/usr/lib/python2.7/dist-packages/csb/bio/io/svg.py is in python-csb 1.2.3+dfsg-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 | """
Build SVG diagrams from various csb objects.
"""
import math
import csb.core
from csb.bio.structure import SecondaryStructure, SecStructures
class SSCartoonBuilder(object):
"""
Creates 2D vector diagrams from L{SecondaryStructure} objects.
@param ss: source secondary structure (either a SS string or a SS object)
@type ss: str or L{SecondaryStructure}
@param width: output width of the diagram in pixels
@type width: int
@param height: output height of the diagram in pixels
@type height: int
@param thickness: stroke-width (2px by default)
@param helix: SVG color for helicies (red by default)
@param strand: SVG color for strands (blue by default)
@param coil: SVG color for coils (orange by default)
@param gap: SVG color for gaps (grey by default)
@param cap: stroke-linecap (round by default)
"""
def __init__(self, ss, width, height, thickness='2px',
helix='#C24641', strand='#6698FF', coil='#FF8C00', gap='#E0E0E0',
cap='round'):
if ss:
if isinstance(ss, csb.core.string):
self._ss = SecondaryStructure(ss)
else:
self._ss = ss.clone()
self._ss.to_three_state()
self._residues = sum(e.length for e in self._ss)
if self._residues == 0:
raise ValueError('Zero-length secondary structure')
else:
raise ValueError('Invalid secondary structure')
self.thickness = thickness
self.helixcolor = helix
self.strandcolor = strand
self.coilcolor = coil
self.gapcolor = gap
self.cap = cap
self._realwidth = float(width)
self._width = self._realwidth - 2 # this is to compensate for antialiasing and rounded caps
self._height = float(height)
self._x = 0
self._y = 0
self._svg = ''
def build(self):
"""
Build a SVG image using the current size and color settings.
@return: SVG diagram
@rtype: str (SVG document)
"""
self._x = 0
self._y = 0
self._svg = [r'''<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
width="{0._realwidth}" height="{0._height}">
<g transform="translate(0, {1})">'''.format(self, self._height / 2.0)]
for e in self._ss:
if e.type == SecStructures.Helix:
cartoon = self._helix(e.length)
color = self.helixcolor
elif e.type == SecStructures.Strand:
cartoon = self._strand(e.length)
color = self.strandcolor
elif e.type == SecStructures.Coil:
cartoon = self._coil(e.length)
color = self.coilcolor
elif e.type == SecStructures.Gap:
cartoon = self._gap(e.length)
color = self.gapcolor
else:
assert False, "Unhandled SS Type: {0!r}".format(e.type)
path = r''' <path fill="none" stroke="{0}" stroke-width="{1.thickness}" stroke-linecap="{1.cap}"
d="{2}" />'''.format(color, self, cartoon)
self._svg.append(path)
self._svg.append(' </g>')
self._svg.append('</svg>')
return '\n'.join(self._svg)
def _format(self, path):
formatted = []
for i in path:
if i == -0:
i = 0
if isinstance(i, float):
i = round(i, ndigits=7)
if i == -0:
i = 0
formatted.append('{0:.7f}'.format(i))
else:
formatted.append(str(i))
return ' '.join(formatted)
def _helix(self, length, arc_width=3.0):
if length < 1:
return ''
helix_width = float(length) * self._width / self._residues
helix_end = self._x + helix_width
path = ['M', self._x, self._y, 'Q']
arcs = int(helix_width / arc_width)
for i in range(1, arcs + 1):
# quadratic bezier control points: sine curve's min, max and inflection points (0, 1, 0, -1, 0, 1 ...)
# one arc is the curve from 0 to pi/2
if i < arcs:
# inner arc
self._x += arc_width
self._y = math.sin(math.pi * i / 2) * (self._height / 2.0)
path.append(self._x)
path.append(self._y)
else:
# last arc; stretch it to make the helix pixel-precise, ending also at y=0
# also the number of arcs/controlpoints must be even, otherwise the path is broken
# remaining pixels on x
remainder = helix_end - self._x
if i % 2 == 0:
# even number of arcs, just extend the last arc with the remainder
self._x += remainder
self._y = 0
path.append(self._x)
path.append(self._y)
else:
# odd number of arcs
# 1) keep this arc at the expected y, but stretch it half of the x remainder
self._x += remainder / 2.0
self._y = math.sin(math.pi * i / 2) * (self._height / 2.0)
path.append(self._x)
path.append(self._y)
# 2) append a final arc, ending at [helix_end, 0]
self._x += remainder / 2.0
self._y = 0
path.append(self._x)
path.append(self._y)
return self._format(path)
def _strand(self, length, arrow_width=3.0):
offset = 1.0
strand_width = float(length) * self._width / self._residues
path = ['M', self._x, self._y, 'H']
self._x += strand_width
path.append(self._x)
if offset < arrow_width < strand_width:
arrow_start = self._x - offset - arrow_width
path.extend(['M', self._x - offset, self._y])
path.extend(['L', arrow_start, self._y + self._height / 9])
path.extend(['L', arrow_start, self._y - self._height / 9])
path.extend(['L', self._x - offset, self._y])
return self._format(path)
def _coil(self, length):
coil_width = float(length) * self._width / self._residues
path = ['M', self._x, self._y, 'Q']
# first control point
self._x += coil_width / 2.0
self._y = self._height / -2.0
path.append(self._x)
path.append(self._y)
# second
self._x += coil_width / 2.0
self._y = 0
path.append(self._x)
path.append(self._y)
return self._format(path)
def _gap(self, length):
return self._strand(length, arrow_width=0)
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