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
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
|
#!/bin/bash
. ../MasterTest.sh
CleanFiles for.in TRP.vec.dat TRP.rms.dat TRP.CA.dist.dat TRP.tocenter.dat \
nh.dat rms.nofit.dat last10.dat distance.dat nested.agr \
EndToEnd0.dat EndToEnd1.dat EndToEnd2.agr temp.*.dat \
DataOut.dat testset.dist.dat
TESTNAME='Loop tests'
Requires netcdf maxthreads 10
INPUT='-i for.in'
cat > for.in <<EOF
set FNAME= ../tz2.nc
parm ../tz2.parm7
trajin \$FNAME 1 10
for residues T inmask :TRP nvec=1;nvec++
vector v\$nvec \$T center out TRP.vec.dat
rms RMS\$T first \$T out TRP.rms.dat
for atoms A0 inmask @CA
distance d\$T\$A0 \$T \$A0 out TRP.CA.dist.dat
done
distance dcenter\$T \$T :1-12 out TRP.tocenter.dat
done
for atoms A0 inmask :2-4@N atoms A1 inmask :2-4@H
distance d\$A0\$A1 \$A0 \$A1 out nh.dat
done
rms :1-12&!@H=
for residues MyRes inmask :1-12 r=1;r++
rms R\$r \$MyRes&!@H= nofit out rms.nofit.dat
done
show
# Print info for the last 10 atoms. This tests using data set values
# as script variables and replacement of multiple script variables
# in a single argument.
set Natom = atoms inmask *
last10 = \$Natom - 10
show
atoms "@\$last10 - \$Natom" out last10.dat
run
EOF
RunCpptraj "$TESTNAME"
DoTest TRP.vec.dat.save TRP.vec.dat
DoTest TRP.rms.dat.save TRP.rms.dat
DoTest TRP.CA.dist.dat.save TRP.CA.dist.dat
DoTest TRP.tocenter.dat.save TRP.tocenter.dat
DoTest nh.dat.save nh.dat
DoTest rms.nofit.dat.save rms.nofit.dat
DoTest last10.dat.save last10.dat
UNITNAME='Test set command'
CheckFor maxthreads 10
if [ $? -eq 0 ] ; then
cat > for.in <<EOF
parm ../FtuFabI.NAD.TCL.parm7
trajin ../FtuFabI.NAD.TCL.nc
set NATOM = atoms inmask ^1
set NRES = residues inmask ^1
set NMOL = molecules inmask *
show
distance @1 @\$NATOM out testset.dist.dat
distance :1 :\$NRES out testset.dist.dat
distance ^1 ^\$NMOL out testset.dist.dat
EOF
RunCpptraj "$UNITNAME"
DoTest testset.dist.dat.save testset.dist.dat
fi
UNITNAME='Test reading comma-separated list of strings'
CheckFor maxthreads 4
if [ $? -eq 0 ] ; then
cat > for.in <<EOF
parm ../tz2.parm7
# Test reading in a comma-separated list of strings
clear trajin
for TRAJ in ../tz2.nc,../tz2.crd,../tz2.pdb,../tz2.rst7
trajin \$TRAJ lastframe
done
distance D1-12 :1 :12 out distance.dat
run
EOF
RunCpptraj "$UNITNAME"
DoTest distance.dat.save distance.dat
fi
UNITNAME='Test nested loops and variables in loops'
cat > for.in <<EOF
parm ../tz2.parm7
trajin ../tz2.nc
set maxval = 4
set maxval1 = 3
set val = 0
for i=1;i<\$maxval;i++ myval=0;myval+=10
startj = \$i + 1
for j=\$startj;j<=\$maxval1;j++
distance d\$i\$j @\$i @\$j out nested.agr
done
done
run
show
list
EOF
RunCpptraj "$UNITNAME"
DoTest nested.agr nested.agr.save
UNITNAME='Test loop over data set blocks'
CheckFor maxthreads 1
if [ $? -eq 0 ] ; then
cat > for.in <<EOF
parm ../tz2.parm7
starttraj = 1
endtraj = 10
offset = 10
for i=1;i<=10;i++
trajin ../tz2.nc \$starttraj \$endtraj
distance EndToEnd\$endtraj :1 :12
run
starttraj = \$starttraj + \$offset
endtraj = \$endtraj + \$offset
clear trajin
done
writedata EndToEnd0.dat EndToEnd*
trajin ../tz2.nc 1 100
distance EndToEndAll :1 :12
run
for DS datasetblocks EndToEndAll blocksize 10 i=1;i++
set WriteVars1 += " \$DS "
show DS WriteVars1
done
writedata EndToEnd1.dat \$WriteVars1
for ES datasetblocks EndToEndAll blocksize 10 firstblock 50 cumulative j=\$i;j++
set WriteVars2 += " \$ES "
show ES WriteVars2
done
writedata EndToEnd2.agr \$WriteVars2
list
EOF
RunCpptraj "$UNITNAME"
DoTest EndToEnd1.dat.save EndToEnd1.dat
DoTest EndToEnd2.agr.save EndToEnd2.agr
fi
UNITNAME='Test for filename wildcards and oversets'
CheckFor notos windows
if [ $? -eq 0 ] ; then
cat > for.in <<EOF
for FILE in distance.dat.save,last10.dat.save,doesnot*,TRP.*.dat.save
readdata \$FILE
done
for SET1 oversets TRP.rms.dat.save* SET2 oversets TRP.tocenter.dat.save* i=1;i++
show SET1 SET2
NewSet\$i = \$SET1 + \$SET2
set DataOut += " NewSet\$i "
done
writedata DataOut.dat \$DataOut
list datasets
EOF
RunCpptraj "$UNITNAME"
DoTest DataOut.dat.save DataOut.dat
fi
EndTest
exit 0
|
