mmtfPyspark.filters.containsSequenceRegex module¶

References¶

• Sequence motif: https://en.wikipedia.org/wiki/Sequence_motif

Examples¶

Short sequence fragment – NPPTP:

The motif search supports wildcard queries by placing a ‘.’ at the variable residue position. A query for an SH3 domains using the consequence sequence -X-P-P-X-P (where X is a variable residue and P is Proline),can be expressed as: .PP.P

Ranges of variable residues are specified by the {n} notation, where n is the number of variable residues. To query a motif with seven variables between residues W and G and twenty variable residues between G and L use the following notation:

W.{7}G.{20}L

Variable ranges are expressed by the {n,m} notation, where n is the minimum and m the maximum number of repetitions. For example the zinc finger motif that binds Zn in a DNA-binding domain can be expressed as:

C.{2,4}C.{12}H.{3,5}H

The ‘^’ operator searches for sequence motifs at the beginning of a protein sequence. The following two queries find sequences with N-terminal Histidine tags:

^HHHHHH or ^H{6}

Square brackets specify alternative residues at a particular position. The Walker (P loop) motif that binds ATP or GTP can be expressed as:

[AG].{4}GK[ST] A or G are followed by 4 variable residues, then G and K, and finally S or T

class ContainsSequenceRegex(regularExpression)[source]¶

Bases: object

This filter returns true if the polymer sequence motif matches the specified regular expression.

Attributes

regularExpression

(str) The regular expression of protein sequence

Methods

__call__(t)

Call self as a function.