nanosheet.py Command Help

Command: $SCHRODINGER/run nanosheet.py

usage: $SCHRODINGER/run nanosheet.py [-h] [-cg] [-element1 ATOMIC_SYMBOL]
                                     [-element2 ATOMIC_SYMBOL]
                                     [-bondlength BONDLENGTH]
                                     [-edgetype1 {zigzag,armchair}]
                                     [-edgetype2 {zigzag,armchair}]
                                     [-ncell1 NCELL1] [-ncell2 NCELL2]
                                     [-no_double_bonds]
                                     [-termfrag FRAGMENT_NAME]
                                     [-min_term_frags] [-nbilayers NBILAYERS]
                                     [-bilayersep BILAYERSEP]
                                     [-bilayershift BILAYERSHIFT]
                                     [-stacktype {ABAB,ABCD}] [-verbose]
                                     [-version]
                                     [output_mae_name]

Create honeycomb nanosheets of different sizes and shapes. 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 sheet.mae.
                        (default: sheet.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)
  -edgetype1 {zigzag,armchair}
                        Specify the type of edge to use for one set of lattice
                        sides. (default: armchair)
  -edgetype2 {zigzag,armchair}
                        Specify the type of edge to use for the other set of
                        lattice sides. (default: zigzag)
  -ncell1 NCELL1        Specify the number of cells to generate along one
                        lattice dimension. (default: 10)
  -ncell2 NCELL2        Specify the number of cells to generate along the
                        other lattice dimension. (default: 10)
  -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)
  -nbilayers NBILAYERS  Specify the number of bilayers. With the default of
                        zero a single layer, not a single bilayer, will be
                        created, otherwise the specified number of bilayers
                        will be created and the total number of layers will
                        then always be even. Layers can be removed from within
                        Maestro using the 'Molecules' option of the 'Delete'
                        button. (default: 0)
  -bilayersep BILAYERSEP
                        Bilayer separation in units of Angstrom. (default:
                        3.35)
  -bilayershift BILAYERSHIFT
                        Specify the offset in the bilayer in terms of the
                        number of unit cells. This value may be fractional,
                        for example pass 0.0 for AA type (aligned) stacking or
                        0.5 for AB type (close-packed) stacking or multiples
                        thereof for larger offsets. (default: 0.5)
  -stacktype {ABAB,ABCD}
                        Specify how to stack the bilayers. (default: ABAB)
  -verbose              Turn on verbose printing. (default: False)
  -version, -v          Show the script's version number and exit.