Bio rules
================================================================================

        
// IMGT classes of the 20 common amino acids
// https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html

/*
Section: 
'Hydropathy'
 

    Hydrophobic: A, C, I, L, M, F, W, V.
    Neutral: G, H, P, S, T, Y.
    Hydrophilic: R, N, D, Q, E, K.

*/

// .. amino acids and their abbreviations 
// https://i-base.info/ttfa/hiv-and-drug-resistance/appendix-3-list-of-amino-acids-and-their-abbreviations/




// .. amino acids charge
// https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/charge/

/*
Section: 
Charge of the amino acid side chains

    Negative charged (acidic side chains): aspartic acid and glutamic acid
    Positive charged (basic side chains): lysine, arginine and histidine
    Fifteen AA have uncharged side chains. They are: A, N, C, Q, G, I, L, M, F, P, S, T, W, Y, V.
*/


// This table is included for future reference.
// --------------------------------------------
// Amino acid       3-letter abbreviation 	1-letter abbreviation
// Alanine          Ala 	A   Hydrophobic   
// Arginine         Arg 	R                       Hydrophilic (+)
// Asparagine       Asn 	N                       Hydrophilic
// Aspartic acid    Asp 	D                       Hydrophilic (-)
// Cysteine         Cys 	C   Hydrophobic  
// Glutamine        Gln 	Q                       Hydrophilic
// Glutamic acid    Glu 	E                       Hydrophilic (-)
// Glycine          Gly 	G               Neutral
// Histidine        His 	H               Neutral (+)
// Isoleucine       Ile 	I   Hydrophobic
// Leucine          Leu 	L   Hydrophobic
// Lysine           Lys 	K                       Hydrophilic (+)
// Methionine       Met 	M   Hydrophobic
// Phenylalanine    Phe 	F   Hydrophobic   
// Proline          Pro 	P               Neutral
// Serine           Ser 	S               Neutral
// Threonine        Thr 	T               Neutral
// Tryptophan       Trp 	W   Hydrophobic
// Tyrosine         Tyr 	Y               Neutral
// Valine           Val 	V   Hydrophobic


// =====================   rules  ===============
//  --- AA
//  Hydrophobic to Hydrophobic
//  Hydrophylic [+] to Hydrophilic [-]
//  Neutral to Hydrophobic
//  Neutral to Hydrophilic (does not matter [+] or [-])
 
//  --- Secondary Structure
//  H to H  and S to S
//  Note: No S to H on this point
// ===============================================



eod