Index

_

_OPTIONS_REAL (molminer.AbstractLinker.AbstractLinker attribute) (molminer.ChemSpot.ChemSpot attribute) (molminer.OPSIN.OPSIN attribute) (molminer.OSRA.OSRA attribute)

A

AbstractLinker (class in molminer.AbstractLinker) ACCENTS (in module molminer.normalize)

add_options() (in module molminer.cli) APOSTROPHES (in module molminer.normalize)

B

BaseNormalizer (class in molminer.normalize)

build_commands() (molminer.AbstractLinker.AbstractLinker method) (molminer.AbstractLinker.AbstractLinker static method)

C

ChemSpot (class in molminer.ChemSpot) chemspot_default_options (molminer.Extractor.Extractor attribute)

common_subprocess() (in module molminer.utils) CONTROLS (in module molminer.normalize)

D

dict_to_csv() (in module molminer.utils)

DOUBLE_QUOTES (in module molminer.normalize)

E

eprint() (in module molminer.utils)

exit_code (molminer.utils.Output attribute) Extractor (class in molminer.Extractor)

G

get_input_file_type() (in module molminer.utils) get_kwargs() (in module molminer.cli) get_opsin_types() (in module molminer.cli) get_temp_images() (in module molminer.utils) get_text() (in module molminer.utils)

get_text_from_image() (in module molminer.utils) get_text_from_pdf() (in module molminer.utils) get_text_from_pdf_scan() (in module molminer.utils) GM_COMMAND (molminer.OSRA.OSRA attribute) GREEK (in module molminer.normalize) GREEK_WORDS (in module molminer.normalize)

H

help() (molminer.AbstractLinker.AbstractLinker method), [1] (molminer.ChemSpot.ChemSpot method), [1] (molminer.OPSIN.OPSIN method), [1] (molminer.OSRA.OSRA method), [1]

HYPHENS (in module molminer.normalize)

L

logger (molminer.ChemSpot.ChemSpot attribute) (molminer.Extractor.Extractor attribute) (molminer.OPSIN.OPSIN attribute) (molminer.OSRA.OSRA attribute)

M

MINUSES (in module molminer.normalize) molminer (module) molminer.AbstractLinker (module) molminer.ChemSpot (module) molminer.cli (module)

molminer.Extractor (module) molminer.normalize (module) molminer.OPSIN (module) molminer.OSRA (module) molminer.utils (module)

N

NAME_SMALL (in module molminer.normalize) normalize (in module molminer.normalize) normalize() (molminer.normalize.BaseNormalizer method) (molminer.normalize.Normalizer method)

normalize_iupac() (molminer.OPSIN.OPSIN method) normalize_text() (molminer.ChemSpot.ChemSpot static method) Normalizer (class in molminer.normalize) NUMBERS (in module molminer.normalize)

O

OPSIN (class in molminer.OPSIN) opsin_default_options (molminer.Extractor.Extractor attribute) options (molminer.AbstractLinker.AbstractLinker attribute) (molminer.ChemSpot.ChemSpot attribute) (molminer.OPSIN.OPSIN attribute) (molminer.OSRA.OSRA attribute)

options_internal (molminer.AbstractLinker.AbstractLinker attribute) (molminer.ChemSpot.ChemSpot attribute) (molminer.OPSIN.OPSIN attribute) (molminer.OSRA.OSRA attribute) OSRA (class in molminer.OSRA) osra_default_options (molminer.Extractor.Extractor attribute) Output (class in molminer.utils)

P

parse_chemspot() (molminer.ChemSpot.ChemSpot static method) parse_chemspot_iob() (molminer.ChemSpot.ChemSpot static method) path_to_binary (molminer.ChemSpot.ChemSpot attribute) (molminer.OPSIN.OPSIN attribute) (molminer.OSRA.OSRA attribute) pdf_to_images() (in module molminer.utils) PLURAL_PATTERN (molminer.OPSIN.OPSIN attribute)

PLUSES (in module molminer.normalize) PRIMES (in module molminer.normalize) process() (molminer.AbstractLinker.AbstractLinker method), [1] (molminer.ChemSpot.ChemSpot method), [1] (molminer.Extractor.Extractor method), [1] (molminer.OPSIN.OPSIN method), [1] (molminer.OSRA.OSRA method), [1]

Q

QUOTES (in module molminer.normalize)

R

RE_CHARGE (molminer.ChemSpot.ChemSpot attribute)

RE_ION (molminer.ChemSpot.ChemSpot attribute)

S

set_options() (molminer.AbstractLinker.AbstractLinker method) (molminer.ChemSpot.ChemSpot method) (molminer.OPSIN.OPSIN method) (molminer.OSRA.OSRA method) SINGLE_QUOTES (in module molminer.normalize)

SLASHES (in module molminer.normalize) SMALL (in module molminer.normalize) stderr (molminer.utils.Output attribute) stdout (molminer.utils.Output attribute) strict_normalize (in module molminer.normalize)

T

TILDES (in module molminer.normalize)

V

version() (molminer.ChemSpot.ChemSpot static method) (molminer.OSRA.OSRA method), [1]

W

write_empty_file() (in module molminer.utils)