added proper error message for improper experiment definition

Author: lmiq

input/inputfile.inp

@@ -12,7 +12,7 @@ endread ENDMDL  # Use this to stop reading atoms if this keyword is found (comme
 readatoms heavy # Which atoms to consider (all/heavy(no-H)/backbone/backplusCB)
 
 # Output directory for links (comment if you do not want the PDB files, that may be a lot)
-printlinks yes
+printlinks no
 linkdir ./links
 
 # What cross-links to compute (all/reactive/observed)

input/teste.inp

@@ -0,0 +1,98 @@
+#
+# TOPOLINK input file example
+#
+# L. Martinez - Institute of Chemistry, University of Campinas
+# http://leandro.iqm.unicamp.br
+#
+
+# PDB file (can be provided in the command line, overwriting this definition)
+pdbfile ./protein.pdb
+
+endread ENDMDL  # Use this to stop reading atoms if this keyword is found (comment otherwise)
+readatoms heavy # Which atoms to consider (all/heavy(no-H)/backbone/backplusCB)
+
+# Output directory for links (comment if you do not want the PDB files, that may be a lot)
+printlinks no
+linkdir ./links
+
+# What cross-links to compute (all/reactive/observed)
+
+compute observed
+#compute reactive
+#compute all
+
+# If only inter-domain (inter-chain) links are of interested, uncomment the following line
+#interchain
+
+# Only consider observed links with score greater than scorecut
+
+scorecut 0.d0
+
+# Cross-links observed:
+
+experiment 1,6-diaminohexane
+
+  # Possible types of cross-links and maximum distances
+  #        ResType  Chain  ResNum   AtomType    ResType  Chain  ResNum   AtomType  MaxDist 
+  linktype   GLU     all     all      CB          GLU     all     all       CB        15.1
+  linktype   GLU     all     all      CB          ASP     all     all       CB        14.3
+  linktype   ASP     all     all      CB          ASP     all     all       CB        13.5
+
+  observed GLU A 37  GLU A 53
+  observed ASP A 22  GLU A 4
+  observed ASP A 75  GLU A 86
+  observed GLU A 32  GLU A 53
+  observed GLU A 62  GLU A 86
+  observed ASP A 22  GLU A 13
+  observed ASP A 38  GLU A 53
+  observed ASP A 38  GLU A 46
+  observed GLU A 20  GLU A 13
+
+
+
+experiment Zero-length
+
+  # Possible types of cross-links and maximum distances
+  #        ResType  Chain  ResNum   AtomType    ResType  Chain  ResNum   AtomType  MaxDist 
+  linktype   ASP     all     all      CB          LYS     all     all       CB         9.7
+  linktype   GLU     all     all      CB          LYS     all     all       CB        10.5
+  linktype   GLU     all     all      CB          SER     all     all       CB         7.7
+  linktype   ASP     all     all      CB          SER     all     all       CB         7.0
+
+  observed SER A  71  GLU A 86
+  observed SER A 116  GLU A 111
+  observed GLU A  86  LYS A  99
+  observed SER A  71  ASP A 75
+  observed SER A 57   ASP A 75
+
+end experiment zerolength
+
+
+# Optional parameters 
+
+search_range 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
+
+pgood 0.70 # Probability of observing a link which is within link reach
+pbad  0.01 # Probability of observing a link which is NOT within linker reach
+
+vdwrad 3.         # Radius to be used for excluded atom volume computation
+print 0           # Extensive or concise printing
+printnotfound yes # Print data for pairs for which links were not found
+quitgood no       # Quit whenever a valid link is found (stop searching for shortest one)
+dbond 1.5         # Bond distance of link "atoms"
+kbond 10.         # Energy constant for link bonds
+kpath 10.         # Energy constant for the complete path distension, used for computing probability
+kvdw  2.          # Force constant of overlap function
+
+# Technical parameters for the optimization method
+
+ntrial 200  # Maximum number of trials for best link search
+nbest 5     # Number of times the same best link is found until satisfied
+maxfunc 50  # Maximum number of function evaluations of CG-Newton
+maxcg 20    # Maximum number of CG iterations
+seed random # Seed for random number generator (random or integer number)
+
+exit # You can add anything after this
+

src/topolink.f90

@@ -36,7 +36,7 @@ program topolink
   character(len=max_string_length), allocatable :: logline(:)
   character(len=20) :: floatout, intout, intout2
   character(len=13) :: statuschar
-  logical :: error, r1, r2, inexp, warning, interchain
+  logical :: error, r1, r2, inexp, warning, interchain, expstart
 
   external :: computef, computeg
 
@@ -132,6 +132,7 @@ program topolink
 
   nexp = 0
   error = .false.
+  expstart = .false.
   input : do 
     read(10,string_read,iostat=ioerr) record
     if ( ioerr /= 0 ) exit
@@ -163,8 +164,15 @@ program topolink
       case ("linktype") 
         cycle
       case ("experiment")
+        if ( expstart ) then
+          write(*,*) ' ERROR: New experiment defined without ending previous one. '
+          write(*,*) '        At line: ', trim(adjustl(record))
+          stop
+        end if
+        expstart = .true.
         nexp = nexp + 1
       case ("end")
+        expstart = .false.
         cycle
       case ("print")
         record = keyvalue(record,1)