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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,53 +1,54 @@ | ||
| from rdkit import Chem | ||
| from mordred import Chi, ABCIndex, RingCount, Calculator, is_missing, descriptors | ||
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| benzene = Chem.MolFromSmiles('c1ccccc1') | ||
| from multiprocessing import freeze_support | ||
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| # Create empty Calculator instance | ||
| calc1 = Calculator() | ||
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| # Register descriptor instance | ||
| calc1.register(Chi.Chi(type='path_cluster', order=4)) | ||
| from rdkit import Chem | ||
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| # Register descriptor class using preset | ||
| calc1.register(RingCount.RingCount) | ||
| from mordred import Chi, ABCIndex, RingCount, Calculator, is_missing, descriptors | ||
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| # Register all descriptors in module | ||
| calc1.register(ABCIndex) | ||
| if __name__ == "__main__": | ||
| freeze_support() | ||
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| benzene = Chem.MolFromSmiles("c1ccccc1") | ||
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| # Calculate descriptors | ||
| result = calc1(benzene) | ||
| # Create empty Calculator instance | ||
| calc1 = Calculator() | ||
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| print(result) | ||
| # >>> [0.0, 1, 0, 0, 0, 1, (snip) | ||
| # Register descriptor instance | ||
| calc1.register(Chi.Chi(type="path_cluster", order=4)) | ||
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| # Register descriptor class using preset | ||
| calc1.register(RingCount.RingCount) | ||
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| # Calculator constructor can register descriptors | ||
| calc2 = Calculator(Chi.Chi) | ||
| # Register all descriptors in module | ||
| calc1.register(ABCIndex) | ||
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| # Descriptors module contains all descriptors | ||
| calc3 = Calculator(descriptors) | ||
| # Calculate descriptors | ||
| result = calc1(benzene) | ||
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| # User can access all descriptor instances by descriptors property | ||
| print(calc3.descriptors) | ||
| # >>> (mordred.EccentricConnectivityIndex.EccentricConnectivityIndex(), (snip) | ||
| print(result) | ||
| # >>> [0.0, 1, 0, 0, 0, 1, (snip) | ||
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| # Calculator constructor can register descriptors | ||
| calc2 = Calculator(Chi.Chi) | ||
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| # Calculate descriptors | ||
| result = calc3(benzene) | ||
| # Descriptors module contains all descriptors | ||
| calc3 = Calculator(descriptors) | ||
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| # get first missing value | ||
| na1 = next(r for r in result if is_missing(r)) | ||
| # User can access all descriptor instances by descriptors property | ||
| print(calc3.descriptors) | ||
| # >>> (mordred.EccentricConnectivityIndex.EccentricConnectivityIndex(), (snip) | ||
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| # get reason | ||
| print(na1.error) | ||
| # >>> missing 3D coordinate | ||
| # Calculate descriptors | ||
| result = calc3(benzene) | ||
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| # get first missing value | ||
| na1 = next(r for r in result if is_missing(r)) | ||
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| # Delete all missing value | ||
| result = result.dropna() | ||
| # get reason | ||
| print(na1.error) | ||
| # >>> missing 3D coordinate | ||
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| # Delete all missing value | ||
| result = result.drop_missing() | ||
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| # convert to dict | ||
| print(result.asdict()) | ||
| # convert to dict | ||
| print(result.asdict()) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,23 @@ | ||
| from multiprocessing import freeze_support | ||
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| from rdkit import Chem | ||
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| from mordred import Calculator, descriptors | ||
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| mols = [ | ||
| Chem.MolFromSmiles('c1ccccc1'), | ||
| Chem.MolFromSmiles('c1ccccc1Cl'), | ||
| Chem.MolFromSmiles('c1ccccc1C'), | ||
| ] | ||
| if __name__ == "__main__": | ||
| freeze_support() | ||
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| mols = [ | ||
| Chem.MolFromSmiles("c1ccccc1"), | ||
| Chem.MolFromSmiles("c1ccccc1Cl"), | ||
| Chem.MolFromSmiles("c1ccccc1C"), | ||
| ] | ||
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| # Create Calculator | ||
| calc = Calculator(descriptors) | ||
| # Create Calculator | ||
| calc = Calculator(descriptors) | ||
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| # map method calculate multiple molecules (return generator) | ||
| print(list(calc.map(mols))) | ||
| # map method calculate multiple molecules (return generator) | ||
| print(list(calc.map(mols))) | ||
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| # pandas method calculate multiple molecules (return pandas DataFrame) | ||
| print(calc.pandas(mols)) | ||
| # pandas method calculate multiple molecules (return pandas DataFrame) | ||
| print(calc.pandas(mols)) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| import numpy as np | ||
| from pandas import Series, DataFrame | ||
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| from .util import is_missing | ||
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| __all__ = ("MordredDataFrame", "Series") | ||
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| class MordredDataFrame(DataFrame): | ||
| @property | ||
| def _constructor(self): | ||
| return self.__class__ | ||
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| def fill_missing(self, value=np.nan, inplace=False): | ||
| t = self if inplace else self.copy() | ||
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| t[t.applymap(is_missing)] = value | ||
| return t |
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