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306 lines (278 loc) · 8.97 KB
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! calculates the cross correlation for each residue over the selected number
! of modes
! Tom Rodgers 08 04 2011
PROGRAM cross_cor
USE read_files
USE nrutil
IMPLICIT NONE
CHARACTER :: lign80*80, pdbfile*120, hetchoice*20, filename*120, dummy*120
INTEGER :: skipvec, numvec, endvec, startvec, ndim, vector, i, j, k, io, natom, m
INTEGER :: nat, resid, residold, st, en
INTEGER, ALLOCATABLE,DIMENSION(:) :: natvec
REAL(DP), ALLOCATABLE, DIMENSION(:) :: eigenval
REAL(DP), ALLOCATABLE, DIMENSION(:,:) :: eigen, crosscor
REAL(DP) :: sum, dot, lengthi, lengthj
LOGICAL :: hetatm, getoption, qexist,nopdb
INTEGER, ALLOCATABLE,DIMENSION(:) :: atnum,resnum
REAL(DP), ALLOCATABLE,DIMENSION(:) ::x,y,z,occ,bfac
CHARACTER, ALLOCATABLE, DIMENSION(:) :: atom*6,name*4,res*3,chain*1,elem*2,chag*2
IF (getoption('-help',.false.,dummy)) THEN
CALL helptext(0)
CALL exit(0)
END IF
IF(.not.getoption('-i',.true.,filename)) THEN
CALL helptext(0)
CALL exit(0)
END IF
INQUIRE(file=filename,exist=qexist)
IF (.not.qexist) THEN
STOP "eigenfacs file specified does not exist"
END IF
nopdb=.false.
IF(.not.getoption('-pdb',.true.,pdbfile)) THEN
nopdb=.true.
END IF
INQUIRE(file=pdbfile,exist=qexist)
IF (.not.qexist) THEN
nopdb=.true.
END IF
IF (getoption('-d1',.false.,dummy)) THEN
ndim=1
ELSE
ndim=3
END IF
! Start vector
IF(getoption('-s',.true.,dummy)) THEN
READ(dummy,*) startvec
ELSE
startvec=7
END IF
skipvec=startvec-1
! End vector
IF(getoption('-e',.true.,dummy)) THEN
READ(dummy,*) endvec
ELSE
endvec=31
END IF
numvec=endvec-skipvec
IF (getoption('-het',.false.,dummy)) THEN
hetatm=.true.
ELSE
hetatm=.false.
END IF
CALL read_eigenfacs(filename,natom,startvec,endvec,ndim,eigenval,eigen,i)
print*, natom
ALLOCATE(crosscor(natom,natom))
DO i=1,natom
DO j=1,natom
sum=0
DO m=1,numvec
dot=0
lengthi=0
lengthj=0
DO k=1,ndim
dot=dot+eigen((i-1)*ndim+k,m)*eigen((j-1)*ndim+k,m)
lengthi=lengthi+eigen((i-1)*ndim+k,m)**2
lengthj=lengthj+eigen((j-1)*ndim+k,m)**2
END DO
sum=sum+dot/(lengthi**0.5*lengthj**0.5)
END DO
crosscor(i,j)=sum/numvec
END DO
END DO
IF (nopdb) THEN
ALLOCATE(resnum(natom))
DO i=1,natom
resnum(i)=i
END DO
ELSE
CALL read_pdb(pdbfile,hetatm,natom,atom,atnum,name,res,chain,resnum,x,y,z, &
occ,bfac,elem,chag)
END IF
!!$ OPEN(file=pdbfile,form="FORMATTED",status="OLD",unit=2356)
!!$
!!$ DO
!!$ READ(2356,'(A)',IOSTAT=io) lign80
!!$ IF (io > 0) THEN
!!$ WRITE(*,*) 'Check input. Something was wrong'
!!$ STOP
!!$ ! End of file
!!$ ELSE IF (io < 0) THEN
!!$ EXIT
!!$ ! Count up number of atoms
!!$ ELSE
!!$ IF (lign80(1:4).eq.'ATOM') THEN
!!$ READ(lign80,'(22X,I4)') residold
!!$ EXIT
!!$ END IF
!!$ END IF
!!$ END DO
!!$
!!$ REWIND(2356)
!!$
!!$ nat=0
!!$ resid=0
!!$ i=0
!!$ j=1
!!$ ALLOCATE(natvec(natom))
!!$
!!$ DO
!!$ READ(2356,'(A)',IOSTAT=io) lign80
!!$ IF (io > 0) THEN
!!$ WRITE(*,*) 'Check input. Something was wrong'
!!$ STOP
!!$ ! End of file
!!$ ELSE IF (io < 0) THEN
!!$ IF (lign80(1:4).eq.'ATOM') THEN
!!$ nat=nat+1
!!$ natvec(nat)=i
!!$ END IF
!!$ EXIT
!!$ ! Count up number of atoms
!!$ ELSE
!!$ IF (lign80(1:4).eq.'ATOM') THEN
!!$ READ(lign80,'(22X,I4)') resid
!!$ IF (resid.eq.residold) THEN
!!$ i=i+1
!!$ ELSE
!!$ nat=nat+1
!!$ natvec(nat)=i
!!$ i=1
!!$ END IF
!!$ residold=resid
!!$ j=0
!!$ ELSE IF ((lign80(1:6).eq.'HETATM').and.hetatm) THEN
!!$ j=j+1
!!$ IF (j.eq.1) THEN
!!$ nat=nat+1
!!$ natvec(nat)=i
!!$ i=1
!!$ residold=resid
!!$ END IF
!!$ nat=nat+1
!!$ natvec(nat)=1
!!$ ELSE
!!$ END IF
!!$ END IF
!!$ END DO
!!$
!!$ CLOSE(2356)
!!$
!!$ IF (nat.lt.natom) THEN
!!$ WRITE(*,*) "Adjusting cross-correlation in terms of residues"
!!$
!!$ DO j=1,natom
!!$ sum=0
!!$ DO k=1,natvec(1)
!!$ sum=sum+crosscor(k,j)
!!$ END DO
!!$ crosscor(1,j)=sum/natvec(1)
!!$ END DO
!!$
!!$ DO i=2,nat
!!$ st=0
!!$ DO j=1,i-1
!!$ st=st+natvec(j)
!!$ END DO
!!$ en=st+natvec(i)
!!$ st=st+1
!!$
!!$ DO j=1,natom
!!$ sum=0
!!$ DO k=st,en
!!$ sum=sum+crosscor(k,j)
!!$ END DO
!!$ crosscor(i,j)=sum/natvec(i)
!!$ END DO
!!$
!!$ END DO
!!$
!!$ DO j=1,nat
!!$ sum=0
!!$ DO k=1,natvec(1)
!!$ sum=sum+crosscor(j,k)
!!$ END DO
!!$ crosscor(j,1)=sum/natvec(1)
!!$ END DO
!!$
!!$ DO i=2,nat
!!$ st=0
!!$ DO j=1,i-1
!!$ st=st+natvec(j)
!!$ END DO
!!$ en=st+natvec(i)
!!$ st=st+1
!!$
!!$ DO j=1,nat
!!$ sum=0
!!$ DO k=st,en
!!$ sum=sum+crosscor(j,k)
!!$ END DO
!!$ crosscor(j,i)=sum/natvec(i)
!!$ END DO
!!$
!!$ END DO
!!$
!!$ END IF
! OPEN(file="atom",form="FORMATTED",unit=5898)
! WRITE(5898,'(I4)') nat
! CLOSE(5898)
OPEN(file="crosscor.dat",form="FORMATTED",unit=5897)
DO i=1,natom
DO j=1,natom
WRITE(5897,'(1X,I5,1X,I5,1X,G11.4)') resnum(i), resnum(j), crosscor(i,j)
END DO
WRITE(5897,'(1X)')
END DO
CLOSE(5897)
! DEALLOCATE(eigen)
DEALLOCATE(crosscor)
! DEALLOCATE(natvec)
END PROGRAM cross_cor
SUBROUTINE helptext(iunit)
IMPLICIT NONE
INTEGER :: iunit
WRITE(iunit,'(A)')" C R O S C O R "
WRITE(iunit,'(A)')" VERSION 1.0 "
WRITE(iunit,'(A)')" "
WRITE(iunit,'(A)')" Written by: "
WRITE(iunit,'(A)')" Tom Rodgers and David Burnell "
WRITE(iunit,'(A)')" "
WRITE(iunit,'(A)')"This program calculates the average residue cross correlation from an "
WRITE(iunit,'(A)')"eigenfacs formated file which can be produced from the included ENM "
WRITE(iunit,'(A)')"code, GNM code, or the GroAMED packages. "
WRITE(iunit,'(A)')" "
WRITE(iunit,'(A)')"The output file, crosscor.dat can be plotted in gnuplot with the command:"
WRITE(iunit,'(A)')'splot "crosscor.dat" using 1:2:3 notitle '
WRITE(iunit,'(A)')" "
WRITE(iunit,'(A)')" Usage: "
WRITE(iunit,'(A)')" cross_cor -i infile [-s startvec] "
WRITE(iunit,'(A)')" [-e endvec] [-d1] [-het] "
WRITE(iunit,'(A)')" "
WRITE(iunit,'(A)')"Option Type Value Description "
WRITE(iunit,'(A)')"------------------------------------------------------------ "
WRITE(iunit,'(A)')" -i Input First eigenvector file "
! WRITE(iunit,'(A)')" -pdb Input First eigenvector file "
WRITE(iunit,'(A)')" -s Input,Opt 7 First included eigenvector number "
WRITE(iunit,'(A)')" -e Input,Opt 31 Last included eigenvector number "
WRITE(iunit,'(A)')" -d1 Opt Allows 1d vectors with flag "
WRITE(iunit,'(A)')" -het Opt Incudes reading HETATM records with flag"
WRITE(iunit,'(A)')" "
END SUBROUTINE helptext
FUNCTION getoption(flag,getval,cvalue)
IMPLICIT NONE
CHARACTER(*) :: flag,cvalue
CHARACTER(160) :: arg
LOGICAL :: getoption,getval
INTEGER :: l,i,j
getoption=.false.
i=0
DO j=1,iargc()
CALL getarg(j,arg)
IF (arg.eq.flag) i=j
END DO
IF (i.gt.0) THEN
getoption=.true.
END IF
IF (getval) call getarg(i+1,cvalue)
END FUNCTION getoption