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’
: Structure ControlF.H.D. van Batenburg (Batenburg@rulsfb.LeidenUniv.nl)
[Ed: This is the code referred to in Eke’s paper from Vector 17:4.]
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 ׌nc'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=׌nc'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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