Merge pull request #50 from HITS-MBM/issue-48

Issue 48: fix residue coordinates by aligning index group
HITS-MBM · May 16, 2023 · c359ccf · c359ccf
2 parents 100f8e5 + 8154f45
commit c359ccf
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Showing 17 changed files with 1,295 additions and 111 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -10,17 +10,18 @@
     },
     "runArgs": ["--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined"],
 
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": [
-                "ms-vscode.cpptools",
-                "ms-vscode.cmake-tools"
-            ]
-        }
-    },
+	// Configure tool-specific properties.
+	"customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"ms-vscode.cpptools",
+				"ms-vscode.cmake-tools",
+				"DavidSchuldenfrei.gtest-adapter"
+			]
+		}
+	},
 
     // Use 'forwardPorts' to make a list of ports inside the container available locally.
     // "forwardPorts": [],

diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -28,7 +28,7 @@
             "type": "cppdbg",
             "request": "launch",
             "program": "${workspaceFolder}/build/bin/fda-graph-test",
-            "args": [],
+            "args": ["--gtest_filter=AllFDAGraphTests/FDAGraphTest.text/8"],
             "stopAtEntry": false,
             "cwd": "${workspaceFolder}",
             "environment": [],

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -87,5 +87,31 @@
         "numbers": "cpp",
         "semaphore": "cpp",
         "stop_token": "cpp"
-    }
+    },
+    "editor.tokenColorCustomizations": {
+        "textMateRules": [
+            {
+                "scope": "googletest.failed",
+                "settings": {
+                    "foreground": "#f00"
+                }
+            },
+            {
+                "scope": "googletest.passed",
+                "settings": {
+                    "foreground": "#0f0"
+                }
+            },
+            {
+                "scope": "googletest.run",
+                "settings": {
+                    "foreground": "#0f0"
+                }
+            }
+        ]
+    },
+    "gtest-adapter.debugConfig": [
+        "(gdb) fda-graph-test"
+    ],
+    "gtest-adapter.supportLocation": false
 }
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -4,6 +4,7 @@ pipeline {
 
   agent {
     dockerfile {
+      label 'docker-gpu-host'
       filename 'devel/Dockerfile'
     }
   }

diff --git a/src/gromacs/gmxana/fda/tests/CMakeLists.txt b/src/gromacs/gmxana/fda/tests/CMakeLists.txt
@@ -8,6 +8,7 @@ gmx_add_gtest_executable(
     FDAGraphTest.cpp
     FDAShortestPathTest.cpp
     FDAViewStressTest.cpp
+    GraphTest.cpp
     PDBTest.cpp
 )
 

diff --git a/src/gromacs/gmxana/fda/tests/FDAGraphTest.cpp b/src/gromacs/gmxana/fda/tests/FDAGraphTest.cpp
@@ -118,15 +118,15 @@ TEST_P(FDAGraphTest, binary)
 }
 
 INSTANTIATE_TEST_CASE_P(AllFDAGraphTests, FDAGraphTest, ::testing::Values(
-    TestDataStructure(
+    TestDataStructure( // 0
         "maxime_all_prot",
         {"-i", "cap0_all_prot.pfr", "-diff", "cap1_all_prot.pfr", "-s", "1G6N.pdb",
          "-n", "index.ndx", "-frame", "0", "-t", "100", "-min", "2", "-convert"},
         "C-alpha",
         "result.pdb",
         "FDAGraphTest.ref0.pdb"
     ),
-    TestDataStructure(
+    TestDataStructure( // 1
         "maxime_all_prot",
         {"-i", "cap0_all_prot.pfr", "-diff", "cap1_all_prot.pfr", "-s", "1G6N.pdb",
          "-n", "index.ndx", "-frame", "0", "-t", "20", "-min", "2", "-convert"},
@@ -141,21 +141,21 @@ INSTANTIATE_TEST_CASE_P(AllFDAGraphTests, FDAGraphTest, ::testing::Values(
         "result.pdb",
         "FDAGraphTest.ref2.pdb"
     ),
-    TestDataStructure(
+    TestDataStructure( // 3
         "alagly",
         {"-i", "fda.pfa", "-s", "conf.gro", "-frame", "all", "-t", "1000", "-pymol", "result.pml"},
         "",
         "result.pdb",
         "FDAGraphTest.ref3.pdb"
     ),
-    TestDataStructure(
+    TestDataStructure( // 4
         "alagly",
         {"-i", "fda.pfa", "-s", "conf.gro", "-frame", "skip 3", "-t", "1000", "-pymol", "result.pml"},
         "",
         "result.pdb",
         "FDAGraphTest.ref4.pdb"
     ),
-    TestDataStructure(
+    TestDataStructure( // 5
         "alagly",
         {"-i", "fda.pfa", "-s", "conf.gro", "-frame", "average 3", "-t", "1000", "-pymol", "result.pml"},
         "",
@@ -169,13 +169,20 @@ INSTANTIATE_TEST_CASE_P(AllFDAGraphTests, FDAGraphTest, ::testing::Values(
         "result.pdb",
         "FDAGraphTest.ref6.pdb"
     ),
-    TestDataStructure(
+    TestDataStructure( // 7
         "maxime_all_prot",
         {"-i", "cap0_all_prot.pfr", "-diff", "cap1_all_prot.pfr", "-s", "1G6N.pdb",
          "-n", "index.ndx", "-frame", "0", "-t", "100", "-min", "4", "-convert", "-big"},
         "C-alpha",
         "result.pdb",
         "FDAGraphTest.ref7.pdb"
+    ),
+    TestDataStructure( // 8
+        "alagly",
+        {"-i", "fda.pfr", "-s", "conf.gro", "-n", "index.ndx", "-frame", "0"},
+        "C-alpha",
+        "result.pdb",
+        "FDAGraphTest.ref8.pdb"
     )
 ));
 

diff --git a/src/gromacs/gmxana/fda/tests/GraphTest.cpp b/src/gromacs/gmxana/fda/tests/GraphTest.cpp
@@ -0,0 +1,36 @@
+/*
+ * GraphTest.cpp
+ *
+ *  Created on: Oct 17, 2022
+ *      Author: Bernd Doser, HITS gGmbH <[email protected]>
+ */
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <gtest/gtest.h>
+#include "gromacs/gmxana/fda/Graph.h"
+#include "testutils/cmdlinetest.h"
+
+using namespace fda_analysis;
+
+//! Test fixture for FDA
+class GraphTest : public gmx::test::CommandLineTestBase
+{};
+
+TEST_F(GraphTest, empty)
+{
+    Graph graph;
+}
+
+TEST_F(GraphTest, residue)
+{
+    std::vector<double> forceMatrix{1.0, 1.0, 1.0, 1.0};
+    rvec coord_traj[3] = {{1.0, 1.1, 1.2}, {2.0, 2.1, 2.2}, {3.0, 3.1, 3.2}};
+    int index[2] = {0, 1};
+    int isize = 2;
+
+    Graph graph(forceMatrix, coord_traj, index, isize);
+
+    std::cout << graph << std::endl;
+}
diff --git a/src/gromacs/gmxana/fda/tests/data/alagly/FDAGraphTest.ref8.pdb b/src/gromacs/gmxana/fda/tests/data/alagly/FDAGraphTest.ref8.pdb
@@ -0,0 +1,4 @@
+ATOM      1              2      -0.000   0.060  -0.490  1.003437.44      AA
+ATOM      2              3       3.700   0.320  -1.170  1.003437.44      AA
+CONECT    1    2
+ENDMDL
diff --git a/src/gromacs/gmxana/fda/tests/data/alagly/index.ndx b/src/gromacs/gmxana/fda/tests/data/alagly/index.ndx
@@ -1,46 +1,22 @@
-[ all ]
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-17
-18
-19
-20
-
-[ ala ]
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-
-[ gly ]
-13
-14
-15
-16
-17
-18
-19
-20
-
+[ System ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+  16   17   18   19   20
+[ Protein ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+  16   17   18   19   20
+[ Protein-H ]
+   1    5    7   11   12   13   15   18   19   20
+[ C-alpha ]
+   1    1    5   15
+[ Backbone ]
+   1    5   11   13   15   18
+[ MainChain ]
+   1    5   11   12   13   15   18   19   20
+[ MainChain+Cb ]
+   1    5    7   11   12   13   15   18   19   20
+[ MainChain+H ]
+   1    2    3    4    5   11   12   13   14   15   18   19   20
+[ SideChain ]
+   6    7    8    9   10   16   17
+[ SideChain-H ]
+   7
diff --git a/src/gromacs/gmxana/fda/tests/data/alagly/result.pdb b/src/gromacs/gmxana/fda/tests/data/alagly/result.pdb
@@ -0,0 +1,41 @@
+ATOM      1              2      -0.410  -1.740  -1.310  1.003437.44      AA
+ATOM      2              3      -0.410  -1.740   0.330  1.003437.44      AA
+CONECT    1    2
+ENDMDL
+ATOM      1              2      -0.414  -1.736  -1.304  1.003012.43      AA
+ATOM      2              3      -0.358  -1.713   0.330  1.003012.43      AA
+CONECT    1    2
+ENDMDL
+ATOM      1              2      -0.415  -1.736  -1.301  1.002642.37      AA
+ATOM      2              3      -0.306  -1.687   0.331  1.002642.37      AA
+CONECT    1    2
+ENDMDL
+ATOM      1              2      -0.412  -1.739  -1.304  1.001851.51      AA
+ATOM      2              3      -0.255  -1.664   0.332  1.001851.51      AA
+CONECT    1    2
+ENDMDL
+ENDMDL
+ATOM      1              2      -0.398  -1.752  -1.316  1.001287.64      AA
+ATOM      2              3      -0.175  -1.620   0.323  1.001287.64      AA
+CONECT    1    2
+ENDMDL
+ATOM      1              2      -0.391  -1.758  -1.321  1.002612.83      AA
+ATOM      2              3      -0.151  -1.599   0.311  1.002612.83      AA
+CONECT    1    2
+ENDMDL
+ATOM      1              2      -0.384  -1.762  -1.322  1.003843.68      AA
+ATOM      2              3      -0.136  -1.581   0.296  1.003843.68      AA
+CONECT    1    2
+ENDMDL
+ATOM      1              2      -0.380  -1.761  -1.318  1.004795.50      AA
+ATOM      2              3      -0.131  -1.566   0.281  1.004795.50      AA
+CONECT    1    2
+ENDMDL
+ATOM      1              2      -0.378  -1.758  -1.310  1.005377.95      AA
+ATOM      2              3      -0.131  -1.558   0.270  1.005377.95      AA
+CONECT    1    2
+ENDMDL
+ATOM      1              2      -0.377  -1.754  -1.301  1.005551.85      AA
+ATOM      2              3      -0.133  -1.557   0.266  1.005551.85      AA
+CONECT    1    2
+ENDMDL
diff --git a/src/gromacs/gmxana/fda/tests/data/alagly_binary/FDAGraphTest.ref8.pdb b/src/gromacs/gmxana/fda/tests/data/alagly_binary/FDAGraphTest.ref8.pdb
@@ -0,0 +1,4 @@
+ATOM      1              2      -0.000   0.060  -0.490  1.003437.44      AA
+ATOM      2              3       3.700   0.320  -1.170  1.003437.44      AA
+CONECT    1    2
+ENDMDL
diff --git a/src/gromacs/gmxana/fda/tests/data/alagly_binary/index.ndx b/src/gromacs/gmxana/fda/tests/data/alagly_binary/index.ndx
@@ -1,46 +1,22 @@
-[ all ]
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-17
-18
-19
-20
-
-[ ala ]
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-
-[ gly ]
-13
-14
-15
-16
-17
-18
-19
-20
-
+[ System ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+  16   17   18   19   20
+[ Protein ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+  16   17   18   19   20
+[ Protein-H ]
+   1    5    7   11   12   13   15   18   19   20
+[ C-alpha ]
+   1    1    5   15
+[ Backbone ]
+   1    5   11   13   15   18
+[ MainChain ]
+   1    5   11   12   13   15   18   19   20
+[ MainChain+Cb ]
+   1    5    7   11   12   13   15   18   19   20
+[ MainChain+H ]
+   1    2    3    4    5   11   12   13   14   15   18   19   20
+[ SideChain ]
+   6    7    8    9   10   16   17
+[ SideChain-H ]
+   7
diff --git a/src/gromacs/gmxana/gmx_fda_graph.cpp b/src/gromacs/gmxana/gmx_fda_graph.cpp
@@ -178,7 +178,15 @@ int gmx_fda_graph(int argc, char *argv[])
         // Convert from kJ/mol/nm into pN
         if (convert) for (auto & f : forceMatrix) f *= 1.66;
 
+        std::cout << "isize " << isize << std::endl;
+        std::cout << "index ";
+        for (int i = 0; i != isize; ++i) {
+            std::cout << index[i] << " ";
+        }
+        std::cout << std::endl;
         Graph graph(forceMatrix, coord, index, isize);
+        std::cout << graph << std::endl;
+
         if (resultFormat == PDB)
             graph.convertInPDBMinGraphOrder(opt2fn("-o", NFILE, fnm), threshold, minGraphOrder, onlyBiggestNetwork, false);
         else if (resultFormat == DIMACS)
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,7 @@ pipeline { @@
       agent {
         dockerfile {
+          label 'docker-gpu-host'
           filename 'devel/Dockerfile'
         }
       }
@@ Expand Down @@