multicomplex_builder_driver.py Command Help

Command: $SCHRODINGER/run multicomplex_builder_gui_dir/multicomplex_builder_driver.py

usage: $SCHRODINGER/run multicomplex_builder_gui_dir/multicomplex_builder_driver.py
       [-h] -metal ATOMIC_SYMBOL [-geom VSEPR_GEOMETRY] [-isomer ISOMER] -site
       COORDINATING_ATOM,DELETED_ATOM [-sentinel SENTINEL]
       [-sentinel_site COORDINATING_ATOM,DELETED_ATOM]
       [-sentinel_copies SENTINEL_COPIES]
       [-slots COORDINATION_SITE1,COORDINATION_SITE2,COORDINATION_SITE3,COORDINATION_SITE4]
       [-minimize METHOD]
       INPUT_FILE

Driver for building complexes of selected ligands, with optionally one or two
ligands remaining constant throughout all complexes. Copyright Schrodinger,
LLC. All rights reserved.

positional arguments:
  INPUT_FILE            Input file containing ligand structures. Each
                        structure will be used to make a new complex.
                        Structures must have the same atom numbering for the
                        atoms used with the site flags.

options:
  -h, -help             Show this help message and exit.
  -metal ATOMIC_SYMBOL, -m ATOMIC_SYMBOL
                        Atomic symbol of the central atom of the complex.
                        (default: None)
  -geom VSEPR_GEOMETRY  VSEPR geometry of the complex. Choices are octahedral,
                        trigonal_bipyramidal, square_planar, tetrahedral,
                        trigonal_planar, linear, pentagonal_bipyramidal,
                        square_antiprismatic, tricapped_trigonal_prismatic,
                        square_pyramidal. (default: octahedral)
  -isomer ISOMER, -i ISOMER
                        The complex isomer - only valid for bidentate ligands.
                        For octahedral complexes, only facial and meridional
                        are valid choices. For square planer complexes, only
                        cis and trans are valid choices. For tetrahedral, only
                        none is a valid choice. The default is facial, cis or
                        none depending on the geometry. (default: None)
  -site COORDINATING_ATOM,DELETED_ATOM, -s COORDINATING_ATOM,DELETED_ATOM
                        Comma-separated grouping of two atom numbers. The
                        first atom number is the atom that should be
                        coordinated to the central metal atom. The second atom
                        number is the atom that should be removed from the
                        ligand when the complex is made. For dative sites
                        (sites that coordinate without removing an atom), use
                        0 for the DELETED_ATOM number. Atom numbers should
                        begin at 1 and correspond to the atom order in the
                        input file. Note that all ligands in the input file
                        will use the same site atom numbers. For bidentate
                        ligands, use the site flag twice (i.e. -site 5,8 -site
                        9,0) for the two sites. Use -1 for the DELETED_ATOM
                        number to specify that the lone hydrogen attached to
                        the COORDINATING_ATOM is to be deleted. This is useful
                        for structures where the hydrogen numbering may not be
                        consistent from one structure to the next. (default:
                        None)
  -sentinel SENTINEL    Sentinel structure. (default: None)
  -sentinel_site COORDINATING_ATOM,DELETED_ATOM
                        See -site description. (default: None)
  -sentinel_copies SENTINEL_COPIES
                        Number of sentinel copies to be placed. (default: 1)
  -slots COORDINATION_SITE1,COORDINATION_SITE2,COORDINATION_SITE3,COORDINATION_SITE4
                        Comma-separated ligand coordination sites as defined
                        in Specify Ligand Coordination Sites diagram from
                        Single Complex Builder. For octahedral geometry, 6
                        values are expected, i.e. -slots 1,2,3,4,5,6. For
                        square planar, 4 values are expected, for trigonal
                        pyramidal 5 values are expected. The slots are filled
                        first by sentinel ligands and their copies (if
                        provided). Followed by -sites of the ligands. Sites
                        for bidentate ligands are used in order given on
                        command line. (default: None)
  -minimize METHOD      Clean up the built structure using the specified
                        method. Options are ff for a force field minimization
                        or xtb for xTB minimization. (default: None)