1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
|
#!/bin/bash
. ../MasterTest.sh
CleanFiles ms.in pp2.rst7 hairpin.rst7 dihedrals.dat dihedrals?.dat fromref.rst7 fromref.pdb.1
INPUT="-i ms.in"
TESTNAME='Make structure tests'
Requires maxthreads 1
# Tests
MS1() {
UNITNAME='Basic makestructure test'
CheckFor netcdf
if [ $? -eq 0 ] ; then
cat > ms.in <<EOF
parm ../tz2.parm7
trajin ../tz2.nc 1 1
# Tests SS arg
makestructure pp2:1-13
outtraj pp2.rst7 time0 1.0
# Tests SS arg and custom turn arg
makestructure extended:1,12 custom1:2-5:-80.0:130.0:-130.0:140.0 typeI':6-7 custom2:8-11:-140.0:170.0:-100.0:140.0
multidihedral phi psi resrange 1-13 out dihedrals.dat
# Tests custom dih arg and custom ss arg
makestructure customdih:5:phi:90 custom:6,7:-70:60
multidihedral phi psi resrange 5-7 out dihedrals2.dat
# Test custom dih definition
makestructure chi1:8:N:CA:CB:CG:35
dihedral chi1 :8@N :8@CA :8@CB :8@CG out dihedrals3.dat
EOF
RunCpptraj "$UNITNAME"
DoTest pp2.rst7.save pp2.rst7
DoTest dihedrals.dat.save dihedrals.dat -a 0.00001
DoTest dihedrals2.dat.save dihedrals2.dat
DoTest dihedrals3.dat.save dihedrals3.dat
fi
}
Ref() {
# Test SS from reference
cat > ms.in <<EOF
parm ../tz2.parm7
reference ../tz2.rst7
trajin pp2.rst7.save
makestructure "ref:1-13:tz2.rst7"
rmsd reference
trajout fromref.pdb multi chainid ' '
EOF
RunCpptraj "Makestructure test with reference."
#DoTest ../tz2.rst7 fromref.rst7
DoTest fromref.pdb.save fromref.pdb.1
}
MS1
Ref
EndTest
exit 0
|
