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TkVisualizationCanvas.py

# This module defines a 3D wireframe visualization widget
# for Tk user interfaces.
#
# Written by Konrad Hinsen <hinsen@cnrs-orleans.fr>
# Last revision: 2002-3-22
#

from Tkinter import *
from Canvas import Line
import Numeric, string
from Scientific.Geometry import Vector
from Scientific.Geometry.Transformation import Rotation

"""This module provides a special widget for Tk user interfaces
which permits the display of 3D wireframe structures with interactive
manipulation.

Note that this module can become sluggish if two many lines are to
be displayed. An OpenGL widget should be used for serious visualization
needs. The advantage of this module is that it requires no special
graphics libraries in addition to Tk.
"""

class PolyPoints3D:

    def __init__(self, points, attr):
        self.points = Numeric.array(points)
      self.scaled = self.points
        self.attributes = {}
        for name, value in self._attributes.items():
            try:
                value = attr[name]
            except KeyError: pass
            self.attributes[name] = value

    def boundingBox(self):
        return Numeric.minimum.reduce(self.points), \
               Numeric.maximum.reduce(self.points)

    def project(self, axis, plane):
        self.depth = Numeric.dot(self.points, axis)
        self.projection = Numeric.dot(self.points, plane)

    def boundingBoxPlane(self):
        return Numeric.minimum.reduce(self.projection), \
               Numeric.maximum.reduce(self.projection)

    def scaleAndShift(self, scale=1, shift=0):
        self.scaled = scale*self.projection+shift


00052 class PolyLine3D(PolyPoints3D):

    """Multiple connected lines

    Constructor: PolyLine(|points|, **|attr|), where |points| is
    any sequence of (x, y, z) number triples and |attr| stands for line
    attributes specified by keyword arguments, which are
    'width' (an integer) and 'color' (a string whose value is one of
    the color names defined in Tk). The default is a black line
    of width 1.
    """

    def __init__(self, points, **attr):
        PolyPoints3D.__init__(self, points, attr)

    _attributes = {'color': 'black',
                   'width': 1}

    def lines(self):
      color = self.attributes['color']
      width = self.attributes['width']
        lines = []
        depths = []
      for i in range(len(self.scaled)-1):
          x1, y1 = self.scaled[i]
          x2, y2 = self.scaled[i+1]
            lines.append((x1, y1, x2, y2,
                          color, width))
            depths.append(min(self.depth[i], self.depth[i+1]))
        return lines, depths


00084 class VisualizationGraphics:

    """Compound graphics object

    Constructor: VisualizationGraphics(|objects|), where |objects| is a list
    whose elements can be instances of the classes PolyLine3D and
    VisualizationGraphics.
    """
    
    def __init__(self, objects):
        self.objects = objects

    def boundingBox(self):
      p1, p2 = self.objects[0].boundingBox()
      for o in self.objects[1:]:
          p1o, p2o = o.boundingBox()
          p1 = Numeric.minimum(p1, p1o)
          p2 = Numeric.maximum(p2, p2o)
      return p1, p2

    def project(self, axis, plane):
      for o in self.objects:
          o.project(axis, plane)

    def boundingBoxPlane(self):
      p1, p2 = self.objects[0].boundingBoxPlane()
      for o in self.objects[1:]:
          p1o, p2o = o.boundingBoxPlane()
          p1 = Numeric.minimum(p1, p1o)
          p2 = Numeric.maximum(p2, p2o)
      return p1, p2

    def scaleAndShift(self, scale=1, shift=0):
      for o in self.objects:
          o.scaleAndShift(scale, shift)

    def lines(self):
        items = []
        depths = []
      for o in self.objects:
            i, d = o.lines()
          items = items + i
            depths = depths + d
        return items, depths

    def __len__(self):
      return len(self.objects)

    def __getitem__(self, item):
      return self.objects[item]


00136 class VisualizationCanvas(Frame):

    """Tk visualization widget

    Constructor: VisualizationCanvas(|master|, |width|, |height|,
                                     **|attributes|).
    The arguments have the same meaning as for a standard Tk canvas.
    The default background color is white and the default font is
    Helvetica at 10 points.

    VisualizationCanvas objects support all operations of Tk widgets.

    Interactive manipulation of the display is possible with
    click-and-drag operations. The left mouse button rotates the
    objects, the middle button translates it, and the right button
    scales it up or down.
    """
    
    def __init__(self, master, width, height, background='white', **attr):
        apply(Frame.__init__, (self, master), attr)
      self.canvas = Canvas(self, width=width, height=height,
                       background=background)
      self.canvas.pack(fill=BOTH, expand=YES)
        border_w = self.canvas.winfo_reqwidth() - \
                   string.atoi(self.canvas.cget('width'))
        border_h = self.canvas.winfo_reqheight() - \
                   string.atoi(self.canvas.cget('height'))
        self.border = (border_w, border_h)
        self.canvas.bind('<Configure>', self.reconfigure)
        self.canvas.bind('<1>', self.clickhandler1)
        self.canvas.bind('<ButtonRelease-1>', self.releasehandler1)
        self.canvas.bind('<2>', self.clickhandler2)
        self.canvas.bind('<ButtonRelease-2>', self.releasehandler2)
        self.canvas.bind('<3>', self.clickhandler3)
        self.canvas.bind('<ButtonRelease-3>', self.releasehandler3)
      self._setsize()
        self.scale = None
        self.translate = Numeric.array([0., 0.])
      self.last_draw = None
        self.axis = Numeric.array([0.,0.,1.])
        self.plane = Numeric.array([[1.,0.], [0.,1.], [0.,0.]])

    def reconfigure(self, event):
        new_width = event.width-self.border[0]
        new_height = event.height-self.border[1]
        width = string.atoi(self.canvas.cget('width'))
        height = string.atoi(self.canvas.cget('height'))
        if new_width == width and new_height == height:
            return
        self.canvas.configure(width=new_width, height=new_height)
        self._setsize()
        self.clear(1)
        self.redraw()

    def _setsize(self):
      self.width = string.atoi(self.canvas.cget('width'))
      self.height = string.atoi(self.canvas.cget('height'))
      self.plotbox_size = 0.97*Numeric.array([self.width, -self.height])
      xo = 0.5*(self.width-self.plotbox_size[0])
      yo = self.height-0.5*(self.height+self.plotbox_size[1])
      self.plotbox_origin = Numeric.array([xo, yo])

    def copyViewpointFrom(self, other):
        self.axis = other.axis
        self.plane = other.plane
        self.scale = other.scale
        self.translate = other.translate

    def setViewpoint(self, axis, plane, scale=None, translate=None):
        self.axis = axis
        self.plane = plane
        if scale is not None:
            self.scale = scale
        if translate is not None:
            self.translate = translate

00212     def draw(self, graphics):
        """Draws the graphics object |graphics|, which can be
        a PolyLine3D or a VisualizationGraphics object."""
      self.last_draw = (graphics, )
      self.configure(cursor='watch')
      self.update_idletasks()
        graphics.project(self.axis, self.plane)
      p1, p2 = graphics.boundingBoxPlane()
        center = 0.5*(p1+p2)
      scale = self.plotbox_size / (p2-p1)
        sign = scale/Numeric.fabs(scale)
        if self.scale is None:
            minscale = Numeric.minimum.reduce(Numeric.fabs(scale))
            self.scale = 0.9*minscale
        scale = sign*self.scale
        box_center = self.plotbox_origin + 0.5*self.plotbox_size
      shift = -center*scale + box_center + self.translate
      graphics.scaleAndShift(scale, shift)
      items, depths = graphics.lines()
        sort = Numeric.argsort(depths)
        for index in sort:
            x1, y1, x2, y2, color, width = items[index]
            Line(self.canvas, x1, y1, x2, y2, fill=color, width=width)
      self.configure(cursor='top_left_arrow')
      self.update_idletasks()

    def redraw(self):
      if self.last_draw is not None:
          apply(self.draw, self.last_draw)

    def clear(self, keepscale = 0):
        "Clears the canvas."
        self.canvas.delete('all')
        if not keepscale:
            self.scale = None

    def clickhandler1(self, event):
        self.click1x = event.x
        self.click1y = event.y
      self.configure(cursor='exchange')
      self.update_idletasks()

    def clickhandler2(self, event):
        self.click2x = event.x
        self.click2y = event.y
      self.configure(cursor='fleur')
      self.update_idletasks()

    def clickhandler3(self, event):
        self.click3x = event.x
        self.click3y = event.y
      self.configure(cursor='sizing')
      self.update_idletasks()

    def releasehandler1(self, event):
      self.configure(cursor='top_left_arrow')
      self.update_idletasks()
        try:
            dx = event.x - self.click1x
            dy = event.y - self.click1y
        except AttributeError:
            return
        if dx != 0 or dy != 0:
            normal = Vector(self.axis)
            move = Vector(-dx*self.plane[:,0]+dy*self.plane[:,1])
            axis = normal.cross(move) / \
                   Numeric.minimum.reduce(Numeric.fabs(self.plotbox_size))
            rot = Rotation(axis.normal(), axis.length())
            self.axis = rot(normal).array
            self.plane[:,0] = rot(Vector(self.plane[:,0])).array
            self.plane[:,1] = rot(Vector(self.plane[:,1])).array
            self.clear(1)
            self.redraw()

    def releasehandler2(self, event):
      self.configure(cursor='top_left_arrow')
      self.update_idletasks()
        try:
            dx = event.x - self.click2x
            dy = event.y - self.click2y
        except AttributeError:
            return
        if dx != 0 or dy != 0:
            self.translate = self.translate + Numeric.array([dx, dy])
            self.clear(1)
            self.redraw()

    def releasehandler3(self, event):
      self.configure(cursor='top_left_arrow')
      self.update_idletasks()
        try:
            dy = event.y - self.click3y
        except AttributeError:
            return
        if dy != 0:
            ratio = -dy/self.plotbox_size[1]
            self.scale = self.scale * (1.+ratio)
            self.clear(1)
            self.redraw()


if __name__ == '__main__':

    from Scientific.IO.TextFile import TextFile
    from Scientific.IO.FortranFormat import FortranFormat, FortranLine
    import string

    generic_format = FortranFormat('A6')
    atom_format = FortranFormat('A6,I5,1X,A4,A1,A3,1X,A1,I4,A1,' +
                                '3X,3F8.3,2F6.2,7X,A4,2A2')

    # Read the PDB file and make a list of all C-alpha positions
    def readCAlphaPositions(filename):
        positions = []
        chains = [positions]
        for line in TextFile(filename):
            record_type = FortranLine(line, generic_format)[0]
            if record_type == 'ATOM  ' or record_type == 'HETATM':
                data = FortranLine(line, atom_format)
                atom_name = string.strip(data[2])
                position = Numeric.array(data[8:11])
                if atom_name == 'CA':
                    positions.append(position)
                elif atom_name == 'OXT':
                    positions = []
                    chains.append(positions)
        if len(chains[-1]) == 0:
            del chains[-1]
        return chains

    conf = readCAlphaPositions('myoglobin.pdb')
    colors = ['black', 'red', 'green', 'blue', 'yellow']
    colors = (len(conf)*colors)[:len(conf)]
    objects = []
    for chain, color in map(None, conf, colors):
        objects.append(PolyLine3D(chain, color=color))
    graphics = VisualizationGraphics(objects)

    window = Frame()
    window.pack(fill=BOTH, expand=YES)

    c = VisualizationCanvas(window, "100m", "100m", relief=SUNKEN, border=2)
    c.pack(side=TOP, fill=BOTH, expand=YES)
    c.draw(graphics)

    Button(window, text='Draw',
           command=lambda o=graphics: c.draw(o)).pack(side=LEFT)
    Button(window, text='Clear', command=c.clear).pack(side=LEFT)
    Button(window, text='Redraw', command=c.redraw).pack(side=LEFT)
    Button(window, text='Quit', command=window.quit).pack(side=RIGHT)

    window.mainloop()

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