Merge pull request #161 from i-VRESSE/sasasscore

Add sasascore module
i-VRESSE · Oct 17, 2024 · 79919f5 · 79919f5
2 parents bd4d98c + 620afe0
commit 79919f5
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diff --git a/app/catalogs/haddock3.easy.json b/app/catalogs/haddock3.easy.json
@@ -1,5 +1,6 @@
 {
   "title": "Haddock 3 on easy level",
+  "nodeLegend": "Module",
   "categories": [
     {
       "name": "topology",
@@ -2062,6 +2063,93 @@
         }
       }
     },
+    {
+      "id": "sasascore",
+      "category": "scoring",
+      "label": "Surface accessibility scoring module.",
+      "description": "HADDOCK3 module to perform accessibility scoring.",
+      "schema": {
+        "type": "object",
+        "properties": {
+          "cutoff": {
+            "default": 0.4,
+            "title": "relative side chain surface accessibility cutoff",
+            "description": "relative side chain surface accessibility cutoff",
+            "$comment": "relative side chain surface accessibility cutoff. Residues with a relative side chain surface accessibility below this value are considered buried.",
+            "type": "number",
+            "maximum": 1,
+            "minimum": 0
+          },
+          "resdic_buried": {
+            "default": {},
+            "title": "List of residues supposed to be buried",
+            "description": "List of residues supposed to be buried",
+            "$comment": "resdic_buried_* is an expandable parameter. You can provide resdic_buried_A, resdic_buried_B, resdic_buried_C, etc, where the last capital letter is the chain identifier.",
+            "type": "object",
+            "additionalProperties": {
+              "type": "array",
+              "items": {
+                "type": "number",
+                "format": "residue",
+                "minItems": 0,
+                "maxItems": 100
+              },
+              "uniqueItems": true,
+              "default": []
+            },
+            "propertyNames": {
+              "pattern": "^[A-Z]$",
+              "format": "chain"
+            },
+            "maxPropertiesFrom": "molecules"
+          },
+          "resdic_accessible": {
+            "default": {},
+            "title": "List of residues supposed to be accessible",
+            "description": "List of residues supposed to be accessible",
+            "$comment": "resdic_* is an expandable parameter. You can provide resdic_accessible_A, resdic_accessible_B, resdic_accessible_C, etc, where the last capital letter is the chain identifier.",
+            "type": "object",
+            "additionalProperties": {
+              "type": "array",
+              "items": {
+                "type": "number",
+                "format": "residue",
+                "minItems": 0,
+                "maxItems": 100
+              },
+              "uniqueItems": true,
+              "default": []
+            },
+            "propertyNames": {
+              "pattern": "^[A-Z]$",
+              "format": "chain"
+            },
+            "maxPropertiesFrom": "molecules"
+          }
+        },
+        "required": [],
+        "additionalProperties": false
+      },
+      "uiSchema": {
+        "cutoff": {
+          "ui:group": "scoring"
+        },
+        "resdic_buried": {
+          "ui:group": "analysis"
+        },
+        "resdic_accessible": {
+          "ui:group": "analysis"
+        }
+      },
+      "tomlSchema": {
+        "resdic_buried": {
+          "indexed": true
+        },
+        "resdic_accessible": {
+          "indexed": true
+        }
+      }
+    },
     {
       "id": "seletop",
       "category": "analysis",

diff --git a/app/catalogs/haddock3.expert.json b/app/catalogs/haddock3.expert.json
@@ -1,5 +1,6 @@
 {
   "title": "Haddock 3 on expert level",
+  "nodeLegend": "Module",
   "categories": [
     {
       "name": "topology",
@@ -8662,6 +8663,105 @@
         }
       }
     },
+    {
+      "id": "sasascore",
+      "category": "scoring",
+      "label": "Surface accessibility scoring module.",
+      "description": "HADDOCK3 module to perform accessibility scoring.",
+      "schema": {
+        "type": "object",
+        "properties": {
+          "cutoff": {
+            "default": 0.4,
+            "title": "relative side chain surface accessibility cutoff",
+            "description": "relative side chain surface accessibility cutoff",
+            "$comment": "relative side chain surface accessibility cutoff. Residues with a relative side chain surface accessibility below this value are considered buried.",
+            "type": "number",
+            "maximum": 1,
+            "minimum": 0
+          },
+          "resdic_buried": {
+            "default": {},
+            "title": "List of residues supposed to be buried",
+            "description": "List of residues supposed to be buried",
+            "$comment": "resdic_buried_* is an expandable parameter. You can provide resdic_buried_A, resdic_buried_B, resdic_buried_C, etc, where the last capital letter is the chain identifier.",
+            "type": "object",
+            "additionalProperties": {
+              "type": "array",
+              "items": {
+                "type": "number",
+                "format": "residue",
+                "minItems": 0,
+                "maxItems": 100
+              },
+              "uniqueItems": true,
+              "default": []
+            },
+            "propertyNames": {
+              "pattern": "^[A-Z]$",
+              "format": "chain"
+            },
+            "maxPropertiesFrom": "molecules"
+          },
+          "resdic_accessible": {
+            "default": {},
+            "title": "List of residues supposed to be accessible",
+            "description": "List of residues supposed to be accessible",
+            "$comment": "resdic_* is an expandable parameter. You can provide resdic_accessible_A, resdic_accessible_B, resdic_accessible_C, etc, where the last capital letter is the chain identifier.",
+            "type": "object",
+            "additionalProperties": {
+              "type": "array",
+              "items": {
+                "type": "number",
+                "format": "residue",
+                "minItems": 0,
+                "maxItems": 100
+              },
+              "uniqueItems": true,
+              "default": []
+            },
+            "propertyNames": {
+              "pattern": "^[A-Z]$",
+              "format": "chain"
+            },
+            "maxPropertiesFrom": "molecules"
+          },
+          "probe_radius": {
+            "default": 1.4,
+            "title": "Probe radius",
+            "description": "Probe radius",
+            "$comment": "Sets the probe radius (in Angstrom) used to compute solvent accessible surface area.",
+            "type": "number",
+            "maximum": 10,
+            "minimum": 0
+          }
+        },
+        "required": [],
+        "additionalProperties": false
+      },
+      "uiSchema": {
+        "cutoff": {
+          "ui:group": "scoring"
+        },
+        "resdic_buried": {
+          "ui:group": "analysis"
+        },
+        "resdic_accessible": {
+          "ui:group": "analysis"
+        },
+        "probe_radius": {
+          "ui:group": "analysis"
+        }
+      },
+      "tomlSchema": {
+        "resdic_buried": {
+          "indexed": true
+        },
+        "resdic_accessible": {
+          "indexed": true
+        }
+      }
+    },
     {
       "id": "seletop",
       "category": "analysis",

diff --git a/app/catalogs/haddock3.guru.json b/app/catalogs/haddock3.guru.json
@@ -1,5 +1,6 @@
 {
   "title": "Haddock 3 on guru level",
+  "nodeLegend": "Module",
   "categories": [
     {
       "name": "topology",
@@ -9084,6 +9085,105 @@
         }
       }
     },
+    {
+      "id": "sasascore",
+      "category": "scoring",
+      "label": "Surface accessibility scoring module.",
+      "description": "HADDOCK3 module to perform accessibility scoring.",
+      "schema": {
+        "type": "object",
+        "properties": {
+          "cutoff": {
+            "default": 0.4,
+            "title": "relative side chain surface accessibility cutoff",
+            "description": "relative side chain surface accessibility cutoff",
+            "$comment": "relative side chain surface accessibility cutoff. Residues with a relative side chain surface accessibility below this value are considered buried.",
+            "type": "number",
+            "maximum": 1,
+            "minimum": 0
+          },
+          "resdic_buried": {
+            "default": {},
+            "title": "List of residues supposed to be buried",
+            "description": "List of residues supposed to be buried",
+            "$comment": "resdic_buried_* is an expandable parameter. You can provide resdic_buried_A, resdic_buried_B, resdic_buried_C, etc, where the last capital letter is the chain identifier.",
+            "type": "object",
+            "additionalProperties": {
+              "type": "array",
+              "items": {
+                "type": "number",
+                "format": "residue",
+                "minItems": 0,
+                "maxItems": 100
+              },
+              "uniqueItems": true,
+              "default": []
+            },
+            "propertyNames": {
+              "pattern": "^[A-Z]$",
+              "format": "chain"
+            },
+            "maxPropertiesFrom": "molecules"
+          },
+          "resdic_accessible": {
+            "default": {},
+            "title": "List of residues supposed to be accessible",
+            "description": "List of residues supposed to be accessible",
+            "$comment": "resdic_* is an expandable parameter. You can provide resdic_accessible_A, resdic_accessible_B, resdic_accessible_C, etc, where the last capital letter is the chain identifier.",
+            "type": "object",
+            "additionalProperties": {
+              "type": "array",
+              "items": {
+                "type": "number",
+                "format": "residue",
+                "minItems": 0,
+                "maxItems": 100
+              },
+              "uniqueItems": true,
+              "default": []
+            },
+            "propertyNames": {
+              "pattern": "^[A-Z]$",
+              "format": "chain"
+            },
+            "maxPropertiesFrom": "molecules"
+          },
+          "probe_radius": {
+            "default": 1.4,
+            "title": "Probe radius",
+            "description": "Probe radius",
+            "$comment": "Sets the probe radius (in Angstrom) used to compute solvent accessible surface area.",
+            "type": "number",
+            "maximum": 10,
+            "minimum": 0
+          }
+        },
+        "required": [],
+        "additionalProperties": false
+      },
+      "uiSchema": {
+        "cutoff": {
+          "ui:group": "scoring"
+        },
+        "resdic_buried": {
+          "ui:group": "analysis"
+        },
+        "resdic_accessible": {
+          "ui:group": "analysis"
+        },
+        "probe_radius": {
+          "ui:group": "analysis"
+        }
+      },
+      "tomlSchema": {
+        "resdic_buried": {
+          "indexed": true
+        },
+        "resdic_accessible": {
+          "indexed": true
+        }
+      }
+    },
     {
       "id": "seletop",
       "category": "analysis",

diff --git a/deploy/Dockerfile.bartenderhaddock3 b/deploy/Dockerfile.bartenderhaddock3
@@ -65,7 +65,7 @@ RUN pip install .
 
 # haddock3 ============================================================================================================
 WORKDIR /opt/haddock3
-RUN echo cachebust=12 && git clone --depth 1 -b ${HADDOCK3_VERSION} https://github.com/${HADDOCK3_GHORG}/haddock3.git .
+RUN echo cachebust=13 && git clone --depth 1 -b ${HADDOCK3_VERSION} https://github.com/${HADDOCK3_GHORG}/haddock3.git .
 RUN pip install .
 # For restraints web service
 RUN pip install fastapi uvicorn