rstoolbox.components.FragmentFrame

class rstoolbox.components.FragmentFrame(*args, **kw)

Data container for Fragment data.

Extends pandas.DataFrame adding some functionalities in order to facilitate analysis, plotting and comparisson.

Filled through the functions provided through this library, each row represents a position of a fragment, while columns describe the properties.

. rubric:: Example

In [1]: from rstoolbox.io import parse_rosetta_fragments
   ...: import pandas as pd
   ...: pd.set_option('display.width', 1000)
   ...: pd.set_option('display.max_columns', 500)
   ...: df = parse_rosetta_fragments("../rstoolbox/tests/data/wauto.200.3mers.gz")
   ...: df.head()
   ...: 
Out[1]: 
    pdb  frame  neighbors  neighbor  position  size aa sse      phi      psi    omega
0  2hox  1      200        1         1         3     S  L  -154.974  117.297  176.201
1  2hox  1      200        1         2         3     E  E  -133.145  153.460  177.064
2  2hox  1      200        1         3         3     Y  E  -77.588   132.516  177.184
3  1ihu  1      200        2         1         3     I  L  -60.621   119.545 -179.669
4  1ihu  1      200        2         2         3     Q  E  -130.878  145.002 -179.783

Methods

add_quality_measure(filename[, pdbfile]) Add RMSD quality measure to the fragment data.
add_source_file(file) Adds a source file to the FragmentFrame.
has_source_file() Checks if there is a source file added.
slice_region(ini, end) Retrieve only fragments within certain positions.
top_limit(limit) Remove all frames whose position puts the frames over a given limit.
is_comparable(df) Evaluate if the current FragmentFrame is comparable to the provided one.
renumber([ini]) Make the fragment set start at the given position.
sample_top_neighbors([max_count]) Limit to the top selected neighbors for each frame.
coerce() Make fragment data coherent.
order() Properly reorder the FragmentFrame.
add_fragments(fragments, ini[, how]) Add to a given position a set of fragments more fragments.
renumber([ini]) Make the fragment set start at the given position.
sample_top_neighbors([max_count]) Limit to the top selected neighbors for each frame.
select_quantile([quantile]) Returns fragments under the rmsd threshold of the specified uantile.
make_sequence_matrix([frequency, round_data]) Generate a PSSM-like matrix from the fragments.
make_per_position_frequency_network() Generate a graph representation of the per-residue frequency.
make_frequency_network([use_rmsd]) Generate a graph with per-position frequency between residue types at each position.
quick_consensus_sequence() Consensus sequence with the highest representative per position.
quick_consensus_secondary_structure() Consensus secondary structure with the highest representative per position.