X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Freadrtns.F;h=6b59d69374adb84fd4bc34735694dcc46fa943dd;hb=96d29f8250d30733e8a1f624f918388ef4f4050f;hp=74ba3d8a94e4b0c5287d73b717467f32843dc05b;hpb=b1ac4ec5292a0d8ddcc3ad64e27a5ab3a4febe39;p=unres.git

diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index 74ba3d8..6b59d69 100644
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -2581,6 +2581,7 @@ c      call flush(iout)
       call readi(controlcard,"NPAIR",npair_,0)
       call readi(controlcard,"NDIST",ndist_,0)
       call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
+      call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
       call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
       call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
       call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
@@ -2761,6 +2762,16 @@ c Alternative: reading from input
  
       call readi(controlcard,"HOMOL_NSET",homol_nset,1)       
       read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
+      start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0)
+      if(.not.read2sigma.and.start_from_model) then
+          write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA'
+          start_from_model=.false.
+      endif
+      if(start_from_model) write(iout,*) 'START_FROM_MODELS is ON'
+      if(start_from_model .and. rest) then 
+        write(iout,*) 'START_FROM_MODELS is OFF'
+        write(iout,*) 'remove restart keyword from input'
+      endif
       if (homol_nset.gt.1)then
          call card_concat(controlcard)
          read(controlcard,*) (waga_homology(i),i=1,homol_nset) 
@@ -2857,8 +2868,8 @@ c         write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
      &                                idomain_tmp
              i_tmp=i_tmp+nnt-1
              idomain(k,i_tmp)=idomain_tmp
-             rescore(k,i_tmp)=0.5d0*(rescore_tmp+0.5d0)
-             rescore2(k,i_tmp)=0.5d0*(rescore2_tmp+0.5d0)
+             rescore(k,i_tmp)=rescore_tmp
+             rescore2(k,i_tmp)=rescore2_tmp
             else
              idomain(k,irec)=1
              read (ientin,*,end=1401) rescore_tmp
@@ -2875,8 +2886,15 @@ c           write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
           do i = nnt,nct-2 
             do j=i+2,nct 
 
-            if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0) then
-                  
+              x12=c(1,i)-c(1,j)
+              y12=c(2,i)-c(2,j)
+              z12=c(3,i)-c(3,j)
+              distal=dsqrt(x12*x12+y12*y12+z12*z12) 
+
+
+            if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+     &            .and. distal.le.dist2_cut ) then
+
               ii=ii+1
               ii_in_use(ii)=1
               l_homo(k,ii)=.true.
@@ -2886,13 +2904,6 @@ c             write (iout,*) "i",i," j",j," constr_homology",
 c    &                       constr_homology
               ires_homo(ii)=i
               jres_homo(ii)=j
-c
-c Attempt to replace dist(i,j) by its definition in ...
-c
-              x12=c(1,i)-c(1,j)
-              y12=c(2,i)-c(2,j)
-              z12=c(3,i)-c(3,j)
-              distal=dsqrt(x12*x12+y12*y12+z12*z12)
               odl(k,ii)=distal
               if (read2sigma) then
                 sigma_odl(k,ii)=0
@@ -2904,30 +2915,18 @@ c
      &        sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
               else
                 if (odl(k,ii).le.dist_cut) then
-                 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j) ! other exprs possible
-c                sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)
+                 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j) 
                 else
 #ifdef OLDSIGMA
-                 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error 
+                 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* 
      &                      dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
 #else
-                 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error 
+                 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* 
      &                      dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
 #endif
                 endif
               endif
-c   Following expr replaced by a positive exp argument
-c             sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
-c    &                      dexp(-0.5d0*(odl(k,ii)/dist_cut)**2)
-
-c             sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)*
-c    &                      dexp(-0.5d0*(odl(k,ii)/dist_cut)**2)
-c
-              sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii)) ! rescore ~ error
-c             sigma_odl(k,ii)=sigma_odl(k,ii)*sigma_odl(k,ii)
-c
-c             sigma_odl(k,ii)=sigma_odl_temp(i,j,k)* ! new var read from file (?)
-c    &                        sigma_odl_temp(i,j,k)  ! not inverse because of use of res. similarity
+              sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii)) 
             else
               ii=ii+1
               l_homo(k,ii)=.false.