readers

Reads oxDNA configuration and topology files.

readers.py includes the class: LorenzoReader

class readers.LorenzoReader(configuration, topology, check_overlap=False)

Reader for oxDNA configurations and topologies.

Parameters:

• configuration – oxDNA configuration/trajectory file
• topology – oxDNA topology file
• check_overlap – boolean. If true, check for nucleotide overlaps in the configuration.

get_system(only_strand_ends=False, N_skip=0)

Returns a base.System object by reading one configuration from the given configuration/trajectory file. After reaching the end of the configuration file, returns False.

Parameters:

• only_strand_ends – boolean. If true, a strand will contain only the first and the last nucleotide.
• N_skip – number of configurations to skip in the trajectory file