Index

A

append() (reacnetgenerator.utils.WriteBuffer method)

appendIfNotNone() (in module reacnetgenerator.utils) atom_index (reacnetgenerator.timedoutput.Molecule attribute)

B

bonds (reacnetgenerator.timedoutput.Molecule attribute)

buff (reacnetgenerator.utils.WriteBuffer attribute) bytestolist() (in module reacnetgenerator.utils)

C

calculate_rate() (in module reacnetgenerator.tools) check() (reacnetgenerator.utils.WriteBuffer method) check_zero_signal() (in module reacnetgenerator.utils)

checksha256() (in module reacnetgenerator.utils) compare_semantic_manifests() (in module reacnetgenerator.timedoutput) compress() (in module reacnetgenerator.utils) count (reacnetgenerator.timedoutput.ReactionEvent attribute)

D

decompress() (in module reacnetgenerator.utils) download_file() (in module reacnetgenerator.utils)

download_multifiles() (in module reacnetgenerator.utils) dps() (in module reacnetgenerator.dps) dps_reaction() (in module reacnetgenerator.dps)

E

enable_viewboxing (reacnetgenerator.utils.SCOUROPTIONS attribute)

end_frame (reacnetgenerator.timedoutput.MoleculeRange attribute) extend() (reacnetgenerator.utils.WriteBuffer method)

F

flush() (reacnetgenerator.utils.WriteBuffer method)

Frame (class in reacnetgenerator.timedoutput) frame (reacnetgenerator.timedoutput.Frame attribute)

G

gather_download_files() (in module reacnetgenerator.utils) get_timestep_value() (in module reacnetgenerator.utils)

GUI (class in reacnetgenerator.gui) gui() (in module reacnetgenerator.gui) (reacnetgenerator.gui.GUI method)

I

idx_to_signal() (in module reacnetgenerator.utils) iter_frames() (in module reacnetgenerator.timedoutput) iter_molecule_ranges() (in module reacnetgenerator.timedoutput)

iter_molecules() (in module reacnetgenerator.timedoutput) iter_reaction_events() (in module reacnetgenerator.timedoutput) iter_reaction_types() (in module reacnetgenerator.timedoutput) iter_species() (in module reacnetgenerator.timedoutput)

L

listtobytes() (in module reacnetgenerator.utils)

listtostirng() (in module reacnetgenerator.utils)

M

main() (in module reacnetgenerator.timedoutputcheck) main_parser() (in module reacnetgenerator.commandline) module reacnetgenerator reacnetgenerator.commandline reacnetgenerator.dps reacnetgenerator.gui reacnetgenerator.reacnetgen reacnetgenerator.schemas reacnetgenerator.timedoutput reacnetgenerator.timedoutputcheck reacnetgenerator.tools reacnetgenerator.utils

Molecule (class in reacnetgenerator.timedoutput) molecule_id (reacnetgenerator.timedoutput.Molecule attribute) (reacnetgenerator.timedoutput.MoleculeRange attribute) MoleculeRange (class in reacnetgenerator.timedoutput) multiopen() (in module reacnetgenerator.utils) must_be_list() (in module reacnetgenerator.utils)

N

newlines (reacnetgenerator.utils.SCOUROPTIONS attribute)

P

parm2cmd() (in module reacnetgenerator.commandline)

produce() (in module reacnetgenerator.utils)

R

reacnetgenerator module ReacNetGenerator (class in reacnetgenerator) reacnetgenerator.commandline module reacnetgenerator.dps module reacnetgenerator.gui module reacnetgenerator.reacnetgen module reacnetgenerator.schemas module reacnetgenerator.timedoutput module reacnetgenerator.timedoutputcheck module reacnetgenerator.tools module

reacnetgenerator.utils module reaction_type_id (reacnetgenerator.timedoutput.ReactionEvent attribute) ReactionEvent (class in reacnetgenerator.timedoutput) read_compressed_block() (in module reacnetgenerator.utils) read_metadata() (in module reacnetgenerator.timedoutput) read_reactions() (in module reacnetgenerator.tools) read_schema_descriptor() (in module reacnetgenerator.timedoutput) read_species() (in module reacnetgenerator.tools) remove_descriptions (reacnetgenerator.utils.SCOUROPTIONS attribute) remove_descriptive_elements (reacnetgenerator.utils.SCOUROPTIONS attribute) remove_metadata (reacnetgenerator.utils.SCOUROPTIONS attribute) remove_titles (reacnetgenerator.utils.SCOUROPTIONS attribute) returnkeys() (reacnetgenerator.utils.SharedRNGData method) root (reacnetgenerator.gui.GUI property) run() (in module reacnetgenerator) run_mp() (in module reacnetgenerator.utils)

S

SCOUROPTIONS (class in reacnetgenerator.utils) semantic_manifest() (in module reacnetgenerator.timedoutput) SharedRNGData (class in reacnetgenerator.utils) shorten_ids (reacnetgenerator.utils.SCOUROPTIONS attribute) source_frame (reacnetgenerator.timedoutput.Frame attribute) source_id (reacnetgenerator.timedoutput.Frame attribute)

species_id (reacnetgenerator.timedoutput.Molecule attribute) start_frame (reacnetgenerator.timedoutput.MoleculeRange attribute) strip_comments (reacnetgenerator.utils.SCOUROPTIONS attribute) strip_ids (reacnetgenerator.utils.SCOUROPTIONS attribute) strip_xml_prolog (reacnetgenerator.utils.SCOUROPTIONS attribute) strip_xml_space_attribute (reacnetgenerator.utils.SCOUROPTIONS attribute)

T

timestep (reacnetgenerator.timedoutput.Frame attribute)

transition (reacnetgenerator.timedoutput.ReactionEvent attribute)

V

validate_timed_output() (in module reacnetgenerator.timedoutput)

W

WriteBuffer (class in reacnetgenerator.utils)