//  All these alphabets use the separation distance to be the acceptor
//	to the donor (so that an alpha-helix is always +4).
//  In this way, it allows the user to see the helical areas easier
//	because they will be the same character in both of the files.

// The NOtor torsion angle is the torsion angle for  C(i-1)-N(i)---O(j)-N(j+1)
// which can be used to characterize beta strand connections.
				

ClassName = Alphabet

        // n_notor looks at the hydrogen bonds formed by the backbone N atom
	// and classifies by the "notor" torsion angle when the
	//	partner is a backbone O (except for separation 3 and
	//	4, which are special)

    Name = n_notor
    IsNucleic = 0
    NormalChars = GHPABSMN
    AllMatch = X
    CharName = G sep_3	3_10_helix_or_turn // notor approx -14
    CharName = H sep_4	alpha_helix  // notor approx 101     
    CharName = P parallel	parallel_beta_strand // notor approx 170 (<-133 or >76)
    CharName = B notor_-83	antiparallel_notor_-83	// [-133,-17]
    CharName = A notor_23	antiparallel_notor_23	// (-17,76]
    CharName = S sidechain	sidechain_hbond
    CharName = M multiple	multiple_hbonds
    CharName = N none	 no_hbond

EndClassName = Alphabet

ClassName = Alphabet

    Name = o_notor
    IsNucleic = 0
    NormalChars = GHPABSMN
    AllMatch = X
    CharName = G sep_3	3_10_helix_or_turn // notor approx -14 
    CharName = H sep_4	alpha_helix  // notor approx 101
    CharName = P parallel	parallel_beta_strand // notor approx 170 (<-133 or >76)
    CharName = B notor_-83	antiparallel_notor_-83	// [-133,-17]
    CharName = A notor_23	antiparallel_notor_23	// (-17,76]
    CharName = S sidechain	sidechain_hbond
    CharName = M multiple	multiple_hbonds
    CharName = N none	no_hbond

EndClassName = Alphabet

ClassName = Alphabet
    
    // n_sep looks at the hydrogen bonds formed by the backbone N atom
    // and classifies by the separation if the partner is a backbone O.
    
    Name = n_sep
    IsNucleic = 0
    NormalChars = GHIJKLMNPQRSTUVWABCD
    AllMatch = X
    CharName = G sep_+3	3_10_helix_or_turn
    CharName = H sep_+4	alpha_helix
    CharName = I sep_+5	sep_+5
    CharName = J sep_+6	sep_+6
    CharName = K sep_+7	sep_+7
    CharName = L sep_+8	sep_+8
    CharName = M sep_+9	sep_+9
    CharName = N sep_+10	sep_+10
    CharName = P sep_-3	sep_-3
    CharName = Q sep_-4	sep_-4
    CharName = R sep_-5	sep_-5
    CharName = S sep_-6	sep_-6
    CharName = T sep_-7	sep_-7
    CharName = U sep_-8	sep_-8
    CharName = V sep_-9	sep_-9
    CharName = W sep_-10	sep_-10
    CharName = A other	other_backbone
    CharName = B multiple	multiple_hbonds
    CharName = C sidechain	sidechain_hbond
    CharName = D none	no_hbond

EndClassName = Alphabet

ClassName = Alphabet

    // o_sep looks at the hydrogen bonds formed by the backbone O atom
    // and classifies by the separation if the partner is a backbone N.
    
    Name = o_sep
    IsNucleic = 0
    NormalChars = GHIJKLMNPQRSTUVWABCD
    AllMatch = X
    CharName = G sep_+3	sep_+3
    CharName = H sep_+4	sep_+4  
    CharName = I sep_+5	sep_+5
    CharName = J sep_+6	sep_+6
    CharName = K sep_+7	sep_+7
    CharName = L sep_+8	sep_+8
    CharName = M sep_+9	sep_+9
    CharName = N sep_+10	sep_+10
    CharName = P sep_-3	sep_-3
    CharName = Q sep_-4	sep_-4
    CharName = R sep_-5	sep_-5
    CharName = S sep_-6	sep_-6
    CharName = T sep_-7	sep_-7
    CharName = U sep_-8	sep_-8
    CharName = V sep_-9	sep_-9
    CharName = W sep_-10	sep_-10
    CharName = A other	other_backbone
    CharName = B multiple	multiple_hbonds
    CharName = C sidechain	sidechain_hbond
    CharName = D none	no_hbond

EndClassName = Alphabet

ClassName = Alphabet

        // n_notor2 is a modified version of n_notor.  It classifies
	//    the alphabet based on the notor angle, but also uses 
	//    a separation of 5, and classifies multiple hydrogen bonds
	//    into three categories:  3 and 4, 4 and 5, and other.

    Name = n_notor2
    IsNucleic = 0
    NormalChars = GHIPABSFJMN
    AllMatch = X
    CharName = G sep_3	3_10_helix_or_turn // notor approx -14
    CharName = H sep_4	alpha_helix  // notor approx 101 
    CharName = I sep_5	pi_helix_or_cap // notor approx 96
    CharName = P parallel	parallel_beta_strand // notor approx 170 (<-133 or >76)
    CharName = B notor_-83	antiparallel_notor_-83	// [-133,-17]
    CharName = A notor_23	antiparallel_notor_23	// (-17,76]
    CharName = S sidechain	sidechain_hbond
    CharName = F multiple_3_and_4	multiple_hbonds_sep_3_and_4 // multiple hydrogen bonds with the bonds having a separation of three and four
    CharName = J multiple_4_and_5	multiple_hbonds_sep_4_and_5 // multiple hydrogen bonds with the bonds having a separation of four and five
    CharName = M multiple_other	multiple_hbonds_other // any other multiple hydrogen bonds
    CharName = N none	 no_hbond

EndClassName = Alphabet

ClassName = Alphabet

        // o_notor2 is a modified version of o_notor.  It classifies
	//    the alphabet based on the notor angle, but also uses 
	//    a separation of 5, and classifies multiple hydrogen bonds
	//    into three categories:  3 and 4, 4 and 5, and other.

    Name = o_notor2
    IsNucleic = 0
    NormalChars = GHIPABSFJMN
    AllMatch = X
    CharName = G sep_3	3_10_helix_or_turn // notor approx -14 
    CharName = H sep_4	alpha_helix  // notor approx 101
    CharName = I sep_5	pi_helix_or_cap // notor approx 96
    
    CharName = P parallel	parallel_beta_strand // notor approx 170 (<-133 or >76)
    CharName = B notor_-83	antiparallel_notor_-83	// [-133,-17]
    CharName = A notor_23	antiparallel_notor_23	// (-17,76]
    CharName = S sidechain	sidechain_hbond
    CharName = F multiple_3_and_4	multiple_hbonds_sep_3_and_4 // multiple hydrogen bonds with the bonds having a separation of three and four
    CharName = J multiple_4_and_5	multiple_hbonds_sep_4_and_5 // multiple hydrogen bonds with the bonds having a separation of four and five
    CharName = M multiple_other	multiple_hbonds_other // any other multiple hydrogen bonds
    CharName = N none	no_hbond

EndClassName = Alphabet