mmdg {<mmdg-statement>} end

<mmdg-statement> :==

  ?
  --{Prints current status.}
  writebounds=<filename>
  --{Smoothed bounds matrices are written to this file, no 
     metrization or embedding are performed.}
  readbounds=<filename>
  --{Read smoothed bounds matrices from this file, then metrization
     and embedding are performed.}
  storebounds
  --{Smoothed bounds matrices are stored in memory, no metrization
     or embedding are performed. This is required for subsequent 
     calls with recallbounds or for using the dg energy term.}
  recallbounds 
  --{Recall smoothed bounds matrices from memory, metrization and 
     embedding are then performed.}
  reference=parameter|coordinate
  --{Use parameters or coordinates to fill distances for bonds, 
     angles, and unique dihedrals or impropers. Takes information
     from reference coordinates for refe=coordinate.}
  verbose=<logical>
  --{Prints verbose information. Default=false}
  baccuracy=<real>
  --{Accuracy for bounds based on bonds (in Angstroms).}
  taccuracy=<real>
  --{Accuracy for bounds based on angles (degrees).}
  paccuracy=<real>
  --{Accuracy for bounds based on dihedrals (degrees).}
  iaccuracy=<real>
  --{Accuracy for bounds based in impropers (degrees).}
  group <atom-selection> <real>
  --{Atom selection and accuracy for rigid group. Takes information 
     from the main coordinates.}
  substructure=<atom-selection>
  --{Selects atoms to be embedded. Default=(all)}
  metrization <atom-selection> <real>
  --{Atom selection and number of picked subset of atoms that are 
     used for metrization. Bound smoothing is applied to other
     atoms. Default=(none)}
  random|ordered
  --{Mutually exclusive options for ordered or random metrization.}
  shortest_path_algorithm=auto|full|sparse
  --{select shortest path algorithm for bound smoothing. Default=auto}
  scale=<real>
  --{Scale factor for the dg energy term.}
  exponent=<integer>
  --{Exponent for dg energy term.}
  selection=<atom-selection>
  --{Select atoms to be included in distance geometry energy term.}

  --{All steps of distance geometry calculations (initialization, 
     metrization, smoothing, and embedding) are executed by default
     unless storebounds, writebounds, recallbounds or readbounds are
     specified.}
  --{For automatic pseudoatom correction a template coordinate set 
     must be present in the reference coordinate set (refx, refy, refz).}