PyMOL-RosettaServer Namespace Reference

Classes
class	StartUpError
	Exceptions. More...
class	PR_UDPServer
class	PR_PyMOLServer
class	XYZCoord
class	PlanePoints
class	Matrix

Functions
def	add_vectors (v1, v2)
def	scalar_multiply (v, n)
def	normalize (normal)
def	rotation_matrix_radians (axis, theta)
def	multiply_matrix (matrix, vector)
def	rotate_vector (vector, theta, axis)
def	compute_plane_positions (center, normal, thickness, rg, npoints=4)
def	draw_membrane_planes (plane_points, normal_vector)
def	make_axis (name, ends, dr, scale=False, axis_color='', num=0)
	Graphing methods. More...
def	scale_axes (name='x_axis or y_axis or z_axis')
def	get_ends (data)
def	extract_coords (name)
def	make_data (name, x_array, y_array, z_array, data_color='red')
def	add_point (name, point, connect='', rescale=False, scale=False, axis_color='', num=0, banner='')
def	rescale_cartesian (data, scale, axis_color, num)
def	connect_points (name, color='red')
def	plot3d (name, x_array, y_array, z_array=[], connect='red', scale=True, axis_color='blue', num=0)
def	set_spectrum (low='blue', high='red')
	PyMOL spectrum coloring. More...
def	main (ip, port)
	Main PyMOLPyRosettaServer.py routines. More...
def	start_rosetta_server (ip='', port=65000)

Variables
bool	_terminate_ = False
dictionary	COLOR_LIB
	Constants. More...
dictionary	X11_COLORS

Function Documentation

add_point()

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(), and str().

Referenced by PyMOL-RosettaServer.Matrix.__init__(), and PyMOL-RosettaServer.PR_PyMOLServer.process_packet().

add_vectors()

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().

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(), range, and rotate_vector().

Referenced by PyMOL-RosettaServer.Matrix.__init__(), and PyMOL-RosettaServer.PR_PyMOLServer.process_packet().

connect_points()

def PyMOL-RosettaServer.connect_points	(		name,
			color = 'red'
	)

Draws colored lines between consecutive points.

References range, and str().

Referenced by PyMOL-RosettaServer.Matrix.__init__(), and plot3d().

draw_membrane_planes()

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().

extract_coords()

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().

get_ends()

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().

main()

def PyMOL-RosettaServer.main	(		ip,
			port
	)

Main PyMOLPyRosettaServer.py routines.

References print().

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

make_axis()

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 run_backbone.float, range, scale_axes(), and str().

Referenced by PyMOL-RosettaServer.Matrix.__init__(), and rescale_cartesian().

make_data()

def PyMOL-RosettaServer.make_data	(		name,
			x_array,
			y_array,
			z_array,
			data_color = 'red'
	)

Generate a data object from three arrays.

References ObjexxFCL.len(), range, and str().

Referenced by PyMOL-RosettaServer.Matrix.__init__(), and plot3d().

multiply_matrix()

def PyMOL-RosettaServer.multiply_matrix	(		matrix,
			vector
	)

multiply matrix by 3D vector

Referenced by PyMOL-RosettaServer.Matrix.__init__(), and rotate_vector().

normalize()

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().

plot3d()

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__(), and PyMOL-RosettaServer.PR_PyMOLServer.process_packet().

rescale_cartesian()

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(), make_axis(), and str().

Referenced by PyMOL-RosettaServer.Matrix.__init__(), add_point(), and plot3d().

rotate_vector()

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().

rotation_matrix_radians()

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().

scalar_multiply()

def PyMOL-RosettaServer.scalar_multiply	(		v,
			n
	)

Multiply a vector by some scalar factor

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

scale_axes()

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().

set_spectrum()

def PyMOL-RosettaServer.set_spectrum	(		low = 'blue',
			high = 'red'
	)

PyMOL spectrum coloring.

Sets the energy coloring spectrum using the above COLOR_LIB dictionary.

References print(), range, and x.

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

start_rosetta_server()

def PyMOL-RosettaServer.start_rosetta_server	(		ip = '',
			port = 65000
	)

References print(), and range.

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

Variable Documentation

_terminate_

bool PyMOL-RosettaServer._terminate_ = False

private

COLOR_LIB

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.

X11_COLORS

dictionary PyMOL-RosettaServer.X11_COLORS