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Rosetta
2020.50
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Classes | |
class | Matrix |
class | PlanePoints |
class | PR_PyMOLServer |
class | PR_UDPServer |
class | StartUpError |
Exceptions. More... | |
class | XYZCoord |
Functions | |
def | add_vectors |
def | scalar_multiply |
def | normalize |
def | rotation_matrix_radians |
def | multiply_matrix |
def | rotate_vector |
def | compute_plane_positions |
def | draw_membrane_planes |
def | make_axis |
Graphing methods. More... | |
def | scale_axes |
def | get_ends |
def | extract_coords |
def | make_data |
def | add_point |
def | rescale_cartesian |
def | connect_points |
def | plot3d |
def | set_spectrum |
PyMOL spectrum coloring. More... | |
def | main |
Main PyMOLPyRosettaServer.py routines. More... | |
def | start_rosetta_server |
Variables | |
_terminate_ = False | |
dictionary | COLOR_LIB |
Constants. More... | |
dictionary | X11_COLORS |
def PyMOL-RosettaServer.add_point | ( | name, | |
point, | |||
connect = '' , |
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rescale = False , |
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scale = False , |
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axis_color = '' , |
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num = 0 , |
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banner = '' |
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) |
Adds a point to existing data, reconnecting points optionally. Adds 'point' to 'name' and connects it with color 'connect' (empty for no connection). 'rescale' will rescale the axes; 'scale' will label the scales; 'axis_color' determines the axis color; 'num' the intermediate scales, 'banner' is a resn name at 'point'.
References rescale_cartesian().
Referenced by PyMOL-RosettaServer.Matrix.__init__(), make_data(), and PyMOL-RosettaServer.PR_PyMOLServer.process_packet().
def PyMOL-RosettaServer.add_vectors | ( | v1, | |
v2 | |||
) |
Add a pair of vectors represented as XYZcoord classes (see above)
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and compute_plane_positions().
def PyMOL-RosettaServer.compute_plane_positions | ( | center, | |
normal, | |||
thickness, | |||
rg, | |||
npoints = 4 |
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) |
Compute the position of the membrane planes based on provided normal, center, thickness, and radius of gyration
References add_vectors(), ObjexxFCL.len(), basic::options::OptionKeys::relax::range.range, and rotate_vector().
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and PyMOL-RosettaServer.PR_PyMOLServer.process_packet().
def PyMOL-RosettaServer.connect_points | ( | name, | |
color = 'red' |
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) |
Draws colored lines between consecutive points.
References plot3d(), and basic::options::OptionKeys::relax::range.range.
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and plot3d().
def PyMOL-RosettaServer.draw_membrane_planes | ( | plane_points, | |
normal_vector | |||
) |
Draw CGO Planes Representing the upper & lower membrane planes Adapted from Evan Baugh's Draw Object code by Rebecca Alford to work with the framework
References normalize().
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and PyMOL-RosettaServer.PR_PyMOLServer.process_packet().
def PyMOL-RosettaServer.extract_coords | ( | name | ) |
Returns the coords of a data container as three arrays.
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and rescale_cartesian().
def PyMOL-RosettaServer.get_ends | ( | data | ) |
Determines the ends for axes from list. Defaults to min, max, but if not pos/neg. Determines based on closest point.
References ObjexxFCL.abs(), max(), and min().
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and rescale_cartesian().
def PyMOL-RosettaServer.main | ( | ip, | |
port | |||
) |
Main PyMOLPyRosettaServer.py routines.
References fmt.print().
Referenced by PyMOL-RosettaServer.Matrix.__init__().
def PyMOL-RosettaServer.make_axis | ( | name, | |
ends, | |||
dr, | |||
scale = False , |
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axis_color = '' , |
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num = 0 |
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) |
Graphing methods.
Make an axis 'name' from 'ends[0]' to 'ends[1]' on the 'dr' (direction). 'scale' bool tells to label axis or not; 'axis_color' determines the axis color; 'num' allows intermediate scale points.
References basic::options::OptionKeys::relax::range.range, and scale_axes().
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and rescale_cartesian().
def PyMOL-RosettaServer.make_data | ( | name, | |
x_array, | |||
y_array, | |||
z_array, | |||
data_color = 'red' |
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) |
Generate a data object from three arrays.
References add_point(), ObjexxFCL.len(), and basic::options::OptionKeys::relax::range.range.
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and plot3d().
def PyMOL-RosettaServer.multiply_matrix | ( | matrix, | |
vector | |||
) |
multiply matrix by 3D vector
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and rotate_vector().
def PyMOL-RosettaServer.normalize | ( | normal | ) |
Ensure that the provided normal is a unit normal_vector
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and draw_membrane_planes().
def PyMOL-RosettaServer.plot3d | ( | name, | |
x_array, | |||
y_array, | |||
z_array = [] , |
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connect = 'red' , |
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scale = True , |
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axis_color = 'blue' , |
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num = 0 |
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) |
Default plotting tool with optional z points, connection, and axis color.
References connect_points(), ObjexxFCL.len(), make_data(), and rescale_cartesian().
Referenced by PyMOL-RosettaServer.Matrix.__init__(), connect_points(), and PyMOL-RosettaServer.PR_PyMOLServer.process_packet().
def PyMOL-RosettaServer.rescale_cartesian | ( | data, | |
scale, | |||
axis_color, | |||
num | |||
) |
Rescales the 'data' axes (x, y, z) based on 'data' data: 'num', 'axis_color', 'scale'
References extract_coords(), get_ends(), and make_axis().
Referenced by PyMOL-RosettaServer.Matrix.__init__(), add_point(), and plot3d().
def PyMOL-RosettaServer.rotate_vector | ( | vector, | |
theta, | |||
axis | |||
) |
Rotate some vector about a specified axis by some angle theta
References multiply_matrix(), and rotation_matrix_radians().
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and compute_plane_positions().
def PyMOL-RosettaServer.rotation_matrix_radians | ( | axis, | |
theta | |||
) |
Compute and return the rotation matrix associated with rotation about the given axis by theta radians
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and rotate_vector().
def PyMOL-RosettaServer.scalar_multiply | ( | v, | |
n | |||
) |
Multiply a vector by some scalar factor
Referenced by PyMOL-RosettaServer.Matrix.__init__().
def PyMOL-RosettaServer.scale_axes | ( | name = 'x_axis or y_axis or z_axis' | ) |
Labels the selection name. Used here for convenience: axis point value str in resn.
Referenced by PyMOL-RosettaServer.Matrix.__init__(), and make_axis().
def PyMOL-RosettaServer.set_spectrum | ( | low = 'blue' , |
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high = 'red' |
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) |
PyMOL spectrum coloring.
Sets the energy coloring spectrum using the above COLOR_LIB dictionary.
References fmt.print(), basic::options::OptionKeys::relax::range.range, and numeric::crick_equations.x().
Referenced by PyMOL-RosettaServer.Matrix.__init__().
def PyMOL-RosettaServer.start_rosetta_server | ( | ip = '' , |
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port = 65000 |
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) |
References fmt.print(), and basic::options::OptionKeys::relax::range.range.
Referenced by PyMOL-RosettaServer.Matrix.__init__().
PyMOL-RosettaServer._terminate_ = False |
dictionary PyMOL-RosettaServer.COLOR_LIB |
Constants.
dictionary PyMOL-RosettaServer.X11_COLORS |