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
|
#!/bin/bash
. ../MasterTest.sh
CleanFiles nc.in nc.hp1.ca.dat nc.hp2.ca.dat nc.all.res.dat cmap.dat \
native.cmap.gnu nonnative.cmap.gnu native.resmap.gnu nonnative.resmap.gnu \
nc1.pdb nc2.contacts.dat nc2.res.dat NC2.series.dat \
nc4.dat nc4.nn.dat nc4.res.dat nc4.contacts.dat nc4.nn.pdb \
NC5.series.dat NC5.respresent.dat NC5.nnseries.dat NC6.ressum.dat \
nc7.dat
TESTNAME='Nativecontacts tests'
Requires netcdf
INPUT="-i nc.in"
cat > nc.in <<EOF
parm ../DPDP.parm7
trajin ../DPDP.nc
reference ../DPDP.nc 1
nativecontacts name NC1 :1-12@CA out nc.hp1.ca.dat mindist maxdist \
map mapout cmap.gnu contactpdb nc1.pdb
nativecontacts name NC2 :10-14@CA :17-21@CA out nc.hp2.ca.dat mindist maxdist \
writecontacts nc2.contacts.dat resout nc2.res.dat \
series seriesout NC2.series.dat
nativecontacts name NC3 :1-21&!@H= byresidue out nc.all.res.dat mindist maxdist \
distance 3.0 reference map mapout resmap.gnu
EOF
RunCpptraj "NativeContacts test."
DoTest nc.hp1.ca.dat.save nc.hp1.ca.dat
DoTest nc1.pdb.save nc1.pdb
DoTest nc.hp2.ca.dat.save nc.hp2.ca.dat
DoTest nc2.contacts.dat.save nc2.contacts.dat
DoTest nc2.res.dat.save nc2.res.dat
DoTest NC2.series.dat.save NC2.series.dat
DoTest nc.all.res.dat.save nc.all.res.dat
DoTest native.resmap.gnu.save native.resmap.gnu
DoTest nonnative.resmap.gnu.save nonnative.resmap.gnu
UNITNAME='NativeContacts test, save non-native contacts, residue time series'
CheckFor notparallel
if [ $? -eq 0 ] ; then
cat > nc.in <<EOF
parm ../DPDP.parm7
trajin ../DPDP.nc
reference ../DPDP.nc 1
nativecontacts name NC4 :1-21@CA out nc4.dat savenonnative series \
reference seriesnnout nc4.nn.dat resout nc4.res.dat \
writecontacts nc4.contacts.dat \
nncontactpdb nc4.nn.pdb
nativecontacts name NC5 :10-11@CA,N :18-20@CA,N series savenonnative \
resseries present resseriesout NC5.respresent.dat
nativecontacts name NC6 :10-11@CA,N :18-20@CA,N series savenonnative \
resseries sum resseriesout NC6.ressum.dat
EOF
RunCpptraj "$UNITNAME"
DoTest nc4.dat.save nc4.dat
DoTest nc4.nn.dat.save nc4.nn.dat
DoTest nc4.res.dat.save nc4.res.dat
DoTest nc4.contacts.dat.save nc4.contacts.dat
DoTest nc4.nn.pdb.save nc4.nn.pdb
DoTest NC5.respresent.dat.save NC5.respresent.dat
DoTest NC6.ressum.dat.save NC6.ressum.dat
fi
UNITNAME='NativeContacts test, orthorhombic imaging.'
CheckFor maxthreads 2
if [ $? -eq 0 ] ; then
cat > nc.in <<EOF
parm ../dna30.parm7
trajin ../Test_AutoImage/split.duplex.nc
reference ../Test_AutoImage/split.duplex.nc 1
nativecontacts name NC7 @N= @O= out nc7.dat distance 3.0
EOF
RunCpptraj "$UNITNAME"
DoTest nc7.dat.save nc7.dat
fi
EndTest
exit 0
|
