Merge pull request #56 from BOINC/vko_simplify_json

[boinc-autodock-vina] Simplify json schema.
BOINC · Jun 16, 2022 · a8f95ad · a8f95ad
2 parents 4b715c6 + c527f73
commit a8f95ad
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Showing 13 changed files with 438 additions and 583 deletions.
diff --git a/boinc-autodock-vina/README.md b/boinc-autodock-vina/README.md
diff --git a/boinc-autodock-vina/samples/basic_docking/1iep_vina.json b/boinc-autodock-vina/samples/basic_docking/1iep_vina.json
@@ -1,22 +1,12 @@
 {
-    "input": {
-        "receptor": "1iep_receptor.pdbqt",
-        "ligands": [
-            "1iep_ligand.pdbqt"
-        ]
-    },
-    "search_area": {
-        "center_x": 15.190,
-        "center_y": 53.903,
-        "center_z": 16.917,
-        "size_x": 20.0,
-        "size_y": 20.0,
-        "size_z": 20.0
-    },
-    "misc": {
-        "exhaustiveness": 4
-    },
-    "output": {
-        "out": "1iep_ligand_vina_out.pdbqt"
-    }
+    "receptor": "1iep_receptor.pdbqt",
+    "ligand": "1iep_ligand.pdbqt",
+    "center_x": 15.190,
+    "center_y": 53.903,
+    "center_z": 16.917,
+    "size_x": 20.0,
+    "size_y": 20.0,
+    "size_z": 20.0,
+    "exhaustiveness": 4,
+    "out": "1iep_ligand_vina_out.pdbqt"
 }
diff --git a/boinc-autodock-vina/samples/basic_docking_full/1iep_vina.json b/boinc-autodock-vina/samples/basic_docking_full/1iep_vina.json
@@ -1,24 +1,12 @@
 {
-    "prepare_receptors": {
-        "receptors": [
-            "1iep_receptor.pdb"
-        ]
-    },
-    "prepare_ligands": {
-        "ligand": "1iep_ligand.sdf"
-    },
-    "search_area": {
-        "center_x": 15.190,
-        "center_y": 53.903,
-        "center_z": 16.917,
-        "size_x": 20.0,
-        "size_y": 20.0,
-        "size_z": 20.0
-    },
-    "misc": {
-        "exhaustiveness": 4
-    },
-    "output": {
-        "out": "1iep_ligand_vina_out.pdbqt"
-    }
+    "receptor": "1iep_receptor.pdb",
+    "ligand": "1iep_ligand.sdf",
+    "center_x": 15.190,
+    "center_y": 53.903,
+    "center_z": 16.917,
+    "size_x": 20.0,
+    "size_y": 20.0,
+    "size_z": 20.0,
+    "exhaustiveness": 4,
+    "out": "1iep_ligand_vina_out.pdbqt"
 }
diff --git a/boinc-autodock-vina/samples/basic_docking_full_generator_test/1iep_vina.json b/boinc-autodock-vina/samples/basic_docking_full_generator_test/1iep_vina.json
@@ -1,25 +1,15 @@
 {
-    "prepare_receptors": {
-        "receptors": [
-            "1iep_receptor.pdb",
-            "1iep_receptor_copy.pdb"
-        ]
-    },
-    "prepare_ligands": {
-        "ligand": "1iep_ligand.sdf"
-    },
-    "search_area": {
-        "center_x": 15.190,
-        "center_y": 53.903,
-        "center_z": 16.917,
-        "size_x": 20.0,
-        "size_y": 20.0,
-        "size_z": 20.0
-    },
-    "misc": {
-        "exhaustiveness": 4
-    },
-    "output": {
-        "out": "1iep_ligand_vina_out.pdbqt"
-    }
+    "receptors": [
+        "1iep_receptor.pdb",
+        "1iep_receptor_copy.pdb"
+    ],
+    "ligand": "1iep_ligand.sdf",
+    "center_x": 15.190,
+    "center_y": 53.903,
+    "center_z": 16.917,
+    "size_x": 20.0,
+    "size_y": 20.0,
+    "size_z": 20.0,
+    "exhaustiveness": 4,
+    "out": "1iep_ligand_vina_out.pdbqt"
 }
diff --git a/boinc-autodock-vina/samples/basic_docking_full_generator_test/1iep_vina_copy.json b/boinc-autodock-vina/samples/basic_docking_full_generator_test/1iep_vina_copy.json
@@ -1,25 +1,15 @@
 {
-    "prepare_receptors": {
-        "receptors": [
-            "1iep_receptor.pdb",
-            "1iep_receptor_copy.pdb"
-        ]
-    },
-    "prepare_ligands": {
-        "ligand": "1iep_ligand.sdf"
-    },
-    "search_area": {
-        "center_x": 15.190,
-        "center_y": 53.903,
-        "center_z": 16.917,
-        "size_x": 20.0,
-        "size_y": 20.0,
-        "size_z": 20.0
-    },
-    "misc": {
-        "exhaustiveness": 4
-    },
-    "output": {
-        "out": "1iep_ligand_vina_out.pdbqt"
-    }
+    "receptors": [
+        "1iep_receptor.pdb",
+        "1iep_receptor_copy.pdb"
+    ],
+    "ligand": "1iep_ligand.sdf",
+    "center_x": 15.190,
+    "center_y": 53.903,
+    "center_z": 16.917,
+    "size_x": 20.0,
+    "size_y": 20.0,
+    "size_z": 20.0,
+    "exhaustiveness": 4,
+    "out": "1iep_ligand_vina_out.pdbqt"
 }
diff --git a/boinc-autodock-vina/src/boinc-autodock-vina/boinc-autodock-vina.cpp b/boinc-autodock-vina/src/boinc-autodock-vina/boinc-autodock-vina.cpp
@@ -132,7 +132,7 @@ int perform_docking(const std::string& in_zip, const std::string& out_zip) noexc
             return 1;
         }
 
-        if (!conf.validate()) {
+        if (!conf.validate(true)) {
             std::cerr << boinc_msg_prefix(buf, sizeof(buf)) << "Config validation failed, cannot proceed further" << std::endl;
             boinc_finish(1);
             return 1;

diff --git a/boinc-autodock-vina/src/boinc-autodock-vina/calculate.cpp b/boinc-autodock-vina/src/boinc-autodock-vina/calculate.cpp
@@ -27,8 +27,8 @@ bool calculator::calculate(const config& config, const int& ncpus, const std::fu
         config.misc.seed, vina_verbosity, config.advanced.no_refine,
         const_cast<std::function<void(double)>*>(&progress_callback));
 
-    if (!config.input.receptor.empty() || !config.input.flex.empty()) {
-        vina.set_receptor(config.input.receptor, config.input.flex);
+    if (!config.input.receptors.empty() || !config.input.flex.empty()) {
+        vina.set_receptor(config.input.receptors.front(), config.input.flex);
     }
 
     if (config.input.scoring == scoring::vina) {
@@ -53,7 +53,7 @@ bool calculator::calculate(const config& config, const int& ncpus, const std::fu
     }
 
     if (!config.input.ligands.empty()) {
-        vina.set_ligand_from_file(config.input.ligands);
+        vina.set_ligand_from_file(config.input.ligands.front());
 
         if (config.input.scoring == scoring::vina || config.input.scoring == scoring::vinardo) {
             if (!config.search_area.maps.empty()) {