Open-Systems-Pharmacology / PK-Sim

PK-Sim® is a comprehensive software tool for whole-body physiologically based pharmacokinetic modeling
Other
102 stars 50 forks source link

Export of compound snapshot (json) #305

Closed msevestre closed 7 years ago

msevestre commented 7 years ago

This is the snapshot structure, encompassing alternatives, processes etc..

{
  "Name": "Test",
  "IsSmallMolecule": true,
  "PlasmaProteinBindingPartner": "Glycoprotein",
  "Lipophilicity": [
    {
      "Name": "Lipo",
      "IsDefault": true,
      "Parameters": [
        {
          "Name": "Lipophilicity",
          "Value": 1.0,
          "Unit": "Log Units"
        }
      ]
    },
    {
      "Name": "lipo2",
      "IsDefault": false,
      "Parameters": [
        {
          "Name": "Lipophilicity",
          "Value": 2.0,
          "Unit": "Log Units"
        }
      ]
    }
  ],
  "FractionUnbound": [
    {
      "Name": "Fu1",
      "IsDefault": false,
      "Species": "Monkey",
      "Parameters": [
        {
          "Name": "Fraction unbound (plasma, reference value)",
          "Value": 0.3
        }
      ]
    },
    {
      "Name": "Fu2",
      "IsDefault": true,
      "Species": "Dog",
      "Parameters": [
        {
          "Name": "Fraction unbound (plasma, reference value)",
          "Value": 0.4
        }
      ]
    }
  ],
  "Solubility": [
    {
      "Name": "Sol1",
      "IsDefault": true,
      "Parameters": [
        {
          "Name": "Solubility at reference pH",
          "Value": 8.0,
          "Unit": "mg/l"
        },
        {
          "Name": "Reference pH",
          "Value": 9.0
        },
        {
          "Name": "Solubility gain per charge",
          "Value": 10.0
        }
      ]
    }
  ],
  "IntestinalPermeability": [
    {
      "Name": "IntestinalPerm1",
      "IsDefault": false,
      "Parameters": [
        {
          "Name": "Specific intestinal permeability (transcellular)",
          "Value": 1.0,
          "Unit": "cm/s"
        }
      ]
    }
  ],
  "Permeability": [
    {
      "Name": "Spec Int 1",
      "IsDefault": false,
      "Parameters": [
        {
          "Name": "Permeability",
          "Value": 1.0,
          "Unit": "cm/s"
        }
      ]
    }
  ],
  "PkaTypes": [
    {
      "Type": "Base",
      "Pka": 6.0
    },
    {
      "Type": "Acid",
      "Pka": 7.0
    }
  ],
  "Processes": [
    {
      "InternalName": "MetabolizationIntrinsic_FirstOrder",
      "DataSource": "Lab",
      "Species": "Human",
      "Molecule": "CYP3A4",
      "Metabolite": "",
      "Parameters": [
        {
          "Name": "Volume (liver)",
          "Value": 1.0,
          "Unit": "l"
        },
        {
          "Name": "Fraction intracellular (liver)",
          "Value": 0.2
        },
        {
          "Name": "Intrinsic clearance",
          "Value": 3.0,
          "Unit": "l/min"
        },
        {
          "Name": "Specific clearance",
          "Value": 5.0,
          "Unit": "1/min"
        }
      ]
    },
    {
      "InternalName": "MetabolizationIntrinsic_FirstOrder",
      "DataSource": "Lab2",
      "Species": "Human",
      "Molecule": "CYP3A4",
      "Parameters": [
        {
          "Name": "Volume (liver)",
          "Value": 1.0,
          "Unit": "l"
        },
        {
          "Name": "Fraction intracellular (liver)",
          "Value": 0.2
        },
        {
          "Name": "Intrinsic clearance",
          "Value": 3.0,
          "Unit": "l/min"
        }
      ]
    },
    {
      "InternalName": "CompetitiveInhibition",
      "DataSource": "Lab3",
      "Molecule": "CYP3A4",
      "Parameters": [
        {
          "Name": "Ki",
          "Value": 22.0,
          "Unit": "µmol/l"
        }
      ]
    }
  ],
  "CalculationMethods": [
    "Cellular partition coefficient method - Rodgers and Rowland",
    "Cellular permeability - Charge dependent Schmitt"
  ],
  "Parameters": [
    {
      "Name": "Molecular weight",
      "Value": 555.0,
      "Unit": "g/mol"
    }
  ]
}
msevestre commented 7 years ago

/cc @Yuri05