""" 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'''') 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)