Class TotalSurfaceAreaPredictor

    • Field Detail

      • cNonPolarAtomTypeName

        public static final java.lang.String[] cNonPolarAtomTypeName
    • Constructor Detail

      • TotalSurfaceAreaPredictor

        public TotalSurfaceAreaPredictor()
    • Method Detail

      • getNonPolarAtomTypeCount

        public static int getNonPolarAtomTypeCount()
      • assessTotalSurfaceArea

        public float assessTotalSurfaceArea​(StereoMolecule mol)
        Calculates the topological total surface area (TPSA) of a molecule as a sum of contributions of its polar and non-atom-types. This method the contributions of all polar atoms. Contributions of polar and non-polar atom types were calculated as follows: 92879 unique reliable active structures with molecular weights between 200 and 700 were selected from the ChEMBL_20 database. For every structure one conformer was generated and minimized by the MMFF94 forcefield. Total surface areas were calculated as solvent accessible surface using Van der Waals radii and a probe of 1.4 angstrom radius. Surface contribution values were for 43 polar and 20 non polar atom types were calculated as a multi-linear regression with a PLS approach.
        Parameters:
        mol -
        Returns:
      • assessPolarSurfaceArea

        public float assessPolarSurfaceArea​(StereoMolecule mol)
        Calculates the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types. This method the contributions of all polar atoms. Contributions of polar and non-polar atom types were calculated as follows: 92879 unique reliable active structures with molecular weights between 200 and 700 were selected from the ChEMBL_20 database. For every structure one conformer was generated and minimized by the MMFF94 forcefield. Total surface areas were calculated as solvent accessible surface using Van der Waals radii and a probe of 1.4 angstrom radius. Surface contribution values were for 43 polar and 20 non polar atom types were calculated as a multi-linear regression with a PLS approach.
        Parameters:
        mol -
        Returns:
      • assessNonPolarSurfaceArea

        public float assessNonPolarSurfaceArea​(StereoMolecule mol)
        Calculates the topological non-polar surface area (TPSA) of a molecule as a sum of contributions of its non-polar atom-types. This method the contributions of all polar atoms. Contributions of polar and non-polar atom types were calculated as follows: 92879 unique reliable active structures with molecular weights between 200 and 700 were selected from the ChEMBL_20 database. For every structure one conformer was generated and minimized by the MMFF94 forcefield. Total surface areas were calculated as solvent accessible surface using Van der Waals radii and a probe of 1.4 angstrom radius. Surface contribution values were for 43 polar and 20 non polar atom types were calculated as a multi-linear regression with a PLS approach.
        Parameters:
        mol -
        Returns:
      • assessRelativePolarSurfaceArea

        public float assessRelativePolarSurfaceArea​(StereoMolecule mol)
        Calculates the relative (fractional) polar surface area from polar and non-polar atom contributions. This method does not use the Peter Ertl increments.
        Parameters:
        mol -
        Returns:
      • getNonPolarAtomTypeCounts

        public int[] getNonPolarAtomTypeCounts​(StereoMolecule mol)