rstoolbox.analysis.
secondary_structure_percentage
(df, seqID, key_residues=None)¶Calculate the percentage of the different secondary structure types.
Requires secondary structure data.
Adds 3 new columns to the data container:
New Column | Data Content |
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structure_<seqID>_H | Percentage of alpha helices in the structure. |
structure_<seqID>_E | Percentage of beta sheets in the structure. |
structure_<seqID>_L | Percentage of loops in the structure. |
Parameters: |
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Returns: | Union[ |
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Raises: |
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Example
In [1]: from rstoolbox.io import parse_rosetta_file
...: from rstoolbox.analysis import secondary_structure_percentage
...: import pandas as pd
...: pd.set_option('display.width', 1000)
...: pd.set_option('display.max_columns', 500)
...: df = parse_rosetta_file("../rstoolbox/tests/data/input_ssebig.minisilent.gz",
...: {'scores': ['score'], 'structure': 'C'})
...: df = secondary_structure_percentage(df, 'C')
...: df.head()
...:
Out[1]:
score structure_C structure_C_H structure_C_E structure_C_L
0 -64.070 LEEEEEEELLLEEEEEEELLLLHHHHHHHHHHHHLLLLLLLLLLLEEEELLLEEEELL 0.206897 0.379310 0.413793
1 -70.981 LEEEEEEELLEEEEEEEELLLLHHHHHHHHHHHLLLLLLLLLLLEEEELLLLLEEEEL 0.189655 0.396552 0.413793
2 -43.863 LEEEEEEELLEEEEEEEELLLLHHHHHHHHHHHHLLLLLLLLLLEEEEELLLEEEEEL 0.206897 0.431034 0.362069
3 -75.847 LLLEEEEELLEEEEEELLLLLLHHHHHHHHHHHHLLLLLLLLLLEEEEELLLEEEEEL 0.206897 0.362069 0.431034
4 -55.347 LEEEEEEELLLEEEEEEELLLLHHHHHHHHHHHHLLLLLLLLLLLEEEELLLEEEELL 0.206897 0.379310 0.413793