path: root/cad/src/graphics/display_styles/DnaCylinderChunks.py

# Copyright 2008-2009 Nanorex, Inc.  See LICENSE file for details. 
"""
DnaCylinderChunks.py -- defines I{DNA Cylinder} display mode, which draws 
axis chunks as a cylinder in the chunk's color.

@author: Mark, Piotr
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc.  See LICENSE file for details. 

History:

Mark 2008-02-12: Created by making a copy of CylinderChunks.py

piotr 080310: I have rewritten most of the code here from scratch. Most of 
the code computed within this function has to be moved to "getmemo" 
for a speed optimization. There are several issues with this rendering code,
including lack of highlighting and selection support, and some
weird behavior when modeltree is used to select individual strands.

The DNA display style requires DNA updater to be enabled.

There are four independent structures within the DNA display style:
axis, strands, struts and bases. Properties of these parts can be set
in the User Preferences dialog.

piotr 080317: Added POV-Ray rendering routines.

piotr 080318: Moved most of the data generation code to "getmemo"
Highlighting and selection now works. Thank you, Ninad!!!

("rainbow" strands still can't be selected nor highlighted, this will 
be fixed later)

piotr 080328: Added several "interactive" features: labels, base orientation
indicators, "2D" style.

piotr 080509: Code refactoring.

piotr 080520: Further code cleanup..

"""

import sys
import foundation.env as env
from graphics.drawing.CS_draw_primitives import drawcylinder
from graphics.drawing.CS_draw_primitives import drawpolycone
from graphics.drawing.CS_draw_primitives import drawpolycone_multicolor
from graphics.drawing.CS_draw_primitives import drawsphere
from graphics.drawing.drawers import drawCircle
from graphics.drawing.drawers import drawFilledCircle
from graphics.drawing.drawers import drawtext

from math import sin, cos, pi
from Numeric import dot, argmax, argmin, sqrt

from graphics.display_styles.displaymodes import ChunkDisplayMode

from geometry.VQT import V, Q, norm, cross, angleBetween

from utilities.debug import print_compact_traceback
from utilities.debug_prefs import debug_pref, Choice, Choice_boolean_True, Choice_boolean_False

from utilities.prefs_constants import hoverHighlightingColor_prefs_key
from utilities.prefs_constants import selectionColor_prefs_key
from utilities.constants import ave_colors, black, red, blue, white

from utilities.prefs_constants import atomHighlightColor_prefs_key

# 3D and 2D rendition display styles. Mark 2008-05-15
from utilities.prefs_constants import dnaRendition_prefs_key

# piotr 080309: user pereferences for DNA style
from utilities.prefs_constants import dnaStyleStrandsColor_prefs_key
from utilities.prefs_constants import dnaStyleAxisColor_prefs_key
from utilities.prefs_constants import dnaStyleStrutsColor_prefs_key
from utilities.prefs_constants import dnaStyleBasesColor_prefs_key
from utilities.prefs_constants import dnaStyleStrandsShape_prefs_key
from utilities.prefs_constants import dnaStyleBasesShape_prefs_key
from utilities.prefs_constants import dnaStyleStrandsArrows_prefs_key
from utilities.prefs_constants import dnaStyleAxisShape_prefs_key
from utilities.prefs_constants import dnaStyleStrutsShape_prefs_key
from utilities.prefs_constants import dnaStyleStrandsScale_prefs_key
from utilities.prefs_constants import dnaStyleAxisScale_prefs_key
from utilities.prefs_constants import dnaStyleBasesScale_prefs_key
from utilities.prefs_constants import dnaStyleAxisEndingStyle_prefs_key
from utilities.prefs_constants import dnaStyleStrutsScale_prefs_key

# piotr 080325 added more user preferences
from utilities.prefs_constants import dnaStrandLabelsEnabled_prefs_key
from utilities.prefs_constants import dnaStrandLabelsColor_prefs_key
from utilities.prefs_constants import dnaStrandLabelsColorMode_prefs_key
from utilities.prefs_constants import dnaBaseIndicatorsEnabled_prefs_key
from utilities.prefs_constants import dnaBaseIndicatorsColor_prefs_key
from utilities.prefs_constants import dnaBaseInvIndicatorsEnabled_prefs_key
from utilities.prefs_constants import dnaBaseInvIndicatorsColor_prefs_key
from utilities.prefs_constants import dnaBaseIndicatorsPlaneNormal_prefs_key
from utilities.prefs_constants import dnaStyleBasesDisplayLetters_prefs_key

try:
    from OpenGL.GLE import glePolyCone
    from OpenGL.GLE import gleGetNumSides 
    from OpenGL.GLE import gleSetNumSides 
    from OpenGL.GLE import gleExtrusion
    from OpenGL.GLE import gleTwistExtrusion
    from OpenGL.GLE import glePolyCylinder 
    from OpenGL.GLE import gleSetJoinStyle
    from OpenGL.GLE import TUBE_NORM_EDGE 
    from OpenGL.GLE import TUBE_NORM_PATH_EDGE 
    from OpenGL.GLE import TUBE_JN_ROUND
    from OpenGL.GLE import TUBE_JN_ANGLE
    from OpenGL.GLE import TUBE_CONTOUR_CLOSED 
    from OpenGL.GLE import TUBE_JN_CAP 
except:
    print "DNA Cylinder: GLE module can't be imported. Now trying _GLE"
    from OpenGL._GLE import glePolyCone 
    from OpenGL._GLE import gleGetNumSides 
    from OpenGL._GLE import gleSetNumSides 
    from OpenGL._GLE import gleExtrusion
    from OpenGL._GLE import gleTwistExtrusion    
    from OpenGL._GLE import glePolyCylinder 
    from OpenGL._GLE import gleSetJoinStyle
    from OpenGL._GLE import TUBE_NORM_EDGE 
    from OpenGL._GLE import TUBE_NORM_PATH_EDGE 
    from OpenGL._GLE import TUBE_JN_ROUND
    from OpenGL._GLE import TUBE_JN_ANGLE
    from OpenGL._GLE import TUBE_CONTOUR_CLOSED 
    from OpenGL._GLE import TUBE_JN_CAP 

# OpenGL functions are called by "realtime" draw methods.
from OpenGL.GL import glBegin
from OpenGL.GL import GL_BLEND
from OpenGL.GL import glEnd
from OpenGL.GL import glVertex3f
from OpenGL.GL import glVertex3fv
from OpenGL.GL import glColor3f
from OpenGL.GL import glColor3fv
from OpenGL.GL import glTranslatef
from OpenGL.GL import GL_LINE_STRIP        
from OpenGL.GL import GL_LINES
from OpenGL.GL import GL_POLYGON
from OpenGL.GL import glEnable
from OpenGL.GL import glDisable
from OpenGL.GL import GL_LIGHTING
from OpenGL.GL import GL_SMOOTH
from OpenGL.GL import glShadeModel
from OpenGL.GL import GL_COLOR_MATERIAL
from OpenGL.GL import GL_TRIANGLES
from OpenGL.GL import GL_FRONT_AND_BACK
from OpenGL.GL import GL_AMBIENT_AND_DIFFUSE
from OpenGL.GL import glMaterialfv
from OpenGL.GL import glPushMatrix
from OpenGL.GL import glPopMatrix
from OpenGL.GL import glRotatef
from OpenGL.GL import glScalef
from OpenGL.GL import glLineWidth
from OpenGL.GL import GL_QUADS
from OpenGL.GL import GL_LINE_SMOOTH

import colorsys

from OpenGL.GLU import gluUnProject

from dna.model.DnaLadderRailChunk import DnaStrandChunk

from model.chunk import Chunk

chunkHighlightColor_prefs_key = atomHighlightColor_prefs_key # initial kluge

# piotr 080519: made this method a global function
# it needs to be moved to a more appropriate location
def get_dna_base_orientation_indicators(chunk, normal):
    """
    Returns two lists for DNA bases perpendicular and anti-perpendicular
    to a plane specified by the plane normal vector.
    
    @param normal: normal vector defining a plane
    @type normal: float[3]
    """
    
    from utilities.prefs_constants import dnaBaseIndicatorsAngle_prefs_key
    from utilities.prefs_constants import dnaBaseIndicatorsDistance_prefs_key

    indicators_angle = env.prefs[dnaBaseIndicatorsAngle_prefs_key]
    indicators_distance = env.prefs[dnaBaseIndicatorsDistance_prefs_key]

    indicators = []
    inv_indicators = []

    if chunk.isStrandChunk(): 
        if chunk.ladder.axis_rail:
            n_bases = chunk.ladder.baselength()
            if chunk == chunk.ladder.strand_rails[0].baseatoms[0].molecule:
                chunk_strand = 0
            else:
                chunk_strand = 1
            for pos in range(0, n_bases):
                atom1 = chunk.ladder.strand_rails[chunk_strand].baseatoms[pos]
                atom2 = chunk.ladder.axis_rail.baseatoms[pos]
                vz = normal
                v2 = norm(atom1.posn()-atom2.posn())
                # calculate the angle between this vector 
                # and the vector towards the viewer
                a = angleBetween(vz, v2)
                if abs(a) < indicators_angle:
                    indicators.append(atom1)
                if abs(a) > (180.0 - indicators_angle):
                    inv_indicators.append(atom1)
    
    return (indicators, inv_indicators)


def get_all_available_dna_base_orientation_indicators(chunk, 
                                                      normal,
                                                      reference_indicator_dict = {},                                           
                                                      skip_isStrandChunk_check = False):
    """
    
    """
    # by Ninad
    #@TODO: Move this and other methods out of this file, into a general
    #helper pkg and module -- Ninad 2008-06-01
    from utilities.prefs_constants import dnaBaseIndicatorsAngle_prefs_key
    from utilities.prefs_constants import dnaBaseIndicatorsDistance_prefs_key

    indicators_angle = env.prefs[dnaBaseIndicatorsAngle_prefs_key]
    indicators_distance = env.prefs[dnaBaseIndicatorsDistance_prefs_key]

    all_indicators_dict = {}
        
    if skip_isStrandChunk_check:
        pass
        #caller has already done this check and is explicitely asking to
        #skip isStrandChunk test (for optimization) 
    else:        
        if chunk.isStrandChunk():
            return {}, {}
     
    if chunk.ladder.axis_rail:
        n_bases = chunk.ladder.baselength()
        if chunk == chunk.ladder.strand_rails[0].baseatoms[0].molecule:
            chunk_strand = 0
        else:
            chunk_strand = 1
        for pos in range(0, n_bases):
            atom1 = chunk.ladder.strand_rails[chunk_strand].baseatoms[pos]
            atom2 = chunk.ladder.axis_rail.baseatoms[pos]
            vz = normal
            v2 = norm(atom1.posn()-atom2.posn())
            # calculate the angle between this vector 
            # and the vector towards the viewer
            a = angleBetween(vz, v2)
            if abs(a) < indicators_angle:
                if not reference_indicator_dict.has_key(id(atom1)):
                    all_indicators_dict[id(atom1)] = atom1
            if abs(a) > (180.0 - indicators_angle):
                if not reference_indicator_dict.has_key(id(atom1)):
                    all_indicators_dict[id(atom1)] = atom1
    
    return all_indicators_dict
    


def get_dna_base_orientation_indicator_dict(chunk, 
                                            normal,
                                            reference_indicator_dict = {},
                                            reference_inv_indicator_dict = {},
                                            skip_isStrandChunk_check = False):
    """
    Returns two  dictionaries for DNA bases perpendicular and anti-perpendicular
    to a plane specified by the plane normal vector.
    """
    # by Ninad
    #@TODO: Move this and other methods out of this file, into a general
    #helper pkg and module -- Ninad 2008-06-01
    
    from utilities.prefs_constants import dnaBaseIndicatorsAngle_prefs_key
    from utilities.prefs_constants import dnaBaseIndicatorsDistance_prefs_key

    indicators_angle = env.prefs[dnaBaseIndicatorsAngle_prefs_key]
    indicators_distance = env.prefs[dnaBaseIndicatorsDistance_prefs_key]

    indicators_dict = {}
    inv_indicators_dict = {}
        
    if skip_isStrandChunk_check:
        pass
        #caller has already done this check and is explicitely asking to
        #skip isStrandChunk test (for optimization) 
    else:        
        if chunk.isStrandChunk():
            return {}, {}
     
    if chunk.ladder.axis_rail:
        n_bases = chunk.ladder.baselength()
        if chunk == chunk.ladder.strand_rails[0].baseatoms[0].molecule:
            chunk_strand = 0
        else:
            chunk_strand = 1
        for pos in range(0, n_bases):
            atom1 = chunk.ladder.strand_rails[chunk_strand].baseatoms[pos]
            atom2 = chunk.ladder.axis_rail.baseatoms[pos]
            vz = normal
            v2 = norm(atom1.posn()-atom2.posn())
            # calculate the angle between this vector 
            # and the vector towards the viewer
            a = angleBetween(vz, v2)
            if abs(a) < indicators_angle:
                if not reference_indicator_dict.has_key(id(atom1)) and \
                   not reference_inv_indicator_dict.has_key(id(atom1)):
                    indicators_dict[id(atom1)] = atom1
            if abs(a) > (180.0 - indicators_angle):
                if not reference_indicator_dict.has_key(id(atom1)) and \
                   not reference_inv_indicator_dict.has_key(id(atom1)):
                    inv_indicators_dict[id(atom1)] = atom1
    
    return (indicators_dict, inv_indicators_dict)

   
class DnaCylinderChunks(ChunkDisplayMode):
    """
    Implements DNA Cylinder display mode, which draws PAM-model DNA objects
    using simplified represenations for individual components.
    
    There are four components treated independently: "axis", "strands", "struts"
    and "nucleotides". Each of these components has its own set of settings.

    @note: Nothing else is rendered (no atoms, sugar atoms, etc) when 
        set to this display mode. 
        piotr 080316: Some of these features can be displayed as "nucleotides"

    @attention: This is still considered experimental.
    """
    # OLD limitations/known bugs, mostly fixed
    #
    # - Cylinders are always straight. DNA axis chunks with atoms that are not 
    # aligned in a straight line are not displayed correctly (i.e. they don't
    # follow a curved axis path. -- fixed 080310 piotr
    # - Hover highlighting does not work. fixed 080318 piotr: thank you, Ninad! 
    # - Selected chunks are not colored in the selection color. fix 080318 piotr 
    # - Cannot drag/move a selected cylinder interactively. fix 080318 piotr
    # - DNA Cylinders are not written to POV-Ray file. piotr: fixed 080317
    # - DNA Cylinders are not written to PDB file and displayed in QuteMolX.
    # --- this is a more general problem related to limitation of QuteMolX

    # mmp_code must be a unique 3-letter code, distinct from the values in 
    # constants.dispNames or in other display modes
    mmp_code = 'dna'  
    disp_label = 'DNA Cylinder' # label for statusbar fields, menu text, etc.
    featurename = "Set Display DNA Cylinder"
    
    icon_name = "modeltree/DnaCylinder.png"
    hide_icon_name = "modeltree/DnaCylinder-hide.png"
    ### also should define icon as an icon object or filename, 
    ### either in class or in each instance
    ### also should define a featurename for wiki help
    
    # Several of the methods below should be split into their own files.
    # piotr 082708
    
    def _compute_spline(self, data, idx, t):
        """
        Implements a Catmull-Rom spline. Interpolates between data[idx] 
        and data[idx+1]. 0.0 <= t <= 1.0.
        
        @param data: array with at least four values to be used for 
        interpolation. The following values are used: data[idx-1], data[idx],
        data[idx+1], data[idx+2]
        
        @param t: position (0 <= t <= 1)
        @type t: float
        
        @return: spline value at t
        """
        t2 = t * t
        t3 = t2 * t
        x0 = data[idx-1]
        x1 = data[idx]
        x2 = data[idx+1]
        x3 = data[idx+2]
        res = 0.5 * ((2.0 * x1) +
                     t * (-x0 + x2) +
                     t2 * (2.0 * x0 - 5.0 * x1 + 4.0 * x2 - x3) +
                     t3 * (-x0 + 3.0 * x1 - 3.0 * x2 + x3))
        return res

    def _get_rainbow_color(self, hue, saturation, value):
        """
        Gets a color of a hue range limited to 0 - 0.667 (red - blue color range).
        
        @param hue: color hue (0..1)
        @type hue: float
        
        @param saturation: color saturation (0..1)
        @type saturation: float
        
        @param value: color value (0..1)
        @type value: float
        
        @return: color for given (h,s,v) 
        """

        hue = 0.666 * (1.0 - hue)
        if hue < 0.0: 
            hue = 0.0
        if hue > 0.666: 
            hue = 0.666
        return colorsys.hsv_to_rgb(hue, saturation, value)

    def _get_full_rainbow_color(self, hue, saturation, value):
        """
        Gets a color from a full hue range (red - red). Can be used for
        color wrapping (color at hue == 0 is the same as color at hue == 1).
        
        @param hue: color hue (0..1)
        @type hue: float
        
        @param saturation: color saturation (0..1)
        @type saturation: float
        
        @param value: color value (0..1)
        @type value: float
        
        @return: color for given (h,s,v)         
        """
        if hue < 0.0: 
            hue = 0.0
        if hue > 1.0: 
            hue = 1.0
        return colorsys.hsv_to_rgb(hue, saturation, value)

    def _get_nice_rainbow_color(self, hue, saturation, value):
        """
        Gets a color of a hue limited to red-magenta range.

        @param hue: color hue (0..1)
        @type hue: float
        
        @param saturation: color saturation (0..1)
        @type saturation: float
        
        @param value: color value (0..1)
        @type value: float
        
        @return: color for given (h,s,v)                 
        """
        hue *= 0.8
        if hue < 0.0: 
            hue = 0.0
        if hue > 1.0: 
            hue = 1.0
        return colorsys.hsv_to_rgb(hue, saturation, value)

    def _get_base_color(self, base):
        """
        Returns a color according to DNA base type.
        Two-ring bases (G and A) have darker colors.
        
        G = red
        C = orange
        A = blue
        T = cyan
        
        @note: there should be a user pref setting for these
        
        @param base: DNA base symbol
        @type base: 1-char string
        
        @return: color corresponding to a given base
        """
        
        if base == "G":
            color = [1.0, 0.0, 0.0]
        elif base == "C":
            color = [1.0, 0.5, 0.0]
        elif base == "A":
            color = [0.0, 0.3, 0.9]
        elif base == "T":
            color = [0.0, 0.7, 0.8]
        else:
            color = [0.5, 0.5, 0.5]
        return color
    
    def _get_rainbow_color_in_range(self, pos, count, saturation, value):
        """
        Gets a color of a hue range limited to 0 - 0.667 (red - blue color range)
        correspoding to a "pos" value from (0..count) range.
        
        @param pos: position in (0..count range) 
        @type pos: integer
        
        @param count: limits the range of allowable values
        @type count: integer
        
        @param saturation: color saturation (0..1)
        @type saturation: float
        
        @param value: color value (0..1)
        @type value: float
        
        @return: color for given (pos, s, v) 
        """
        if count > 1: 
            count -= 1
        hue = float(pos)/float(count)        
        if hue < 0.0: 
            hue = 0.0
        if hue > 1.0: 
            hue = 1.0
        return self._get_rainbow_color(hue, saturation, value)

    def _get_full_rainbow_color_in_range(self, pos, count, saturation, value):
        """
        Gets a color from a full hue range (red to red). Can be used for
        color wrapping (color at hue == 0 is the same as color at hue == 1).
        The color corresponds to a "pos" value from (0..count) range.
        
        @param pos: position in (0..count range) 
        @type pos: integer
        
        @param count: limits the range of allowable values
        @type count: integer
        
        @param saturation: color saturation (0..1)
        @type saturation: float
        
        @param value: color value (0..1)
        @type value: float
        
        @return: color for given (pos, s, v) 
        """
        if count > 1: 
            count -= 1
        hue = float(pos)/float(count)        
        if hue < 0.0: 
            hue = 0.0
        if hue > 1.0: 
            hue = 1.0
        return self._get_full_rainbow_color(hue, saturation, value)

    def _get_nice_rainbow_color_in_range(self, pos, count, saturation, value):
        """
        Gets a color of a hue range limited to red-magenta range.
        The color corresponds to a "pos" value from (0..count) range.
        
        @param pos: position in (0..count) range 
        @type pos: integer
        
        @param count: limits the range of allowable values
        @type count: integer
        
        @param saturation: color saturation (0..1)
        @type saturation: float
        
        @param value: color value (0..1)
        @type value: float
        
        @return: color for given (pos, s, v) 
        """
        if count > 1: 
            count -= 1
        hue = float(pos)/float(count)        
        if hue < 0.0: 
            hue = 0.0
        if hue > 1.0: 
            hue = 1.0
        return self._get_nice_rainbow_color(hue, saturation, value)
    
    def _make_curved_strand(self, points, colors, radii):
        """
        Converts a polycylinder tube to a smooth, curved tube
        by spline interpolating of points, colors and radii.
        
        Assumes that len(points) == len(colors) == len(radii)
        
        @param points: consecutive points to be interpolated
        @type points: list of V or list of float[3]
        
        @param colors: colors corresponding to the points
        @type colors: list of colors
        
        @param radii: radii correspoding to individual points
        @type radii: list of radii
        
        @return: tuple of interpolated (points, colors, radii)
        """
        n = len(points)
        if n > 3:
            # Create lists for the interpolated positions, colors, and radii.
            new_points = [ None ] * (4*(n-2)-1)
            new_colors = [ None ] * (4*(n-2)-1)
            new_radii = [ 0.0 ] * (4*(n-2)-1)
            for p in range(0, (4*(n-2)-1)):
                new_points[p] = [ 0.0 ] * 3
                new_colors[p] = [ 0.0 ] * 3
            o = 1
            # Fill-in the lists by computing spline values at consecutive points.
            # Assume that the spline resolution equals 4.
            for p in range (1, n-2):
                for m in range (0, 4):
                    t = 0.25 * m
                    new_points[o] = self._compute_spline(points, p, t)
                    new_colors[o] = self._compute_spline(colors, p, t)
                    new_radii[o] = self._compute_spline(radii, p, t)
                    o += 1        
                    
            # Fill-in terminal positions.
            new_points[o] = self._compute_spline(points, p, 1.0)
            new_colors[o] = self._compute_spline(colors, p, 1.0)
            new_radii[o] = self._compute_spline(radii, p, 1.0)
            o += 1
            new_points[0] = 3.0 * new_points[1] \
                      - 3.0 * new_points[2] \
                      + new_points[3] 
            new_points[o] = 3.0 * new_points[o-1] \
                      - 3.0 * new_points[o-2] \
                      + new_points[o-3] 
            new_colors[0] = new_colors[1]
            new_colors[o] = new_colors[o - 1]
            new_radii[0] = new_radii[1]
            new_radii[o] = new_radii[o - 1]
            return (new_points, new_colors, new_radii)
        else:
            # if not enough points, just return the initial lists
            return (points, colors, radii)

    def _get_axis_positions(self, chunk, atom_list, color_style):
        """
        From an atom list create a list of positions extended by two dummy 
        positions at both ends. The list looks different depending on the
        used color style.

        Uses the chunk to convert atom coordinates to molecule-relative coords.
        
        @param chunk: chunk
        @type chunk: Chunk
        
        @param atom_list: list of axis chunk atoms
        @type atom_list: list of Atoms
        
        @param color_style: color style to be used to render the axis
        @type color_style: int
        
        @return: positions of the DNA axis cylinder 
        """
        n_atoms = len(atom_list)
        if color_style == 2 or color_style == 3: 
            # Use discrete colors. Below is an explanation of how the "discrete"
            # colors work. piotr 080827
            # The GLE "polycylinder" (and related methods, e.g. glePolyCone) 
            # interpolates colors between consecutive links. To create a sharp,
            # "discrete" color transition between two links, a new virtual link
            # of length 0 has to be introduced. The virtual link will be not
            # drawn, its purpose is only to make the color transitions sharp.
            # The virtual links are introduced in-between existing links,
            # for example:
            # Original sequence: (P0,C0) - (P1,C1) - (P2,C2)
            # will be replaced by:
            # New sequence: (P0,C0) - (P1,C0) - (P1,C1) - (P2,C1) - (P2,C2)
            # where (Px,Cx) is a (position,color) pair of an individual link.
            positions = [None] * (2 * n_atoms + 2)
            pos = 2
            for i in range (1, n_atoms):
                pos1 = chunk.abs_to_base(atom_list[i-1].posn())
                pos2 = chunk.abs_to_base(atom_list[i].posn())                
                positions[pos] = 0.5*(pos1 + pos2)
                positions[pos + 1] = 0.5*(pos1 + pos2)
                pos += 2
            positions[1] = chunk.abs_to_base(atom_list[0].posn())
            positions[0] = 2 * positions[1] - positions[2]
            positions[pos] = chunk.abs_to_base(atom_list[n_atoms - 1].posn())
            positions[pos + 1] = 2 * positions[pos] - positions[pos - 1]
        else:    
            positions = [None] * (n_atoms + 2)
            for i in range(1, n_atoms + 1):
                positions[i] = chunk.abs_to_base(atom_list[i-1].posn())
            if n_atoms > 1:
                positions[0] = 2 * positions[1] - positions[2]
            else:
                positions[0] = positions[1]
            if n_atoms > 1:    
                positions[n_atoms + 1] = 2 * positions[n_atoms] - positions[n_atoms - 1]
            else:
                positions[n_atoms + 1] = positions[n_atoms]                    
        return positions

    def _get_axis_atom_color_per_base(self, pos, strand_atoms_lists):
        """
        Gets a color of an axis atom depending on a base type.
        
        If the axis cylinder is colored 'per base', it uses two distinct
        colors: orange for G-C pairs, and teal for A-T pairs.
        Unknown bases are colored gray. 
        
        @param pos: atom position in axis chunk
        @type pos: integer
        
        @param strand_atoms_lists: lists of strand atoms (used to find out
        the name of DNA base).
        
        @return: axis atom color
        """
        color = [0.5, 0.5, 0.5]
        if len(strand_atoms_lists) > 1:
            if strand_atoms_lists[0] and strand_atoms_lists[1]:
                len1 = len(strand_atoms_lists[0])
                len2 = len(strand_atoms_lists[1])
                if pos>=0 and pos < len1 and pos < len2:
                    base_name = strand_atoms_lists[0][pos].getDnaBaseName()
                    if base_name == 'A' or base_name == 'T':
                        color = [0.0, 1.0, 0.5]
                    elif base_name == 'G' or base_name == 'C':
                        color = [1.0, 0.5, 0.0]
        return color                    

    def _get_axis_colors(self, atom_list, strand_atoms_lists, \
                         color_style, chunk_color, group_color):
        """
        Create a list of colors from an axis atom list, depending on the
        used color style.
        
        @param atom_list: list of axis atoms
        
        @param strand_atoms_list: lists of strand atoms
        
        @param color_style: color style used to draw the axis chunk
        
        @param chunk_color: color of the chunk
        
        @param group_color: 
        """
        n_atoms = len(atom_list)
        if color_style == 2 or \
           color_style == 3: 
            # Discrete colors.
            # For discrete color scheme, the number of internal nodes has to be
            # duplicated in order to deal with (defult) color interpolation
            # in glePolyCylinder routine (colors are interpolated on links
            # with zero length, so the interpolation effects are not visible.)
            # Also, look at comments in _get_axis_positions.
            colors = [None] * (2 * n_atoms + 2)
            pos = 2
            for i in range (1, n_atoms):
                if color_style == 2: 
                    color1 = self._get_rainbow_color_in_range(
                        i-1, n_atoms, 0.75, 1.0)
                    color2 = self._get_rainbow_color_in_range(
                        i, n_atoms, 0.75, 1.0)
                elif color_style == 3:
                    color1 = self._get_axis_atom_color_per_base(
                        i-1, strand_atoms_lists)
                    color2 = self._get_axis_atom_color_per_base(
                        i, strand_atoms_lists)
                colors[pos] = color1
                colors[pos + 1] = color2
                pos += 2
            colors[1] = colors[2] 
            colors[0] = colors[1] 
            colors[pos] = colors[pos - 1] 
            colors[pos + 1] = colors[pos] 
        else:
            colors = [None] * (n_atoms + 2)
            if color_style == 1:                    
                for i in range(1, n_atoms + 1):
                    colors[i] = self._get_rainbow_color_in_range(
                        i-1, n_atoms, 0.75, 1.0)
            elif color_style == 4:
                for i in range(1, n_atoms + 1):
                    colors[i] = group_color
            else:
                for i in range(1, n_atoms + 1):
                    colors[i] = chunk_color
            colors[0] = colors[1]
            colors[n_atoms + 1] = colors[n_atoms]

        return colors

    def _get_axis_radii(self, atom_list, color_style, shape, scale, ending_style):
        """
        Create a list of radii from the axis atom list.
        
        @param atom_list: list of axis atoms
        
        @param strand_atoms_list: lists of strand atoms
        
        @param color_style: color style used to draw the axis chunk
        
        @param shape: shape of the axis component
        
        @param scale: scale of the axis component
        
        @param ending_style: ending style of the axis component (blunt/tapered)
        """
        if shape == 1:
            rad = 7.0 * scale
        else:    
            rad = 2.0 * scale
        n_atoms = len(atom_list)
        if color_style == 2 or color_style == 3: 
            # Discrete colors.
            # For discrete colors duplicate a number of nodes.
            length = 2 * n_atoms + 2
            radii = [rad] * (length)
            # Append radii for the virtual ends.
            if ending_style == 2 or ending_style == 3:
                radii[1] = 0.0
                radii[2] = 0.5 * rad
                radii[3] = 0.5 * rad
            if ending_style == 1 or ending_style == 3:
                radii[length-4] = 0.5 * rad
                radii[length-3] = 0.5 * rad
                radii[length-2] = 0.0
        else:
            length = n_atoms + 2
            radii = [rad] * (length)
            if ending_style == 2 or ending_style == 3:
                radii[1] = 0.0
                radii[2] = 0.66 * rad
            if ending_style == 1 or ending_style == 3:
                radii[length-3] = 0.66 * rad
                radii[length-2] = 0.0        

        return radii

    def _get_strand_positions(self, chunk, atom_list):
        """
        From an strand atom list create a list of positions
        extended by two dummy positions at both ends.
        
        @param chunk: current chunk
        
        @param atom_list: list of strand atom positions 
        """
        n_atoms = len(atom_list)
        positions = [None] * (n_atoms + 2)
        for i in range(1, n_atoms + 1):
            positions[i] = chunk.abs_to_base(atom_list[i-1].posn())
        if n_atoms < 3:
            positions[0] = positions[1]
            positions[n_atoms + 1] = positions[n_atoms]
        else:
            positions[0] = 3.0 * positions[1] \
                     - 3.0 * positions[2] \
                     + positions[3]
            positions[n_atoms + 1] = 3.0 * positions[n_atoms] \
                     - 3.0 * positions[n_atoms - 1] \
                     + positions[n_atoms - 2] 

        return positions

    def _get_atom_rainbow_color(self, idx, n_atoms, start, end, length):
        """ 
        Calculates a "rainbow" color for a single atom.
        This code is partially duplicated in get_strand_colors.
        
        @param idx: atom index relative to the chunk length
        @type idx: integer
        
        @param n_atoms: number of atoms in the chunk
        @type n_atoms: integer
        
        @param start: index of the first chunk atom relative to the total strand length
        @type start: integer

        @param end: index of the last chunk atom relative to the total strand length
        @type end: integer
        
        @param length: total length of the strand
        @type length: integer
        """
        if n_atoms > 1:
            step = float(end - start)/float(n_atoms - 1)
        else:
            step = 0.0
        if length > 1:
            ilength = 1.0 / float(length - 1)
        else:
            ilength = 1.0
        q = ilength * (start + step * idx)
        ### if strand_direction == -1:
        ###    q = 1.0 - q
        return self._get_rainbow_color(q, 0.75, 1.0)


    def _get_strand_colors(self, atom_list, color_style, start, end, \
                           length, chunk_color, group_color):
        """
        From the strand atom list create a list of colors extended by two dummy 
        positions at both ends.
        
        @param atom_list: list of the strand atoms
        
        @param color_style: color style used to draw the axis chunk
        
        @param start: index of the first chunk atom relative to the total strand length
        @type start: integer

        @param end: index of the last chunk atom relative to the total strand length
        @type end: integer
        
        @param length: total length of the strand
        @type length: integer

        @param chunk_color: color of the chunk
        
        @param group_color: color of the group        
        """
        n_atoms = len(atom_list)
        colors = [None] * (n_atoms + 2)
        pos = 0
        if n_atoms > 1:
            step = float(end - start)/float(n_atoms - 1)
        else:
            step = 0.0
        if length > 1:
            ilength = 1.0 / float(length - 1)
        else:
            ilength = 1.0
        r = start
        for i in range(0, n_atoms):
            if color_style == 0:
                col = chunk_color
            elif color_style == 1:
                q =  r * ilength
                #if strand_direction == -1:
                #    q = 1.0 - q
                col = self._get_rainbow_color(q, 0.75, 1.0)
                r += step
            else:
                col = group_color
            colors[i + 1] = V(col[0], col[1], col[2])
            # Has to convert to array, otherwise spline interpolation
            # doesn't work (why - I suppose because tuples are immutable ?)
        colors[0] = colors[1]
        colors[n_atoms + 1] = colors[n_atoms]
        return colors

    def _get_strand_radii(self, atom_list, radius):
        """
        From the atom list create a list of radii extended by two dummy positions 
        at both ends.
        
        @param atom_list: list of strand atoms
        
        @param radius: scale factor of the strands
        """
        n_atoms = len(atom_list)
        radii = [None] * (n_atoms + 2)
        for i in range(1, n_atoms + 1):
            radii[i] = radius
        radii[0] = radii[1]
        radii[n_atoms + 1] = radii[n_atoms]
        return radii


    def _make_discrete_polycone(self, positions, colors, radii):
        """
        Converts a polycone_multicolor colors from smoothly interpolated 
        gradient to discrete (sharp edged) color scheme. The number of nodes 
        will be duplicated.
        
        @param positions: list of positions
        
        @param colors: list of colors
        
        @param radii: list of radii
        
        @return: (positions, colors, radii) tuple 
        
        @note: The method is written so it can be called in a following way:        
        pos, col, rad = _make_discrete_polycone(pos, col, rad)
        """
        # See a comment in "_get_axis_positions"
        n = len(positions)
        new_positions = []
        new_colors = []
        new_radii = []
        for i in range(0, n - 1):
            new_positions.append(positions[i])
            new_positions.append(positions[i])
            new_colors.append(colors[i])
            new_colors.append(colors[i+1])
            new_radii.append(radii[i])
            new_radii.append(radii[i])
        return (new_positions, new_colors, new_radii)


    def drawchunk(self, glpane, chunk, memo, highlighted):
        """
        Draw chunk in glpane in the whole-chunk display mode represented by 
        this ChunkDisplayMode subclass.

        Assume we're already in chunk's local coordinate system (i.e. do all
        drawing using atom coordinates in chunk.basepos, not chunk.atpos).

        If highlighted is true, draw it in hover-highlighted form (but note 
        that it may have already been drawn in unhighlighted form in the same
        frame, so normally the highlighted form should augment or obscure the
        unhighlighted form).

        Draw it as unselected, whether or not chunk.picked is true. See also
        self.drawchunk_selection_frame. (The reason that's a separate method
        is to permit future drawing optimizations when a chunk is selected
        or deselected but does not otherwise change in appearance or position.)

        If this drawing requires info about chunk which it is useful to 
        precompute (as an optimization), that info should be computed by our
        compute_memo method and will be passed as the memo argument
        (whose format and content is whatever self.compute_memo returns). 
        That info must not depend on the highlighted variable or on whether
        the chunk is selected.        
        """
        # ---------------------------------------------------------------------

        if not memo: 
            # nothing to render
            return

        if self.dnaExperimentalMode > 0: 
            # experimental models is drawn in drawchunk_realtime
            return

        positions, colors, radii, \
        arrows, struts_cylinders, base_cartoons = memo

        # render the axis cylinder        
        if chunk.isAxisChunk() and \
           positions: 
            # fixed bug 2877 (exception when "positions" 
            # is set to None) - piotr 080516
            n_points = len(positions)            
            if self.dnaStyleAxisShape > 0:
                # spherical ends    
                if self.dnaStyleAxisEndingStyle == 4:
                    drawsphere(colors[1], 
                                      positions[1], 
                                      radii[1], 2)
                    drawsphere(colors[n_points - 2], 
                                      positions[n_points - 2], 
                                      radii[n_points - 2], 2)                    

                # set polycone parameters
                gleSetJoinStyle(TUBE_JN_ANGLE | TUBE_NORM_PATH_EDGE 
                                | TUBE_JN_CAP | TUBE_CONTOUR_CLOSED) 
                
                # draw the polycone                
                if self.dnaStyleAxisColor == 1 \
                   or self.dnaStyleAxisColor == 2 \
                   or self.dnaStyleAxisColor == 3: 
                    # render discrete colors                
                    drawpolycone_multicolor([0, 0, 0, -2], 
                                                   positions, 
                                                   colors, 
                                                   radii)
                else:   
                    drawpolycone(colors[1], 
                                        positions, 
                                        radii)

        elif chunk.isStrandChunk(): # strands, struts and bases 
            gleSetJoinStyle(TUBE_JN_ANGLE | TUBE_NORM_PATH_EDGE 
                            | TUBE_JN_CAP | TUBE_CONTOUR_CLOSED) 

            if positions:                    
                if self.dnaStyleStrandsColor == 1:
                    # opacity value == -2 is a flag enabling 
                    # the "GL_COLOR_MATERIAL" mode, the
                    # color argument is ignored and colors array
                    # is used instead
                    ### positions, colors, radii = self._make_discrete_polycone(positions, colors, radii)
                    drawpolycone_multicolor([0, 0, 0, -2], 
                                                   positions,
                                                   colors,
                                                   radii)
                else:
                    drawpolycone(colors[1], 
                                        positions,
                                        radii)
    
                n_points = len(positions)
                
                # draw the ending spheres
                drawsphere(
                    colors[1], 
                    positions[1], 
                    radii[1], 2) 
                
                drawsphere(
                    colors[n_points - 2], 
                    positions[n_points - 2], 
                    radii[n_points - 2], 2) 
                
                # draw the arrows
                for color, pos, rad in arrows:
                    drawpolycone(color, pos, rad)
            # render struts
            for color, pos1, pos2, rad in struts_cylinders:
                drawcylinder(color, pos1, pos2, rad, True)
                
            # render nucleotides            
            if self.dnaStyleBasesShape > 0:
                for color, a1pos, a2pos, a3pos, normal, bname in base_cartoons:
                    if a1pos:
                        if self.dnaStyleBasesShape == 1: # sugar spheres
                            drawsphere(color, a1pos, self.dnaStyleBasesScale, 2)
                        elif self.dnaStyleBasesShape == 2: 
                            if a2pos:
                                # draw a schematic 'cartoon' shape
                                aposn = a1pos + 0.50 * (a2pos - a1pos)
                                bposn = a1pos + 0.66 * (a2pos - a1pos)
                                cposn = a1pos + 0.75 * (a2pos - a1pos)
                                
                                drawcylinder(color, 
                                    a1pos, 
                                    bposn, 
                                    0.20 * self.dnaStyleBasesScale, True) 
                                
                                if bname == 'G' or \
                                   bname == 'A': 
                                    # draw two purine rings                                
                                    drawcylinder(color, 
                                        aposn - 0.25 * self.dnaStyleBasesScale * normal,
                                        aposn + 0.25 * self.dnaStyleBasesScale * normal,
                                        0.7 * self.dnaStyleBasesScale, True)                            
                                    drawcylinder(color, 
                                        cposn - 0.25 * self.dnaStyleBasesScale * normal,
                                        cposn + 0.25 * self.dnaStyleBasesScale * normal,
                                        0.9 * self.dnaStyleBasesScale, True)
                                else:
                                    drawcylinder(color, 
                                        bposn - 0.25 * self.dnaStyleBasesScale * normal,
                                        bposn + 0.25 * self.dnaStyleBasesScale * normal,
                                        0.9 * self.dnaStyleBasesScale, True)                            
                            
    def drawchunk_selection_frame(self, glpane, chunk, selection_frame_color, memo, highlighted):
        """
        Given the same arguments as drawchunk, plus selection_frame_color, 
        draw the chunk's selection frame.

        (Drawing the chunk itself as well would not cause drawing errors
        but would presumably be a highly undesirable slowdown, especially if
        redrawing after selection and deselection is optimized to not have to
        redraw the chunk at all.)

        @note: in the initial implementation of the code that calls this method,
        the highlighted argument might be false whether or not we're actually
        hover-highlighted. And if that's fixed, then just as for drawchunk, 
        we might be called twice when we're highlighted, once with 
        highlighted = False and then later with highlighted = True.
        """
        drawchunk(self, glpane, chunk, selection_frame_color, memo, highlighted)
        return

    def drawchunk_realtime(self, glpane, chunk, highlighted=False):
        """
        Draws the chunk style that may depend on a current view.
        These are experimental features, work in progress as of 080319.
        For the DNA style, draws base orientation indicators and strand labels.
        080321 piotr: added better label positioning
        and 
        """

        def _realTextSize(text, fm):
            """
            Returns a pair of vectors corresponding to a width
            and a height vector of a rendered text. 
            Beware, this call is quite expensive.

            @params: text - text to be measured
                     fm - font metrics created for the text font:
                     fm = QFontMetrics(font)

            @returns: (v1,v2) - pair of vector covering the text rectangle
                                expressed in world coordinates
            """
            textwidth = fm.width(text)
            textheight = fm.ascent()
            x0, y0, z0 = gluUnProject(0, 0, 0)
            x1, y1, z1 = gluUnProject(textwidth, 0, 0)
            x2, y2, z2 = gluUnProject(0, textheight, 0)
            return (V(x1-x0, y1-y0, z1-z0),V(x2-x0, y2-y0, z2-z0))

        def _get_screen_position_of_strand_atom(strand_atom):
            """
            For a given strand atom, find its on-screen position.
            """

            axis_atom = strand_atom.axis_neighbor()
            
            if axis_atom:
                mol = axis_atom.molecule
                axis_atoms = mol.ladder.axis_rail.baseatoms
                if axis_atoms is None:
                    return None
                n_bases = len(axis_atoms)
                pos = axis_atoms.index(axis_atom)
                atom0 = axis_atom
                if pos < n_bases - 1:
                    atom1 = axis_atoms[pos + 1]
                    dpos = atom1.posn() - atom0.posn()
                else:
                    atom1 = axis_atoms[pos - 1]
                    atom2 = axis_atoms[pos]
                    dpos = atom2.posn() - atom1.posn()
                last_dpos = dpos
                out = mol.quat.unrot(glpane.out)
                if flipped:
                    dvec = norm(cross(dpos, -out))
                else:
                    dvec = norm(cross(dpos, out))
                pos0 = axis_atom.posn()
                if not highlighted:
                    pos0 = chunk.abs_to_base(pos0)
                pos1 = pos0 + ssep * dvec
                pos2 = pos0 - ssep * dvec
                if mol.ladder.strand_rails[0].baseatoms[pos] == strand_atom:
                    return (pos1, dpos)
                elif mol.ladder.strand_rails[1].baseatoms[pos] == strand_atom:
                    return (pos2, -dpos)

            return (None, None)

        
        def _draw_arrow(atom):
            """
            Draws a 2-D arrow ending of a DNA strand at 3' atom.
            
            @return: True if arrow was drawn, False if this is not a 3' atom.
            """
            if atom:
                strand = atom.molecule.parent_node_of_class(
                    atom.molecule.assy.DnaStrand)
                if atom == strand.get_three_prime_end_base_atom():
                    ax_atom = atom.axis_neighbor()
                    a_neighbors = ax_atom.axis_neighbors()
                    pos0, dvec = _get_screen_position_of_strand_atom(atom)
                    ovec = norm(cross(dvec, chunk.quat.unrot(glpane.out)))
                    pos1 = pos0 + 0.5 * dvec
                    if mode == 1:
                        pos1 += 1.0 * dvec
                    glVertex3fv(pos0)
                    glVertex3fv(pos1)
                    dvec = norm(dvec)
                    avec2 = pos1 - 0.5 * (dvec - ovec) - dvec
                    glVertex3fv(pos1)
                    glVertex3fv(avec2)
                    avec3 = pos1 - 0.5 * (dvec + ovec) - dvec
                    glVertex3fv(pos1)
                    glVertex3fv(avec3)
                    return True
            return False
        
        def _draw_external_bonds():
            """
            Draws external bonds between different chunks of the same group.
            """
            # note: this is a local function inside 'def drawchunk_realtime'.
            # it has no direct relation to ChunkDrawer._draw_external_bonds.
            for bond in chunk.externs:
                if bond.atom1.molecule.dad == bond.atom2.molecule.dad: # same group
                    if bond.atom1.molecule != bond.atom2.molecule: # but different chunks
                        pos0, dvec = _get_screen_position_of_strand_atom(bond.atom1)
                        pos1, dvec = _get_screen_position_of_strand_atom(bond.atom2)
                        if pos0 and pos1:
                            glVertex3f(pos0[0], pos0[1], pos0[2])
                            glVertex3f(pos1[0], pos1[1], pos1[2])
        
        def _light_color(color):
            """
            Make a lighter color.
            """
            lcolor = [0.0, 0.0, 0.0]
            lcolor[0] = 0.5 * (1.0 + color[0])
            lcolor[1] = 0.5 * (1.0 + color[1])
            lcolor[2] = 0.5 * (1.0 + color[2])
            return lcolor

        # note: this starts the body of def drawchunk_realtime,
        # after it defines several local functions.
        
        from utilities.constants import lightgreen
        from PyQt4.Qt import QFont, QString, QColor, QFontMetrics
        from widgets.widget_helpers import RGBf_to_QColor
        from dna.model.DnaLadderRailChunk import DnaStrandChunk

        labels_enabled = env.prefs[dnaStrandLabelsEnabled_prefs_key]
        indicators_enabled = env.prefs[dnaBaseIndicatorsEnabled_prefs_key]

        if chunk.color: # sometimes the chunk.color is not defined
            chunk_color = chunk.color
        else:
            chunk_color = white

        hhColor = env.prefs[hoverHighlightingColor_prefs_key]
        selColor = env.prefs[selectionColor_prefs_key]

        if self.dnaExperimentalMode == 0:

            if indicators_enabled: # draw the orientation indicators
                self.dnaStyleStrandsShape = env.prefs[dnaStyleStrandsShape_prefs_key]
                self.dnaStyleStrutsShape = env.prefs[dnaStyleStrutsShape_prefs_key]
                self.dnaStyleBasesShape = env.prefs[dnaStyleBasesShape_prefs_key]
                indicators_color = env.prefs[dnaBaseIndicatorsColor_prefs_key]
                inv_indicators_color = env.prefs[dnaBaseInvIndicatorsColor_prefs_key]                
                inv_indicators_enabled = env.prefs[dnaBaseInvIndicatorsEnabled_prefs_key]

                plane_normal_idx = env.prefs[dnaBaseIndicatorsPlaneNormal_prefs_key]
                
                plane_normal = glpane.up
                
                if plane_normal_idx == 1:
                    plane_normal = glpane.out
                elif plane_normal_idx == 2:
                    plane_normal = glpane.right
                    
                indicators, inv_indicators = get_dna_base_orientation_indicators(chunk, plane_normal)
                 
                if highlighted:
                    for atom in indicators:
                        drawsphere(
                            indicators_color, 
                            atom.posn(), 1.5, 2)
                    if inv_indicators_enabled:
                        for atom in inv_indicators:
                            drawsphere(
                                inv_indicators_color, 
                                atom.posn(), 1.5, 2)
                else:
                    for atom in indicators:
                        drawsphere(
                            indicators_color, 
                            chunk.abs_to_base(atom.posn()), 1.5, 2)                
                    if inv_indicators_enabled:
                        for atom in inv_indicators:
                            drawsphere(
                                inv_indicators_color, 
                                chunk.abs_to_base(atom.posn()), 1.5, 2)
    
            if chunk.isStrandChunk():       
                if hasattr(chunk, "_dnaStyleExternalBonds"):
                    for exbond in chunk._dnaStyleExternalBonds:
                        atom1, atom2, color = exbond
                        pos1 = atom1.posn()
                        pos2 = atom2.posn()
                        if chunk.picked:
                            color = selColor
                        if highlighted:
                            color = hhColor
                        else:
                            pos1 = chunk.abs_to_base(pos1)
                            pos2 = chunk.abs_to_base(pos2)
                        drawsphere(color, pos1, self.dnaStyleStrandsScale, 2)
                        drawsphere(color, pos2, self.dnaStyleStrandsScale, 2)
                        drawcylinder(color, pos1, pos2, self.dnaStyleStrandsScale, True)              

                if self.dnaStyleBasesDisplayLetters: 
                    # calculate text size
                    font_scale = int(500.0 / glpane.scale)
                    if sys.platform == "darwin":
                        font_scale *= 2                        
                    if font_scale < 9:
                        font_scale = 9
                    if font_scale > 50:
                        font_scale = 50

                    # create the label font
                    labelFont = QFont( QString("Lucida Grande"), font_scale)
                    # get font metrics for the current font
                    fm = QFontMetrics(labelFont)
                    glpane.qglColor(RGBf_to_QColor(black))
                    # get text size in world coordinates
                    label_text = QString("X")
                    dx, dy = _realTextSize(label_text, fm)
                    # disable lighting
                    glDisable(GL_LIGHTING)            
                    for atom in chunk.atoms.itervalues():
                        # pre-compute atom position
                        if not highlighted:
                            textpos = chunk.abs_to_base(atom.posn()) + 3.0 * glpane.out
                        else:
                            textpos = atom.posn() + 3.0 * glpane.out
                        # get atom base name
                        label_text = QString(atom.getDnaBaseName())
                        # move the text center to the atom position
                        textpos -= 0.5*(dx + dy)   
                        # render the text
                        glpane.renderText(textpos[0], textpos[1], textpos[2], 
                                          label_text, labelFont)                    

                    # done, enable lighting
                    glEnable(GL_LIGHTING)

                if labels_enabled: 
                    # draw the strand labels

                    self.dnaStyleStrandsShape = env.prefs[dnaStyleStrandsShape_prefs_key]
                    self.dnaStyleStrutsShape = env.prefs[dnaStyleStrutsShape_prefs_key]
                    self.dnaStyleBasesShape = env.prefs[dnaStyleBasesShape_prefs_key]

                    labels_color_mode = env.prefs[dnaStrandLabelsColorMode_prefs_key]

                    if labels_color_mode == 1:
                        labels_color = black
                    elif labels_color_mode == 2:
                        labels_color = white
                    else: 
                        labels_color = env.prefs[dnaStrandLabelsColor_prefs_key]

                    # calculate the text size
                    font_scale = int(500.0 / glpane.scale)
                    if sys.platform == "darwin":
                        font_scale *= 2                        
                    if font_scale < 9:
                        font_scale = 9
                    if font_scale > 50:
                        font_scale = 50

                    if chunk.isStrandChunk():                
                        if self.dnaStyleStrandsShape > 0 or \
                           self.dnaStyleBasesShape > 0 or \
                           self.dnaStyleStrutsShape > 0:                   

                            # REVIEW: Is the following comment still valid?
                            #
                            # Q. the following is copied from DnaStrand.py
                            # I need to find a 5' sugar atom of the strand
                            # is there any more efficient way of doing that?
                            # this is terribly slow... I need something like
                            # "get_strand_chunks_in_bond_direction"...
                            #
                            # A [bruce 081001]: yes, there is an efficient way.
                            # The strand rail atoms are in order, and it's possible
                            # to determine which end is 5'. I forget the details.

                            strandGroup = chunk.parent_node_of_class(chunk.assy.DnaStrand)
                            if strandGroup is None:
                                strand = chunk
                            else:
                                    #dna_updater case which uses DnaStrand object for 
                                    #internal DnaStrandChunks
                                strand = strandGroup                  

                            # the label is positioned at 5' end of the strand
                            # get the 5' strand atom
                            atom = strand.get_five_prime_end_base_atom()
                            if atom:

                                # and the next atom for extra positioning
                                next_atom = atom.strand_next_baseatom(1)

                                if atom.molecule is chunk and atom and next_atom: 
                                    # draw labels only for the first chunk

                                    # vector to move the label slightly away from the atom center
                                    halfbond = 0.5*(atom.posn()-next_atom.posn())

                                    # create the label font
                                    labelFont = QFont( QString("Helvetica"), font_scale)

                                    # define a color of the label
                                    if highlighted:
                                        glpane.qglColor(RGBf_to_QColor(hhColor))
                                    elif chunk.picked:
                                        glpane.qglColor(RGBf_to_QColor(selColor))
                                    else:
                                        if labels_color_mode == 0:
                                            glpane.qglColor(RGBf_to_QColor(chunk_color))
                                        else:
                                            glpane.qglColor(RGBf_to_QColor(labels_color))
    
                                        
                                    # get font metrics to calculate text extents
                                    fm = QFontMetrics(labelFont)
                                    label_text = QString(strand.name)+QString(" ")
                                    textsize = fm.width(label_text)

                                    # calculate the text position
                                    # move a bit into viewers direction
                                    if not highlighted:
                                        textpos = chunk.abs_to_base(atom.posn()) + halfbond + 5.0 * glpane.out 
                                    else:
                                        textpos = atom.posn() + halfbond + 5.0 * glpane.out 
                                        
                                    # calculate shift for right aligned text
                                    dx, dy = _realTextSize(label_text, fm)

                                    # check if the right alignment is necessary
                                    if dot(glpane.right,halfbond)<0.0:
                                        textpos -= dx

                                    # center the label vertically
                                    textpos -= 0.5 * dy

                                    # draw the label
                                    glDisable(GL_LIGHTING)
                                    glpane.renderText(textpos[0], textpos[1], textpos[2], 
                                                      label_text, labelFont)
                                    glEnable(GL_LIGHTING)


        if self.dnaExperimentalMode > 0:
            # Very exprimental, buggy and undocumented 2D DNA display mode.
            # The helices are flattened, so sequence ond overall topology
            # can be visualized in a convenient way. Particularly
            # useful for short structural motifs and origami structures.
            # As of 080415, this work is still considered very preliminary
            # and experimental.
            
            # As of 080520, this code is less buggy, but still quite slow.
            # REVIEW: Suggestions for speedup?
            # suggestion added by piotr 080910:
            # The 2D representation is drawn in intermediate mode. 
            # This code uses multiple individual OpenGL calls (glVertex, 
            # glColor). These calls should be replaced by single OpenGL
            # array call. 
            
            # The structure will follow a 2D projection of the central axis.
            # Note: this mode doesn't work well for PAM5 models.
            
            axis = chunk.ladder.axis_rail

            flipped = False
            
            mode = self.dnaExperimentalMode - 1

            no_axis = False
            
            if axis is None:
                axis = chunk.ladder.strand_rails[0]
                no_axis = True
                
            if axis:
                # Calculate the font scale.
                if mode == 0:
                    font_scale = int(500.0 / glpane.scale)
                else:
                    font_scale = int(300.0 / glpane.scale)
                    
                # Rescale font scale for OSX.
                if sys.platform == "darwin":
                    font_scale *= 2         
    
                # Limit the font scale.            
                if font_scale < 9:
                    font_scale = 9
                if font_scale > 100:
                    font_scale = 100
    
                # Number of bases
                n_bases = len(axis)
                
                
                # Disable lighting, we are drawing only text and lines.                
                glDisable(GL_LIGHTING)

                # Calculate the line width.
                if mode == 0 \
                   or mode == 2:
                    lw = 1.0 + 100.0 / glpane.scale

                if mode == 1:
                    lw = 2.0 + 200.0 / glpane.scale
 
                labelFont = QFont( QString("Lucida Grande"), font_scale)
                fm = QFontMetrics(labelFont)
                
                # Calculate the font extents
                dx, dy = _realTextSize("X", fm)

                # Get the axis atoms
                axis_atoms = axis.baseatoms 
                
                # Get the strand atoms
                strand_atoms = [None, None]
                for i in range(0, len(chunk.ladder.strand_rails)):
                    strand_atoms[i] = chunk.ladder.strand_rails[i].baseatoms
                            
                base_list = []
                    
                if mode == 0:
                    ssep = 7.0
                elif mode == 1 \
                     or mode == 2:
                    ssep = 7.0
                
                # Prepare a list of bases to render and their positions.
                for pos in range(0, n_bases):
                    atom0 = axis_atoms[pos]
                    if pos < n_bases - 1:
                        atom1 = axis_atoms[pos + 1]
                        dpos = atom1.posn() - atom0.posn()
                    else:
                        atom1 = axis_atoms[pos - 1]
                        atom2 = axis_atoms[pos]
                        dpos = atom2.posn() - atom1.posn()                           
                    last_dpos = dpos
                    # Project the axis atom position onto a current view plane
                    out = chunk.quat.unrot(glpane.out)
                    if flipped:
                        dvec = norm(cross(dpos, -out))
                    else:
                        dvec = norm(cross(dpos, out))                    
                    pos0 = atom0.posn()
                    if not highlighted:
                        pos0 = chunk.abs_to_base(pos0)
                    s_atom0 = s_atom1 = None
                    if strand_atoms[0]:
                        if pos < len(strand_atoms[0]):
                            s_atom0 = strand_atoms[0][pos]
                    if strand_atoms[1]:
                        if pos < len(strand_atoms[1]):
                            s_atom1 = strand_atoms[1][pos]
                    s_atom0_pos = pos0 + ssep * dvec
                    s_atom1_pos = pos0 - ssep * dvec
                    str_atoms = [s_atom0, s_atom1]
                    str_pos = [s_atom0_pos, s_atom1_pos]
                    base_list.append((atom0, pos0, 
                                      str_atoms, str_pos)) 
                
                if chunk.isStrandChunk():
                    
                    glLineWidth(lw)

                    for str in [0, 1]:
                        # Draw the strand
                        atom = None
                        for base in base_list:
                            ax_atom, ax_atom_pos, str_atoms, str_atoms_pos = base
                            if str_atoms[str] != None:
                                atom = str_atoms[str]
                                break
        
                        if atom and \
                           chunk == atom.molecule:
                            if atom.molecule.color:
                                strand_color = atom.molecule.color
                            else:
                                strand_color = lightgreen
                            
                            if chunk.picked:
                                strand_color = selColor
                             
                            if highlighted:
                                strand_color = hhColor
                                
                            glColor3fv(strand_color)
                            
                            glBegin(GL_LINES)
                            last_str_atom_pos = None
                            for base in base_list:
                                ax_atom, ax_atom_pos, str_atoms, str_atoms_pos = base
                                if str_atoms[str]:
                                    if last_str_atom_pos:
                                        glVertex3fv(last_str_atom_pos)
                                        glVertex3fv(str_atoms_pos[str])
                                    last_str_atom_pos = str_atoms_pos[str]
                                else:
                                    last_str_atom_pos = None
                            glEnd()
                            
                            if mode == 0 \
                               or mode == 2:
                                glLineWidth(lw)
                            elif mode == 1:
                                glLineWidth(0.5 * lw)
                            
                            glBegin(GL_LINES)
                            # Draw an arrow on 3' atom    
                            if not _draw_arrow(atom):
                                # Check out the other end
                                atom = None
                                for base in base_list:
                                    ax_atom, ax_atom_pos, str_atoms, str_atoms_pos = base
                                    if str_atoms[str] != None:
                                        atom = str_atoms[str]                        
                                # Draw an arrow on 3' atom    
                                _draw_arrow(atom)                                
                            glEnd()
                            
                            glLineWidth(lw)

                            glBegin(GL_LINES)
                            
                            # draw the external bonds
                            _draw_external_bonds()
                                # note: this calls a local function defined
                                # earlier (not a method, thus the lack of self),
                                # which has no direct relation to
                                # ChunkDrawer._draw_external_bonds.
            
                            # Line drawing done
                            glEnd()
                            
                            # Draw the base letters
                            if mode == 0:
                                for base in base_list:
                                    ax_atom, ax_atom_pos, str_atoms, str_atoms_pos = base
                                    if str_atoms[str]:
                                        textpos = ax_atom_pos + 0.5 * (str_atoms_pos[str] - ax_atom_pos)
                                        base_name = str_atoms[str].getDnaBaseName()
                                        label_text = QString(base_name)
                                        textpos -= 0.5 * (dx + dy)  
                                        color = black
                                        
                                        if chunk.picked:
                                            glColor3fv(selColor)                                        
                                            color = selColor
                                        else:
                                            base_color = self._get_base_color(base_name)
                                            glColor3fv(base_color)
                                            color = base_color
                                            
                                        if highlighted:
                                            glColor3fv(hhColor)
                                            color = hhColor
                                            
                                        ### drawtext(label_text, color, textpos, font_scale, glpane)
                                        glpane.renderText(textpos[0], 
                                                          textpos[1], 
                                                          textpos[2], 
                                                          label_text, labelFont)                    
                            elif mode == 1 \
                                 or mode == 2:
                                if no_axis == False:
                                    glLineWidth(lw)
                                    glBegin(GL_LINES)
                                    if chunk.picked:
                                        glColor3fv(selColor)
                                    elif highlighted:
                                        glColor3fv(hhColor)
                                    for base in base_list:
                                        ax_atom, ax_atom_pos, str_atoms, str_atoms_pos = base
                                        if str_atoms[str]:
                                            if not chunk.picked and \
                                               not highlighted:
                                                base_color = self._get_base_color(
                                                    str_atoms[str].getDnaBaseName())
                                                glColor3fv(base_color)   
                                            glVertex3fv(str_atoms_pos[str])
                                            glVertex3fv(ax_atom_pos)                                
                                    glEnd()
                                
                                if mode == 1:
                                    # draw circles interior
                                    for base in base_list:
                                        if chunk.picked:
                                            lcolor = _light_color(selColor)
                                        elif highlighted:
                                            lcolor = hhColor
                                        else:
                                            lcolor = _light_color(strand_color)
                                        ax_atom, ax_atom_pos, str_atoms, str_atoms_pos = base
                                        if str_atoms[str]:
                                            drawFilledCircle(
                                                lcolor, 
                                                str_atoms_pos[str] + 3.0 * chunk.quat.unrot(glpane.out), 
                                                1.5, chunk.quat.unrot(glpane.out))                                     
                                
                                    # draw circles border
                                    glLineWidth(3.0)
                                    #glColor3fv(strand_color)
                                    for base in base_list:
                                        ax_atom, ax_atom_pos, str_atoms, str_atoms_pos = base
                                        if str_atoms[str]:
                                            drawCircle(
                                                strand_color, 
                                                str_atoms_pos[str] + 3.1 * chunk.quat.unrot(glpane.out), 
                                                1.5, chunk.quat.unrot(glpane.out)) 
                                    glLineWidth(1.0)
                    
                if chunk.isAxisChunk():
                    if mode == 0:
                        # Draw filled circles in the center of the axis rail.
                        if chunk.picked:
                            color = selColor
                        elif highlighted:
                            color = hhColor
                        else:
                            color = black
                        for base in base_list:
                            ax_atom, ax_atom_pos, str_atoms, str_atoms_pos = base
                            if str_atoms[0] and str_atoms[1]:
                                drawFilledCircle(color, ax_atom_pos, 0.5, chunk.quat.unrot(glpane.out))
                            else:
                                drawFilledCircle(color, ax_atom_pos, 0.15, chunk.quat.unrot(glpane.out))

                glEnable(GL_LIGHTING)              
                
                glLineWidth(1.0)             
                # line width should be restored to initial value
                # but I think 1.0 is maintained within the program

    def writepov(self, chunk, memo, file):
        """
        Renders the chunk to a POV-Ray file.

        This is an experimental feature as of 080319.

        
        @param chunk: chunk to be rendered
        @type chunk: Chunk
        
        @param memo: a tuple describing the reduced representation
        @type memo: a tuple
        """

        from graphics.rendering.povray.povheader import povpoint
        from geometry.VQT import vlen

        def writetube(points, colors, radii, rainbow, smooth):
            """ 
            Writes a smooth tube in a POV-Ray format.
            
            @param points: list of tube points
            
            @param colors: list of tube colors
            
            @param radii: list of tube radii
            
            @param rainbow: use rainbow gradient to color the tube
            
            @param smooth: if True, use smooth tube, otherwise draw it
            as connected cylinders
            @type smooth: boolean
            """
            file.write("sphere_sweep {\n")
            if smooth == True:
                file.write("  linear_spline\n")
            else:
                # REVIEW: What should the non-smooth version be?
                # The non-smooth version should just draw straight
                # cylinders with spherical joints. This is not implemented.
                file.write("  linear_spline\n")
            file.write("  %d,\n" % (len(points)))
            n = len(points)
            for i in range(0,n):
                file.write("  " + povpoint(chunk.base_to_abs(points[i])) +", %g\n" % radii[i]);
            
            file.write("  pigment {\n")
            vec = points[n-1]-points[0]
            nvec = radii[0] * norm(vec)
            vec += 2.0 * nvec
            file.write("    gradient <%g,%g,%g> scale %g translate " % 
                       (vec[0], vec[1], vec[2], vlen(vec)))
            file.write(povpoint(chunk.base_to_abs(points[0] - nvec)) + "\n")
            file.write("    color_map { RainbowMap }\n")
            file.write("  }\n")
            
            file.write("}\n")

        def writecylinder(start, end, rad, color):
            """
            Write a POV-Ray cylinder starting at start and ending at end,
            of radius rad, using given color.
            """
            file.write("cylinder {\n")
            file.write("  " + povpoint(chunk.base_to_abs(start)) + ", " + povpoint(chunk.base_to_abs(end)))
            file.write(", %g\n" % (rad))
            file.write("  pigment {color <%g %g %g>}\n" % (color[0], color[1], color[2]))
            file.write("}\n")

        def writesphere(color, pos, rad):
            """
            Write a POV-Ray sphere at position pos of radius rad using given color.
            """
            file.write("sphere {\n")
            file.write("  " + povpoint(chunk.base_to_abs(pos)))
            file.write(", %g\n" % rad)
            file.write("  pigment {color <%g %g %g>}\n" % (color[0], color[1], color[2]))
            file.write("}\n")
        
        def writecone(color, pos1, pos2, rad1, rad2):            
            """
            Write a POV-Ray cone starting at pos1 ending at pos2 using
            radii rad1 and rad2 in given color.
            """
            file.write("cone {\n")
            file.write("  " + povpoint(chunk.base_to_abs(pos1)))
            file.write(", %g\n" % rad1)
            file.write("  " + povpoint(chunk.base_to_abs(pos2)))
            file.write(", %g\n" % rad2)
            file.write("  pigment {color <%g %g %g>}\n" % (color[0], color[1], color[2]))
            file.write("}\n")

        # Write a POV-Ray file.
        
        # Make sure memo is precomputed.
        if memo is None:
            return
        
        positions, colors, radii, \
        arrows, struts_cylinders, base_cartoons = memo

        if positions is None:
            return
        
        # Render the axis cylinder        
        n_points = len(positions)            
        if self.dnaStyleAxisShape > 0:
            # spherical ends    
            if self.dnaStyleAxisEndingStyle == 4:
                writesphere(colors[1], 
                            positions[1], 
                            radii[1])                
                writesphere(colors[n_points - 2], 
                            positions[n_points - 2], 
                            radii[n_points - 2])                    
            
            # draw the polycone
            writetube(positions, colors, radii, False, True)

        elif chunk.isStrandChunk(): # strands, struts and bases 

            writetube(positions, colors, radii, False, True)

            # draw the arrows
            for color, pos, rad in arrows:
                writecone(color, pos[1], pos[2], rad[1], rad[2])

            # render struts
            for color, pos1, pos2, rad in struts_cylinders:
                writecylinder(pos1, pos2, rad, color)
                
            # render nucleotides            
            if self.dnaStyleBasesShape > 0:
                for color, a1pos, a2pos, a3pos, normal, bname in base_cartoons:
                    if a1pos:
                        if self.dnaStyleBasesShape == 1: # sugar spheres
                            writesphere(color, a1pos, self.dnaStyleBasesScale)
                        elif self.dnaStyleBasesShape == 2: 
                            if a2pos:
                                # draw a schematic 'cartoon' shape
                                aposn = a1pos + 0.50 * (a2pos - a1pos)
                                bposn = a1pos + 0.66 * (a2pos - a1pos)
                                cposn = a1pos + 0.75 * (a2pos - a1pos)
                                writecylinder( 
                                    a1pos, 
                                    bposn, 
                                    0.20 * self.dnaStyleBasesScale, color) 
                                if bname == 'G' \
                                   or bname == 'A': # draw two purine rings                                
                                    writecylinder(
                                        aposn - 0.25 * self.dnaStyleBasesScale * normal,
                                        aposn + 0.25 * self.dnaStyleBasesScale * normal,
                                        0.7 * self.dnaStyleBasesScale, color)                            
                                    writecylinder( 
                                        cposn - 0.25 * self.dnaStyleBasesScale * normal,
                                        cposn + 0.25 * self.dnaStyleBasesScale * normal,
                                        0.9 * self.dnaStyleBasesScale, color)
                                else:
                                    writecylinder( 
                                        bposn - 0.25 * self.dnaStyleBasesScale * normal,
                                        bposn + 0.25 * self.dnaStyleBasesScale * normal,
                                        0.9 * self.dnaStyleBasesScale, color)                            
        
    def compute_memo(self, chunk):
        """
        If drawing chunks in this display mode can be optimized by precomputing
        some info from chunk's appearance, compute that info and return it.

        If this computation requires preference values, access them as 
        env.prefs[key], and that will cause the memo to be removed (invalidated)
        when that preference value is changed by the user.

        This computation is assumed to also depend on, and only on, chunk's
        appearance in ordinary display modes (i.e. it's invalidated whenever
        havelist is). There is not yet any way to change that, so bugs will 
        occur if any ordinarily invisible chunk info affects this rendering,
        and potential optimizations will not be done if any ordinarily visible
        info is not visible in this rendering. These can be fixed if necessary
        by having the real work done within class Chunk's _recompute_ rules,
        with this function or drawchunk just accessing the result of that
        (and sometimes causing its recomputation), and with whatever 
        invalidation is needed being added to appropriate setter methods of 
        class Chunk. If the real work can depend on more than chunk's ordinary
        appearance can, the access would need to be in drawchunk;
        otherwise it could be in drawchunk or in this method compute_memo().

        @param chunk: The chunk
        @type  chunk: Chunk
        """

        # REVIEW: Does this take into account curved strand shapes?
        #
        # for this example, we'll turn the chunk axes into a cylinder.
        # Since chunk.axis is not always one of the vectors chunk.evecs 
        # (actually chunk.poly_evals_evecs_axis[2]),
        # it's best to just use the axis and center, then recompute 
        # a bounding cylinder.

        # piotr 080910 comment: yes, it is not a straight cylinder representing
        # the chunk axis anymore. It is a glePolyCone object
        # drawn along a path of DNA axis chunk. Similarly, the strand chunks
        # are represented by curved polycone objects. 
        
        # import the style preferences from User Preferences
        self.dnaStyleStrandsShape = env.prefs[dnaStyleStrandsShape_prefs_key]
        self.dnaStyleStrandsColor = env.prefs[dnaStyleStrandsColor_prefs_key]
        self.dnaStyleStrandsScale = env.prefs[dnaStyleStrandsScale_prefs_key]
        self.dnaStyleStrandsArrows = env.prefs[dnaStyleStrandsArrows_prefs_key]        
        self.dnaStyleAxisShape = env.prefs[dnaStyleAxisShape_prefs_key]
        self.dnaStyleAxisColor = env.prefs[dnaStyleAxisColor_prefs_key]
        self.dnaStyleAxisScale = env.prefs[dnaStyleAxisScale_prefs_key]
        self.dnaStyleAxisEndingStyle = env.prefs[dnaStyleAxisEndingStyle_prefs_key]
        self.dnaStyleStrutsShape = env.prefs[dnaStyleStrutsShape_prefs_key]
        self.dnaStyleStrutsColor = env.prefs[dnaStyleStrutsColor_prefs_key]
        self.dnaStyleStrutsScale = env.prefs[dnaStyleStrutsScale_prefs_key]                
        self.dnaStyleBasesShape = env.prefs[dnaStyleBasesShape_prefs_key]
        self.dnaStyleBasesColor = env.prefs[dnaStyleBasesColor_prefs_key]
        self.dnaStyleBasesScale = env.prefs[dnaStyleBasesScale_prefs_key]
        self.dnaStyleBasesDisplayLetters = env.prefs[dnaStyleBasesDisplayLetters_prefs_key]        
        self.dnaExperimentalMode = env.prefs[dnaRendition_prefs_key]

        # Four components of the reduced DNA style can be created and
        # controlled independently: central axis, strands, structs, and bases.
        
        if not hasattr(chunk, 'ladder'):
            # DNA updater is off? Don't render 
            # (should display a warning message?)
            return None

        if not chunk.atoms or not chunk.ladder: 
            # nothing to display - return
            return None

        n_bases = chunk.ladder.baselength()    
        if n_bases < 1: 
            # no bases - return
            return None

        # make sure there is a chunk color
        if chunk.color:
            chunk_color = chunk.color
        else:
            # sometimes the chunk.color is not defined, use white color
            # in this case. this may happen when a strand or segment
            # are being interactively edited. 
            chunk_color = white

        # atom positions in strand and axis
        strand_positions = axis_positions = None

        # number of strand in the ladder
        num_strands = chunk.ladder.num_strands()

        # current strand 
        current_strand = 0

        # get both lists of strand atoms
        strand_atoms = [None] * num_strands
        for i in range(0, num_strands):
            strand_atoms[i] = chunk.ladder.strand_rails[i].baseatoms
            if chunk.ladder.strand_rails[i].baseatoms[0].molecule is chunk:
                current_strand = i

        # empty list for strand colors
        strand_colors = [None] * num_strands

        # list of axis atoms
        axis_atoms = None
        if chunk.ladder.axis_rail:
            axis_atoms = chunk.ladder.axis_rail.baseatoms

        # group color (white by default)
        group_color = white

        # 5' and 3' end atoms of current strand (used for drawing arrowheads)
        five_prime_atom = three_prime_atom = None
        
        # current strand chunk direction
        strand_direction = 0

        # start and end positions of the current strand chunk (or corresponding
        # axis segment chunk) relative to the length of the entire strand
        start_index = end_index = 0
        total_strand_length = 1

        # positions, colors and radii to be used for model drawing
        positions = None
        colors = None
        radii = None
        
        # pre-calculate polycylinder positions (main drawing primitive
        # for strands and/or central axis)

        arrows = []
        struts_cylinders = []
        base_cartoons = []
        
        if chunk.isAxisChunk() \
           and axis_atoms \
           and num_strands > 1: 

            if self.dnaStyleAxisColor == 4: 
                # color according to position along the longest strand.
                longest_rail = None
                longest_wholechain = None
                longest_length = 0
                
                # Find a longest rail and wholechain
                strand_rails = chunk.ladder.strand_rails      
                for rail in strand_rails:
                    length = len(rail.baseatoms[0].molecule.wholechain)
                    if length > longest_length:
                        longest_length = length
                        longest_rail = rail
                        longest_wholechain = rail.baseatoms[0].molecule.wholechain
                        
                wholechain = longest_wholechain
                
                # Get first and last positions of the wholechain
                pos0, pos1 = wholechain.wholechain_baseindex_range()
                
                # index of the first wholechain base in the longest rail
                idx = wholechain.wholechain_baseindex(longest_rail, 0)
                
                # The "group_color" is a uniform color used for entire chunk
                # Calculate the group color according to relative position
                # of the wholechain using the "nice rainbow" coloring scheme.
                # For circular structures, the exact starting position 
                # is unpredictable, but the whole color range is still
                # properly displayed.
                group_color = self._get_nice_rainbow_color_in_range(
                    idx - pos0, 
                    pos1 - pos0, 
                    0.75,
                    1.0) 
            
            # Make sure there are two strands present in the rail
            # piotr 080430 (fixed post-FNANO Top 20 bugs - exception in
            # DNA cylinder chunks)
            positions = self._get_axis_positions(
                chunk, 
                axis_atoms, 
                self.dnaStyleAxisColor)
            colors = self._get_axis_colors(
                axis_atoms, 
                strand_atoms, 
                self.dnaStyleAxisColor, 
                chunk_color, 
                group_color)
            radii = self._get_axis_radii(axis_atoms, 
                self.dnaStyleAxisColor, 
                self.dnaStyleAxisShape,
                self.dnaStyleAxisScale,
                self.dnaStyleAxisEndingStyle)
            
        elif chunk.isStrandChunk() and \
            (strand_atoms[0] or 
             strand(atoms[1])):

            n_atoms = len(strand_atoms[current_strand])
            
            strand_group = chunk.getDnaGroup()
            if strand_group:
                strands = strand_group.getStrands()
                # find out strand color
                group_color = self._get_rainbow_color_in_range(
                    strands.index(chunk.dad), len(strands), 0.75, 1.0)
                strand = chunk.parent_node_of_class(chunk.assy.DnaStrand)
                if strand:
                    # determine 5' and 3' end atoms of the strand the chunk 
                    # belongs to, and find out the strand direction
                    five_prime_atom = strand.get_five_prime_end_base_atom()
                    three_prime_atom = strand.get_three_prime_end_base_atom()
                    strand_direction = chunk.idealized_strand_direction()
                    
                    wholechain = chunk.wholechain
    
                    # determine strand and end atom indices
                    # within the entire strand.
    
                    all_atoms = strand.get_strand_atoms_in_bond_direction()
                        
                    start_atom = strand_atoms[current_strand][0]
                    end_atom = strand_atoms[current_strand][len(strand_atoms[0])-1]
                    
                    # find out first and last strand chunk atom positions relative
                    # to the length of the entire strand
                    if  start_atom in all_atoms and \
                        end_atom in all_atoms:
                        start_index = all_atoms.index(start_atom) - 1
                        end_index = all_atoms.index(end_atom) - 1
                        total_strand_length = len(all_atoms) - 2           
                    
            if self.dnaStyleStrandsShape > 0: 
            
                # Get positions, colors and radii for current strand chunk
                positions = self._get_strand_positions(
                    chunk, strand_atoms[current_strand])
                
                colors = self._get_strand_colors(
                    strand_atoms[current_strand], 
                    self.dnaStyleStrandsColor,
                    start_index, end_index, total_strand_length,
                    chunk_color, group_color)
                
                radii = self._get_strand_radii(
                    strand_atoms[current_strand], 
                    self.dnaStyleStrandsScale)
    
                if self.dnaStyleStrandsShape == 2:
                    # strand shape is a tube
                    positions, \
                    colors, \
                    radii = self._make_curved_strand( 
                        positions, 
                        colors, 
                        radii )
    
                # Create a list of external bonds.
                # Moved drawing to draw_realtime, otherwise the struts are not
                # updated. piotr 080411
                
                # These bonds need to be drawn in draw_realtime
                # to reflect position changes of the individual chunks.                
    
                chunk._dnaStyleExternalBonds = []
                
                for bond in chunk.externs:
                    if bond.atom1.molecule.dad == bond.atom2.molecule.dad: # same group
                        if bond.atom1.molecule != bond.atom2.molecule: # but different chunks
                            if bond.atom1.molecule is chunk:
                                idx = strand_atoms[current_strand].index(bond.atom1)
                                if self.dnaStyleStrandsColor == 0:
                                    color = chunk.color
                                elif self.dnaStyleStrandsColor == 1:
                                    color = self._get_atom_rainbow_color(
                                        idx, n_atoms, start_index, end_index, 
                                        total_strand_length)
                                else:
                                    color = group_color                                
                                chunk._dnaStyleExternalBonds.append(
                                    (bond.atom1, bond.atom2, color))         
                    
                # Make the strand arrows.
                # Possibly, this code is too complicated... make sure that 
                # the conditions below are not redundant.
                
                arrlen = 5.0                
                n = len(positions)
                
                if strand_direction == 1:                
                    draw_5p = (strand_atoms[current_strand][0] == five_prime_atom)
                    draw_3p = (strand_atoms[current_strand][n_atoms - 1] == three_prime_atom)
                    if draw_5p and (self.dnaStyleStrandsArrows == 1 or 
                                    self.dnaStyleStrandsArrows == 3):
                        arrvec = arrlen * norm(positions[2] - positions[1])                    
                        arrows.append((colors[1],
                                      [positions[1] + arrvec,
                                       positions[1] + arrvec,
                                       positions[1] - arrvec,
                                       positions[1] - arrvec],
                                       [0.0, 0.0, 
                                        radii[1]*2.0, 
                                        radii[1]*2.0]))
                        
                    if draw_3p and (self.dnaStyleStrandsArrows == 2 or 
                                    self.dnaStyleStrandsArrows == 3):
                        arrvec = arrlen * norm(positions[n-3] - positions[n-2])
                        arrows.append((colors[n-2],
                                            [positions[n-2],
                                             positions[n-2],
                                             positions[n-2] - arrvec,
                                             positions[n-2] - arrvec],
                                             [radii[n-2]*2.0, 
                                              radii[n-2]*2.0, 
                                              0.0, 0.0]))
                else:
                    draw_5p = (strand_atoms[current_strand][n_atoms - 1] == five_prime_atom)
                    draw_3p = (strand_atoms[current_strand][0] == three_prime_atom)
                    if draw_3p and (self.dnaStyleStrandsArrows == 2 or 
                                    self.dnaStyleStrandsArrows == 3):
                        arrvec = arrlen * norm(positions[2] - positions[1])
                        arrows.append((colors[1],
                                            [positions[1],
                                             positions[1],
                                             positions[1] - arrvec,
                                             positions[1] - arrvec],
                                             [radii[1]*2.0, 
                                              radii[1]*2.0, 
                                              0.0, 0.0]))
                        
                    if draw_5p and (self.dnaStyleStrandsArrows == 1 or 
                                    self.dnaStyleStrandsArrows == 3):
                        arrvec = arrlen * norm(positions[n-3] - positions[n-2])
                        arrows.append((colors[n-2],
                                            [positions[n-2] + arrvec,
                                             positions[n-2] + arrvec,
                                             positions[n-2] - arrvec,
                                             positions[n-2] - arrvec],
                                             [0.0, 0.0, 
                                              radii[n-2]*2.0, 
                                              radii[n-2]*2.0]))
   
                        
            # Make struts.            
            if self.dnaStyleStrutsShape > 0:
                if num_strands > 1:
                    for pos in range(0, n_atoms):
                        atom1 = strand_atoms[current_strand][pos]
                        atom3 = strand_atoms[1 - current_strand][pos]
                        if self.dnaStyleStrutsShape == 1: 
                            # strand-axis-strand type
                            atom2_pos = chunk.abs_to_base(axis_atoms[pos].posn())   
                        elif self.dnaStyleStrutsShape == 2: 
                            # strand-strand type
                            atom2_pos = chunk.abs_to_base(0.5 * (atom1.posn() + atom3.posn()))
                        if self.dnaStyleStrutsColor == 0:
                            # color by chunk color
                            color = chunk_color
                        elif self.dnaStyleStrutsColor == 1:
                            # color by base order
                            color = self._get_rainbow_color_in_range(
                                pos, n_atoms, 0.75, 1.0)                        
                        else:
                            # color by base type
                            color = self._get_base_color(atom1.getDnaBaseName())

                        struts_cylinders.append(
                            (color,
                             chunk.abs_to_base(atom1.posn()),
                             atom2_pos,
                             0.5 * self.dnaStyleStrutsScale))

            # Make nucleotides.            
            if self.dnaStyleBasesShape > 0:
                atom1_pos = None
                atom2_pos = None
                atom3_pos = None
                normal = None
                for pos in range(0, n_atoms):
                    atom = strand_atoms[current_strand][pos]
                    bname = atom.getDnaBaseName()
                    if self.dnaStyleBasesColor == 0:
                        # color by chunk color
                        color = chunk_color
                    elif self.dnaStyleBasesColor == 1:
                        # color by base order
                        color = self._get_rainbow_color_in_range(pos, n_atoms, 0.75, 1.0)
                    elif self.dnaStyleBasesColor == 2:
                        # color by group color
                        color = group_color
                    else:
                        # color by base type
                        color = self._get_base_color(atom.getDnaBaseName())

                    if self.dnaStyleBasesShape == 1: 
                        # draw spheres
                        atom1_pos = chunk.abs_to_base(atom.posn())
                    elif self.dnaStyleBasesShape == 2 and \
                         num_strands > 1: 
                        # draw a schematic 'cartoon' shape
                        atom1_pos = chunk.abs_to_base(strand_atoms[current_strand][pos].posn())
                        atom3_pos = chunk.abs_to_base(strand_atoms[1 - current_strand][pos].posn())                        
                        atom2_pos = chunk.abs_to_base(axis_atoms[pos].posn())                        
                        # figure out a normal to the bases plane
                        v1 = atom1_pos - atom2_pos
                        v2 = atom1_pos - atom3_pos
                        normal = norm(cross(v1, v2))
                    
                    base_cartoons.append((
                        color, atom1_pos, atom2_pos, atom3_pos, normal, bname))
        
        # For current chunk, returns: list of positions, colors, radii, arrows, 
        # strut cylinders and base cartoons
        return (positions,
                colors,
                radii,
                arrows,
                struts_cylinders,
                base_cartoons)

    pass # end of class DnaCylinderChunks

ChunkDisplayMode.register_display_mode_class(DnaCylinderChunks)

# end