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Merge branch 'release-2018-fda' into release-2019-fda
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@BerndDoser
BerndDoser committed Apr 29, 2020
2 parents 3a1d750 + 0547b4b commit 9936923
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Showing 6 changed files with 204 additions and 220 deletions.
14 changes: 8 additions & 6 deletions src/gromacs/gmxana/fda/Graph.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -84,17 +84,19 @@ void Graph::updateCoordinates(rvec *coord, int *index, int isize)
if (iterFind == indices_.end()) gmx_fatal(FARGS, "Error in insertPDBInfo.");
int pos = std::distance(indices_.begin(), iterFind);

nodes_[pos].x_ = coord[index[i]][0];
nodes_[pos].y_ = coord[index[i]][1];
nodes_[pos].z_ = coord[index[i]][2];
/// Values will be converted from nm into Angstrom.
nodes_[pos].x_ = coord[index[i]][0] * 10.0;
nodes_[pos].y_ = coord[index[i]][1] * 10.0;
nodes_[pos].z_ = coord[index[i]][2] * 10.0;
}
// atomic-based
} else {
for (size_t i = 0; i != indices_.size(); ++i)
{
nodes_[i].x_ = coord[indices_[i]][0];
nodes_[i].y_ = coord[indices_[i]][1];
nodes_[i].z_ = coord[indices_[i]][2];
/// Values will be converted from nm into Angstrom.
nodes_[i].x_ = coord[indices_[i]][0] * 10.0;
nodes_[i].y_ = coord[indices_[i]][1] * 10.0;
nodes_[i].z_ = coord[indices_[i]][2] * 10.0;
}
}
}
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88 changes: 44 additions & 44 deletions src/gromacs/gmxana/fda/tests/data/glycine_trimer/FDAGraphTest.ref6.pdb
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Original file line number Diff line number Diff line change
@@ -1,77 +1,77 @@
ATOM 1 0 0.317 0.205 -0.060 1.001054.83 AA
ATOM 2 1 -0.218 0.398 0.015 1.001054.83 AA
ATOM 3 1 -0.218 0.398 0.015 1.002056.08 AA
ATOM 4 2 -0.052 -0.041 -0.011 1.002056.08 AA
ATOM 1 0 3.170 2.050 -0.600 1.001054.83 AA
ATOM 2 1 -2.180 3.980 0.150 1.001054.83 AA
ATOM 3 1 -2.180 3.980 0.150 1.002056.08 AA
ATOM 4 2 -0.520 -0.410 -0.110 1.002056.08 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.206 -0.060 1.001048.76 AA
ATOM 2 1 -0.218 0.398 0.015 1.001048.76 AA
ATOM 3 1 -0.218 0.398 0.015 1.002069.92 AA
ATOM 4 2 -0.052 -0.042 -0.011 1.002069.92 AA
ATOM 1 0 3.171 2.059 -0.603 1.001048.76 AA
ATOM 2 1 -2.181 3.976 0.153 1.001048.76 AA
ATOM 3 1 -2.181 3.976 0.153 1.002069.92 AA
ATOM 4 2 -0.522 -0.418 -0.107 1.002069.92 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.207 -0.060 1.001046.82 AA
ATOM 2 1 -0.218 0.397 0.016 1.001046.82 AA
ATOM 3 1 -0.218 0.397 0.016 1.002072.41 AA
ATOM 4 2 -0.052 -0.042 -0.010 1.002072.41 AA
ATOM 1 0 3.170 2.069 -0.604 1.001046.82 AA
ATOM 2 1 -2.181 3.971 0.158 1.001046.82 AA
ATOM 3 1 -2.181 3.971 0.158 1.002072.41 AA
ATOM 4 2 -0.522 -0.425 -0.102 1.002072.41 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.208 -0.060 1.001046.88 AA
ATOM 2 1 -0.218 0.397 0.016 1.001046.88 AA
ATOM 3 1 -0.218 0.397 0.016 1.002061.24 AA
ATOM 4 2 -0.052 -0.043 -0.010 1.002061.24 AA
ATOM 1 0 3.169 2.080 -0.603 1.001046.88 AA
ATOM 2 1 -2.181 3.966 0.163 1.001046.88 AA
ATOM 3 1 -2.181 3.966 0.163 1.002061.24 AA
ATOM 4 2 -0.523 -0.430 -0.097 1.002061.24 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.209 -0.060 1.001047.06 AA
ATOM 2 1 -0.218 0.396 0.017 1.001047.06 AA
ATOM 3 1 -0.218 0.396 0.017 1.002041.35 AA
ATOM 4 2 -0.052 -0.043 -0.009 1.002041.35 AA
ATOM 1 0 3.168 2.090 -0.601 1.001047.06 AA
ATOM 2 1 -2.180 3.962 0.167 1.001047.06 AA
ATOM 3 1 -2.180 3.962 0.167 1.002041.35 AA
ATOM 4 2 -0.523 -0.433 -0.094 1.002041.35 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.210 -0.060 1.001046.26 AA
ATOM 2 1 -0.218 0.396 0.017 1.001046.26 AA
ATOM 3 1 -0.218 0.396 0.017 1.002023.51 AA
ATOM 4 2 -0.053 -0.044 -0.009 1.002023.51 AA
ATOM 1 0 3.168 2.099 -0.599 1.001046.26 AA
ATOM 2 1 -2.179 3.959 0.170 1.001046.26 AA
ATOM 3 1 -2.179 3.959 0.170 1.002023.51 AA
ATOM 4 2 -0.525 -0.435 -0.092 1.002023.51 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.211 -0.060 1.001045.06 AA
ATOM 2 1 -0.218 0.396 0.017 1.001045.06 AA
ATOM 3 1 -0.218 0.396 0.017 1.002019.26 AA
ATOM 4 2 -0.053 -0.044 -0.009 1.002019.26 AA
ATOM 1 0 3.170 2.107 -0.598 1.001045.06 AA
ATOM 2 1 -2.177 3.958 0.171 1.001045.06 AA
ATOM 3 1 -2.177 3.958 0.171 1.002019.26 AA
ATOM 4 2 -0.528 -0.437 -0.093 1.002019.26 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.211 -0.060 1.001045.67 AA
ATOM 2 1 -0.217 0.396 0.017 1.001045.67 AA
ATOM 3 1 -0.217 0.396 0.017 1.002037.09 AA
ATOM 4 2 -0.053 -0.044 -0.010 1.002037.09 AA
ATOM 1 0 3.174 2.113 -0.598 1.001045.67 AA
ATOM 2 1 -2.175 3.959 0.171 1.001045.67 AA
ATOM 3 1 -2.175 3.959 0.171 1.002037.09 AA
ATOM 4 2 -0.533 -0.440 -0.096 1.002037.09 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.318 0.212 -0.060 1.001051.13 AA
ATOM 2 1 -0.217 0.396 0.017 1.001051.13 AA
ATOM 3 1 -0.217 0.396 0.017 1.002081.11 AA
ATOM 4 2 -0.054 -0.044 -0.010 1.002081.11 AA
ATOM 1 0 3.180 2.118 -0.598 1.001051.13 AA
ATOM 2 1 -2.171 3.961 0.172 1.001051.13 AA
ATOM 3 1 -2.171 3.961 0.172 1.002081.11 AA
ATOM 4 2 -0.538 -0.443 -0.099 1.002081.11 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.319 0.212 -0.060 1.001064.38 AA
ATOM 2 1 -0.217 0.396 0.017 1.001064.38 AA
ATOM 3 1 -0.217 0.396 0.017 1.002151.30 AA
ATOM 4 2 -0.054 -0.045 -0.010 1.002151.30 AA
ATOM 1 0 3.187 2.123 -0.596 1.001064.38 AA
ATOM 2 1 -2.167 3.962 0.173 1.001064.38 AA
ATOM 3 1 -2.167 3.962 0.173 1.002151.30 AA
ATOM 4 2 -0.544 -0.447 -0.102 1.002151.30 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.320 0.213 -0.059 1.001087.35 AA
ATOM 2 1 -0.216 0.396 0.018 1.001087.35 AA
ATOM 3 1 -0.216 0.396 0.018 1.002242.89 AA
ATOM 4 2 -0.055 -0.045 -0.010 1.002242.89 AA
ATOM 1 0 3.195 2.128 -0.593 1.001087.35 AA
ATOM 2 1 -2.162 3.962 0.177 1.001087.35 AA
ATOM 3 1 -2.162 3.962 0.177 1.002242.89 AA
ATOM 4 2 -0.550 -0.452 -0.102 1.002242.89 AA
CONECT 1 2
CONECT 3 4
ENDMDL
88 changes: 44 additions & 44 deletions src/gromacs/gmxana/fda/tests/data/glycine_trimer_binary/FDAGraphTest.ref6.pdb
View file
Original file line number Diff line number Diff line change
@@ -1,77 +1,77 @@
ATOM 1 0 0.317 0.205 -0.060 1.001054.83 AA
ATOM 2 1 -0.218 0.398 0.015 1.001054.83 AA
ATOM 3 1 -0.218 0.398 0.015 1.002056.08 AA
ATOM 4 2 -0.052 -0.041 -0.011 1.002056.08 AA
ATOM 1 0 3.170 2.050 -0.600 1.001054.83 AA
ATOM 2 1 -2.180 3.980 0.150 1.001054.83 AA
ATOM 3 1 -2.180 3.980 0.150 1.002056.08 AA
ATOM 4 2 -0.520 -0.410 -0.110 1.002056.08 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.206 -0.060 1.001048.76 AA
ATOM 2 1 -0.218 0.398 0.015 1.001048.76 AA
ATOM 3 1 -0.218 0.398 0.015 1.002069.92 AA
ATOM 4 2 -0.052 -0.042 -0.011 1.002069.92 AA
ATOM 1 0 3.171 2.059 -0.603 1.001048.76 AA
ATOM 2 1 -2.181 3.976 0.153 1.001048.76 AA
ATOM 3 1 -2.181 3.976 0.153 1.002069.92 AA
ATOM 4 2 -0.522 -0.418 -0.107 1.002069.92 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.207 -0.060 1.001046.82 AA
ATOM 2 1 -0.218 0.397 0.016 1.001046.82 AA
ATOM 3 1 -0.218 0.397 0.016 1.002072.41 AA
ATOM 4 2 -0.052 -0.042 -0.010 1.002072.41 AA
ATOM 1 0 3.170 2.069 -0.604 1.001046.82 AA
ATOM 2 1 -2.181 3.971 0.158 1.001046.82 AA
ATOM 3 1 -2.181 3.971 0.158 1.002072.41 AA
ATOM 4 2 -0.522 -0.425 -0.102 1.002072.41 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.208 -0.060 1.001046.88 AA
ATOM 2 1 -0.218 0.397 0.016 1.001046.88 AA
ATOM 3 1 -0.218 0.397 0.016 1.002061.24 AA
ATOM 4 2 -0.052 -0.043 -0.010 1.002061.24 AA
ATOM 1 0 3.169 2.080 -0.603 1.001046.88 AA
ATOM 2 1 -2.181 3.966 0.163 1.001046.88 AA
ATOM 3 1 -2.181 3.966 0.163 1.002061.24 AA
ATOM 4 2 -0.523 -0.430 -0.097 1.002061.24 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.209 -0.060 1.001047.06 AA
ATOM 2 1 -0.218 0.396 0.017 1.001047.06 AA
ATOM 3 1 -0.218 0.396 0.017 1.002041.35 AA
ATOM 4 2 -0.052 -0.043 -0.009 1.002041.35 AA
ATOM 1 0 3.168 2.090 -0.601 1.001047.06 AA
ATOM 2 1 -2.180 3.962 0.167 1.001047.06 AA
ATOM 3 1 -2.180 3.962 0.167 1.002041.35 AA
ATOM 4 2 -0.523 -0.433 -0.094 1.002041.35 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.210 -0.060 1.001046.26 AA
ATOM 2 1 -0.218 0.396 0.017 1.001046.26 AA
ATOM 3 1 -0.218 0.396 0.017 1.002023.51 AA
ATOM 4 2 -0.053 -0.044 -0.009 1.002023.51 AA
ATOM 1 0 3.168 2.099 -0.599 1.001046.26 AA
ATOM 2 1 -2.179 3.959 0.170 1.001046.26 AA
ATOM 3 1 -2.179 3.959 0.170 1.002023.51 AA
ATOM 4 2 -0.525 -0.435 -0.092 1.002023.51 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.211 -0.060 1.001045.06 AA
ATOM 2 1 -0.218 0.396 0.017 1.001045.06 AA
ATOM 3 1 -0.218 0.396 0.017 1.002019.26 AA
ATOM 4 2 -0.053 -0.044 -0.009 1.002019.26 AA
ATOM 1 0 3.170 2.107 -0.598 1.001045.06 AA
ATOM 2 1 -2.177 3.958 0.171 1.001045.06 AA
ATOM 3 1 -2.177 3.958 0.171 1.002019.26 AA
ATOM 4 2 -0.528 -0.437 -0.093 1.002019.26 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.317 0.211 -0.060 1.001045.67 AA
ATOM 2 1 -0.217 0.396 0.017 1.001045.67 AA
ATOM 3 1 -0.217 0.396 0.017 1.002037.09 AA
ATOM 4 2 -0.053 -0.044 -0.010 1.002037.09 AA
ATOM 1 0 3.174 2.113 -0.598 1.001045.67 AA
ATOM 2 1 -2.175 3.959 0.171 1.001045.67 AA
ATOM 3 1 -2.175 3.959 0.171 1.002037.09 AA
ATOM 4 2 -0.533 -0.440 -0.096 1.002037.09 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.318 0.212 -0.060 1.001051.13 AA
ATOM 2 1 -0.217 0.396 0.017 1.001051.13 AA
ATOM 3 1 -0.217 0.396 0.017 1.002081.11 AA
ATOM 4 2 -0.054 -0.044 -0.010 1.002081.11 AA
ATOM 1 0 3.180 2.118 -0.598 1.001051.13 AA
ATOM 2 1 -2.171 3.961 0.172 1.001051.13 AA
ATOM 3 1 -2.171 3.961 0.172 1.002081.11 AA
ATOM 4 2 -0.538 -0.443 -0.099 1.002081.11 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.319 0.212 -0.060 1.001064.38 AA
ATOM 2 1 -0.217 0.396 0.017 1.001064.38 AA
ATOM 3 1 -0.217 0.396 0.017 1.002151.30 AA
ATOM 4 2 -0.054 -0.045 -0.010 1.002151.30 AA
ATOM 1 0 3.187 2.123 -0.596 1.001064.38 AA
ATOM 2 1 -2.167 3.962 0.173 1.001064.38 AA
ATOM 3 1 -2.167 3.962 0.173 1.002151.30 AA
ATOM 4 2 -0.544 -0.447 -0.102 1.002151.30 AA
CONECT 1 2
CONECT 3 4
ENDMDL
ATOM 1 0 0.320 0.213 -0.059 1.001087.35 AA
ATOM 2 1 -0.216 0.396 0.018 1.001087.35 AA
ATOM 3 1 -0.216 0.396 0.018 1.002242.89 AA
ATOM 4 2 -0.055 -0.045 -0.010 1.002242.89 AA
ATOM 1 0 3.195 2.128 -0.593 1.001087.35 AA
ATOM 2 1 -2.162 3.962 0.177 1.001087.35 AA
ATOM 3 1 -2.162 3.962 0.177 1.002242.89 AA
ATOM 4 2 -0.550 -0.452 -0.102 1.002242.89 AA
CONECT 1 2
CONECT 3 4
ENDMDL
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