# The strand_sep alphabet is a new secondary structure alphabet which 
# classifies strands based on the separation between the beta partners.
# The separations are split differently for anti-parallel and parallel 
# strands

# There are three sections to this alphabet:
#     	Helix letters, based primarily on hydrogen bond patterns
#	Strand letters, based on CA distances and Beta partner separations
#       Other letters, based on the r_rot value and the NO_dist2 value.

# Helix letters:
# 	Like str4, H stands for Oi-2,Ni+2 hydrogen bond and G stands for
#	Oi-2,Ni+1 hydrogen bond

#Strand letters:
#	Strands will be separated into parallel and antiparallel based on
#	whether Calpha distance of Oj or Oj+1 is closer.

#	Antiparallel:
#		Divided into separations of:
#			<-30	 	V
#			-30 to -10 	U
#			-10 to 0 	T
#			0 to 10 	S
#			10 to 30 	R
#			>30 		Q
#			unbonded edge   W
#	Parallel:
#		Divided into separations of:
#			< -52		N
#			-52 to -28	M
#			-27 to -10	L
#			10 to 27	K
#			28 to 52	J
#			>52		I
#			unbonded edge   P

# Other regions (coil) are classified based on r_rot and NO_dist2
# The NO_dist2 cut off is 10
# The r_rot cutoffs are -1, -0.4, and 0.3
# Since one region has few points, it will be merged with another region.  
# The regions will be defined as follows:
#	Regions with NO_dist2 > 10:
#		r_rot < -0.4		A	
#		-0.4 <= r_rot < 0.3 	B
#		r_rot > 0.3		C
#	Regions with NO_dist2 <= 10:
#		r_rot < -0.4		D
#		-0.4 <= r_rot < 0.3	B
#		r_rot >= 0.3		E


ClassName = Alphabet
    Name = strand_sep

    IsNucleic = 0
    NormalChars = ABCDEFGHIJKLMNPQRSTUVW
    AllMatch = X

    # Helix types

    CharName = F other_helical	other_helical_ends
    CharName = G 3_10		3_10_helix
    CharName = H helix		alpha_helix
    
    # Parallel strand types

    CharName = I para_53+	parallel_separation_53+
    CharName = J para_28to52	parallel_separation_28to52
    CharName = K para_10to27	parallel_separation_10to27
    CharName = L para_-10to-27	parallel_separation_-10to-27
    CharName = M para_-28to-52	parallel_separation_-28to-52
    CharName = N para_-53	parallel_separation_-53
    CharName = P para_unbonded	parallel_unbonded_edge

    # Antiparallel strand types

    CharName = Q anti_30+	antiparallel_separation_30+
    CharName = R anti_10to30	antiparallel_separation_10to30
    CharName = S anti_0to10	antiparallel_separation_0to10
    CharName = T anti_-10to0	antiparallel_separation_-10to0
    CharName = U anti_-30to-10	antiparallel_separation_-30to-10
    CharName = V anti_-30	antiparallel_separation_-30
    CharName = W anti_unbonded  antiparallel_unbonded_edge

    # Other types

    CharName = A NOdist_low_rot_r_low	NOdist_low_rot_r_low
    CharName = B rot_r_mid		rot_r_mid
    CharName = C NOdist_low_rot_r_high	NOdist_low_rot_r_high
    CharName = D NOdist_high_rot_r_low	NOdist_high_rot_r_low
    CharName = E NOdist_high_rot_r_high	NOdist_high_rot_r_high

EndClassName = Alphabet