multichain cluster can select number of clusters instead of cutoff

diff --git a/source/cluster/wham/src-M/COMMON.CLUSTER b/source/cluster/wham/src-M/COMMON.CLUSTER
index 4fedc52..a82948d 100644 (file)
--- a/source/cluster/wham/src-M/COMMON.CLUSTER
+++ b/source/cluster/wham/src-M/COMMON.CLUSTER
@@ -4,11 +4,11 @@
       real*4 diss,allcart
       double precision enetb,entfac,totfree,energy,rmstb
       integer ncut,ngr,licz,nconf,iass,icc,mult,list_conf,
-     &  nss_all,ihpb_all,jhpb_all,iass_tot,iscore,nprop
+     &  nss_all,ihpb_all,jhpb_all,iass_tot,iscore,nprop,nclust
       common /clu/ diss(maxdist),energy(0:maxconf),
      &  enetb(max_ene,maxconf),ecut,
      &  entfac(maxconf),totfree(0:maxconf),totfree_gr(maxgr),
-     &  rcutoff(max_cut+1),ncut,min_var,tree,plot_tree,lgrp
+     &  rcutoff(max_cut+1),ncut,nclust,min_var,tree,plot_tree,lgrp
       common /clu1/ ngr,licz(maxgr),nconf(maxgr,maxingr),iass(maxgr),
      &  iass_tot(maxgr,max_cut),list_conf(maxconf)
       common /alles/ allcart(3,maxres2,maxconf),rmstb(maxconf),

diff --git a/source/cluster/wham/src-M/main_clust.F b/source/cluster/wham/src-M/main_clust.F
index a3f8094..9835c01 100644 (file)
--- a/source/cluster/wham/src-M/main_clust.F
+++ b/source/cluster/wham/src-M/main_clust.F
@@ -23,7 +23,7 @@ C
       logical printang(max_cut)
       integer printpdb(max_cut)
       integer printmol2(max_cut)
-      character*240 lineh
+      character*240 lineh,scrachdir2d
       REAL CRIT(maxconf),MEMBR(maxconf)
       REAL CRITVAL(maxconf-1)
       INTEGER IA(maxconf),IB(maxconf)
@@ -34,12 +34,13 @@ C
       DIMENSION NN(maxconf),DISNN(maxconf)
       LOGICAL FLAG(maxconf)
       integer i,j,k,l,m,n,len,lev,idum,ii,ind,ioffset,jj,icut,ncon,
-     & it,ncon_work,ind1,kkk, ijk
+     & it,ncon_work,ind1,kkk, ijk,is,ie,ilen
       double precision t1,t2,tcpu,difconf
       
       double precision varia(maxvar)
       double precision hrtime,mintime,sectime
       logical eof
+      external ilen
 #ifdef MPI
       call MPI_Init( IERROR )
       call MPI_Comm_rank( MPI_COMM_WORLD, me, IERROR )
@@ -79,6 +80,12 @@ c      write (iout,*) "after permut"
 c      call flush(iout)
       print *,'MAIN: nnt=',nnt,' nct=',nct
 
+      if (nclust.gt.0) then
+        PRINTANG(1)=.TRUE.
+        PRINTPDB(1)=outpdb
+        printmol2(1)=outmol2
+        ncut=0
+      else
       DO I=1,NCUT
         PRINTANG(I)=.FALSE.
         PRINTPDB(I)=0
@@ -90,12 +97,21 @@ c      call flush(iout)
           printmol2(i)=outmol2
         ENDIF
       ENDDO
+      endif
+      if (ncut.gt.0) then
       write (iout,*) 'Number of cutoffs:',NCUT
       write (iout,*) 'Cutoff values:'
       DO ICUT=1,NCUT
         WRITE(IOUT,'(8HRCUTOFF(,I2,2H)=,F8.1,2i2)')ICUT,RCUTOFF(ICUT),
      &    printpdb(icut),printmol2(icut)
       ENDDO
+      else if (nclust.gt.0) then
+      write (iout,'("Number of clusters requested",i5)') nclust
+      else
+      if (me.eq.Master)
+     & write (iout,*) "ERROR: Either nclust or ncut must be >0"
+      stop
+      endif
       DO I=1,NRES-3  
         MULT(I)=1
       ENDDO
@@ -180,7 +196,8 @@ c          write (iout,'(2i4,i10,f10.5)') i,j,ind,DISS(IND)
      &     scount(0),idispl(0),MPI_REAL,Master,MPI_COMM_WORLD, IERROR)
       if (me.eq.master) then
 #endif
-      open(80,file='/tmp/distance',form='unformatted')
+      scrachdir2d=scratchdir(:ilen(scratchdir))//'distance'
+      open(80,file=scrachdir2d,form='unformatted')
       do i=1,ndis
         write(80) diss(i)
       enddo
@@ -253,29 +270,39 @@ C
       CALL HCASS(N,IA,IB,CRIT,LEV,ICLASS,HVALS,IORDER,CRITVAL,HEIGHT)
 c      CALL HCDEN(LEV,IORDER,HEIGHT,CRITVAL)
 
+c 3/3/16 AL: added explicit number of cluters
+      if (nclust.gt.0) then
+        is=nclust-1
+        ie=nclust-1
+        icut=1
+      else
+        is=1
+        ie=lev-1
+      endif
       do i=1,maxgr
         licz(i)=0
       enddo
       icut=1
-      i=1
-      NGR=i+1
+      i=is
+      NGR=is+1
       do j=1,n
         licz(iclass(j,i))=licz(iclass(j,i))+1
         nconf(iclass(j,i),licz(iclass(j,i)))=j
 c        write (iout,*) i,j,iclass(j,i),licz(iclass(j,i)),
 c     &    nconf(iclass(j,i),licz(iclass(j,i)))
       enddo        
-      do i=1,lev-1
-
+c      do i=1,lev-1
+      do i=is,ie
          idum=lev-i
          DO L=1,LEV
             IF (HEIGHT(L).EQ.IDUM) GOTO 190
          ENDDO
  190     IDUM=L
-         write(IOUT,*) "i+1",i+1," idum",idum," critval",CRITVAL(IDUM),
-     &    " icut",icut," cutoff",rcutoff(icut)
-         IF (CRITVAL(IDUM).LT. RCUTOFF(ICUT)) THEN
-          WRITE (iout,'(/a,f10.5)') 'AT CUTOFF:',rcutoff(icut)
+c         write(IOUT,*) "i+1",i+1," idum",idum," critval",CRITVAL(IDUM),
+c     &    " icut",icut," cutoff",rcutoff(icut)
+         IF (nclust.gt.0.or.CRITVAL(IDUM).LT. RCUTOFF(ICUT)) THEN
+         if (nclust.le.0) 
+     &    WRITE (iout,'(/a,f10.5)') 'AT CUTOFF:',rcutoff(icut)
           write (iout,'(a,f8.2)') 'Maximum distance found:',
      &              CRITVAL(IDUM)
           CALL SRTCLUST(ICUT,ncon_work,iT)
@@ -288,9 +315,10 @@ c     &    nconf(iclass(j,i),licz(iclass(j,i)))
          do l=1,maxgr
           licz(l)=0
          enddo
+         ii=i-is+1
          do j=1,n
-          licz(iclass(j,i))=licz(iclass(j,i))+1
-          nconf(iclass(j,i),licz(iclass(j,i)))=j
+          licz(iclass(j,ii))=licz(iclass(j,ii))+1
+          nconf(iclass(j,ii),licz(iclass(j,ii)))=j
 c        write (iout,*) i,j,iclass(j,i),licz(iclass(j,i)),
 c     &    nconf(iclass(j,i),licz(iclass(j,i)))
 cd          print *,j,iclass(j,i),

diff --git a/source/cluster/wham/src-M/readrtns.F b/source/cluster/wham/src-M/readrtns.F
index ae8f8a8..a3feaa5 100644 (file)
--- a/source/cluster/wham/src-M/readrtns.F
+++ b/source/cluster/wham/src-M/readrtns.F
@@ -91,7 +91,8 @@ C long axis of side chain
       min_var=(index(controlcard,'MINVAR').gt.0)
       plot_tree=(index(controlcard,'PLOT_TREE').gt.0)
       punch_dist=(index(controlcard,'PUNCH_DIST').gt.0)
-      call readi(controlcard,'NCUT',ncut,1)
+      call readi(controlcard,'NCUT',ncut,0)
+      call readi(controlcard,'NCLUST',nclust,5)
       call readi(controlcard,'SYM',symetr,1)
       write (iout,*) 'sym', symetr
       call readi(controlcard,'NSTART',nstart,0)
@@ -102,7 +103,8 @@ C long axis of side chain
       lgrp=(index(controlcard,'LGRP').gt.0)
       caonly=(index(controlcard,'CA_ONLY').gt.0)
       print_dist=(index(controlcard,'PRINT_DIST').gt.0)
-      call multreada(controlcard,'CUTOFF',rcutoff,ncut,-1.0d0)
+      if (ncut.gt.0) 
+     & call multreada(controlcard,'CUTOFF',rcutoff,ncut,-1.0d0)
       call readi(controlcard,'IOPT',iopt,2) 
       lside = index(controlcard,"SIDE").gt.0
       efree = index(controlcard,"EFREE").gt.0

diff --git a/source/cluster/wham/src-M/wrtclust.f b/source/cluster/wham/src-M/wrtclust.f
index f2f3eb7..917d4f3 100644 (file)
--- a/source/cluster/wham/src-M/wrtclust.f
+++ b/source/cluster/wham/src-M/wrtclust.f
@@ -84,12 +84,14 @@ C 12/8/93 Estimation of "diameters" of the subsequent families.
       ave_dim=0.0
       amax_dim=0.0
 c      write (iout,*) "ecut",ecut
+      emin=totfree(nconf(igr,1))
+c      write (2,*) "emin",emin," ecut",ecut
       do i=2,licz(igr)
         ii=nconf(igr,i)
         if (totfree(ii)-emin .gt. ecut) goto 10
         do j=1,i-1
           jj=nconf(igr,j)
-          if (jj.eq.1) exit
+c          if (jj.eq.1) exit
           if (ii.lt.jj) then
             ind=ioffset(ncon,ii,jj)
           else
@@ -112,9 +114,12 @@ c     &      list_conf(jj),curr_dist
      & '; average distance in the family:',ave_dim 
       rmsave(igr)=0.0d0
       qpart=0.0d0
+      emin=totfree(nconf(igr,1))
       do i=1,licz(igr)
         icon=nconf(igr,i)
-        boltz=dexp(-totfree(icon))
+        boltz=dexp(-totfree(icon)+emin)
+c        write (2,*) "igr",igr," i",i," icon",icon," totfree",
+c     &     totfree(icon)," emin",emin," boltz",boltz," rms",rmstb(icon)
         rmsave(igr)=rmsave(igr)+boltz*rmstb(icon)
         qpart=qpart+boltz
       enddo
@@ -191,8 +196,8 @@ c Write conformations of the family i to PDB files
 c            write (iout,*) i,ncon_out,nconf(i,ncon_out),
 c     &        totfree(nconf(i,ncon_out)),emin1,ecut
           enddo
-          write (iout,*) "ncon_out",ncon_out
-          call flush(iout)
+c          write (iout,*) "ncon_out",ncon_out
+c          call flush(iout)
           do j=1,nres
             tempfac(1,j)=5.0d0
             tempfac(2,j)=5.0d0
@@ -263,9 +268,9 @@ c create InsightII command file for their displaying in different colors
   200 FORMAT (/'FAMILY ',I4,' WITH TOTAL FREE ENERGY',1pE15.5,
      & ' CONTAINS ',I4,' CONFORMATION(S): ')
 c 300 FORMAT ( 8(I4,F6.1))
-  300 FORMAT (5(I4,1pe12.3))
+  300 FORMAT (5(I6,1pe12.3))
   400 FORMAT (//'ASSIGNMENT OF CONSECUTIVE CONFORMATIONS TO FAMILIES:')
-  500 FORMAT (8(2I4,2X)) 
+  500 FORMAT (8(I6,I4,2X)) 
   600 FORMAT ('REMARK FAMILY',I4,' CONFORMATION',I4,' ENERGY ',E15.6)
       RETURN
       END