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A New Life For `’`: Structure Control

F.H.D. van Batenburg (Batenburg@rulsfb.LeidenUniv.nl)

[Ed: This is the code referred to in Eke’s paper from Vector 17:4.]

Appendix

In this paragraph two already structured programs are shown in their original programming style as well as with the new proposal.

    ’ ref„set WProfile name;default;num
[1]   ©’[ref„][set] WProfile name -- Set/Ref .INI Profile data
[2]   ©’name = '#[section]name {=default}' -- '#' and '=default' for ref only; #=return numeric
[3]   default„(Ÿ\'='=name)/name
[4]   name„(-½default)‡name
[5]   num„'#'=1†name
[6]   name„num‡name
[7]   :if ×Œnc'set'
[8]      :if ~(Œdr set)¹82 11 323 645
[9]      :orif 1<½½set
[10]        Œerror 'DOMAIN ERROR'
[11]     :end
[12]     set„•set
[13]     (('¯'=set)/set)„'-'
[14]     set„Œwcall 'W_Ini' (name,'=',set)
[15]  :else
[16]     ref„Œwcall 'W_Ini' name
[17]     :if ''¦ref
[18]        ref„1‡default
[19]     :end
[20]     :if num
[21]        ref„(~0¹Œvi ref)/Œfi ref
[22]     :end
[23]  :end
_____________________________________________

    ’ ref„set WProfile name;default;num
[1]   ©’[ref„][set] WProfile name -- Set/Ref .INI Profile data
[2]   ©’name = '#[section]name {=default}' -- '#' and '=default' for ref only; #=return numeric
[3]   default„(Ÿ\'='=name)/name
[4]   name„(-½default)‡name
[5]   num„'#'=1†name
[6]   name„num‡name
[7]   ’1 0=×Œnc'set'
[8]   :’(1<½½set)Ÿ~(Œdr set)¹82 11 323 645
[9]     Œerror 'DOMAIN ERROR'
[10]   ’
[11]   set„•set
[12]   (('¯'=set)/set)„'-'
[13]   set„Œwcall 'W_Ini' (name,'=',set)
[14]  :ref„Œwcall 'W_Ini' name
[15]   ref„1‡default’''¦ref
[16]   ref„(~0¹Œvi ref)/Œfi ref ’num
[17]  ’

=============================================================

[0]  Z„L RNA_PK‘GUP R;SEQ;STR;A;STM;D1;D2;SEQ1;B
[1]  © compute energy values for given stem (½R=8) that
[2]  © forms a (bulge) pseudoknot with a stem (A) downstream
[3]  © P: S.Gultyaev 2000
[4]  ©    EvanBatenburg 2001.1.17: illegal NA to vector
[5]  
[6]  (SEQ STR A)„L ª STM„R
[7]  STM[6]„STM[7]„STM[8]„999
[8]  B1:…(0<(SEQ STR)RNA_DOMAINS STM[2],A[1])/1+E1
[9]  D1„(SEQ STR)RNA_DOMAINS A[2],STM[3]
[10] D2„(SEQ STR)RNA_DOMAINS STM[4],A[3]
[11] B3:…((0=D1+D2),((D1=1)^D2=0),((D1=0)^D2=1),1<D1+D2)/B3a,B3b,B3c,B3d
[12] B3a:STM[6]„(STM[2],A[2]+1)RNA_PKLOOPDEEP A[2]-A[1]-1
[13] STM[7]„((STM[3]-1),A[3])RNA_PKLOOPSHLW STM[2]-STM[1]-1
[14] STM[8]„STM[5]+STM[6]+STM[7]+RNArulquasijunction[STM[3]-A[2]]-A[6]
[15] BE1:…(STM[3]>A[2]+1)/ŒLC+1ªSTM[8]„STM[8]+RNArulcoax+(STM[2 3],A[3 2])RNA_STACKING SEQ
[16] B4:…(STM[3]¬A[2]+2)/1+E4
[17]  SEQ1„SEQ[STM[2],(A[3]-1),(A[2]+1),STM[3]]
[18]  STM[8]„STM[8]+RNArulcoax+(A[2 3]RNA_MISMINT SEQ)+1 4 RNA_MISMINT SEQ1
[19] E4:
[20]  …1+E3
[21] B3b:B„(STR[;1]=1+(SEQ STR)RNA_SCANSSCHAIN A[2],STM[3])šSTR
[22]  B„B[1;]
[23]  STM„(SEQ STR A B)RNA_PKBLG‘GUP STM[¼4]
[24]  …1+E3
[25] B3c:B„(STR[;1]=1+(SEQ STR)RNA_SCANSSCHAIN STM[4],A[3])šSTR
[26]  B„B[1;]
[27] BE2:…(B[4]<A[3]-2)/ŒLC+1 ª STM„(SEQ STR A B)RNA_PKBLG‘GUP STM[¼4]
[28]  …1+E3
[29] B3d:STM[8]„999
[30] E3:
[31] E1:
[32]  Z„STM
_____________________________________________
  
[0]  Z„L RNA_PK‘GUP R;SEQ;STR;A;STM;D1;D2;SEQ1;B
[1]  © compute energy values for given stem (½R=8) that
[2]  © forms a (bulge) pseudoknot with a stem (A) downstream
[3]  © P: S.Gultyaev 2000
[4]  ©    EvanBatenburg 2001.1.17: illegal NA to vector
[5]  
[6]   (SEQ STR A)„L ª STM„R
[7]   STM[6]„STM[7]„STM[8]„999
[8]   ’~0<(SEQ STR)RNA_DOMAINS STM[2],A[1]
[9]    D1„(SEQ STR)RNA_DOMAINS A[2],STM[3]
[10]   D2„(SEQ STR)RNA_DOMAINS STM[4],A[3]
[11]   ’(0=D1+D2),((D1=1)^D2=0),((D1=0)^D2=1),1<D1+D2
[12]   :STM[6]„(STM[2],A[2]+1)RNA_PKLOOPDEEP A[2]-A[1]-1
[13]    STM[7]„((STM[3]-1),A[3])RNA_PKLOOPSHLW STM[2]-STM[1]-1
[14]    STM[8]„STM[5]+STM[6]+STM[7]+RNArulquasijunction[STM[3]-A[2]]-A[6]
[15]     STM[8]„STM[8]+RNArulcoax+(STM[2 3],A[3 2])RNA_STACKING SEQ’~STM[3]>A[2]+1
[16]    ’~STM[3]¬A[2]+2
[17]     SEQ1„SEQ[STM[2],(A[3]-1),(A[2]+1),STM[3]]
[18]     STM[8]„STM[8]+RNArulcoax+(A[2 3]RNA_MISMINT SEQ)+1 4 RNA_MISMINT SEQ1
[19]    ’
[20]   :B„(STR[;1]=1+(SEQ STR)RNA_SCANSSCHAIN A[2],STM[3])šSTR
[21]    B„B[1;]
[22]    STM„(SEQ STR A B)RNA_PKBLG‘GUP STM[¼4]
[23]   :B„(STR[;1]=1+(SEQ STR)RNA_SCANSSCHAIN STM[4],A[3])šSTR
[24]    B„B[1;]
[25]     STM„(SEQ STR A B)RNA_PKBLG‘GUP STM[¼4] ’ ~B[4]<A[3]-2
[26]   :STM[8]„999
[27]   ’
[28]  ’
[29]  Z„STM

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A New Life For ’: Structure Control

Appendix

A New Life For `’`: Structure Control