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#!/bin/bash
. ../MasterTest.sh
# Clean
CleanFiles atommap.in initial.mol2 atommap.dat reordered.pdb reordered.mol2 \
fit.mol2 rmsd.dat map.chm_to_amb.dat mapped.pdb.? rmsout.dat \
map.byres.chm_to_amb.dat
TESTNAME='Atom map tests'
Requires maxthreads 3
INPUT="-i atommap.in"
UNITNAME='Basic atommap test'
CheckFor maxthreads 1
if [ $? -eq 0 ] ; then
# Test 1
cat > atommap.in <<EOF
noprogress
parm xtallig.mol2
reference xtallig.mol2
parm start.mol2
reference start.mol2 parmindex 1
outtraj initial.mol2 mol2
# xtallig -> start
atommap xtallig.mol2 start.mol2 mapout atommap.dat
trajin xtallig.mol2
outtraj reordered.pdb pdb chainid X model
outtraj reordered.mol2 mol2
rms 1g9v refindex 1 out rmsd.dat
trajout fit.mol2 mol2
EOF
RunCpptraj "AtomMap Test"
DoTest initial.mol2.save initial.mol2
DoTest atommap.dat.save atommap.dat
DoTest reordered.pdb.save reordered.pdb
DoTest reordered.mol2.save reordered.mol2
DoTest rmsd.dat.save rmsd.dat
DoTest fit.mol2.save fit.mol2
fi
# Test 2
UNITNAME="AtomMap with 'rmsfit'"
CheckFor maxthreads 2
if [ $? -eq 0 ] ; then
cat > atommap.in <<EOF
parm xtallig.mol2
reference xtallig.mol2
parm start.mol2
reference start.mol2 parm start.mol2
atommap xtallig.mol2 start.mol2 rmsfit rmsout rmsout.dat 1g9v
trajin xtallig.mol2
EOF
RunCpptraj "AtomMap with 'rmsfit'"
DoTest rmsd.dat.save rmsout.dat
fi
# Test 3
UNITNAME='Atom map charmm->amber atom order'
CheckFor maxthreads 3
if [ $? -eq 0 ] ; then
cat > atommap.in <<EOF
parm cg-amb.topo
reference cg-amb.crds
parm cg-chm.topo
reference cg-chm.crds parmindex 1
atommap cg-amb.crds cg-chm.crds mapout map.chm_to_amb.dat
trajin cg.crd
trajout mapped.pdb pdb multi
EOF
RunCpptraj "Atom map charmm->amber atom order"
DoTest map.chm_to_amb.dat.save map.chm_to_amb.dat
# Test 4
cat > atommap.in <<EOF
parm cg-amb.topo
reference cg-amb.crds
parm cg-chm.topo
reference cg-chm.crds parmindex 1
atommap cg-amb.crds cg-chm.crds mapout map.byres.chm_to_amb.dat maponly mode byres
EOF
RunCpptraj "Atom map charmm->amber atom order, by residue"
DoTest map.chm_to_amb.dat.save map.byres.chm_to_amb.dat
fi
EndTest
exit 0
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