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|
*----------------------------------------------------------------------*
* *
* FORTRAN code for program CONVERT_SEQ *
* conversion of sequence and alignment formats *
* *
*----------------------------------------------------------------------*
* *
* Authors: *
* *
* Reinhard Schneider May, 1994 version 1.0 *
* LION http://www.lion-ag/ *
* D-69120 Heidelberg schneider@lion-ag.de *
* *
* & *
* *
* Burkhard Rost May, 1994 version 1.1 *
* Oct, 1998 version 2.0 *
* EMBL/LION http://www.embl-heidelberg.de/~rost/ *
* D-69012 Heidelberg rost@embl-heidelberg.de *
* *
*----------------------------------------------------------------------*
* *
* General note: - uses library lib-maxhom.f *
* *
* *
*----------------------------------------------------------------------*
PROGRAM MAKE_METRIC
*
C quick hack to produce structure/IO dependent metric used in MaxHom
*
*
*
*
************************************************************************
IMPLICIT NONE
C----
C---- parameters
C----
INTEGER NTRANS,NSTRMAX,NIOMAX,KOUT,KIN
PARAMETER (NTRANS=26,NSTRMAX=3,NIOMAX=3,KOUT=10,KIN=11)
INTEGER NSTR1,NSTR2,NIO1,NIO2,IL,IH,IB,IO,IE,N1,N2,N3,N4
C----
C----
C----
CHARACTER CTRANS*(NTRANS),CSTRUC*3,CIO*3
REAL STRVAL(NSTRMAX,NSTRMAX),IOVAL(NIOMAX,NIOMAX),
+ VALUE(NTRANS)
INTEGER IORANGE(NIOMAX,NIOMAX)
REAL STRIOVAL(1:(NSTRMAX*NIOMAX),1:(NSTRMAX*NIOMAX))
CHARACTER*5 CTEMP,CH
INTEGER ITEMP(3,3),IT1,IT2,IHVEC(1:9),FAC_STR,FAC_SEQ,
+ ISTR1,IO1,I,ISTR2,IO2,J,MTRANS,NUMARGUMENTS
CHARACTER*80 FILE_METRIC_SEQ,FILE_METRIC_OUT,FILE_METRIC_IN
LOGICAL LREAD_METRIC_IN,LHELP
REAL SIMSEQ(NTRANS,NTRANS,NSTRMAX,NIOMAX,NSTRMAX,NIOMAX),
+ SIMSTR
C--------------------------------------------------
C----
C---- init defaults
C----
FILE_METRIC_OUT='Make_metric_new.output'
FILE_METRIC_SEQ=
+ '/home/rost/pub/topits/mat/Maxhom_McLachlan.metric'
FILE_METRIC_IN= 'Make_metric_new.input'
ctrans='VLIMFWYGAPSTCHRKQENDBZX!-.'
C read metric from file?
LREAD_METRIC_IN=.FALSE.
LREAD_METRIC_IN=.TRUE.
* *
C--------------------------------------------------
C---- requesting input files:
C---- McLachlan (seq. metric) + file_in; file_out
C--------------------------------------------------
* *
CALL GET_ARG_NUMBER(NUMARGUMENTS)
IF (NUMARGUMENTS.GT.0) THEN
CALL GET_ARGUMENT(1,FILE_METRIC_IN)
END IF
IF (NUMARGUMENTS.GT.1) THEN
CALL GET_ARGUMENT(2,FILE_METRIC_OUT)
END IF
IF (NUMARGUMENTS.GT.2) THEN
CALL GET_ARGUMENT(3,FILE_METRIC_SEQ)
END IF
IF (NUMARGUMENTS.EQ.0) THEN
WRITE(6,'(T2,A)')'---'
WRITE(6,'(T2,A3,T10,A)')'----',
+ 'you can provide three input arguments:'
WRITE(6,'(T2,A3,T10,A,T35,A)')'----','1: input metric def=',
+ FILE_METRIC_IN
WRITE(6,'(T2,A3,T10,A,T35,A)')'----','2: output metric def=',
+ FILE_METRIC_OUT
WRITE(6,'(T2,A3,T10,A,T35,A)')'----','3: sequence metric def=',
+ FILE_METRIC_SEQ
WRITE(6,'(T2,A)')'---'
END IF
* *
* *
C percentage of match_struc / match_seq:
C (fac_str) * match_str + (10-fac_str) * match_seq
FAC_STR= 10
C number of secondary structure and IO states
NSTR1= 3
NSTR2= 3
NIO1= 2
NIO2= 2
C define secondary structure states: E=beta , H=helix, L= NOT E or H
C cstruc='ELH'
CSTRUC='ELH'
IE=INDEX(CSTRUC,'E')
IL=INDEX(CSTRUC,'L')
IH=INDEX(CSTRUC,'H')
C define match/mismatch between secondary structures states
C "ie,ie" = 3.0 ==> match between two residue in a beta strand
C give a value of 3.0
STRVAL(IE,IE)= 4.0
STRVAL(IE,IL)= -1.0
STRVAL(IE,IH)= -4.0
STRVAL(IL,IE)= -1.0
STRVAL(IL,IL)= 1.0
STRVAL(IL,IH)= -1.0
STRVAL(IH,IE)= -4.0
STRVAL(IH,IL)= -1.0
STRVAL(IH,IH)= 4.0
C define IO states: B=buried , I=inside, O=ouside
C cio='BIO'
CIO='BO'
IB=INDEX(CIO,'B')
C ii=index(cio,'I')
IO=INDEX(CIO,'O')
C define match/mismatch between IO states
C "ib,ib" = 3.0 ==> match between a buried residue with a buried residue
C give a value of 3.0
IOVAL(IB,IB)= 4.0
C IOVAL(IB,II)= -2.0
IOVAL(IB,IO)= -2.0
C IOVAL(II,IB)= -2.0
C IOVAL(II,II)= 1.0
C IOVAL(II,IO)= -2.0
IOVAL(IO,IB)= -2.0
C IOVAL(IO,II)= -2.0
IOVAL(IO,IO)= 1.0
C define IO classes
C "ie,ib" = beta-strand + buried are residues with a %accessibility
C surface area below or equal to 5 percent (depndend on residue type)
IORANGE(IE,IB)= 15
C IORANGE(IE,II)= 16
IORANGE(IE,IO)= 100
IORANGE(IL,IB)= 15
C IORANGE(IL,II)= 16
IORANGE(IL,IO)= 100
IORANGE(IH,IB)= 15
C IORANGE(IH,II)= 16
IORANGE(IH,IO)= 100
C--------------------------------------------------
C---- generate the sequence match matrix
C--------------------------------------------------
C----
C----
CALL GETSIMMETRIC(NTRANS,CTRANS,NSTRMAX,NIOMAX,N1,N2,N3,N4,
+ CTEMP,CTEMP,ITEMP,99,FILE_METRIC_SEQ,SIMSEQ)
C -----------------
C--------------------------------------------------
C define match/mismatch between secondary structures and in/out
C Eb Ee Lb Le Hb He
C Eb 9 2 1 -6 -1 -8
C Ee 7 -6 1 -8 -3
C Lb 6 -1 1 -6
C Le 4 -6 1
C Hb 9 2
C He 7
C
C----
C E->x
STRIOVAL(1,1)= 9.0
STRIOVAL(1,2)= 2.0
STRIOVAL(1,3)= 1.0
STRIOVAL(1,4)= -6.0
STRIOVAL(1,5)= -1.0
STRIOVAL(1,6)= -8.0
STRIOVAL(2,2)= 7.0
C----
C L->x
strioval(3,3)= 6.0
strioval(3,4)= -1.0
strioval(4,4)= 4.0
C----
C symmetrie intuition
STRIOVAL(2,3)=STRIOVAL(1,4)
STRIOVAL(2,4)=STRIOVAL(1,3)
STRIOVAL(2,5)=STRIOVAL(1,6)
STRIOVAL(2,6)=STRIOVAL(1,5)
STRIOVAL(3,5)=STRIOVAL(1,3)
STRIOVAL(3,6)=STRIOVAL(1,4)
STRIOVAL(4,5)=STRIOVAL(1,4)
STRIOVAL(4,6)=STRIOVAL(1,3)
STRIOVAL(5,5)=STRIOVAL(1,1)
STRIOVAL(5,6)=STRIOVAL(1,2)
STRIOVAL(6,6)=STRIOVAL(2,2)
C----
C symmetrie intuition
DO IT1=1,6
DO IT2=1,(IT1-1)
STRIOVAL(IT1,IT2)=STRIOVAL(IT2,IT1)
END DO
END DO
C--------------------------------------------------
C read in factors and metric file?
C--------------------------------------------------
IF (LREAD_METRIC_IN) THEN
OPEN(KIN,FILE=FILE_METRIC_IN,STATUS='UNKNOWN',RECL=150)
write(6,*)'--- read metric in'
READ(KIN,'(A)',END=22114)CH
write(6,'(A,T20,A)')'---',CH
DO IT1=1,NSTR1*NIO1
READ(KIN,'(A3,6I8)',END=22114)CH,
+ (IHVEC(IT2),IT2=1,(NSTR2*NIO2))
write(6,'(A5,I2,A1,A3,T20,6I6)')'read ',IT1,':',CH,
+ (IHVEC(IT2),IT2=1,(NSTR2*NIO2))
DO IT2=1,(NSTR2*NIO2)
STRIOVAL(IT1,IT2)=IHVEC(IT2)/10.
END DO
END DO
LHELP=.TRUE.
DO WHILE (LHELP)
CH=' '
READ(KIN,'(A)',END=22114)CH
IF ( (CH(1:1).EQ.' ').OR.(CH(1:1).EQ.'*') ) THEN
CONTINUE
ELSEIF ( (CH(1:1).NE.'F').AND.
+ (CH(1:1).NE.'f') ) THEN
write(6,*)'x.x ch=',ch(1:5)
LHELP=.FALSE.
ELSE
BACKSPACE(KIN)
READ(KIN,'(A8,I2)',END=22114)CH,FAC_STR
END IF
END DO
22114 CONTINUE
CLOSE(KIN)
END IF
c recompute factors
FAC_SEQ=10-FAC_STR
C----------------------------------------------------------------------
C now summarise the setting
C----------------------------------------------------------------------
c write out onto printer
WRITE(6,*)'--------------------------------------------------'
WRITE(6,'(T5,A)')' '
IF (LREAD_METRIC_IN) THEN
WRITE(6,'(T5,A,T40,A)')'file containing metric asf.:',
+ FILE_METRIC_IN
WRITE(6,'(T5,A,T40,A)')'output will be in:',FILE_METRIC_OUT
WRITE(6,'(T5,A)')'match = n*match_struc + (10-n)*match_seq '
WRITE(6,'(T5,A,T20,I5)')'where n = ',FAC_STR
WRITE(6,'(T5,A)')' '
END IF
WRITE(6,*)' '
WRITE(6,*)'matrix generated:'
WRITE(6,'(T10,6(A2,A1,A1,A2))')
+ ' ',cstruc(1:1),cio(1:1),' ',' ',cstruc(1:1),cio(2:2),' ',
+ ' ',cstruc(2:2),cio(1:1),' ',' ',cstruc(2:2),cio(2:2),' ',
+ ' ',cstruc(3:3),cio(1:1),' ',' ',cstruc(3:3),cio(2:2),' '
DO ISTR1=1,NSTR1
DO IO1=1,NIO1
IT1=(ISTR1-1)*NIO1+IO1
WRITE(6,'(A1,A1,T10,6F6.2)')
+ CSTRUC(ISTR1:ISTR1),CIO(IO1:IO1),
+ (STRIOVAL(IT1,IT2),IT2=1,(NSTR2*NIO2))
END DO
END DO
WRITE(6,*)' '
WRITE(6,*)'--------------------------------------------------'
C----------------------------------------------------------------------
C now write into file
C----------------------------------------------------------------------
OPEN(KOUT,FILE=FILE_METRIC_OUT,STATUS='UNKNOWN',RECL=250)
C write header info
WRITE(KOUT,'(A)')'#========================================='//
+ '=========================================='//
+ '=========================================='//
+ '==============='
WRITE(KOUT,'(A,I3)')'STRUCTURE-STATES_1:',NSTR1
WRITE(KOUT,'(A,I3)')'STRUCTURE-STATES_2:',NSTR2
WRITE(KOUT,'(A,I3)')'I/O-STATES_1:',NIO1
WRITE(KOUT,'(A,I3)')'I/O-STATES_2:',NIO2
WRITE(KOUT,'(A)')'DSSP-STRUCTURE I/O %ACC-RANGE '//
+ '(<= less or equal)'
C write ranges for accessibility classes
DO ISTR1=1,NSTR1
DO IO1=1,NIO1
WRITE(KOUT,'(4X,A,13X,A,7X,I3)')CSTRUC(ISTR1:ISTR1),
+ CIO(IO1:IO1),IORANGE(ISTR1,IO1)
ENDDO
ENDDO
C write seperator lines
WRITE(KOUT,'(A)')'#========================================='//
+ '=========================================='//
+ '=========================================='//
+ '==============='
WRITE(KOUT,'(A)')'AA STR I/O V L I M F '//
+ 'W Y G A P S T '//
+ 'C H R K Q E N '//
+ 'D B Z'
C write metric
MTRANS=22
DO I=1,MTRANS
DO ISTR1=1,NSTR1
DO IO1=1,NIO1
DO ISTR2=1,NSTR2
DO IO2=1,NIO2
C--- old version: combine HEL be
C SIMSTR=
C + strval(istr1,istr2) + ioval(io1,io2)
C--- new version: 6x6 matrix
SIMSTR=STRIOVAL( ((ISTR1-1)*NIO1+IO1),
+ ((ISTR2-1)*NIO2+IO2) )
DO J=1,22
C F*struc + (10-F)*seq
VALUE(J) = (FAC_STR/10. * SIMSTR) +
+ (FAC_SEQ/10. * SIMSEQ(I,J,1,1,1,1))
IF (VALUE(J) .GE. 10.0) VALUE(J)=9.99
IF (VALUE(J) .LE. -10.0) VALUE(J)=-9.99
ENDDO
WRITE(KOUT,'(1X,A,2X,A,A,1X,A,A,1X,22(F5.2,1X))')
+ CTRANS(I:I),CSTRUC(ISTR1:ISTR1),
+ CSTRUC(ISTR2:ISTR2),CIO(IO1:IO1),
+ CIO(IO2:IO2),
+ (VALUE(J),J=1,22)
ENDDO
ENDDO
ENDDO
ENDDO
ENDDO
END
|
