# OAT utilities documentation ## Data structures ```{eval-rst} .. toctree:: :maxdepth: 2 .. currentmodule:: oxDNA_analysis_tools .. autosummary:: :nosignatures: oxDNA_analysis_tools.UTILS.data_structures.Chunk oxDNA_analysis_tools.UTILS.data_structures.ConfInfo oxDNA_analysis_tools.UTILS.data_structures.TrajInfo oxDNA_analysis_tools.UTILS.data_structures.Configuration oxDNA_analysis_tools.UTILS.data_structures.TopInfo oxDNA_analysis_tools.UTILS.data_structures.System oxDNA_analysis_tools.UTILS.data_structures.Strand oxDNA_analysis_tools.UTILS.data_structures.Monomer .. autoclass:: oxDNA_analysis_tools.UTILS.data_structures.Chunk .. autoclass:: oxDNA_analysis_tools.UTILS.data_structures.ConfInfo .. autoclass:: oxDNA_analysis_tools.UTILS.data_structures.TrajInfo .. autoclass:: oxDNA_analysis_tools.UTILS.data_structures.Configuration .. autoclass:: oxDNA_analysis_tools.UTILS.data_structures.TopInfo .. autoclass:: oxDNA_analysis_tools.UTILS.data_structures.System .. autoclass:: oxDNA_analysis_tools.UTILS.data_structures.Strand .. autoclass:: oxDNA_analysis_tools.UTILS.data_structures.Monomer ``` ## Geometry utilities ```{eval-rst} .. toctree:: :maxdepth: 2 .. currentmodule:: oxDNA_analysis_tools .. autosummary:: :nosignatures: oxDNA_analysis_tools.UTILS.geom.fit_plane oxDNA_analysis_tools.UTILS.geom.get_RNA_axis oxDNA_analysis_tools.UTILS.geom.get_DNA_axis .. autofunction:: oxDNA_analysis_tools.UTILS.geom.fit_plane .. autofunction:: oxDNA_analysis_tools.UTILS.geom.get_RNA_axis .. autofunction:: oxDNA_analysis_tools.UTILS.geom.get_DNA_axis ``` ## iPython oxView plugin ```{eval-rst} .. toctree:: :maxdepth: 2 .. currentmodule:: oxDNA_analysis_tools .. autosummary:: :nosignatures: oxDNA_analysis_tools.UTILS.oxview.display_files oxDNA_analysis_tools.UTILS.oxview.from_path oxDNA_analysis_tools.UTILS.oxview.oxdna_conf oxDNA_analysis_tools.UTILS.oxview.loro_patchy_conf oxDNA_analysis_tools.UTILS.oxview.flro_patchy_conf .. autofunction:: oxDNA_analysis_tools.UTILS.oxview.display_files .. autofunction:: oxDNA_analysis_tools.UTILS.oxview.from_path .. autofunction:: oxDNA_analysis_tools.UTILS.oxview.oxdna_conf .. autofunction:: oxDNA_analysis_tools.UTILS.oxview.loro_patchy_conf .. autofunction:: oxDNA_analysis_tools.UTILS.oxview.flro_patchy_conf ``` ## Multiprocesser ```{eval-rst} .. toctree:: :maxdepth: 2 .. currentmodule:: oxDNA_analysis_tools .. autosummary:: :nosignatures: oxDNA_analysis_tools.UTILS.oat_multiprocesser.oat_multiprocesser .. autofunction:: oxDNA_analysis_tools.UTILS.oat_multiprocesser.oat_multiprocesser ``` ## Rye reader ```{eval-rst} .. toctree:: :maxdepth: 2 .. currentmodule:: oxDNA_analysis_tools .. autosummary:: :nosignatures: oxDNA_analysis_tools.UTILS.RyeReader.Chunker oxDNA_analysis_tools.UTILS.RyeReader.linear_read oxDNA_analysis_tools.UTILS.RyeReader.get_confs oxDNA_analysis_tools.UTILS.RyeReader.get_top_info oxDNA_analysis_tools.UTILS.RyeReader.get_top_info_from_traj oxDNA_analysis_tools.UTILS.RyeReader.get_traj_info oxDNA_analysis_tools.UTILS.RyeReader.describe oxDNA_analysis_tools.UTILS.RyeReader.strand_describe oxDNA_analysis_tools.UTILS.RyeReader.get_input_parameter oxDNA_analysis_tools.UTILS.RyeReader.inbox oxDNA_analysis_tools.UTILS.RyeReader.write_conf oxDNA_analysis_tools.UTILS.RyeReader.conf_to_str oxDNA_analysis_tools.UTILS.RyeReader.get_top_string .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.Chunker .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.linear_read .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.get_confs .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.get_top_info .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.get_top_info_from_traj .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.get_traj_info .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.describe .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.strand_describe .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.get_input_parameter .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.inbox .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.write_conf .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.conf_to_str .. autofunction:: oxDNA_analysis_tools.UTILS.RyeReader.get_top_string