forgi.utilities.numbered_dotbracket module¶
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class
forgi.utilities.numbered_dotbracket.NumberedDotbracket(dotbracket_str='', residue_numbers=None, helix_ends=None)[source]¶ Parameters: - dotbracket_str – A string
- numbers (residue) – A list of integers or forgi RESIDS. Same length as dotbracket_str
- helix_ends –
- If a basepair represents a helix or
- stem with missing residues,
The helix end give the last/ first missing(condensed)
residue number which is represented by this basepair.
I.e. the basepair of the helix that is at the 3’ end
of the forward strand.
It is a list with the same length as residue_numers.
- Example 1. Every nucleotide only represents itself::
- dotbracket_str (((..))) residue numbers 12345678 helix_ends 12345678
- Example 2. The same helix as Ex. 1, now condensed.
- The helix 1-3,6-8 is represented by the basepair 1-8:: dotbracket_str (..) residue numbers 1458 helix_ends 3456 Here the nucleotide 1 represents one strand of the helix, going from 1 to 3. The nucleotide 8 represents the other strand, going from 6 to 8.
The value for helix ends for unpaired nucleotides is undefined and should ignored.
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condensed(remove_helices_shorter_than=3)[source]¶ Return input with consecutive basepairs remove_unpaired
Parameters: - dotbracket – A dotbracket string
- residue_numbers – A list of residue numbers, with same length as dotbracket
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without_short_helices(min_length)[source]¶ Check the stems if the correspond to the minimum length given by the Users
Parameters: min_length – minimum stem length
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without_substr(pattern)[source]¶ Return number of occurrences of pattern and a NumberedDotbracket all occurrences removed.
Occurrences of the pattern are removed recursicvely. E.g.: The pattern “ab” will be removed from “aabb” two times. E.g.: two occurrences of “([)]” will be removed from “(([)][)]”