PyMOL-RosettaServer Namespace Reference

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

Function Documentation

def PyMOL-RosettaServer.add_point	(		name,
			point,
			connect = '',
			rescale = False,
			scale = False,
			axis_color = '',
			num = 0,
			banner = ''
	)

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
	)

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'
	)

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,
			axis_color = '',
			num = 0
	)

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'
	)

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 = [],
			connect = 'red',
			scale = True,
			axis_color = 'blue',
			num = 0
	)

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',
			high = 'red'
	)

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 = '',
			port = 65000
	)

References fmt.print(), and basic::options::OptionKeys::relax::range.range.

Referenced by PyMOL-RosettaServer.Matrix.__init__().

Variable Documentation

PyMOL-RosettaServer._terminate_ = False

dictionary PyMOL-RosettaServer.COLOR_LIB

Initial value:

= {
'white':[1,1,1],
'yellow':[1,1,0],
'magenta':[1,0,1],
'cyan':[0,1,1],
'red':[1,0,0],
'blue':[0,0,1],
'green':[0,1,0],
'black':[0,0,0]}

Constants.

dictionary PyMOL-RosettaServer.X11_COLORS