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[DOC] MkDocs Chemistry (#899)
* mkdocstrings on chemistry functions * Minor update to biology.py * Proper config for syntax highlighting * Switch to nord theme for syntax highlighting * [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * FLake8 fix. Co-authored-by: Zero <[email protected]>
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‎janitor/biology.py

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@@ -58,7 +58,6 @@ def join_fasta(
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Method chaining usage example:
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```python
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import pandas as pd
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import janitor.biology
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‎janitor/chemistry.py

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@@ -94,36 +94,38 @@ def smiles2mol(
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Functional usage example:
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.. code-block:: python
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```python
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import pandas as pd
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import janitor.chemistry
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import pandas as pd
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import janitor.chemistry
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df = pd.DataFrame(...)
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df = pd.DataFrame(...)
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df = janitor.chemistry.smiles2mol(
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df=df,
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smiles_column_name='smiles',
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mols_column_name='mols'
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)
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df = janitor.chemistry.smiles2mol(
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df=df,
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smiles_column_name='smiles',
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mols_column_name='mols'
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)
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```
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Method chaining usage example:
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.. code-block:: python
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import pandas as pd
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import janitor.chemistry
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```python
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import pandas as pd
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import janitor.chemistry
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df = pd.DataFrame(...)
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df = pd.DataFrame(...)
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df = df.smiles2mol(smiles_column_name='smiles',
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mols_column_name='mols')
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df = df.smiles2mol(
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smiles_column_name='smiles',
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mols_column_name='mols'
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)
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```
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A progressbar can be optionally used.
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- Pass in "notebook" to show a tqdm notebook progressbar. (ipywidgets must
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be enabled with your Jupyter installation.)
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- Pass in "terminal" to show a tqdm progressbar. Better suited for use
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- Pass in "notebook" to show a `tqdm` notebook progressbar.
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(`ipywidgets` must be enabled with your Jupyter installation.)
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- Pass in "terminal" to show a `tqdm` progressbar. Better suited for use
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with scripts.
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- "none" is the default value - progress bar will be not be shown.
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@@ -180,67 +182,70 @@ def morgan_fingerprint(
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Functional usage example:
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.. code-block:: python
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```python
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import pandas as pd
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import janitor.chemistry
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import pandas as pd
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import janitor.chemistry
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df = pd.DataFrame(...)
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df = pd.DataFrame(...)
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# For "counts" kind
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morgans = janitor.chemistry.morgan_fingerprint(
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df=df.smiles2mol('smiles', 'mols'),
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mols_column_name='mols',
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radius=3, # Defaults to 3
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nbits=2048, # Defaults to 2048
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kind='counts' # Defaults to "counts"
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)
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# For "counts" kind
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morgans = janitor.chemistry.morgan_fingerprint(
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df=df.smiles2mol('smiles', 'mols'),
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mols_column_name='mols',
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radius=3, # Defaults to 3
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nbits=2048, # Defaults to 2048
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kind='counts' # Defaults to "counts"
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)
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# For "bits" kind
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morgans = janitor.chemistry.morgan_fingerprint(
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df=df.smiles2mol('smiles', 'mols'),
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mols_column_name='mols',
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radius=3, # Defaults to 3
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nbits=2048, # Defaults to 2048
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kind='bits' # Defaults to "counts"
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)
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# For "bits" kind
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morgans = janitor.chemistry.morgan_fingerprint(
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df=df.smiles2mol('smiles', 'mols'),
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mols_column_name='mols',
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radius=3, # Defaults to 3
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nbits=2048, # Defaults to 2048
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kind='bits' # Defaults to "counts"
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)
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```
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Method chaining usage example:
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.. code-block:: python
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```python
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import pandas as pd
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import janitor.chemistry
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import pandas as pd
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import janitor.chemistry
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df = pd.DataFrame(...)
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df = pd.DataFrame(...)
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# For "counts" kind
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morgans = (
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df.smiles2mol('smiles', 'mols')
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.morgan_fingerprint(mols_column_name='mols',
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radius=3, # Defaults to 3
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nbits=2048, # Defaults to 2048
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kind='counts' # Defaults to "counts"
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)
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# For "counts" kind
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morgans = (
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df.smiles2mol('smiles', 'mols')
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.morgan_fingerprint(
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mols_column_name='mols',
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radius=3, # Defaults to 3
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nbits=2048, # Defaults to 2048
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kind='counts' # Defaults to "counts"
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)
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)
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# For "bits" kind
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morgans = (
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df.smiles2mol('smiles', 'mols')
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.morgan_fingerprint(mols_column_name='mols',
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radius=3, # Defaults to 3
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nbits=2048, # Defaults to 2048
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kind='bits' # Defaults to "counts"
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)
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# For "bits" kind
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morgans = (
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df
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.smiles2mol('smiles', 'mols')
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.morgan_fingerprint(
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mols_column_name='mols',
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radius=3, # Defaults to 3
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nbits=2048, # Defaults to 2048
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kind='bits' # Defaults to "counts"
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)
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)
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```
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If you wish to join the morgan fingerprints back into the original
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dataframe, this can be accomplished by doing a `join`,
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because the indices are preserved:
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.. code-block:: python
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joined = df.join(morgans)
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```python
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joined = df.join(morgans)
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```
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:param df: A pandas DataFrame.
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:param mols_column_name: The name of the column that has the RDKIT
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The molecular descriptors are from the rdkit.Chem.rdMolDescriptors:
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Chi0n, Chi0v, Chi1n, Chi1v, Chi2n, Chi2v, Chi3n, Chi3v,
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Chi4n, Chi4v, ExactMolWt, FractionCSP3, HallKierAlpha, Kappa1,
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Kappa2, Kappa3, LabuteASA, NumAliphaticCarbocycles,
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NumAliphaticHeterocycles, NumAliphaticRings, NumAmideBonds,
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NumAromaticCarbocycles, NumAromaticHeterocycles, NumAromaticRings,
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NumAtomStereoCenters, NumBridgeheadAtoms, NumHBA, NumHBD,
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NumHeteroatoms, NumHeterocycles, NumLipinskiHBA, NumLipinskiHBD,
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NumRings, NumSaturatedCarbocycles, NumSaturatedHeterocycles,
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NumSaturatedRings, NumSpiroAtoms, NumUnspecifiedAtomStereoCenters,
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TPSA.
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```
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Chi0n, Chi0v, Chi1n, Chi1v, Chi2n, Chi2v, Chi3n, Chi3v,
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Chi4n, Chi4v, ExactMolWt, FractionCSP3, HallKierAlpha, Kappa1,
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Kappa2, Kappa3, LabuteASA, NumAliphaticCarbocycles,
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NumAliphaticHeterocycles, NumAliphaticRings, NumAmideBonds,
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NumAromaticCarbocycles, NumAromaticHeterocycles, NumAromaticRings,
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NumAtomStereoCenters, NumBridgeheadAtoms, NumHBA, NumHBD,
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NumHeteroatoms, NumHeterocycles, NumLipinskiHBA, NumLipinskiHBD,
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NumRings, NumSaturatedCarbocycles, NumSaturatedHeterocycles,
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NumSaturatedRings, NumSpiroAtoms, NumUnspecifiedAtomStereoCenters,
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TPSA.
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```
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Functional usage example:
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.. code-block:: python
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import pandas as pd
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import janitor.chemistry
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```python
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import pandas as pd
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import janitor.chemistry
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df = pd.DataFrame(...)
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df = pd.DataFrame(...)
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mol_desc = janitor.chemistry.molecular_descriptors(
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mol_desc = (
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janitor.chemistry.molecular_descriptors(
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mols_column_name='mols'
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)
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)
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```
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Method chaining usage example:
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.. code-block:: python
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```python
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import pandas as pd
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import janitor.chemistry
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import pandas as pd
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import janitor.chemistry
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df = pd.DataFrame(...)
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df = pd.DataFrame(...)
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mol_desc = (
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df.smiles2mol('smiles', 'mols')
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.molecular_descriptors(mols_column_name='mols')
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)
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mol_desc = (
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df.smiles2mol('smiles', 'mols')
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.molecular_descriptors(mols_column_name='mols')
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)
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```
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If you wish to join the molecular descriptors back into the original
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dataframe, this can be accomplished by doing a `join`,
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because the indices are preserved:
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.. code-block:: python
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joined = df.join(mol_desc)
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```python
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joined = df.join(mol_desc)
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```
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:param df: A pandas DataFrame.
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:param mols_column_name: The name of the column that has the RDKIT mol
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.. code-block:: python
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import pandas as pd
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import janitor.chemistry
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```python
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import pandas as pd
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import janitor.chemistry
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df = pd.DataFrame(...)
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df = pd.DataFrame(...)
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maccs = janitor.chemistry.maccs_keys_fingerprint(
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df=df.smiles2mol('smiles', 'mols'),
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mols_column_name='mols'
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)
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maccs = janitor.chemistry.maccs_keys_fingerprint(
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df=df.smiles2mol('smiles', 'mols'),
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mols_column_name='mols'
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)
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```
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Method chaining usage example:
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.. code-block:: python
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```python
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import pandas as pd
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import janitor.chemistry
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import pandas as pd
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import janitor.chemistry
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df = pd.DataFrame(...)
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df = pd.DataFrame(...)
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maccs = (
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df.smiles2mol('smiles', 'mols')
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.maccs_keys_fingerprint(mols_column_name='mols')
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)
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maccs = (
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df.smiles2mol('smiles', 'mols')
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.maccs_keys_fingerprint(mols_column_name='mols')
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)
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```
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If you wish to join the maccs keys fingerprints back into the
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original dataframe, this can be accomplished by doing a `join`,
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because the indices are preserved:
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.. code-block:: python
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joined = df.join(maccs_keys_fingerprint)
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```python
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joined = df.join(maccs_keys_fingerprint)
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```
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:param df: A pandas DataFrame.
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:param mols_column_name: The name of the column that has the RDKIT mol

‎mkdocs.yml

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# Taken from here: https://squidfunk.github.io/mkdocs-material/extensions/codehilite/
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markdown_extensions:
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- codehilite
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# - codehilite
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- admonition
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- pymdownx.highlight:
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use_pygments: false
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- pymdownx.inlinehilite
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# - pymdownx.tabbed
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# - pymdownx.arithmatex
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# - pymdownx.details
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extra_javascript:
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- https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML
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- https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.7.2/highlight.min.js
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- js/config.js
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extra_css:
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- css/nb_mods.css
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- css/apidocs.css
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# This sets the theme for syntax highlighting.
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# Theme names are available here: https://highlightjs.org/static/demo/
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# Not sure how the theme names map onto CSS filenames though.
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- https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.7.2/styles/nord.min.css
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repo_name: "ericmjl/pyjanitor"
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repo_url: "https://github.com/ericmjl/pyjanitor"

‎mkdocs/js/config.js

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hljs.highlightAll();

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