Command line

crabwurcs convert [--from FORMAT] --to FORMAT [--table off|fallback|check] [INPUT]
crabwurcs normalize-wurcs [--input-file] [INPUT]
crabwurcs mol-to-wurcs --format {mol,sdf,smiles} [FILE]
crabwurcs wurcs-to-mol --format {mol,sdf,smiles} [FILE]
crabwurcs pdb-to-wurcs [--to FORMAT] [--policy coordinates|names|strict] [--quiet] FILE
crabwurcs render [--from FORMAT] [--output FILE] [INPUT]

Omitted notation input is read from standard input. convert and render accept --input-file when their positional argument is a path. Render output is SVG by default; .svg and .png output suffixes select file type.

Both the Cargo and pip distributions provide the same command name and core behavior, so install only one in a given environment.

convert computes every conversion from the parsed glycan. The bundled table of GlycoShape notations is used only on request: --table fallback answers an input that cannot be converted (for example a GlyTouCan accession stored as a name) from its table record, and --table check fails when the input's record holds another structure.

Every command that produces WURCS uses the offline normalizer. The dedicated normalize-wurcs command is strict and exits unsuccessfully rather than claiming an unsupported input was normalized.

pdb-to-wurcs reads every monosaccharide from its coordinates and prints one line per glycan (site<TAB>notation). Where a residue name disagrees with the coordinates, or the coordinates cannot decide part of a residue, a warning: ... line goes to standard error (--quiet silences them). --policy names lets names decide where they say something; --policy strict fails on a disagreement. See PDB and mmCIF extraction.