forgi.graph.sequence module¶

class forgi.graph.sequence.MissingResidue(resid, res_name)[source]¶

Bases: object

Parameters:	resid – A fgr.RESID instance of a string. resname – A string. Probably one of “AUGC”.

classmethod from_bg_fields(parts)[source]¶

Used during loading of the bg_file.

Parameters:	parts – A list of strings. If the first is not “missing”, None is returned
Returns:	Either a MissingResidue instance or None

to_bg_string()[source]¶

class forgi.graph.sequence.SeqidList(arg)[source]¶

Bases: _abcoll.Sequence

index(elem)[source]¶

class forgi.graph.sequence.Sequence(seq, seqids, missing_residues=None, modifications=None)[source]¶

Bases: object

A class holding the RNA sequence.

It supports 2 indexing conventions (see below), missing residues and modified nucleotids.

The two indexing conventions are:

• 1-based indexing into the sequence for which structure information is available This uses indices of type integer. Integer based indexing can not address missing residues!
• Indexing using PDB-style numbers (They can start at any positive or negative number and may contain insertion codes or gaps.) This uses indices of type fgr.RESID PDB-Style indices may address missing residues (Reidues for which only sequence but no structure information is present).

Parameters:	seq – A string missing_residues – A list of dictionaries with the following keys: “res_name”, “chain”, “ssseq”, “insertion”

backbone_breaks_after¶

Breakpoints as 1-based indices

define_length(d)[source]¶

get_bg_str()[source]¶

Used during bg-file creation

is_valid()[source]¶

iter_modifications()[source]¶

Iter over tuples seq_id, modified residue code

iter_resids(start, stop, include_missing)[source]¶

to_integer(resid)[source]¶

to_resid(i)[source]¶

with_missing¶

Allows slices with missing residues!

with_modifications¶

class forgi.graph.sequence.SequenceLoader[source]¶

Load the sequence-related part during loading of bg-files

consume_fields(parts)[source]¶

Read one line from the forgi file.

Returns True, if the line was used/ understood, False otherwise

sequence¶

forgi.graph.sequence.to_0_based(key)[source]¶