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Autogenerated Tag Syntax Documentation:

Used to setup symmetric systems in which the input structures(s) are aligned along the x, y, or z axis.

<SymDofMover name="(&string;)" set_sampler="(true &bool;)"
        auto_range="(false &bool;)" symm_file="(&string;)"
        sym_dof_names="(&string;)"
        sampling_mode="(single_dock &sampling_mode_choices;)"
        flip_input_about_axes="(&type_for_axes_or_zero_cslist;)"
        align_input_axes_to_symdof_axes="(&type_for_axes_cslist;)"
        radial_disps="(&string;)" radial_offsets="(&string;)"
        translation_axes="(&type_for_axes_cslist;)" angles="(&string;)"
        rotation_axes="(&type_for_axes_cslist;)"
        radial_disps_range_min="(&string;)" radial_disps_range_max="(&string;)"
        angles_range_min="(&string;)" angles_range_max="(&string;)"
        angle_steps="(&string;)" radial_disp_steps="(&string;)"
        angle_deltas="(&string;)" radial_disp_deltas="(&string;)" />
  • set_sampler: For use with the GetRBDOFValues filter. If set to false, then the RBDOF values will not be updated when the reported DOF values are not affected by the SymDofMoverSampler. Defaults to true.
  • auto_range: Boolean to set the manner in which the user defined ranges for radial displacements are interpreted. If set to true, then the negative values for min or max displacement are interpreted as moving the structure closer to the origin and positive values away from the origin.
  • symm_file: (REQUIRED) Symmetry definition file.
  • sym_dof_names: (REQUIRED) Names of the sym_dofs in the symmetry definition file along which one wishes to move or rotate the input. NOTE: For multicomponent systems, the order of the displacements, angles, ranges, and steps must correspond with the the order of the sym_dof_names. Passed as a string with comma-separated list (e.g. sym_dof_names='JTP1,JDP1')
  • sampling_mode: Which mode to use to sample around the initial configuration, if desired. 'grid', 'uniform', or 'gaussian'
  • flip_input_about_axes: Rotate subunits 180 degrees about the specified axes prior to applying transtions, rotations, alignment, and symmetry. ie, 'reverse' the component before further manipulation.
  • align_input_axes_to_symdof_axes: If specified, will align the specified axis of each subunit with the corresponding axis of the symdof jump from the symmetry definition file.
  • radial_disps: Initial displacement(s) by which to translate the input structure(s) along the user specified axis. Passed as a string with a comma-separated list (e.g. radial_disps='-65.4,109.2'). Must also specify translationa_axes to apply these along.
  • radial_offsets: Can be used in any sampling mode. Offset value(s) are added to the corresponding radial_disps before grid, uniform, or gaussian sampling is performed. Works with auto_range. For example, if one wants to space out both symdofs a given structure by 2 angstroms, one can pass radial_offsets='2,2' and auto_range=true. Then, regardless of the sign of the radial disps, the subunits will be displaced 2 angstroms further from the origin (assuming the input subunit(s) start at the origin).
  • translation_axes: Need to use this when using radial_disps. Axes (x, y, or z) along which to translate each subunit prior to applying symmetry.
  • angles: Initial angle(s) by which to rotate the input structure(s) about the user specified axis. Passed as a comma-separated list (e.g. angles='-65.4,109.2'). Must also specificy rotation axes to apply these along.
  • rotation_axes: Axes (x, y, or x) along which to rotate each subunit prior to applying symmetry. Need to use this when using angles.
  • radial_disps_range_min: For use with grid or uniform sampling. Minimum distance(s) in Angstroms by which to modify the initial radial_disps. Passed as a string with a comma-separated list (e.g. radial_disps_range_min='-1,-1'.
  • radial_disps_range_max: For use with grid or uniform sampling. Maximum distance(s) in Angstroms by which to modify the initial radial_disps. Passed as a string with a comma-separated list (e.g. radial_disps_range_max='1,1'.
  • angles_range_min: For use with grid or uniform sampling. Minimum angle(s) in degrees by which to rotate the structure around the initial angle(s) provided by the user. Passed as a string with a comma-separated list (e.g. angles_range_min='-1,-1'.
  • angles_range_max: For use with grid or uniform sampling. Maximum angle(s) in degrees by which to rotate the structure around the initial angle(s) provided by the user. Passed as a string with a comma-separated list (e.g. angles_range_max='1,1'.
  • angle_steps: For use with grid sampling. Set the bin size(s) by which to sample within the user defined range(s). Passed as a string with a comma-separated list (e.g. angle_steps='0.5,0.5'.
  • radial_disp_steps: For use with Gaussian sampling. The range within to sample inward and outward around the user specified initial displacement(s). Passed as a string with a comma-separated list (e.g. radial_disp_deltas='0.5,0.5'.
  • angle_deltas: For use with Gaussian sampling. The range within to sample around the user specified initial angle(s). Passed as a string with a comma-separated list (e.g. angle_deltas='0.5,0.5'.
  • radial_disp_deltas: For use with Gaussian sampling. The range within to sample inward and outward around the user specified initial displacement(s). Passed as a string with a comma-separated list (e.g. radial_disp_deltas='0.5,0.5'.

SymDofMover

Used to setup symmetric systems in which the input structures(s) are aligned along the x, y, or z axis. All functionality, except for grid sampling, can handle any number of distinct input structures for multi-component symmetric systems (Grid sampling can handle 1 or 2). Input subunits are first optionally flipped 180 degrees about the specified axes (x, y, or z) to "reverse" the inputs if desired, then translated along the specified axes (x, y, or z) by the values specified by the user in the radial_disps option and rotated about the specified axes by the value specified by the user in the angles option, and lastly, if the user specifies axes for the align_input_axes_to_symdof_axes option, then for each input subunit the user specified axis (x, y, or z) is aligned to the correct axis corresponding to the sym_dof_name in the symmetry definition file. Following these initial manipulations of the input structures, a symmetric pose is generated using the user specified symmetry definition file. If one wishes to sample around the user defined radial_disps and angles, then this can be done either through non-random grid sampling, random sampling from a Gaussian distribution within a user defined range, or random sampling from a uniform distribution within a user defined range. Each sampling method is driven by nstruct. If grid sampling is desired, then the user must specify radial_disps_range_min, radial_disps_range_max, angles_range_min, angle_range_max to define the range within to sample around the docked configuration and the bin sizes in which to sample these displacements and angles, which are set through the radial_disp_steps and angle_steps options. If uniform sampling is desired, then the user must specify radial_disps_range_min, radial_disps_range_max, angles_range_min, and angle_range_max. If Gaussian sampling is desired, then the user must specify the radial_disp_deltas and angle_deltas (a random number derived from a Gaussian distribution between -1 and 1 will then be multiplied by these step values and added to the initial radial_disps or angles). If the auto_range option is set to true, then the ranges set by the user for the grid or uniform sampling will be interpreted by the mover such that negative values move the structures toward the origin and positive values move the structures away from the origin (this is helpful if you have a mix of structures with negative or positive initial displacements, so that you can use a generic xml or run_script for all of them).

  • symm_file - Symmetry definition file.
  • sym_dof_names - Names of the sym_dofs in the symmetry definition file along which one wishes to move or rotate the input. NOTE: For multicomponent systems, the order of the displacements, angles, ranges, and steps must correspond with the the order of the sym_dof_names. Passed as a string with comma-separated list (e.g. sym_dof_names="JTP1,JDP1")
  • flip_input_about_axes - Rotate subunits 180 degrees about the specified axes prior to applying transtions, rotations, alignment, and symmetry. ie, "reverse" the component before further manipulation.
  • translation_axes - Axes (x, y, or z) along which to translate each subunit prior to applying symmetry.
  • rotation_axes - Axes (x, y, or x) along which to rotate each subunit prior to applying symmetry.
  • align_input_axes_to_symdof_axes - If specified, will align the specified axis of each subunit with the corresponding axis of the symdof jump from the symmetry definition file.
  • auto_range - Boolean to set the manner in which the user defined ranges for radial displacements are interpreted. If set to true, then the negative values for min or max displacement are interpreted as moving the structure closer to the origin and positive values away from the origin.
  • sampling_mode - Which mode to use to sample around the initial configuration, if desired. "grid", "uniform", or "gaussian"
  • radial_disps - Initial displacement(s) by which to translate the input structure(s) along the user specified axis. Passed as a string with a comma-separated list (e.g. radial_disps="-65.4,109.2")
  • angles - Initial angle(s) by which to rotate the input structure(s) about the user specified axis. Passed as a comma-separated list (e.g. angles="-65.4,109.2")
  • radial_disps_range_min - For use with grid or uniform sampling. Minimum distance(s) in Angstroms by which to modify the initial radial_disps. Passed as a string with a comma-separated list (e.g. radial_disps_range_min="-1,-1".
  • radial_disps_range_max - For use with grid or uniform sampling. Maximum distance(s) in Angstroms by which to modify the initial radial_disps. Passed as a string with a comma-separated list (e.g. radial_disps_range_max="1,1".
  • angles_range_min - For use with grid or uniform sampling. Minimum angle(s) in degrees by which to rotate the structure around the initial angle(s) provided by the user. Passed as a string with a comma-separated list (e.g. angles_range_min="-1,-1".
  • angles_range_max - For use with grid or uniform sampling. Maximum angle(s) in degrees by which to rotate the structure around the initial angle(s) provided by the user. Passed as a string with a comma-separated list (e.g. angles_range_max="1,1".
  • radial_disp_steps - For use with grid sampling. Set the bin size(s) by which to sample within the user defined range(s). Passed as a string with a comma-separated list (e.g. radial_disps_steps="0.5,0.5".
  • angle_steps - For use with grid sampling. Set the bin size(s) by which to sample within the user defined range(s). Passed as a string with a comma-separated list (e.g. angle_steps="0.5,0.5".
  • radial_disp_deltas - For use with Gaussian sampling. The range within to sample inward and outward around the user specified initial displacement(s). Passed as a string with a comma-separated list (e.g. radial_disp_deltas="0.5,0.5".
  • angle_deltas - For use with Gaussian sampling. The range within to sample around the user specified initial angle(s). Passed as a string with a comma-separated list (e.g. angle_deltas="0.5,0.5".
  • radial_offsets - Can be used in any sampling mode. Offset value(s) are added to the corresponding radial_disps before grid, uniform, or gaussian sampling is performed. Works with auto_range. For example, if one wants to space out both symdofs a given structure by 2 angstroms, one can pass radial_offsets="2,2" and auto_range=true. Then, regardless of the sign of the radial disps, the subunits will be displaced 2 angstroms further from the origin (assuming the input subunit(s) start at the origin).
  • set_sampler - For use with the GetRBDOFValues filter. If set to false, then the RBDOF values will not be updated when the reported DOF values are not affected by the SymDofMoverSampler. Defaults to true.

See Also