@kmansouri kmansouri released this Dec 14, 2018 · 21 commits to master since this release

Assets 4

OPERA v2.1-beta.1
Windows version

Latest update:

  • Added a correction patch for PFAS chemicals for logP and WS models
  • Corrected CATMoS-LD50 experimental values
  • Fixed bug related to running all models as default

Limitations of the current version:

  • Molecular descriptors can only be calculated for:
    * Maximum molecular weight 2000 g/Mol
    * Maximum number of heavy atoms <= 100
    * No nano-materials like shapes (spheres, tubes...)

Files:

  • OPERA2.0_win_web.zip: the installer will automatically download all dependencies if Matlab runtime v94 is not already installed.

  • OPERA2.0_win_offline.zip: the installer is self-contained with all dependencies. No internet connection required during installation.

         *  OPERA v2.0:
    
    • Molecular descriptors:
  • PaDEL (2.21) (https://doi.org/10.1002/jcc.21707 )

  • CDK (2.0) (https://doi.org/10.1186/s13321-017-0220-4)

    • Models:
  • Structural Properties: MolWeight, nbAtoms, nbHeavyAtoms, nbC, nbO, nbN, nbAromAtom, nbRing, nbHeteroRing, Sp3Sp2HybRatio, nbRotBd, nbHBdAcc, ndHBdDon, nbLipinskiFailures, TopoPolSurfAir, MolarRefract, CombDipolPolarizability.

  • pKa: acid dissociation constant

  • LogD: Octanol-water distribution constant. LogD is equivalent to logP for non-ionisable compounds.

  • CERAPP: Collaborative Estrogen Receptor Activity Prediction Project. Binding, Agonist and Antagonist Estrogen Receptor activity (https://ehp.niehs.nih.gov/15-10267/)

  • CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. Binding, Agonist and Antagonist Androgen Receptor activity (https://doi.org/10.13140/RG.2.2.19612.80009, https://doi.org/10.13140/RG.2.2.21850.03520)

  • CATMoS: Collaborative Acute Toxicity Modeling Suite. Very-Toxic, Non-Toxic, EPA categories, GHS categories, LD50 (Log mg/kg) (https://doi.org/10.1016/j.comtox.2018.08.002)

  • OPERA v1.5 models

       *  OPERA v1.5:
    
    • Molecular descriptors:
  • PaDEL (2.21) (https://doi.org/10.1002/jcc.21707 )

    • Models:
  • OH (LogOH) in cm3/molecule-sec: The OH rate constant for the atmospheric, gas-phase reaction between photochemically produced hydroxyl radicals and organic chemicals.

  • BCF (Log): Fish bioconcentration factor

  • Biodeg (LogHalfLife) in days: biodegradation half-life for compounds containing only carbon and hydrogen (i.e. hydrocarbons).

  • Ready_biodeg (classification: 0/1): Ready biodegradability of organic chemicals.

  • BP in deg C: Boiling Point at 760 mm Hg

  • HL (LogHL) in atm-m3/mole: The Henry’s Law constant (air/water partition coefficient) at 25C

  • Km (Log KmHL) half-lives in days: The whole body primary biotransformation rate constant for organic chemicals in fish.

  • KOA (Log): The octanol/air partition coefficient.

  • LogP (Log): Octanol-water partition coefficient, log KOW, of chemicals.

  • MP in deg C: Melting Point

  • Koc (Log) in L/Kg: the soil adsorption coefficient of organic compounds.  The ratio of the amount of chemical adsorbed per unit weight of organic carbon in the soil or sediment to the concentration of the chemical in solution at equilibrium.

  • VP (Log) in mmHg: Vapor Pressure experimental values between 15 and 30 deg C (majority at 25-20C)

  • WS (Log) in Molar moles/L: Water solubility at 25C.

  • RT in minutes: HPLC retention time.

@kmansouri kmansouri released this Dec 14, 2018 · 21 commits to master since this release

Assets 9

OPERA v2.1-beta.1
Linux version

Latest update:

  • Added a correction patch for PFAS chemicals for logP and WS models
  • Corrected CATMoS-LD50 experimental values
  • Fixed bug related to running all models as default

Limitations of the current version:

  • Molecular descriptors can only be calculated for:
    * Maximum molecular weight 2000 g/Mol
    * Maximum number of heavy atoms <= 100
    * No nano-materials like shapes (spheres, tubes...)

Files:

  • OPERA2_bin.tar.gz: contains the binary file to run if MATLAB runtime v94 is already installed

  • OPERA2_web_install.tar.gz: the installer will automatically download all dependencies if Matlab runtime v94 is not already installed.

  • OPERA2_offline_install.tar.gz: the installer is self-contained with all dependencies. No internet connection required during installation.

  • libOPERA2_*.tar.gz: additional libraries in C, C++, Java, and Python to embed in other projects.

         *  OPERA v2.0:
    
    • Molecular descriptors:
  • PaDEL (2.21) (https://doi.org/10.1002/jcc.21707 )

  • CDK (2.0) (https://doi.org/10.1186/s13321-017-0220-4)

    • Models:
  • Structural Properties: MolWeight, nbAtoms, nbHeavyAtoms, nbC, nbO, nbN, nbAromAtom, nbRing, nbHeteroRing, Sp3Sp2HybRatio, nbRotBd, nbHBdAcc, ndHBdDon, nbLipinskiFailures, TopoPolSurfAir, MolarRefract, CombDipolPolarizability.

  • pKa: acid dissociation constant

  • LogD: Octanol-water distribution constant. LogD is equivalent to logP for non-ionisable compounds.

  • CERAPP: Collaborative Estrogen Receptor Activity Prediction Project. Binding, Agonist and Antagonist Estrogen Receptor activity (https://ehp.niehs.nih.gov/15-10267/)

  • CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. Binding, Agonist and Antagonist Androgen Receptor activity (https://doi.org/10.13140/RG.2.2.19612.80009, https://doi.org/10.13140/RG.2.2.21850.03520)

  • CATMoS: Collaborative Acute Toxicity Modeling Suite. Very-Toxic, Non-Toxic, EPA categories, GHS categories, LD50 (Log mg/kg) (https://doi.org/10.1016/j.comtox.2018.08.002)

  • OPERA v1.5 models

       *  OPERA v1.5:
    
    • Molecular descriptors:
  • PaDEL (2.21) (https://doi.org/10.1002/jcc.21707 )

    • Models:
  • OH (LogOH) in cm3/molecule-sec: The OH rate constant for the atmospheric, gas-phase reaction between photochemically produced hydroxyl radicals and organic chemicals.

  • BCF (Log): Fish bioconcentration factor

  • Biodeg (LogHalfLife) in days: biodegradation half-life for compounds containing only carbon and hydrogen (i.e. hydrocarbons).

  • Ready_biodeg (classification: 0/1): Ready biodegradability of organic chemicals.

  • BP in deg C: Boiling Point at 760 mm Hg

  • HL (LogHL) in atm-m3/mole: The Henry’s Law constant (air/water partition coefficient) at 25C

  • Km (Log KmHL) half-lives in days: The whole body primary biotransformation rate constant for organic chemicals in fish.

  • KOA (Log): The octanol/air partition coefficient.

  • LogP (Log): Octanol-water partition coefficient, log KOW, of chemicals.

  • MP in deg C: Melting Point

  • Koc (Log) in L/Kg: the soil adsorption coefficient of organic compounds.  The ratio of the amount of chemical adsorbed per unit weight of organic carbon in the soil or sediment to the concentration of the chemical in solution at equilibrium.

  • VP (Log) in mmHg: Vapor Pressure experimental values between 15 and 30 deg C (majority at 25-20C)

  • WS (Log) in Molar moles/L: Water solubility at 25C.

  • RT in minutes: HPLC retention time.