rstoolbox.io.
parse_rosetta_file
(filename, description=None, multi=False)¶Read a Rosetta score or silent file and returns the design population
in a DesignFrame
.
By default, it will pick the data contained in all the score columns with the exception of positional scores (such as per-residue ddg). The user can specify scores to be ignored.
When working with silent files, extra information can be picked, such as sequence and secondary structure data, residue labels or positional scores. The fine control of these options is explained in detail in tutorial: reading Rosetta.
Some basic usage cases:
# (1) The default scenario, just read scores from a single file.
df = rstoolbox.io.parse_rosetta_file("silentfile")
# (2) Reading from multiple files. Assumes all files start with
# the particular prefix.
df = rstoolbox.io.parse_rosetta_file("silentfile", multi=True)
# (3) Getting all scores and the sequence of each design.
description = {'sequence': 'A'}
df = rstoolbox.io.parse_rosetta_file("silentfile", description)
# (4) Get only total_score and RMSD, and rename total_score to score.
description = {'scores': ['RMSD'], 'scores_rename': {'total_score': 'score'}}
df = rstoolbox.io.parse_rosetta_file("silentfile", description)
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Example
In [1]: from rstoolbox.io import parse_rosetta_file
...: 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_2seq.minisilent.gz")
...: df.head(2)
...:
Out[1]:
score fa_atr fa_rep fa_sol fa_intra_rep fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 rama omega fa_dun p_aa_pp yhh_planarity ref BUNS B_ni_mtcontacts B_ni_rmsd B_ni_rmsd_threshold B_ni_trials GRMSD2Target GRMSD2Template LRMSD2Target LRMSDH2Target LRMSDLH2Target cav_vol design_score packstat rmsd_drift time description
0 -206.678 -1510.021 268.657 853.020 2.921 -145.015 5.825 -150.177 -2.452 -13.326 -36.936 0.0 -28.499 42.312 551.509 -23.219 0.000 -21.277 22.0 57.0 0.568 5.0 1.0 1.976 1.927 4.404 4.055 2.49 387.371 -255.445 0.633 1.677 3194.0 test_3lhp_binder_labeled_00001
1 -214.362 -1490.968 267.328 824.258 3.019 -133.421 6.018 -151.609 -2.452 -12.584 -33.021 0.0 -29.998 38.315 545.056 -23.612 0.003 -20.693 14.0 54.0 0.333 5.0 1.0 2.659 2.417 4.469 4.124 2.73 332.657 -264.239 0.577 2.240 3210.0 test_3lhp_binder_labeled_00002