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Merge branch 'release-2019-fda' into release-2020-fda
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@BerndDoser
BerndDoser committed Sep 1, 2020
2 parents 52ff53c + a87bc97 commit 458e0b9
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Showing 11 changed files with 205 additions and 306 deletions.
16 changes: 0 additions & 16 deletions .vscode/extensions.json
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@@ -1,26 +1,10 @@
{
<<<<<<< HEAD
"recommendations": [
"eamodio.gitlens",
"kriegalex.vscode-cudacpp",
"ms-python.python",
"ms-vscode.cmake-tools",
"ms-vscode.cpptools",
"twxs.cmake"
=======
// See https://go.microsoft.com/fwlink/?LinkId=827846 to learn about workspace recommendations.
// Extension identifier format: ${publisher}.${name}. Example: vscode.csharp

// List of extensions which should be recommended for users of this workspace.
"recommendations": [
"kriegalex.vscode-cudacpp",
"ms-vscode.cmake-tools",
"ms-vscode.cpptools",
"twxs.cmake"
],
// List of extensions recommended by VS Code that should not be recommended for users of this workspace.
"unwantedRecommendations": [

>>>>>>> release-2019-fda
]
}
10 changes: 0 additions & 10 deletions .vscode/launch.json
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Expand Up @@ -5,17 +5,10 @@
"version": "0.2.0",
"configurations": [
{
<<<<<<< HEAD
"name": "(gdb) fda-integration-tests",
"type": "cppdbg",
"request": "launch",
"program": "${workspaceFolder}/build/bin/fda-integration-tests",
=======
"name": "(gdb) Launch",
"type": "cppdbg",
"request": "launch",
"program": "enter program name, for example ${workspaceFolder}/a.out",
>>>>>>> release-2019-fda
"args": [],
"stopAtEntry": false,
"cwd": "${workspaceFolder}",
Expand All @@ -30,7 +23,6 @@
}
]
},
<<<<<<< HEAD
{
"name": "(gdb) fda-graph-test",
"type": "cppdbg",
Expand All @@ -50,7 +42,5 @@
}
]
}
=======
>>>>>>> release-2019-fda
]
}
12 changes: 0 additions & 12 deletions .vscode/settings.json
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@@ -1,17 +1,11 @@
{
<<<<<<< HEAD
"cmake.configureSettings": {
=======
"cmake.configureSettings":
{
>>>>>>> release-2019-fda
"GMX_BUILD_OWN_FFTW": "ON",
"GMX_BUILD_MDRUN_ONLY": "OFF",
"GMX_BUILD_FDA": "ON",
"GMX_DEFAULT_SUFFIX": "OFF",
"GMX_BINARY_SUFFIX": "_fda",
"GMX_SIMD": "NONE",
<<<<<<< HEAD
"GMX_BUILD_UNITTESTS": "ON",
"BOOST_ROOT": "~/.conan/data/boost/1.72.0/_/_/package/f419497daccab81a781a793e5fffd7f228cf234e"
},
Expand Down Expand Up @@ -90,9 +84,3 @@
"filesystem": "cpp"
}
}
=======
"GMX_BUILD_UNITTESTS": "ON"
},
"cmake.generator": "Unix Makefiles"
}
>>>>>>> release-2019-fda
16 changes: 9 additions & 7 deletions src/gromacs/gmxana/fda/Graph.cpp
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Expand Up @@ -81,20 +81,22 @@ void Graph::updateCoordinates(rvec *coord, int *index, int isize)
for (int i = 0; i != isize; ++i)
{
iterFind = std::find(indices_.begin(), indices_.end(), i);
if (iterFind == indices_.end()) gmx_fatal(FARGS, "Error in insertPDBInfo.");
if (iterFind == indices_.end()) continue;
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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110 changes: 44 additions & 66 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
@@ -1,109 +1,87 @@
ATOM 1 0 0.317 0.205 -0.060 1.00635.44 AA
ATOM 2 1 -0.218 0.398 0.015 1.00635.44 AA
ATOM 3 0 0.317 0.205 -0.060 1.00583.03 AA
ATOM 4 2 -0.052 -0.041 -0.011 1.00583.03 AA
ATOM 5 1 -0.218 0.398 0.015 1.001238.60 AA
ATOM 6 2 -0.052 -0.041 -0.011 1.001238.60 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.317 0.206 -0.060 1.00631.78 AA
ATOM 2 1 -0.218 0.398 0.015 1.00631.78 AA
ATOM 3 0 0.317 0.206 -0.060 1.00583.73 AA
ATOM 4 2 -0.052 -0.042 -0.011 1.00583.73 AA
ATOM 5 1 -0.218 0.398 0.015 1.001246.94 AA
ATOM 6 2 -0.052 -0.042 -0.011 1.001246.94 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.317 0.207 -0.060 1.00630.61 AA
ATOM 2 1 -0.218 0.397 0.016 1.00630.61 AA
ATOM 3 0 0.317 0.207 -0.060 1.00585.65 AA
ATOM 4 2 -0.052 -0.042 -0.010 1.00585.65 AA
ATOM 5 1 -0.218 0.397 0.016 1.001248.44 AA
ATOM 6 2 -0.052 -0.042 -0.010 1.001248.44 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.317 0.208 -0.060 1.00630.65 AA
ATOM 2 1 -0.218 0.397 0.016 1.00630.65 AA
ATOM 3 0 0.317 0.208 -0.060 1.00587.74 AA
ATOM 4 2 -0.052 -0.043 -0.010 1.00587.74 AA
ATOM 5 1 -0.218 0.397 0.016 1.001241.71 AA
ATOM 6 2 -0.052 -0.043 -0.010 1.001241.71 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.317 0.209 -0.060 1.00630.76 AA
ATOM 2 1 -0.218 0.396 0.017 1.00630.76 AA
ATOM 3 0 0.317 0.209 -0.060 1.00587.83 AA
ATOM 4 2 -0.052 -0.043 -0.009 1.00587.83 AA
ATOM 5 1 -0.218 0.396 0.017 1.001229.73 AA
ATOM 6 2 -0.052 -0.043 -0.009 1.001229.73 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.317 0.210 -0.060 1.00630.28 AA
ATOM 2 1 -0.218 0.396 0.017 1.00630.28 AA
ATOM 3 0 0.317 0.210 -0.060 1.00583.41 AA
ATOM 4 2 -0.053 -0.044 -0.009 1.00583.41 AA
ATOM 5 1 -0.218 0.396 0.017 1.001218.98 AA
ATOM 6 2 -0.053 -0.044 -0.009 1.001218.98 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.317 0.211 -0.060 1.00629.56 AA
ATOM 2 1 -0.218 0.396 0.017 1.00629.56 AA
ATOM 3 0 0.317 0.211 -0.060 1.00573.48 AA
ATOM 4 2 -0.053 -0.044 -0.009 1.00573.48 AA
ATOM 5 1 -0.218 0.396 0.017 1.001216.42 AA
ATOM 6 2 -0.053 -0.044 -0.009 1.001216.42 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.317 0.211 -0.060 1.00629.92 AA
ATOM 2 1 -0.217 0.396 0.017 1.00629.92 AA
ATOM 3 0 0.317 0.211 -0.060 1.00559.74 AA
ATOM 4 2 -0.053 -0.044 -0.010 1.00559.74 AA
ATOM 5 1 -0.217 0.396 0.017 1.001227.16 AA
ATOM 6 2 -0.053 -0.044 -0.010 1.001227.16 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.318 0.212 -0.060 1.00633.21 AA
ATOM 2 1 -0.217 0.396 0.017 1.00633.21 AA
ATOM 3 0 0.318 0.212 -0.060 1.00545.50 AA
ATOM 4 2 -0.054 -0.044 -0.010 1.00545.50 AA
ATOM 5 1 -0.217 0.396 0.017 1.001253.68 AA
ATOM 6 2 -0.054 -0.044 -0.010 1.001253.68 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.319 0.212 -0.060 1.00641.19 AA
ATOM 2 1 -0.217 0.396 0.017 1.00641.19 AA
ATOM 3 0 0.319 0.212 -0.060 1.00534.01 AA
ATOM 4 2 -0.054 -0.045 -0.010 1.00534.01 AA
ATOM 5 1 -0.217 0.396 0.017 1.001295.97 AA
ATOM 6 2 -0.054 -0.045 -0.010 1.001295.97 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
CONECT 5 6
ENDMDL
ATOM 1 0 0.320 0.213 -0.059 1.00655.03 AA
ATOM 2 1 -0.216 0.396 0.018 1.00655.03 AA
ATOM 3 0 0.320 0.213 -0.059 1.00527.23 AA
ATOM 4 2 -0.055 -0.045 -0.010 1.00527.23 AA
ATOM 5 1 -0.216 0.396 0.018 1.001351.14 AA
ATOM 6 2 -0.055 -0.045 -0.010 1.001351.14 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
CONECT 5 6
Expand Down
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