Class TotalSurfaceAreaPredictor
- java.lang.Object
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- com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
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- com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
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public class TotalSurfaceAreaPredictor extends PolarSurfaceAreaPredictor
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Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
cNonPolarAtomTypeName
static float
cPSAUnknown
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Fields inherited from class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
cPolarAtomTypeName
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Constructor Summary
Constructors Constructor Description TotalSurfaceAreaPredictor()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.float
assessPolarSurfaceArea(StereoMolecule mol)
Calculates the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.float
assessRelativePolarSurfaceArea(StereoMolecule mol)
Calculates the relative (fractional) polar surface area from polar and non-polar atom contributions.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.ParameterizedStringList
getDetail(StereoMolecule mol)
static int
getNonPolarAtomTypeCount()
int[]
getNonPolarAtomTypeCounts(StereoMolecule mol)
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Methods inherited from class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
assessPSA, getPolarAtomTypeCount, getPolarAtomTypeCounts
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Field Detail
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cPSAUnknown
public static final float cPSAUnknown
- See Also:
- Constant Field Values
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cNonPolarAtomTypeName
public static final java.lang.String[] cNonPolarAtomTypeName
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Method Detail
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getNonPolarAtomTypeCount
public static int getNonPolarAtomTypeCount()
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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:
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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:
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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:
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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:
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getDetail
public ParameterizedStringList getDetail(StereoMolecule mol)
- Overrides:
getDetail
in classPolarSurfaceAreaPredictor
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getNonPolarAtomTypeCounts
public int[] getNonPolarAtomTypeCounts(StereoMolecule mol)
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