adsorbant_enumeration_driver.py Command Help

Command: $SCHRODINGER/run adsorbant_enumeration_gui_dir/adsorbant_enumeration_driver.py

usage: $SCHRODINGER/run adsorbant_enumeration_gui_dir/adsorbant_enumeration_driver.py
       [-h] -substrates SUBSTRATE_FILE -adsorbates ADSORBATES_FILE
       [-vdw_scale SCALE_FACTOR] [-direction {auto,c_vector,gap}]
       [-rotations ROTATIONS] [-type TYPE1,TYPE2...] [-radius ANGSTROMS]
       [-neighbor_factor SCALE_FACTOR] [-above] [-deduplicate]
       [-HOST <hostname>] [-D] [-VIEWNAME <viewname>] [-JOBNAME JOBNAME]

Enumerates adsorbate-substrate reaction dimers Copyright Schrodinger, LLC. All
rights reserved.

options:
  -h, -help             Show this help message and exit.
  -substrates SUBSTRATE_FILE
                        The file containing substrate structures (default:
                        None)
  -adsorbates ADSORBATES_FILE
                        The file containing adsorbate structures to dock on
                        the substrates. (default: None)
  -vdw_scale SCALE_FACTOR
                        The scale factor for van der Waals radii when
                        determining if there is a bad gas molecule/substrate
                        contact. A contact is assumed when the distance
                        between the two atoms is less than the sum of the van
                        der Waals radii times the scale factor. (default:
                        0.75)
  -direction {auto,c_vector,gap}
                        The direction of the substrate-gas coordination
                        vector. c_vector will make this vector parallel to the
                        PBC c vector or the Z axis if there is no pbc. gap
                        will place this vector in a gap of the substrate atoms
                        coordination sphere - attempting to create VSEPR-like
                        geometries. auto will choose the option that results
                        in the fewest steric interactions at the shortest
                        distance. (default: auto)
  -rotations ROTATIONS  Create this many structures for each complex by
                        rotating the gas molecule around the the adsorption
                        axis. Each rotation will be the golden angle (137.5
                        degrees) from the previous structure. (default: 1)
  -type TYPE1,TYPE2...  The type of adsorption sites to use. This should be a
                        comma-separated list of one or more site types. The
                        three possible site types are {'hollow', 'bridge',
                        'top'}. top is an atom-centered site, bridge is a site
                        between two atoms, and hollow is a site between three
                        atoms that form an acute triangle. For example,
                        "top,bridge" or "hollow". (default: top)
  -radius ANGSTROMS     Create adsorption complexes not only with the reactive
                        atom but also with any substrate surface atom within
                        this distance of the reactive atom. This flag is
                        required if -type includes any type that requires
                        multiple atoms (bridge or hollow). (default: None)
  -neighbor_factor SCALE_FACTOR
                        Bridge and hollow sites are found between groups of
                        substrate atoms where each pair is within (a + b) * X
                        of each other. a is the covalent diameter of the
                        adsorbate atom, b is the sum of the covalent radii of
                        the two substrate atoms, and X is the neighbor factor.
                        Bridge sites involve 2 atoms, hollow involve 3 atoms.
                        (default: 1.1)
  -above                For each complex, also create a second complex with
                        the gas molecule at a non-bonding distance from the
                        substrate (default: False)
  -deduplicate          Remove symmetry equivalent structures. (default:
                        False)

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)