Index

A

add_argument() (seamm_util.argument_parser.ArgumentParser method) add_argument_group() (seamm_util.argument_parser.ArgumentParser method) add_axis() (seamm_util.plotting.Plot method) add_creator() (seamm_util.zenodo.Record method) add_file() (seamm_util.zenodo.Record method) add_keyword() (seamm_util.zenodo.Record method) add_parser() (seamm_util.argument_parser.ArgumentParser method) add_plot() (seamm_util.plotting.Figure method) add_prolog() (seamm_util.configuration.Configuration method) add_section() (seamm_util.configuration.Configuration method) add_trace() (seamm_util.plotting.Plot method) add_version() (seamm_util.zenodo.Zenodo method)

addHandler() (seamm_util.printing.Printer method) addLevelName() (in module seamm_util.printing) analyze_autocorrelation() (in module seamm_util.md_statistics) append() (seamm_util.printing.PlaceHolder method) ar1() (in module seamm_util.md_statistics) ArgumentParser (class in seamm_util.argument_parser) atom_types() (seamm_util.water_models.SPC method) (seamm_util.water_models.SPC_E method) (seamm_util.water_models.TIP3P method) authors (seamm_util.zenodo.Record property) axes (seamm_util.plotting.Plot property) Axis (class in seamm_util.plotting)

B

basicConfig() (in module seamm_util.printing)

C

callHandlers() (seamm_util.printing.Printer method) check_executable() (in module seamm_util.check_executable) clean() (in module seamm_util.variable_names) CompactJSONEncoder (class in seamm_util.compact_json_encoder) conceptdoi (seamm_util.zenodo.Record property) Configuration (class in seamm_util.configuration)

CONTAINER_TYPES (seamm_util.compact_json_encoder.CompactJSONEncoder attribute) coordinates() (seamm_util.water_models.Water method) copy() (seamm_util.dictionary.Dictionary method) (seamm_util.output.Output method) create_model() (seamm_util.water_models.Water static method) create_record() (seamm_util.zenodo.Zenodo method) creators (seamm_util.zenodo.Record property)

D

data (seamm_util.zenodo.Record attribute) default() (seamm_util.seamm_json.JSONEncoder method) default_units() (in module seamm_util.units) default_uri_handler() (in module seamm_util.include_open) depth (seamm_util.include_open.Open property) description (seamm_util.zenodo.Record property) dict_to_object() (seamm_util.seamm_json.JSONDecoder method)

Dictionary (class in seamm_util.dictionary) disable() (in module seamm_util.printing) disabled (seamm_util.printing.Printer property) doi (seamm_util.zenodo.Record property) download_file() (seamm_util.zenodo.Record method) dump() (seamm_util.plotting.Figure method) dumps() (seamm_util.plotting.Figure method)

E

encode() (seamm_util.compact_json_encoder.CompactJSONEncoder method)

exists() (seamm_util.argument_parser.ArgumentParser method)

F

Figure (class in seamm_util.plotting) File (class in seamm_util.seamm_file) file_exists() (seamm_util.configuration.Configuration method) fileConfig() (in module seamm_util.printing) filename (seamm_util.output.Output property) files() (seamm_util.zenodo.Record method)

find_waters() (seamm_util.water_models.Water static method) findCaller() (seamm_util.printing.Printer method) format_help() (seamm_util.argument_parser.ArgumentParser method) FormattedText (class in seamm_util.printing) from_string() (seamm_util.configuration.Configuration method) fromkeys() (seamm_util.dictionary.Dictionary class method)

G

get() (seamm_util.argument_parser.ArgumentParser method) get_deposit_record() (seamm_util.zenodo.Zenodo method) get_file() (seamm_util.zenodo.Record method) get_ini_files() (seamm_util.argument_parser.ArgumentParser method) get_options() (seamm_util.argument_parser.ArgumentParser method) get_origins() (seamm_util.argument_parser.ArgumentParser method) get_plot() (seamm_util.plotting.Figure method) get_prolog() (seamm_util.configuration.Configuration method)

get_record() (seamm_util.zenodo.Zenodo method) get_values() (seamm_util.configuration.Configuration method) getEffectiveLevel() (seamm_util.printing.Printer method) getLevelName() (in module seamm_util.printing) getParser() (in module seamm_util.argument_parser) getPrinter() (in module seamm_util.printing) (seamm_util.printing.Manager method) grid_plots() (seamm_util.plotting.Figure method)

H

handle() (seamm_util.printing.Printer method)

handlers (seamm_util.printing.Printer property)

I

important() (in module seamm_util.printing) (seamm_util.printing.Printer method) in_progress (seamm_util.zenodo.Record property) indent_str (seamm_util.compact_json_encoder.CompactJSONEncoder property)

is_valid() (in module seamm_util.variable_names) isEnabledFor() (seamm_util.printing.Printer method) iskeyword() (in module seamm_util.variable_names) items() (seamm_util.argument_parser.ArgumentParser method) iterencode() (seamm_util.compact_json_encoder.CompactJSONEncoder method)

J

job() (in module seamm_util.printing) (seamm_util.printing.Printer method)

JSONDecoder (class in seamm_util.seamm_json) JSONEncoder (class in seamm_util.seamm_json)

K

keywords (seamm_util.zenodo.Record property)

L

level (seamm_util.printing.Printer property)

lineno (seamm_util.include_open.Open property)

M

makeRecord() (seamm_util.printing.Printer method) Manager (class in seamm_util.printing) manager (seamm_util.printing.Printer attribute) mass (seamm_util.water_models.Water property) MAX_ITEMS (seamm_util.compact_json_encoder.CompactJSONEncoder attribute) MAX_WIDTH (seamm_util.compact_json_encoder.CompactJSONEncoder attribute) metadata (seamm_util.zenodo.Record attribute) module seamm_util seamm_util.argument_parser seamm_util.check_executable seamm_util.compact_json_encoder seamm_util.configuration seamm_util.dictionary seamm_util.elemental_data seamm_util.include_open seamm_util.list_definition seamm_util.md_statistics seamm_util.output seamm_util.plotting seamm_util.printing seamm_util.seamm_file seamm_util.seamm_json seamm_util.seamm_util seamm_util.units seamm_util.variable_names seamm_util.water_models seamm_util.zenodo

N

name (seamm_util.printing.Printer property)

normal() (in module seamm_util.printing) (seamm_util.printing.Printer method)

O

Open (class in seamm_util.include_open)

optionxform() (seamm_util.argument_parser.ArgumentParser method) Output (class in seamm_util.output)

P

parent (seamm_util.printing.Printer property) parse_args() (seamm_util.argument_parser.ArgumentParser method) parse_list() (in module seamm_util.list_definition) path (seamm_util.configuration.Configuration property) (seamm_util.include_open.Open property) paths (seamm_util.include_open.Open property) pdb() (seamm_util.water_models.Water method) PlaceHolder (class in seamm_util.printing)

Plot (class in seamm_util.plotting) print() (seamm_util.printing.Printer method) print_help() (seamm_util.argument_parser.ArgumentParser method) print_root (seamm_util.printing.Printer attribute) Printer (class in seamm_util.printing) propagate (seamm_util.printing.Printer property) publish() (seamm_util.zenodo.Record method) push() (seamm_util.include_open.Open method)

R

read_header() (seamm_util.seamm_file.File method) Record (class in seamm_util.zenodo) reference() (seamm_util.water_models.SPC_E method)

remove_file() (seamm_util.zenodo.Record method) remove_keyword() (seamm_util.zenodo.Record method) removeHandler() (seamm_util.printing.Printer method) RootPrinter (class in seamm_util.printing)

S

save() (seamm_util.configuration.Configuration method) seamm_parser() (in module seamm_util.argument_parser) seamm_util module seamm_util.argument_parser module seamm_util.check_executable module seamm_util.compact_json_encoder module seamm_util.configuration module seamm_util.dictionary module seamm_util.elemental_data module seamm_util.include_open module seamm_util.list_definition module seamm_util.md_statistics module seamm_util.output module seamm_util.plotting module seamm_util.printing module

seamm_util.seamm_file module seamm_util.seamm_json module seamm_util.seamm_util module seamm_util.units module seamm_util.variable_names module seamm_util.water_models module seamm_util.zenodo module search() (seamm_util.zenodo.Zenodo method) section_exists() (seamm_util.configuration.Configuration method) sections() (seamm_util.configuration.Configuration method) set_value() (seamm_util.configuration.Configuration method) setLevel() (seamm_util.printing.Printer method) setPrinterClass() (in module seamm_util.printing) shutdown() (in module seamm_util.printing) sort_dimensions() (in module seamm_util.units) SPC (class in seamm_util.water_models) SPC_E (class in seamm_util.water_models) split_args() (seamm_util.argument_parser.ArgumentParser method) splitext() (in module seamm_util.include_open) stack() (seamm_util.include_open.Open method) submitted (seamm_util.zenodo.Record property) system() (seamm_util.water_models.Water method)

T

template (seamm_util.plotting.Figure property) terse() (in module seamm_util.printing) (seamm_util.printing.Printer method) TIP3P (class in seamm_util.water_models) title (seamm_util.zenodo.Record property) to_dict() (seamm_util.plotting.Axis method) (seamm_util.plotting.Trace method)

to_string() (seamm_util.configuration.Configuration method) token (seamm_util.zenodo.Record attribute) (seamm_util.zenodo.Zenodo property) total_lines (seamm_util.include_open.Open property) Trace (class in seamm_util.plotting)

U

update_metadata() (seamm_util.zenodo.Record method)

upload_type (seamm_util.zenodo.Record property)

V

verbose() (in module seamm_util.printing) (seamm_util.printing.Printer method)

visited (seamm_util.include_open.Open property)

W

Water (class in seamm_util.water_models)

Z

Zenodo (class in seamm_util.zenodo)