sugar_builder_driver.py Command Help

Command: $SCHRODINGER/run sugar_builder_gui_dir/sugar_builder_driver.py

usage: $SCHRODINGER/run sugar_builder_gui_dir/sugar_builder_driver.py
       [-h] [-building_mode {glycosylation,polysaccharide}]
       [-glyco_notation GLYCO_NOTATION] [-glyco_graph GLYCO_GRAPH]
       [-anchor_amino_acid {Asn,Ser,Thr}] [-minimize]
       [-polysaccharide_info POLYSACCHARIDE_INFO] [-length LENGTH]
       [-HOST <hostname>] [-D] [-VIEWNAME <viewname>] [-JOBNAME JOBNAME]

Build sugar molecules from monosaccharide units using predefined or custom
definitions. Copyright Schrodinger, LLC. All rights reserved.

options:
  -h, -help             Show this help message and exit.
  -building_mode {glycosylation,polysaccharide}
                        Build mode deciding the molecule category and input
                        format. (default: polysaccharide) (default:
                        polysaccharide)
  -glyco_notation GLYCO_NOTATION
                        IUPAC-condensed glycan notation (e.g.,
                        "Gal-b1,4-GlcNAc") (default: None)
  -glyco_graph GLYCO_GRAPH
                        JSON file with glycan graph structure (default: None)
  -anchor_amino_acid {Asn,Ser,Thr}
                        Amino acid anchor for glycan attachment (default:
                        None)
  -minimize             Minimize the final glycosylation structure. (default:
                        False)
  -polysaccharide_info POLYSACCHARIDE_INFO
                        Path to JSON file defining the polysaccharide
                        structure. (default: None)
  -length LENGTH        Number of repeating units in the polysaccharide chain.
                        (default: 10)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -D, -DEBUG            Show details of Job Control operation. (default:
                        False)
  -VIEWNAME <viewname>  Specifies viewname used in job filtering in maestro.
                        (default: False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)