rstoolbox.components.
SequenceFrame
(*args, **kwargs)¶Per position frequency occurrence for a set of decoys.
The SequenceFrame
extends pandas.DataFrame
.
Ideally, in this pandas.DataFrame
, each column represents a ResidueType
(or NucleotideType) and each row a sequence position.
A reference_sequence
can be provided, but it has to be the exact same
length as the sequence expressed in the pandas.DataFrame
.
As it represents sequence, unless the SequenceFrame
is generated by
slicing another, one should expect the index to start in 1.
Methods
add_reference (seqID[, sequence, structure, …]) |
Single access to add_reference_sequence() , add_reference_structure() and add_reference_shift() . |
add_reference_sequence (seqID, sequence) |
Add a reference_sequence attached to chain seqID . |
add_reference_shift (seqID, shift[, shift_labels]) |
Add a reference_shift attached to a chain seqID . |
add_reference_structure (seqID, structure) |
Add a reference_structure attached to chain seqID . |
delete_empty ([pick]) |
Setter/Getter for the delete empty configuration. |
delete_extra ([pick]) |
Setter/Getter for the delete extra configuration. |
delete_reference (seqID[, shift_labels]) |
Remove all reference data regarding a particular seqID. |
get_available_references () |
List which decoy chain identifiers have some kind of reference data. |
get_key_residues ([key_residues]) |
Get positions of interest. |
get_reference_sequence (seqID[, key_residues]) |
Get the reference_sequence attached to chain seqID . |
get_reference_shift (seqID) |
Get a reference_shift attached to a particular seqID . |
get_reference_structure (seqID[, key_residues]) |
Get the reference_structure attached to chain seqID . |
has_reference_sequence (seqID) |
Checks if there is a reference_sequence for sequID . |
has_reference_structure (seqID) |
Checks if there is a reference_structure for seqID . |
is_transposed () |
Assert if the SequenceFrame is found as expected (ResidueType as column) or transposed. |
to_bits () |
Change the sequenceFrame from frequency to bits. |
transfer_reference (df) |
Transfer reference data from one container to another. |