nanotube.py Command Help

Command: $SCHRODINGER/run nanotube.py

usage: $SCHRODINGER/run nanotube.py [-h] [-cg] [-element1 ATOMIC_SYMBOL]
                                    [-element2 ATOMIC_SYMBOL]
                                    [-bondlength BONDLENGTH] [-nindex NINDEX]
                                    [-mindex MINDEX] [-ncells NCELLS]
                                    [-no_double_bonds]
                                    [-termfrag FRAGMENT_NAME]
                                    [-min_term_frags] [-up_to_nindex]
                                    [-up_to_mindex] [-nwalls NWALLS]
                                    [-wallsep WALLSEP] [-verbose] [-version]
                                    [output_mae_name]

Enumerate single- and multi-walled nanotubes. Copyright Schrodinger, LLC. All
rights reserved.

positional arguments:
  output_mae_name       Specify the name of the output Maestro file that will
                        contain all built structures, for example tube.mae.
                        (default: tube.mae)

options:
  -h, -help             Show this help message and exit.
  -cg                   Build a coarse grain structure. (default: False)
  -element1 ATOMIC_SYMBOL
                        Elemental symbol for one of the two atoms in the
                        asymmetric unit is the case of atomistic systems.
                        Coarse grain particle name can be passed while
                        building a coarse grain structure. (default: C)
  -element2 ATOMIC_SYMBOL
                        Elemental symbol for the other of the two atoms in the
                        asymmetric unit is the case of atomistic systems.
                        Coarse grain particle name can be passed while
                        building a coarse grain structure. (default: C)
  -bondlength BONDLENGTH
                        Bond length of the asymmetric unit in Angstrom.
                        (default: 1.418)
  -nindex NINDEX        Specify the first chiral index, i.e. n in (n, m).
                        (default: 6)
  -mindex MINDEX        Specify the second chiral index, i.e. m <= n in (n,
                        m). (default: 6)
  -ncells NCELLS        Specify the number of unit cells. (default: 2)
  -no_double_bonds      Returns a structure containing only single bonds. This
                        option is ignored for coarse grain structure.
                        (default: False)
  -termfrag FRAGMENT_NAME
                        For an atomistic system choose a fragment from the
                        following list to terminate the lattice: none,
                        hydrogen, oxide, hydroxyl, fluoro, chloro, bromo,
                        carbonyl, methyl, carboxyl, amine, planar amine,
                        silyl, thiol, phosphyl. Coarse grain systems support
                        only a single particle fragment with the passed name.
                        (default: hydrogen)
  -min_term_frags       Minimize the geometry of terminating fragments.
                        (default: False)
  -up_to_nindex         Enumerate nanotubes on the first chiral index, i.e.
                        return a set of (n, m) for all n >= m. (default:
                        False)
  -up_to_mindex         Enumerate nanotubes on the second chiral index, i.e.
                        return a set of (n, m) for all m <= n. (default:
                        False)
  -nwalls NWALLS        Specify the number of walls for a multi-walled
                        nanotube. (default: 1)
  -wallsep WALLSEP      Specify the wall separation in units of Angstrom for a
                        multi-walled nanotube. (default: 3.35)
  -verbose              Turn on verbose printing. (default: False)
  -version, -v          Show the script's version number and exit.