generateΒΆ

Generates oxDNA configuration and topology files.

Usage:

python generate.py filename box_side
Args:
  • filename: path to text file with a format described below
  • box_side: length of box side

Reads a text file with the following format:

  • Each line contains the sequence for a single strand (A,C,T,G). The nucleotides can be specified by (case insensitive) letter (A, C, G, T), random (X), strong (S) and weak (W).
  • Options: DOUBLE, CIRCULAR, DOUBLE CIRCULAR
Example:

  • Two ssDNA (single stranded DNA):

    ATATATA

    GCGCGCG

  • Two strands, one double stranded, the other single stranded:

    DOUBLE AGGGCT

    CCTGTA

  • One dsDNA that frays only on one side:

    DOUBLE SSXXXXXXWW

  • One dsDNA that frays very little but has TATA in the middle:

    DOUBLE SSXXXXTATAXXXXSS

  • Two strands, one double stranded circular, the other single stranded circular:

    DOUBLE CIRCULAR AGAGGTAGGAGGATTTGCTTGAGCTTCGAGAGCTTCGAGATTCGATCAGGGCT

    CIRCULAR CCTGTAAGGAGATCGGAGAGATTCGAGAGGATCTGAGAGCTTAGCT