Merge pull request #156 from i-VRESSE/openmm

Add openmm module to catalog and docker image

app/catalogs/haddock3.easy.json

@@ -1675,6 +1675,215 @@
       },
       "tomlSchema": {}
     },
+    {
+      "id": "openmm",
+      "category": "refinement",
+      "label": "OpenMM refinement module for HADDOCK3.",
+      "description": "HADDOCK3 OpenMM module.",
+      "schema": {
+        "type": "object",
+        "properties": {
+          "forcefield": {
+            "default": "amber14-all.xml",
+            "title": "Forcefield used by OpenMM.",
+            "description": "Forcefields that can be used by OpenMM.",
+            "$comment": "Forcefields that can be used by OpenMM.",
+            "type": "string",
+            "minLength": 10,
+            "maxLength": 100,
+            "enum": [
+              "amber14-all.xml",
+              "amber14/protein.ff14SB.xml",
+              "amber14/protein.ff15ipq.xml",
+              "amber14/DNA.OL15.xml",
+              "amber14/DNA.bsc1.xml",
+              "amber14/RNA.OL3.xml",
+              "amber14/lipid17.xml",
+              "amber14/GLYCAM_06j-1.xml",
+              "charmm36.xml"
+            ]
+          },
+          "explicit_solvent_model": {
+            "default": "amber14/tip3p.xml",
+            "title": "Explicit solvent models.",
+            "description": "Solvent models supported by the OpenMM modeller to build the water solvation box.",
+            "$comment": "Solvent models supported by the OpenMM modeller to build the water solvation box.",
+            "type": "string",
+            "minLength": 0,
+            "maxLength": 100,
+            "enum": [
+              "amber14/tip3p.xml",
+              "amber14/spce.xml",
+              "charmm36/spce.xml",
+              "amber14/tip4pew.xml",
+              "charmm36/tip4pew.xml",
+              "charmm36/tip5p.xml"
+            ]
+          },
+          "keep_solvent": {
+            "default": false,
+            "title": "Whether-or-not solvent be removed from provided structures.",
+            "description": "Whether-or-not solvent be removed from provided structures.",
+            "$comment": "Whether-or-not solvent be removed from provided structures. If 'false', all HETATM atoms will be removed.",
+            "type": "boolean"
+          },
+          "implicit_solvent": {
+            "default": false,
+            "title": "Indicate use of implicit solvent.",
+            "description": "Indicate use of implicit solvent, avoids building a water solvation box around pdbs.",
+            "$comment": "Indicate use of implicit solvent, avoids building a water solvation box around pdbs.",
+            "type": "boolean"
+          },
+          "implicit_solvent_model": {
+            "default": "implicit/hct.xml",
+            "title": "Implicit solvent models.",
+            "description": "Implicit solvent models supported by OpenMM.",
+            "$comment": "Implicit solvent models supported by OpenMM.",
+            "type": "string",
+            "minLength": 0,
+            "maxLength": 100,
+            "enum": [
+              "implicit/hct.xml",
+              "implicit/obc1.xml",
+              "implicit/obc2.xml",
+              "implicit/gbn.xml",
+              "implicit/gbn2.xml"
+            ]
+          },
+          "add_extra_particles_for_forcefield": {
+            "default": false,
+            "title": "Add extra particles for forcefield.",
+            "description": "Add extra particles for forcefield if needed such as e.g. Drude particles.",
+            "$comment": "Add extra particles for forcefield if needed such as e.g. Drude particles.",
+            "type": "boolean"
+          },
+          "constraints": {
+            "default": "HBonds",
+            "title": "Integration constraints.",
+            "description": "Integration constraints used to allow for larger integration time step.",
+            "$comment": "Integration constraints used to allow for larger integration time step. For extra info see http://docs.openmm.org/latest/userguide/application/02_running_sims.html#constraints",
+            "type": "string",
+            "minLength": 1,
+            "maxLength": 20,
+            "enum": ["None", "HBonds", "AllBonds", "HAngles"]
+          },
+          "sampling_factor": {
+            "default": 1,
+            "title": "Number of simulation replicas.",
+            "description": "Number of simulation replicas.",
+            "$comment": "Number of simulation replicas.",
+            "type": "number",
+            "maximum": 20,
+            "minimum": 1
+          },
+          "temperature_kelvin": {
+            "default": 298.15,
+            "title": "Average temperature.",
+            "description": "Average temperature used by e.g. the integrator or by for temperature coupling.",
+            "$comment": "Average temperature used by e.g. the integrator or by for temperature coupling.",
+            "type": "number",
+            "maximum": 1000,
+            "minimum": 1
+          },
+          "remove_center_of_mass_motion": {
+            "default": true,
+            "title": "Remove center of mass motion.",
+            "description": "Remove center of mass motion when overall molecular drift is detected.",
+            "$comment": "Remove center of mass motion when overall molecular drift is detected.",
+            "type": "boolean"
+          },
+          "generate_ensemble": {
+            "default": true,
+            "title": "Generate ensemble of configurations.",
+            "description": "Generate ensemble of configurations.",
+            "$comment": "If 'true', generates 1 single ensemble .pdb file holding various configurations; composed of the equilibrated one, all intermediates and the final one. If 'false', only return the last configuration obtained after 'simulation_timesteps' steps.",
+            "type": "boolean"
+          },
+          "rigid_water": {
+            "default": true,
+            "title": "Use rigid water.",
+            "description": "Use of rigid water in the simulation.",
+            "$comment": "Use of rigid water in the simulation. Flexible water molecules usually require a slower taken timestep by the used integrator.",
+            "type": "boolean"
+          },
+          "iniseed": {
+            "default": 917,
+            "title": "Simulation seed.",
+            "description": "Set a pseudo-random seed for the simulation.",
+            "$comment": "Set a pseudo-random seed for the simulation. This defines how the initial velocities are created, but has no effect on the randomicity of the solvation box.",
+            "type": "number",
+            "maximum": 1000000,
+            "minimum": 0
+          },
+          "ion_concentration": {
+            "default": 0.15,
+            "title": "Ion concentration.",
+            "description": "Ion concentration in Molar.",
+            "$comment": "Ion concentration in Molar.",
+            "type": "number",
+            "maximum": 5,
+            "minimum": 0
+          },
+          "solv_equilibration": {
+            "default": true,
+            "title": "Process the solvent equilibration phase.",
+            "description": "Process the solvent equilibration phase.",
+            "$comment": "Process the solvent equilibration phase. If 'true', the solvent will be equilibrated while constraining proteins positions to intial ones.",
+            "type": "boolean"
+          }
+        },
+        "required": [],
+        "additionalProperties": false
+      },
+      "uiSchema": {
+        "forcefield": {
+          "ui:group": "force field"
+        },
+        "explicit_solvent_model": {
+          "ui:group": "force field"
+        },
+        "keep_solvent": {
+          "ui:group": "post processing"
+        },
+        "implicit_solvent": {
+          "ui:group": "force field"
+        },
+        "implicit_solvent_model": {
+          "ui:group": "force field"
+        },
+        "add_extra_particles_for_forcefield": {
+          "ui:group": "force field"
+        },
+        "constraints": {
+          "ui:group": "restraints"
+        },
+        "sampling_factor": {
+          "ui:group": "sampling"
+        },
+        "temperature_kelvin": {
+          "ui:group": "sampling"
+        },
+        "remove_center_of_mass_motion": {
+          "ui:group": "sampling"
+        },
+        "generate_ensemble": {
+          "ui:group": "post processing"
+        },
+        "rigid_water": {
+          "ui:group": "restraints"
+        },
+        "iniseed": {
+          "ui:group": "sampling"
+        },
+        "ion_concentration": {
+          "ui:group": "sampling"
+        },
+        "solv_equilibration": {
+          "ui:group": "sampling"
+        }
+      },
+      "tomlSchema": {}
+    },
     {
       "id": "rigidbody",
       "category": "sampling",