apbs/data/input-schema.json

{
  "$schema": "http://json-schema.org/draft-04/schema#",
  "$id": "https://json.schemastore.org/apbs-input.json",
  "title": "APBS input",
  "description": "Input file schema for APBS electrostatics software (https://apbs.readthedocs.io/)",
  "type": "object",
  "properties": {
    "read": {
      "description": "Specify input files for APBS calculation.",
      "type": "object",
      "properties": {
        "charge": {
          "description": "Specify input file for fixed (molecular) charge density function mapped to a mesh. The inputs are maps of charge densities; these values have units of e_c Å^{-3}, where e_c is the electron charge.",
          "type": "object",
          "properties": {
            "format": {
              "description": "Input file format",
              "type": "object",
              "oneOf": [
                { "$ref": "#/$defs/dx" },
                { "$ref": "#/$defs/gz" }
              ]
            },
            "path": {
              "description": "Path to input file",
              "type": "string"
            }
          },
          "required": [
            "format",
            "path"
          ]
        },
        "dielectric": {
          "description": "Specify input file for dielectric maps, the dielectric function mapped to 3 meshes shifted by one-half grid spacing in the x, y, and z directions. The inputs are maps of dielectric variables between the solvent and biomolecular dielectric constants; these values are unitless. If you choose this option and have a non-zero ionic strength, you must also include a kappa input map.",
          "type": "object",
          "properties": {
            "format": {
              "description": "Input file format",
              "type": "object",
              "oneOf": [
                {
                  "$ref": "#/$defs/dx"
                },
                {
                  "$ref": "#/$defs/gz"
                }
              ]
            },
            "path-x": {
              "description": "x-shifted dielectric map",
              "type": "string"
            },
            "path-y": {
              "description": "y-shifted dielectric map",
              "type": "string"
            },
            "path-z": {
              "description": "z-shifted dielectric map",
              "type": "string"
            }
          },
          "required": [
            "format",
            "path-x",
            "path-y",
            "path-z"
          ]
        },
        "ion accessibility": {
          "description": "Specify input file for ion-accessibility function mapped to a mesh. The inputs are maps of ion accessibility values which range between 0 and the value of the Debye-Hückel screening parameter; these values have units of Å^{-2}.",
          "type": "object",
          "properties": {
            "format": {
              "description": "Input file format",
              "type": "object",
              "oneOf": [
                {
                  "$ref": "#/$defs/dx"
                },
                {
                  "$ref": "#/$defs/gz"
                }
              ]
            },
            "path": {
              "description": "Path to input file",
              "type": "string"
            }
          },
          "required": [
            "format",
            "path"
          ]
        },
        "molecule": {
          "description": "Specify input file for molecular structure data.",
          "type": "object",
          "properties": {
            "format": {
              "description": "Input file format",
              "type": "object",
              "oneOf": [
                {
                  "$ref": "#/$defs/pqr"
                },
                {
                  "$ref": "#/$defs/pdb"
                }
              ]
            },
            "path": {
              "description": "Path to input file",
              "type": "string"
            }
          },
          "required": [
            "format",
            "path"
          ]
        },
        "parameter": {
          "description": "Specify the charge and radius data to be used with PDB-format molecule files.",
          "type": "object",
          "properties": {
            "format": {
              "description": "Input file format",
              "type": "object",
              "oneOf": [
                {
                  "$ref": "#/$defs/xml"
                },
                {
                  "$ref": "#/$defs/flat"
                }
              ]
            },
            "path": {
              "description": "Path to input file",
              "type": "string"
            }
          },
          "required": ["format", "path"]
        },
        "potential": {
          "description": "Specify the electrostatic potential data (in units of k T/e_c) from previous calculations.",
          "type": "object",
          "properties": {
            "format": {
              "description": "Input file format",
              "type": "object",
              "oneOf": [
                {
                  "$ref": "#/$defs/dx"
                },
                {
                  "$ref": "#/$defs/gz"
                }
              ]
            },
            "path": {
              "description": "Path to input file",
              "type": "string"
            }
          },
          "required": ["format", "path"]
        }
      },
      "required": [
        "mol"
      ]
    },
    "polar": {
      "description": "Specify configuration of an electrostatics (polar solvation) calculation",
      "type": "object",
      "properties": {
        "name": {
          "description": "A name for your calculation.",
          "type": "string"
        },
        "type": {
          "description": "The type of calculation to perform"
        }
      }
    }
  },
  "$defs": {
    "dx": {
      "description": "OpenDX scalar data format"
    },
    "flat": {
      "description": "Flat-format parameter file"
    },
    "gz": {
      "description": "Gzip-compressed OpenDX scalar data format"
    },
    "pdb": {
      "description": "Protein DataBank (PDB) old format"
    },
    "pqr": {
      "description": "PQR (PDB with charge and radius information) format"
    },
    "xml": {
      "description": "XML format parameter file"
    }
  },
  "required": [
    "read"
  ]
}