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
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
|
#!/bin/bash
. ../MasterTest.sh
# Clean
CleanFiles rms.in rmsd.dat rms.mass.in rmsd.mass.dat rms.reftraj.in \
rmsd.reftraj.dat tz2.norotate.crd tz2.rotate.crd rmatrices.dat \
rmsd.refcoords.dat rms.dat NoMod.dat NoMod.crd.save NoMod.crd \
vecs.dat Previous.dat distances.agr
TESTNAME='RMSD tests'
Requires netcdf
# Test rmsd, mass-weighted rmsd, rmsd to reference traj.
UNITNAME='Basic RMSD tests'
CheckFor maxthreads 10
if [ $? -eq 0 ] ; then
TOP='../tz2.truncoct.parm7'
INPUT='rms.in'
cat > rms.in <<EOF
noprogress
trajin ../tz2.truncoct.nc
rms Res2-11 first :2-11 out rmsd.dat
rms Res2-11_mass first :2-11 out rmsd.mass.dat mass \
savevectors combined vecsout vecs.dat
rms Res2_11_traj reftraj ../tz2.truncoct.nc :2-11 out rmsd.reftraj.dat
run
removedata Res2_11_traj
loadtraj ../tz2.truncoct.nc name TZ2
rms Res2_11_traj reftraj TZ2 :2-11 out rmsd.refcoords.dat
EOF
RunCpptraj "$UNITNAME"
DoTest rmsd.dat.save rmsd.dat
DoTest rmsd.mass.dat.save rmsd.mass.dat
DoTest vecs.dat.save vecs.dat -a 0.000001
DoTest rmsd.reftraj.dat.save rmsd.reftraj.dat
DoTest rmsd.reftraj.dat.save rmsd.refcoords.dat
fi
# Test RMS rotate/norotate, generation of rotation matrices
UNITNAME='RMS coordinate rotation/rotation matrices test'
CheckFor maxthreads 10
if [ $? -eq 0 ] ; then
TOP=''
INPUT='-i rms.in'
cat > rms.in <<EOF
parm ../tz2.parm7 [NOWAT]
reference ../tz2.nc parm [NOWAT] 1 [first]
parm ../tz2.truncoct.parm7 [WAT]
trajin ../tz2.truncoct.nc parm [WAT]
strip :WAT
rms NOROT ref [first] norotate @CA
outtraj tz2.norotate.crd parm [WAT]
rms ROT ref [first] out rms.dat @CA savematrices matricesout rmatrices.dat
outtraj tz2.rotate.crd parm [WAT]
EOF
RunCpptraj "$UNITNAME"
DoTest tz2.norotate.crd.save tz2.norotate.crd
DoTest tz2.rotate.crd.save tz2.rotate.crd
DoTest rmatrices.dat.save rmatrices.dat
fi
# Test RMS nomod
TOP=''
INPUT="-i rms.in"
cat > rms.in <<EOF
parm ../tz2.parm7
trajin ../tz2.nc
outtraj NoMod.crd.save
rms First_CA :2-12@CA out NoMod.dat nomod
trajout NoMod.crd
EOF
RunCpptraj "RMS fit with no coordinates modification test."
DoTest NoMod.dat.save NoMod.dat
DoTest NoMod.crd.save NoMod.crd
# Test RMS 'previous'
UNITNAME='RMS fit to previous test'
CheckFor notparallel
if [ $? -eq 0 ] ; then
TOP=''
INPUT='-i rms.in'
cat > rms.in <<EOF
parm ../tz2.parm7
trajin ../tz2.nc
rms ToPrevious :2-12@CA previous out Previous.dat
EOF
RunCpptraj "$UNITNAME"
DoTest Previous.dat.save Previous.dat
fi
# Test imaging after unit cell rotation
UNITNAME='RMS: imaging after unit cell rotation'
TOP='-p ../tz2.ortho.parm7'
INPUT='-i rms.in'
cat > rms.in <<EOF
noprogress
trajin ../tz2.ortho.nc
rms :1-13 first
distance NoImage :559 :1412 noimage out distances.agr
distance Image :559 :1412 out distances.agr
run
EOF
RunCpptraj "$UNITNAME"
DoTest distances.agr.save distances.agr
EndTest
exit 0
|
