The converters module¶

This module contains some high-level utility functions to interconvert between different file formats. When installed it also creates the following standalone executable scripts:

oxDNA_LAMMPS input_file [bond_file], which calls oxDNA_LAMMPS_command_line().
oxDNA_cogli input_file, which calls oxDNA_cogli_command_line().
LAMMPS_cogli input_file, which calls LAMMPS_cogli_command_line().

`oxDNA_LAMMPS`	Convert an oxDNA configuration into a LAMMPS data file.
`oxDNA_LAMMPS_command_line`	Convert the command-line supplied oxDNA configuration into a LAMMPS data file.
`oxDNA_cogli`	Convert an oxDNA configuration into a cogli file.
`oxDNA_cogli_command_line`	Convert the command-line supplied oxDNA configuration into a cogli file.
`LAMMPS_cogli`	Convert a LAMMPS data/dump file into a cogli file.
`LAMMPS_cogli_command_line`	Convert the command-line supplied LAMMPS data/dump file into a cogli file.

baggianalysis.converters.oxDNA_LAMMPS(input_file, output_file, bond_file=None, datafile_type=None)¶

Convert an oxDNA configuration into a LAMMPS data file.

Parameters

input_file (str) – The name of the input oxDNA configuration
output_file (str) – The name of the output LAMMPS data file
bond_file (str) – The name of the bond file that contains the system’s topology
datafile_type (str) – The type of the LAMMPS data file, which by default is “atomic”

baggianalysis.converters.oxDNA_LAMMPS_command_line()¶

Convert the command-line supplied oxDNA configuration into a LAMMPS data file.

The name of the output file is the same as the input file plus ‘.lammps’.

baggianalysis.converters.oxDNA_cogli(input_file, output_file)¶

Convert an oxDNA configuration into a cogli file.

Parameters

input_file (str) – The name of the input oxDNA configuration
output_file (str) – The name of the output cogli file

baggianalysis.converters.oxDNA_cogli_command_line()¶

Convert the command-line supplied oxDNA configuration into a cogli file.

The name of the output file is the same as the input file plus ‘.mgl’.

baggianalysis.converters.LAMMPS_cogli(input_file, output_file)¶

Convert a LAMMPS data/dump file into a cogli file.

Parameters

input_file (str) – The name of the LAMMPS data file
output_file (str) – The name of the output cogli file

baggianalysis.converters.LAMMPS_cogli_command_line()¶

Convert the command-line supplied LAMMPS data/dump file into a cogli file.

The name of the output file is the same as the input file plus ‘.mgl’.