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#!/bin/bash
. ../MasterTest.sh
CleanFiles pdb.in test.pdb tz2.pqr.gb.pdb tz2.pqr.parse.pdb \
tz2.pqr.vdw.pdb chainA.dat oresnum.dat tz2.plain.pdb \
2b5t.fromparm.pdb altloca.pdb tz2.het.pdb
INPUT="-i pdb.in"
TESTNAME='PDB format tests'
Requires maxthreads 1
# Test read/write of residue numbers, insertion / altloc codes, etc
Test1() {
UNITNAME='PDB format read/write test'
cat > pdb.in <<EOF
parm 2b5t.pdb noconect
resinfo ::A out chainA.dat
resinfo :;2 out oresnum.dat
trajin 2b5t.pdb
trajout test.pdb teradvance sg "P 1"
EOF
RunCpptraj "$UNITNAME"
DoTest test.pdb.save test.pdb
DoTest chainA.dat.save chainA.dat
DoTest oresnum.dat.save oresnum.dat
}
# Test writing PQR files with various radii options
Test2() {
UNITNAME='PQR file write with various radii'
CheckFor notparallel
if [ $? -eq 0 ] ; then
cat > pdb.in <<EOF
parm ../tz2.parm7
trajin ../tz2.rst7
trajout tz2.pqr.gb.pdb dumpq # GB radii
trajout tz2.pqr.parse.pdb parse # PARSE radii
trajout tz2.pqr.vdw.pdb dumpr* # VDW radii
# Test default chain ID write
trajout tz2.plain.pdb pdbres
trajout tz2.het.pdb conectmode het
EOF
RunCpptraj "$UNITNAME"
DoTest tz2.pqr.gb.pdb.save tz2.pqr.gb.pdb
DoTest tz2.pqr.parse.pdb.save tz2.pqr.parse.pdb
DoTest tz2.pqr.vdw.pdb.save tz2.pqr.vdw.pdb
DoTest tz2.plain.pdb.save tz2.plain.pdb
DoTest tz2.het.pdb.save tz2.het.pdb
fi
}
# Test filtering out alternate atom locations
Test3() {
UNITNAME='PDB filter alternate atom location IDs test'
cat > pdb.in <<EOF
parm 2b5t.pdb noconect keepaltloc A
trajin 2b5t.pdb keepaltloc A
strip !(:1-5)
trajout altloca.pdb teradvance sg "P 1"
EOF
RunCpptraj "$UNITNAME"
DoTest altloca.pdb.save altloca.pdb
}
# Test adding back PDB info
Test4() {
UNITNAME='Adding PDB info to topology'
cat > pdb.in <<EOF
parm 2b5t.segment.pdb
trajin 2b5t.segment.pdb
change oresnums of :1 min 186 max 186
change oresnums of :6 min 187 max 187
change icodes of :2-5 min A max D resnum 186
change chainid of :1-6 to B
trajout 2b5t.fromparm.pdb
EOF
RunCpptraj "$UNITNAME"
DoTest 2b5t.fromparm.pdb.save 2b5t.fromparm.pdb
}
Test1
Test2
Test3
Test4
EndTest
exit 0
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