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authorPiotr Rotkiewicz <piotr@pirx.com>2008-09-05 21:52:26 +0000
committerPiotr Rotkiewicz <piotr@pirx.com>2008-09-05 21:52:26 +0000
commit2271b377573ef0b0653373d47042dd223a78b92a (patch)
tree6b8ce879ad507dd50c205f1ce660d0e4ed2b2a68
parent8aff664f2ded4d672a1c6b83837554bc8021b039 (diff)
downloadnanoengineer-theirix-2271b377573ef0b0653373d47042dd223a78b92a.tar.gz
nanoengineer-theirix-2271b377573ef0b0653373d47042dd223a78b92a.zip
=ProteinChunks.py for review.
Diffstat
-rw-r--r--cad/src/graphics/display_styles/ProteinChunks.py394
1 files changed, 300 insertions, 94 deletions
diff --git a/cad/src/graphics/display_styles/ProteinChunks.py b/cad/src/graphics/display_styles/ProteinChunks.py
index 72493c4db..559c02a23 100644
--- a/cad/src/graphics/display_styles/ProteinChunks.py
+++ b/cad/src/graphics/display_styles/ProteinChunks.py
@@ -22,6 +22,8 @@ piotr 080729: Code cleanup.
piotr 080804: Further code cleanup, adding docstrings.
+piotr 080904: Added missing docstrings, prepared for review.
+
"""
import foundation.env as env
@@ -66,6 +68,17 @@ from utilities.constants import yellow
from graphics.drawing.CS_workers import drawcylinder_worker
from graphics.drawing.CS_workers import drawsphere_worker
+# Protein display style preferences
+from utilities.prefs_constants import proteinStyle_prefs_key
+from utilities.prefs_constants import proteinStyleColors_prefs_key
+from utilities.prefs_constants import proteinStyleQuality_prefs_key
+from utilities.prefs_constants import proteinStyleScaleFactor_prefs_key
+from utilities.prefs_constants import proteinStyleScaling_prefs_key
+from utilities.prefs_constants import proteinStyleHelixColor_prefs_key
+from utilities.prefs_constants import proteinStyleStrandColor_prefs_key
+from utilities.prefs_constants import proteinStyleCoilColor_prefs_key
+from utilities.prefs_constants import proteinStyleSmooth_prefs_key
+
try:
from OpenGL.GLE import glePolyCone
from OpenGL.GLE import gleGetNumSides
@@ -128,6 +141,10 @@ PROTEIN_STYLE_SIMPLE_CARTOONS = 9
PROTEIN_STYLE_FANCY_CARTOONS = 10
PROTEIN_STYLE_PEPTIDE_TILES = 11
+# I plan to change the following color schemes so they use less
+# intrusive colors (maybe just blue-to-white-to-red scale instad
+# of red-green-blue spectrum). piotr 080902
+
# coloring according to amino acid hydropathy scale (Kyte-Doolittle)
AA_COLORS_HYDROPATHY = {
"ALA" : orange,
@@ -175,6 +192,7 @@ AA_COLORS_POLARITY = {
"VAL" : red }
# coloring according to amino acid acidity
+
AA_COLORS_ACIDITY = {
"ALA" : green,
"ARG" : blue,
@@ -199,9 +217,23 @@ AA_COLORS_ACIDITY = {
def compute_spline(data, idx, t):
"""
- Implements a Catmull-Rom spline.
- Interpolates between data[idx] and data[idx+1].
- 0.0 <= t <= 1.0.
+ Implements a Catmull-Rom spline. Interpolates between data[idx] and
+ data[idx+1] using data[idx-1], data[idx], data[idx+1] and data[idx+2]
+ points.
+
+ @param data: list of data points to interpolate. it needs to have at least
+ data points, otherwise will cause an exception
+
+ @param idx: index of data points to be interpolated between
+ @type idx: int
+
+ @param t: interpolation ratio (0.0 <= t <= 1.0)
+ @type t: float
+
+ @note: this method is basically identical to the one in DnaCylinderChunks,
+ so it should be splitted out from here and moved to another, more general
+ file
+
"""
t2 = t*t
t3 = t2*t
@@ -215,10 +247,35 @@ def compute_spline(data, idx, t):
t3 * (-x0 + 3.0 * x1 - 3.0 * x2 + x3))
return res
-def make_tube(points, colors, radii, dpos, resolution=8, trim=True):
+def make_tube(points, colors, radii, dpos, resolution=3):
"""
- Converts a polycylinder tube into a smooth, curved tube
- using spline interpolation of points, colors and radii.
+ Converts a polycylinder tube into a smooth, curved tube using spline
+ interpolation of points, colors and radii.
+
+ If there is not enough data points, returns the original lists.
+ Thus, it can be used in the following way:
+
+ pos, col, rad, dpos = make_tube(pos, col, rad, dpos, resolution)
+
+ 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
+
+ @param dpos: dpos vectors correspoding to individual points
+ @type dpos: list of dpos vectors
+
+ @param resolution: specifies a number of points intepolated in-between
+ two consecutive input points
+ @type resolution: integer
+
+ @return: tuple of interpolated (points, colors, radii, dpos)
"""
n = len(points)
if n > 3:
@@ -260,9 +317,23 @@ def make_tube(points, colors, radii, dpos, resolution=8, trim=True):
else:
return (points, colors, radii, dpos)
+# These two methods are identical to these found in DnaCylinderChunks.
+
def get_rainbow_color(hue, saturation, value):
"""
Gets a color of a hue range limited to 0 - 0.667 (red - blue)
+
+ @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)
@@ -274,7 +345,22 @@ def get_rainbow_color(hue, saturation, value):
def get_rainbow_color_in_range(pos, count, saturation, value):
"""
- Create a rainbow color from a range (0, pos/count).
+ 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
@@ -305,7 +391,31 @@ class ProteinChunks(ChunkDisplayMode):
def _get_aa_color(self, chunk, pos, n_pos, sec, aa, c_sec, n_sec):
"""
- Returns an amino acid color according to current colormode.
+ Returns an amino acid color according to the current color mode.
+
+ @param chunk: Protein chunk
+ @type chunk: Chunk with protein attribute available
+
+ @param pos: residue sequence position
+ @type pos: int
+
+ @param n_pos: length of the protein sequence
+ @type n_pos: int
+
+ @param sec: secondary structure type (SS_HELIX, SS_STRAND, or SS_COIL)
+ @type sec: int
+
+ @param aa: amino acid name (3-letter code)
+ @type aa: string
+
+ @param c_sec: index of secondary structure element
+ @type c_sec: int
+
+ @param n_sec: number of secondary structure elements
+ @type n_sec: int
+
+ @return: residue color according to curreny color mode, or gray
+ if wrong parameters were specified
"""
color = gray
@@ -348,14 +458,21 @@ class ProteinChunks(ChunkDisplayMode):
def drawchunk(self, glpane, chunk, memo, highlighted):
"""
- Draws reduced representation of a protein chunk. This method is called
- per chunk, but in fact draws individual secondary structure elements,
+ Draws a reduced representation of a protein chunk. This method is called
+ per chunk, but in fact it draws individual secondary structure elements,
i.e. consecutive part of the protein chain composed of a single type
- of secondary structure.
+ of secondary structure.
"""
+ # Note: If the protein model is going to be re-factored in the future
+ # so that every individual chunk corresponds to a single, homogenoeous
+ # secondary structure element, this method could be used without
+ # much changes.
+
+ # Retrieve parameters from memo
structure, total_length, ca_list, n_sec = memo
+ # Get display style settings
style = self.proteinStyle
scaleFactor = self.proteinStyleScaleFactor
resolution = self.proteinStyleQuality
@@ -363,7 +480,8 @@ class ProteinChunks(ChunkDisplayMode):
smooth = self.proteinStyleSmooth
# Set nice joint style for gle Polycone primitives.
- gleSetJoinStyle(TUBE_JN_ANGLE | TUBE_NORM_PATH_EDGE | TUBE_JN_CAP | TUBE_CONTOUR_CLOSED )
+ gleSetJoinStyle(TUBE_JN_ANGLE | TUBE_NORM_PATH_EDGE \
+ | TUBE_JN_CAP | TUBE_CONTOUR_CLOSED )
# Iterate over consecutive secondary structure elements.
current_sec = 0
@@ -373,6 +491,7 @@ class ProteinChunks(ChunkDisplayMode):
# The length should be at least 3.
if n_atoms >= 3:
# Alpha carbon trace styles. Simple but fast.
+ # Use either lines or cylinder to connect consecutive alpha carbons.
if style == PROTEIN_STYLE_CA_WIRE or \
style == PROTEIN_STYLE_CA_CYLINDER or \
style == PROTEIN_STYLE_CA_BALL_STICK:
@@ -396,12 +515,6 @@ class ProteinChunks(ChunkDisplayMode):
width=5,
isSmooth=True)
- #drawline(color,
- # pos1,
- # pos1 + dpos1,
- # width=5,
- # isSmooth=True)
-
if pos2:
drawline(color,
pos1,
@@ -430,7 +543,10 @@ class ProteinChunks(ChunkDisplayMode):
capped=1)
elif style == PROTEIN_STYLE_PEPTIDE_TILES:
- # Peptide tiles (not implemented yet)
+ # Peptide tiles: not implemented yet.
+ # piotr 080903: this option should be removed
+ # from Protein Display Style PM.
+ """
for n in range( 1, n_atoms-2 ):
pos0, ss0, aa0, idx0, dpos0, cbpos0 = sec[n - 1]
pos1, ss1, aa1, idx1, dpos1, cbpos1 = sec[n]
@@ -444,7 +560,7 @@ class ProteinChunks(ChunkDisplayMode):
tri = []
nor = []
col = []
-
+ """
elif style == PROTEIN_STYLE_TUBE or \
style == PROTEIN_STYLE_LADDER or \
@@ -454,7 +570,7 @@ class ProteinChunks(ChunkDisplayMode):
style == PROTEIN_STYLE_SIMPLE_CARTOONS or \
style == PROTEIN_STYLE_FANCY_CARTOONS:
- # All these styles use the same interpolated cubic spline
+ # All of these styles use the same interpolated cubic spline
# that connects alpha carbon atoms.
# The following lists store positions, colors, radii and
@@ -466,6 +582,9 @@ class ProteinChunks(ChunkDisplayMode):
tube_rad = []
tube_dpos = []
+ # Fill-in the position, color, radius and peptide position
+ # lists.
+
for n in range( 2, n_atoms-2 ):
pos00, ss00, a00, idx00, dpos00, cbpos00 = sec[n - 2]
pos0, ss0, aa0, idx0, dpos0, cbpos0 = sec[n - 1]
@@ -584,7 +703,6 @@ class ProteinChunks(ChunkDisplayMode):
# Strands just shrink at the C-terminal end.
width = scaleFactor * 1.0
dw = (1.5 * scaleFactor) / ((1.5 * resolution) - 3)
- print "dw = ", dw
if style == PROTEIN_STYLE_FLAT_RIBBON or \
style == PROTEIN_STYLE_SOLID_RIBBON or \
@@ -611,7 +729,7 @@ class ProteinChunks(ChunkDisplayMode):
nor_arr3 = []
col_arr3 = []
- # This should be done faster... are separate
+ # This should be done faster... are individual
# copies of the tube positions really necessary?
###from copy import copy
@@ -636,13 +754,32 @@ class ProteinChunks(ChunkDisplayMode):
reset = False
if self.proteinStyle == PROTEIN_STYLE_ZIGZAG:
- drawline(col, last_pos-dpos1, pos-dpos2, width=3)
- drawline(col, last_pos+dpos1, pos+dpos2, width=3)
- drawline(col, last_pos-dpos1, pos+dpos2, width=1)
- drawline(col, pos-dpos2, pos+dpos2, width=1)
- drawline(col, last_pos-dpos1, last_pos+dpos1, width=1)
+ # The line calls below draw an outline
+ # of ribbon triangles.
+ drawline(col,
+ last_pos-dpos1,
+ pos-dpos2,
+ width=3)
+ drawline(col,
+ last_pos+dpos1,
+ pos+dpos2,
+ width=3)
+ drawline(col,
+ last_pos-dpos1,
+ pos+dpos2,
+ width=1)
+ drawline(col,
+ pos-dpos2,
+ pos+dpos2,
+ width=1)
+ drawline(col,
+ last_pos-dpos1,
+ last_pos+dpos1,
+ width=1)
if self.proteinStyle == PROTEIN_STYLE_FLAT_RIBBON:
+ # Flat ribbon only draws a single
+ # layer of triangles.
if pos != last_pos:
nvec1 = norm(cross(dpos1, pos-last_pos))
@@ -669,9 +806,22 @@ class ProteinChunks(ChunkDisplayMode):
if self.proteinStyle == PROTEIN_STYLE_SOLID_RIBBON or \
self.proteinStyle == PROTEIN_STYLE_SIMPLE_CARTOONS or \
self.proteinStyle == PROTEIN_STYLE_FANCY_CARTOONS:
-
+ # These three styles are similar.
+ # The difference between "solid ribbon"
+ # and "fancy cartoons" is that the
+ # cartoons mode uses rounded edges
+ # on helices, while solid ribbon uses
+ # just a flat edge. The difference between
+ # simple cartoons and fancy cartoons or
+ # solid ribbon is that the simple cartoons
+ # mode use simple straight cylinders to
+ # represent alpha helices.
if secondary > 0:
-
+
+ # Prepare traiangle strips positioned
+ # along interpolated curve connecting
+ # consecutive alpha carbon atoms
+
col3 = col4 = V(gray)
if pos != last_pos:
@@ -781,27 +931,43 @@ class ProteinChunks(ChunkDisplayMode):
width -= dw
###new_tube_dpos[n] = dpos1
-
+ # Append dummy positions at both ends for
+ # GLE polycone rendering.
tube_pos_left.append(tube_pos[-2])
tube_pos_right.append(tube_pos[-2])
tube_pos_left.append(tube_pos[-1])
tube_pos_right.append(tube_pos[-1])
if self.proteinStyle == PROTEIN_STYLE_FLAT_RIBBON:
- drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr0, nor_arr0, col_arr0)
+ # Note: the "-2" opacity component in the color list
+ # tells the ColorSorter that this is a multi color
+ # object and "color material" should be enabled
+ # while rendering it.
+ drawtriangle_strip(
+ [1.0,1.0,0.0,-2.0], tri_arr0, nor_arr0, col_arr0)
if self.proteinStyle == PROTEIN_STYLE_SOLID_RIBBON or \
self.proteinStyle == PROTEIN_STYLE_SIMPLE_CARTOONS or \
self.proteinStyle == PROTEIN_STYLE_FANCY_CARTOONS:
if secondary == 0:
- drawpolycone_multicolor([0,0,0,-2], tube_pos, tube_col, tube_rad)
+ drawpolycone_multicolor(
+ [0,0,0,-2], tube_pos, tube_col, tube_rad)
else:
- if (secondary == 1 and self.proteinStyle == PROTEIN_STYLE_SOLID_RIBBON) or \
+ if (secondary == 1 and
+ self.proteinStyle == PROTEIN_STYLE_SOLID_RIBBON) or \
secondary == 2:
- drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr0, nor_arr0, col_arr0)
- drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr1, nor_arr1, col_arr1)
- drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr2, nor_arr2, col_arr2)
- drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr3, nor_arr3, col_arr3)
+ drawtriangle_strip(
+ [1.0,1.0,0.0,-2.0],
+ tri_arr0, nor_arr0, col_arr0)
+ drawtriangle_strip(
+ [1.0,1.0,0.0,-2.0],
+ tri_arr1, nor_arr1, col_arr1)
+ drawtriangle_strip(
+ [1.0,1.0,0.0,-2.0],
+ tri_arr2, nor_arr2, col_arr2)
+ drawtriangle_strip([1.0,1.0,0.0,-2.0],
+ tri_arr3, nor_arr3, col_arr3)
+
# Fill in the strand N-terminal end.
quad_tri = []
quad_nor = []
@@ -818,25 +984,40 @@ class ProteinChunks(ChunkDisplayMode):
quad_col.append(col_arr3[0])
quad_col.append(col_arr2[1])
quad_col.append(col_arr3[1])
- drawtriangle_strip([1.0,1.0,1.0,-2.0],quad_tri,quad_nor,quad_col)
+ drawtriangle_strip(
+ [1.0,1.0,1.0,-2.0], quad_tri, quad_nor,quad_col)
if (secondary == 1 and self.proteinStyle == PROTEIN_STYLE_FANCY_CARTOONS):
# Draw smooth tubes at the edges of the
- # helices.
- drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr0, nor_arr0, col_arr0)
- drawtriangle_strip([1.0,1.0,0.0,-2.0], tri_arr1, nor_arr1, col_arr1)
- drawpolycone_multicolor([0,0,0,-2], tube_pos_left, tube_col, tube_rad)
- drawpolycone_multicolor([0,0,0,-2], tube_pos_right, tube_col, tube_rad)
+ # helices.
+ drawtriangle_strip(
+ [1.0,1.0,0.0,-2.0],
+ tri_arr0, nor_arr0, col_arr0)
+ drawtriangle_strip([
+ 1.0,1.0,0.0,-2.0],
+ tri_arr1, nor_arr1, col_arr1)
+ drawpolycone_multicolor(
+ [0,0,0,-2],
+ tube_pos_left, tube_col, tube_rad)
+ drawpolycone_multicolor(
+ [0,0,0,-2],
+ tube_pos_right, tube_col, tube_rad)
if (secondary == 1 and style == PROTEIN_STYLE_SIMPLE_CARTOONS):
- drawcylinder(tube_col[0][0], tube_pos[1], tube_pos[-3], 2.5, capped=1)
+ drawcylinder(tube_col[0][0],
+ tube_pos[1],
+ tube_pos[-3], 2.5, capped=1)
if style == PROTEIN_STYLE_LADDER or \
style == PROTEIN_STYLE_TUBE:
- # Draw the tube.
- drawpolycone_multicolor([0,0,0,-2], tube_pos, tube_col, tube_rad)
-
- # increase secondary structure element counter
+ # Draw a smooth tube connecting alpha carbon positions.
+ drawpolycone_multicolor([0,0,0,-2],
+ tube_pos,
+ tube_col,
+ tube_rad)
+
+ # Increase secondary structure element counter (for coloring
+ # by "secondary structure elements order").
current_sec += 1
def drawchunk_selection_frame(self, glpane, chunk, selection_frame_color, memo, highlighted):
@@ -872,12 +1053,26 @@ class ProteinChunks(ChunkDisplayMode):
piotr 080801: Backbone atoms are omitted.
"""
+ # Draw rotamers using a display list. Create it if necessary.
+
+ # Note: the only command that uses this feature is Edit
+ # Rotamers. The purpose of this feature is to have
+ # an atomistic-like display style on top of a reduced
+ # representation.
+
+ # Note: this implementation may have bugs. The major problem
+ # is that the display list is never explicitly deleted,
+ # so using this feature may introduce memory leaks (I am
+ # not sure about that).
+
+ # The rotamer is rendered using a style resembling "Tubes".
+
if chunk.protein:
if highlighted:
# If highlighhting, just draw everything without using
# the display list.
- aa_list = chunk.protein.get_amino_acids()
color = yellow
+ aa_list = chunk.protein.get_amino_acids()
glMaterialfv(
GL_FRONT_AND_BACK,
GL_AMBIENT_AND_DIFFUSE,
@@ -906,17 +1101,19 @@ class ProteinChunks(ChunkDisplayMode):
0.2,
True))
else:
- # Draw rotamers using a display list. Create it if necessary.
+ """
from PyQt4.Qt import QFont, QString, QColor, QFontMetrics
-
labelFont = QFont( QString("Lucida Grande"), 16)
fm = QFontMetrics(labelFont)
-
+ """
if not chunk.protein.residues_dl:
+ # Create a new residues display list if one is not present.
chunk.protein.residues_dl = glGenLists(1)
glNewList(chunk.protein.residues_dl, GL_COMPILE)
aa_list = chunk.protein.get_amino_acids()
for aa in aa_list:
+ # Iterate over amino acids and check if any rotamer
+ # is in 'expanded' state.
if chunk.protein.is_expanded(aa):
aa_atom_list = aa.get_side_chain_atom_list()
for atom in aa_atom_list:
@@ -929,14 +1126,15 @@ class ProteinChunks(ChunkDisplayMode):
GL_FRONT_AND_BACK,
GL_AMBIENT_AND_DIFFUSE,
color[:3])
- drawsphere_worker((pos1, 0.2, 1))
- _name = aa.get_atom_name(atom)
- textpos = chunk.abs_to_base(atom.posn()) + 2.0 * glpane.out
- glColor3f(1,1,1)
-
- chunk.glpane.renderText(textpos[0], textpos[1], textpos[2], _name, labelFont)
+ drawsphere_worker((pos1, 0.2, 1, 1))
+ ### _name = aa.get_atom_name(atom)
+ ### textpos = chunk.abs_to_base(atom.posn()) + 2.0 * glpane.out
+ ### glColor3f(1,1,1)
+ ### chunk.glpane.renderText(textpos[0], textpos[1], textpos[2], _name, labelFont)
+
+ # Draw bonds
for bond in atom.bonds:
if bond.atom2 in aa_atom_list:
if atom == bond.atom1:
@@ -959,6 +1157,7 @@ class ProteinChunks(ChunkDisplayMode):
True))
glEndList()
+ # Call the residues display list
glCallList(chunk.protein.residues_dl)
return
@@ -1000,48 +1199,48 @@ class ProteinChunks(ChunkDisplayMode):
def _get_ss(aa):
"""
- Returns secondary structure for an amino acid.
+ Returns secondary structure for a residue, or SS_COIL if
+ aa is None
+
+ @param aa: amino acid
+ @type aa: Residue
"""
if aa:
return aa.get_secondary_structure()
- return 0
+ return SS_COIL
def _get_aa(aa):
"""
- Returns a three-letter amino acid code.
+ Returns a three-letter amino acid code for a residue,
+ or "UNK" if aa is None.
+
+ @param aa: amino acid
+ @type aa: Residue
"""
if aa:
return aa.get_three_letter_code()
+
return "UNK"
+ # Return None if the chunk is None
if chunk is None:
return None
+ # Return None if the chunk is not a protein.
if chunk.protein is None:
return None
+ # List of secondary structure elements
structure = []
- from utilities.prefs_constants import proteinStyle_prefs_key
- from utilities.prefs_constants import proteinStyleColors_prefs_key
- from utilities.prefs_constants import proteinStyleQuality_prefs_key
- from utilities.prefs_constants import proteinStyleScaleFactor_prefs_key
- from utilities.prefs_constants import proteinStyleScaling_prefs_key
- from utilities.prefs_constants import proteinStyleHelixColor_prefs_key
- from utilities.prefs_constants import proteinStyleStrandColor_prefs_key
- from utilities.prefs_constants import proteinStyleCoilColor_prefs_key
- from utilities.prefs_constants import proteinStyleSmooth_prefs_key
-
+ # Retrieve protein style properties from user preferences.
self.proteinStyle = env.prefs[proteinStyle_prefs_key] + 1
-
self.proteinStyleSmooth = env.prefs[proteinStyleSmooth_prefs_key]
self.proteinStyleQuality = 2 * env.prefs[proteinStyleQuality_prefs_key]
self.proteinStyleScaling = env.prefs[proteinStyleScaling_prefs_key]
self.proteinStyleScaleFactor = env.prefs[proteinStyleScaleFactor_prefs_key]
-
self.proteinStyleColors = env.prefs[proteinStyleColors_prefs_key]
-
self.proteinStyleAuxColors = 0
self.proteinStyleCustomColor = gray
self.proteinStyleAuxCustomColor = gray
@@ -1051,10 +1250,10 @@ class ProteinChunks(ChunkDisplayMode):
self.proteinStyleCoilColor = env.prefs[proteinStyleCoilColor_prefs_key]
# Extract secondary structure elements
- # Every element is a list of consecutive, non-broken C-alpha atoms
- # in the same secondary structure conformation. The list also includes
+ # Every element is a list of consecutive C-alpha atoms of the same
+ # secondary structure conformation. The list also includes
# two "dummy" atoms - either preceding and following residues, or
- # pre-computed chain extensions.
+ # pre-computed dummy atoms extensions.
# Empty SS element.
sec = []
@@ -1069,7 +1268,8 @@ class ProteinChunks(ChunkDisplayMode):
# "dpos" vectors can be flipped so the angle between consecutive
# "dpos" vectors is less than 90 degree to avoid visual problems.
- # dictionary of corresponding Ca-Cb atoms for rendering "Ladder" style.
+ # dictionary of corresponding Ca-Cb atoms for rendering of the
+ # "Ladder" style.
ca_cb = {}
n_ca = 0
@@ -1078,6 +1278,8 @@ class ProteinChunks(ChunkDisplayMode):
last_dpos = None
last_ca_atom = None
+ # Calculate "dpos" vectors paralles to the peptide planes.
+
for aa in chunk.protein.get_amino_acids():
last_c_atom = aa.get_c_atom()
last_o_atom = aa.get_o_atom()
@@ -1094,7 +1296,8 @@ class ProteinChunks(ChunkDisplayMode):
n0 = last_dpos
n1 = dpos
d = dot(n0, n1)
- # Flip dpos if > 90 deg.
+ # Flip dpos if the angle between consecutive planes
+ # is > 90 deg.
if d < 0.0:
dpos = -1.0 * dpos
last_dpos = dpos
@@ -1120,8 +1323,10 @@ class ProteinChunks(ChunkDisplayMode):
anum = 0
- # Smoothing of helices and beta-strands.
-
+ # Smoothing alpha-helices and beta-strands. The consecutive "dpos"
+ # vectors are smoothed using a sliding windows and weighted average.
+ # Beta-strands use longer averaging window than alpha-helices.
+
if self.proteinStyleSmooth and \
(self.proteinStyle == PROTEIN_STYLE_TUBE or
self.proteinStyle == PROTEIN_STYLE_LADDER or
@@ -1154,23 +1359,23 @@ class ProteinChunks(ChunkDisplayMode):
next_aa = None
next_dpos = None
- if (ss == 2 or prev_ss == 2 or next_ss == 2) and prev_ca and next_ca:
- ca_pos = 0.5 * (0.5 * (prev_ca_pos + next_ca_pos) + ca_pos)
- if next_ss == 2 and prev_ss == 2:
+ if (ss == 1 or prev_ss == 1 or next_ss == 1) and prev_ca and next_ca:
+ if prev_dpos and next_dpos:
dpos = norm(prev_dpos + dpos + next_dpos)
smooth_list.append((ca, ca_pos, ss, aa, dpos, i))
- #if ss == 1:
- if (ss == 1 or prev_ss == 1 or next_ss == 1) and prev_ca and next_ca:
- if prev_dpos and next_dpos:
+ if (ss == 2 or prev_ss == 2 or next_ss == 2) and prev_ca and next_ca:
+ ca_pos = 0.5 * (0.5 * (prev_ca_pos + next_ca_pos) + ca_pos)
+ if next_ss == 2 and prev_ss == 2:
dpos = norm(prev_dpos + dpos + next_dpos)
smooth_list.append((ca, ca_pos, ss, aa, dpos, i))
for ca, ca_pos, ss, aa, dpos, i in smooth_list:
ca_list[i] = (ca, ca_pos, ss, aa, dpos)
+ # Build the list of secondary structure elements.
+
n_sec = 0
-
for i in range( n_ca ):
ca, ca_pos, ss, aa, dpos = ca_list[i]
@@ -1223,8 +1428,8 @@ class ProteinChunks(ChunkDisplayMode):
# inside a continuous secondary structure chain fragment
# (ss element) and FOUR dummy atom positions (two at
# each of both terminals).
- #
- # The dummy atom positions can be None and therefore
+
+ # The dummy atom positions can't be None and therefore
# the spline interpolator has to compute fake positions
# of the terminal atoms.
@@ -1235,7 +1440,7 @@ class ProteinChunks(ChunkDisplayMode):
pos1, ss1, aa1, idx1, dpos1, cbpos1 = sec[1]
pos2, ss2, aa2, idx2, dpos2, cbpos2 = sec[2]
pos3, ss3, aa3, idx3, dpos3, cbpos3 = sec[3]
- #pos4, ss4, aa4, idx4, dpos4, cbpos4 = sec[4]
+ ### pos4, ss4, aa4, idx4, dpos4, cbpos4 = sec[4]
if pos1 == pos2:
pos1 = pos1 - (pos3 - pos2)
sec[1] = (pos1, ss1, aa1, idx1, dpos1, cbpos1)
@@ -1243,13 +1448,14 @@ class ProteinChunks(ChunkDisplayMode):
pos1, ss1, aa1, idx1, dpos1, cbpos1 = sec[-2]
pos2, ss2, aa2, idx2, dpos2, cbpos2 = sec[-3]
pos3, ss3, aa3, idx3, dpos3, cbpos3 = sec[-4]
- #pos4, ss4, aa4, idx4, dpos4, cbpos4 = sec[-5]
+ ### pos4, ss4, aa4, idx4, dpos4, cbpos4 = sec[-5]
if pos1 == pos2:
pos1 = pos1 - (pos3 - pos2)
sec[-2] = (pos1, ss1, aa1, idx1, dpos1, cbpos1)
# Make sure that the interior surface of helices
- # is properly oriented.
+ # is properly oriented. This is important for "Fancy Cartoons"
+ # display style.
if ss == 1:
pos2, ss2, aa2, idx2, dpos2, cbpos2 = sec[2]
generated by cgit v1.2.3 (git 2.39.1) at 2025-04-09 11:33:06 +0000