changed search_range for search_limit, and added the corresponding options

Author: lmiq

input/inputfile.inp

@@ -97,7 +97,7 @@ end experiment DSS
 
 # Optional parameters 
 
-search_range 1.5  # Search for topological distances of up to search_range*dmaxlink
+search_limit relative 1.5  # Search for topological distances of up to search_range*dmaxlink
 
 printallfound no  # Prints, or not, the structure of the links that were found but violate the distances
 

src/inputoptions.f90

@@ -18,7 +18,8 @@ module inputoptions
   double precision :: pgood
   double precision :: pbad
   double precision :: scorecut
-  double precision :: search_range
+  double precision :: search_limit
+  integer :: search_limit_type
 
   character(len=max_string_length) :: pdbfile
   character(len=max_string_length) :: readlog

src/printdata.f90

@@ -75,19 +75,14 @@ subroutine printdata(print,link)
     ib = 9 - len(trim(adjustl(chardist)))
     chardist(ib:ib) = " "
 
-  ! Otherwise, report that it is greater than dsearch, or than the 
-  ! the euclidean distance, if this one is greater still
-
   else
-    if ( link%status == 3 ) then 
-      write(chardist,"( f9.3 )") link%euclidean
-      ib = 9 - len(trim(adjustl(chardist)))
-      chardist(ib:ib) = ">"
-    else
-      write(chardist,"( f9.3 )") link%dsearch
-      ib = 9 - len(trim(adjustl(chardist)))
-      chardist(ib:ib) = ">"
-    end if
+
+  ! Otherwise, report that it is greater than dsearch, or than 
+  ! the euclidean distance, the one which is greater
+
+    write(chardist,"( f9.3 )") max(link%dsearch,link%euclidean)
+    ib = 9 - len(trim(adjustl(chardist)))
+    chardist(ib:ib) = ">"
   end if
 
   ra1 = "Y" ; if ( .not. link%atom1%residue%accessible ) ra1 = "N"

src/topolink.f90

@@ -86,7 +86,8 @@ program topolink
   printaccessible = .false.
   warning = .false.
   interchain = .false.
-  search_range = 1.5
+  search_limit = 1.5
+  search_limit_type = 1
 
   ! Format of output
   floatout="(tr1,a,f12.7)"
@@ -201,9 +202,20 @@ program topolink
         if ( keyvalue(record,1) == 'observed' ) compute = 1
         if ( keyvalue(record,1) == 'reactive' ) compute = 2
         if ( keyvalue(record,1) == 'all' ) compute = 3
-      case ("search_range") 
-        record = keyvalue(record,1)
-        read(record,*) search_range
+      case ("search_limit") 
+        if ( keyvalue(record,1) == 'relative' ) then
+          search_limit_type = 1
+        else if ( keyvalue(record,1) == 'sum' ) then
+          search_limit_type = 2
+        else if ( keyvalue(record,1) == 'fixed' ) then
+          search_limit_type = 3
+        else
+          write(*,*) ' ERROR: search_limit must be relative, sum, or fixed. '
+          write(*,*) '        Default: search_limit relative 1.5 '
+          stop
+        end if
+        record = keyvalue(record,2)
+        read(record,*) search_limit
       case ("pgood") 
         record = keyvalue(record,1)
         read(record,*) pgood
@@ -1092,7 +1104,13 @@ program topolink
       if ( link(i)%exp(iexp)%obs_reactive ) link(i)%obs_reactive = .true.
       if ( link(i)%exp(iexp)%type_reactive ) link(i)%type_reactive = .true.
     end do
-    link(i)%dsearch = search_range*link(i)%dmaxlink
+    if ( search_limit_type == 1 ) then
+      link(i)%dsearch = search_limit*link(i)%dmaxlink
+    else if ( search_limit_type == 2 ) then
+      link(i)%dsearch = search_limit + link(i)%dmaxlink
+    else if ( search_limit_type == 3 ) then
+      link(i)%dsearch = search_limit
+    end if
     link(i)%nbeads = int(link(i)%dsearch/dbond)+1
     link(i)%topodist = -1.d0
     nmax = max(nmax,link(i)%nbeads)