BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992)
+HENS920103 BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)
+HENS920104 BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992)
+JOHM930101 Structure-based amino acid scoring table (Johnson-Overington, 1993)
+JOND920103 The 250 PAM PET91 matrix (Jones et al., 1992)
+JOND940101 The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994)
+KANM000101 Substitution matrix (OPTIMA) derived by maximizing discrimination between homologs and non-homologs (Kann et al., 2000)
+KAPO950101 (Kapp et al., 1995)
+KESO980101 Quasichemical transfer energy derived from interfacial regions of protein-protein complexes
+KESO980102 Quasichemical energy in an average protein environment derived from interfacial regions of protein-protein complexes
+KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
+KOLA930101 Statistical potential derived by the quasichemical approximation
+KOSJ950115 Context-dependent optimal substitution matrices for all residues (Koshi-Goldstein, 1995)
+LEVJ860101 The secondary structure similarity matrix (Levin et al., 1986)
+LINK010101 Substitution matrices from an neural network model (Lin et al., 2001)
+LIWA970101 Modified version of the Miyazawa-Jernigan transfer energy
+LUTR910101 Structure-based comparison table for outside other class (Luthy et al., 1991)
+LUTR910102 Structure-based comparison table for inside other class (Luthy et al., 1991)
+LUTR910103 Structure-based comparison table for outside alpha class (Luthy et al., 1991)
+LUTR910104 Structure-based comparison table for inside alpha class (Luthy et al., 1991)
+LUTR910105 Structure-based comparison table for outside beta class (Luthy et al., 1991)
+LUTR910106 Structure-based comparison table for inside beta class (Luthy et al., 1991)
+LUTR910107 Structure-based comparison table for other class (Luthy et al., 1991)
+LUTR910108 Structure-based comparison table for alpha helix class (Luthy et al., 1991)
+LUTR910109 Structure-based comparison table for beta strand class (Luthy et al., 1991)
+MCLA710101 The similarity of pairs of amino acids (McLachlan, 1971)
+MCLA720101 Chemical similarity scores (McLachlan, 1972)
+MEHP950101 (Mehta et al., 1995)
+MEHP950102 (Mehta et al., 1995)
+MEHP950103 (Mehta et al., 1995)
+MICC010101 Optimization-derived potential
+MIRL960101 Statistical potential derived by the maximization of the harmonic mean of Z scores
+MIYS850102 Quasichemical energy of transfer of amino acids from water to the protein environment
+MIYS850103 Quasichemical energy of interactions in an average buried environment
+MIYS930101 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
+MIYS960101 Quasichemical energy of transfer of amino acids from water to the protein environment
+MIYS960102 Quasichemical energy of interactions in an average buried environment
+MIYS960103 Number of contacts between side chains derived from 1168 x-ray protein structures
+MIYS990106 Quasichemical energy of transfer of amino acids from water to the protein environment
+MIYS990107 Quasichemical energy of interactions in an average buried environment
+MIYT790101 Amino acid pair distance (Miyata et al., 1979)
+MOHR870101 EMPAR matrix (Mohana Rao, 1987)
+MOOG990101 Quasichemical potential derived from interfacial regions of protein-protein complexes
+MUET010101 Non-symmetric substitution matrix (SLIM) for detection of homologous transmembrane proteins (Mueller et al., 2001)
+MUET020101 Substitution matrix (VTML160) obtained by maximum likelihood estimation (Mueller et al., 2002)
+MUET020102 Substitution matrix (VTML250) obtained by maximum likelihood estimation (Mueller et al., 2002)
+NAOD960101 Substitution matrix derived from the single residue interchanges at spatially conserved regions of proteins (Naor et al., 1996)
+NGPC000101 Substitution matrix (PHAT) built from hydrophobic and transmembrane regions of the Blocks database (Ng et al., 2000)
+NIEK910101 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991)
+NIEK910102 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991)
+OGAK980101 Substitution matrix derived from structural alignments by maximizing entropy (Ogata et al., 1998)
+OVEJ920101 STR matrix from structure-based alignments (Overington et al., 1992)
+OVEJ920102 Environment-specific amino acid substitution matrix for alpha residues (Overington et al., 1992)
+OVEJ920103 Environment-specific amino acid substitution matrix for beta residues (Overington et al., 1992)
+PARB960101 Statistical contact potential derived by the quasichemical approximation
+PARB960102 Modified version of the Miyazawa-Jernigan transfer energy
+PRLA000101 Structure derived matrix (SDM) for alignment of distantly related sequences (Prlic et al., 2000)
+PRLA000102 Homologous structure dereived matrix (HSDM) for alignment of distantly related sequences (Prlic et al., 2000)
+QUIB020101 STROMA score matrix for the alignment of known distant homologs (Qian-Goldstein, 2002)
+QU_C930101 Cross-correlation coefficients of preference factors main chain (Qu et al., 1993)
+QU_C930102 Cross-correlation coefficients of preference factors side chain (Qu et al., 1993)
+QU_C930103 The mutant distance based on spatial preference factor (Qu et al., 1993)
+RIER950101 Hydrophobicity scoring matrix (Riek et al., 1995)
+RISJ880101 Scoring matrix (Risler et al., 1988)
+ROBB790102 Interaction energies derived from side chain contacts in the interiors of known protein structures
+RUSR970101 Substitution matrix based on structural alignments of analogous proteins (Russell et al., 1997)
+RUSR970102 Substitution matrix based on structural alignments of remote homolous proteins (Russell et al., 1997)
+RUSR970103 Substitution matrix based on structural alignments of analogous and remote homolous proteins (Russell et al., 1997)
+SIMK990101 Distance-dependent statistical potential (contacts within 0-5 Angstrooms)
+SIMK990102 Distance-dependent statistical potential (contacts within 5-7.5 Angstrooms)
+SIMK990103 Distance-dependent statistical potential (contacts within 7.5-10 Angstrooms)
+SIMK990104 Distance-dependent statistical potential (contacts within 10-12 Angstrooms)
+SIMK990105 Distance-dependent statistical potential (contacts longer than 12 Angstrooms)
+SKOJ000101 Statistical quasichemical potential with the partially composition-corrected pair scale
+SKOJ000102 Statistical quasichemical potential with the composition-corrected pair scale
+SKOJ970101 Statistical potential derived by the quasichemical approximation
+TANS760101 Statistical contact potential derived from 25 x-ray protein structures
+TANS760102 Number of contacts between side chains derived from 25 x-ray protein structures
+THOP960101 Mixed quasichemical and optimization-based protein contact potential
+TOBD000101 Optimization-derived potential obtained for small set of decoys
+TOBD000102 Optimization-derived potential obtained for large set of decoys
+TUDE900101 isomorphicity of replacements (Tudos et al., 1990)
+VENM980101 Statistical potential derived by the maximization of the perceptron criterion
+VOGG950101 (Vogt et al., 1995)
+WEIL970101 WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997)
+WEIL970102 Difference matrix obtained by subtracting the BLOSUM62 from the WAC matrix (Wei et al., 1997)
+ZHAC000101 Environment-dependent residue contact energies (rows = helix, cols = helix)
+ZHAC000102 Environment-dependent residue contact energies (rows = helix, cols = strand)
+ZHAC000103 Environment-dependent residue contact energies (rows = helix, cols = coil)
+ZHAC000104 Environment-dependent residue contact energies (rows = strand, cols = strand)
+ZHAC000105 Environment-dependent residue contact energies (rows = strand, cols = coil)
+ZHAC000106 Environment-dependent residue contact energies (rows = coil, cols = coil)