Merge branch 'master' of https://gitlab.eps.surrey.ac.uk/mw00368/GromacsOnEUREKA

amp_stats.py

@@ -260,6 +260,21 @@ if args.dna_hydrogen_bonds is not None:
   mout.headerOut("Found "+mcol.result+str(len(dg_chainlist))+mcol.arg+" DG Residues")
   mout.headerOut("Found "+mcol.result+str(len(dc_chainlist))+mcol.arg+" DC Residues")
 
+  no_AT_pairs=False
+  no_GC_pairs=False
+
+  # Do some checks:
+  if len(da_chainlist) + len(dt_chainlist) + len(dg_chainlist) + len(dc_chainlist) < 2:
+    mout.errorOut("Less than two bases",fatal=True)
+  if len(da_chainlist) == 0 ^ len(dt_chainlist) == 0:
+    mout.warningOut("Not enough bases for AT pairs")
+    no_AT_pairs=True
+  if len(dg_chainlist) == 0 ^ len(dc_chainlist) == 0:
+    mout.warningOut("Not enough bases for GC pairs")
+    no_GC_pairs=True
+  if no_AT_pairs and no_GC_pairs:
+    mout.errorOut("No matching base pairs",fatal=True)
+
   # read in the first image of the pdb
   mout.out("Reading timestep into Atoms object...")
   atoms = amp.read(infile,index="0",printScript=False,verbosity=0)

gmx_funcs.sh

@@ -27,6 +27,7 @@ function finishUp {
     mkdir ${SLURM_SUBMIT_DIR}/${SLURM_JOBID}_${SLURM_JOB_NAME}
     cp -r * ${SLURM_SUBMIT_DIR}/${SLURM_JOBID}_${SLURM_JOB_NAME}/
     mv ${SLURM_SUBMIT_DIR}/${SLURM_JOBID}_${SLURM_JOB_NAME}.? ${SLURM_SUBMIT_DIR}/${SLURM_JOBID}_${SLURM_JOB_NAME}/
+    rm -rf "/users/mw00368/parallel_scratch/"${SLURM_JOBID}_${SLURM_JOB_NAME}/
     exit $1
   fi
 }