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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;)" />
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).