def __getTextSize(self, text, padding=2, format='pdf'):
try:
import cairocffi as cairo
except ImportError:
import cairo
# Use dummy surface to determine text extents
surface = createNewSurface(format)
cr = cairo.Context(surface)
cr.set_font_size(self.options['fontSizeNormal'])
extents = cr.text_extents(text)
width = extents[2] + 2 * padding
height = extents[3] + 2 * padding
return [0, 0, width, height]
def draw(self, network, format, path=None):
"""
Draw the potential energy surface for the given `network` as a Cairo
surface of the given `format`. If `path` is given, the surface is
saved to that location on disk.
"""
try:
import cairocffi as cairo
except ImportError:
try:
import cairo
except ImportError:
logging.warning('Cairo not found; potential energy surface will not be drawn.')
return
self.network = network
# The order of wells is as follows:
# - Reactant channels come first (to the left)
# - Isomers are in the middle
# - Product channels come last (to the right)
# This is done because most people will read the PES from left to right
wells = []
wells.extend(network.reactants)
wells.extend(network.isomers)
wells.extend(network.products)
# Generate the bounding rectangles for each configuration label
labelRects = []
for well in wells:
labelRects.append(self.__getLabelSize(well, format=format))
# Get energy range (use kJ/mol internally)
E0min, E0max = self.__getEnergyRange()
E0min *= 0.001; E0max *= 0.001
# Drawing parameters
padding = self.options['padding']
wellWidth = self.options['wellWidth']
wellSpacing = self.options['wellSpacing']
Eslope = self.options['Eslope']
TSwidth = self.options['TSwidth']
E0_offset = self.options['E0offset'] * 0.001
# Choose multiplier to convert energies to desired units (on figure only)
Eunits = self.options['Eunits']
try:
Emult = {'J/mol': 1.0, 'kJ/mol': 0.001, 'cal/mol': 1.0/4.184, 'kcal/mol': 1.0/4184., 'cm^-1': 1.0/11.962}[Eunits]
except KeyError:
raise Exception('Invalid value "{0}" for Eunits parameter.'.format(Eunits))
# Determine height required for drawing
Eheight = self.__getTextSize('0.0', format=format)[3] + 6
y_E0 = (E0max - 0.0) * Eslope + padding + Eheight
height = (E0max - E0min) * Eslope + 2 * padding + Eheight + 6
for i in range(len(wells)):
if 0.001 * wells[i].E0 == E0min:
height += labelRects[i][3]
break
# Determine naive position of each well (one per column)
coordinates = numpy.zeros((len(wells), 2), numpy.float64)
x = padding
for i in range(len(wells)):
well = wells[i]
rect = labelRects[i]
thisWellWidth = max(wellWidth, rect[2])
E0 = 0.001 * well.E0
y = y_E0 - E0 * Eslope
coordinates[i] = [x + 0.5 * thisWellWidth, y]
x += thisWellWidth + wellSpacing
width = x + padding - wellSpacing
# Determine the rectangles taken up by each well
# We'll use this to merge columns safely so that wells don't overlap
wellRects = []
for i in range(len(wells)):
l, t, w, h = labelRects[i]
x, y = coordinates[i,:]
if w < wellWidth: w = wellWidth
t -= 6 + Eheight
h += 6 + Eheight
wellRects.append([l + x - 0.5 * w, t + y + 6, w, h])
# Squish columns together from the left where possible until an isomer is encountered
oldLeft = numpy.min(coordinates[:,0])
Nleft = wells.index(network.isomers[0])-1
columns = []
for i in range(Nleft, -1, -1):
top = wellRects[i][1]
bottom = top + wellRects[i][3]
for j in range(len(columns)):
for c in columns[j]:
top0 = wellRects[c][1]
bottom0 = top + wellRects[c][3]
if (top >= top0 and top <= bottom0) or (top <= top0 and top0 <= bottom):
# Can't put it in this column
break
else:
# Can put it in this column
columns[j].append(i)
break
else:
# Needs a new column
columns.append([i])
for column in columns:
columnWidth = max([wellRects[c][2] for c in column])
x = coordinates[column[0]+1,0] - 0.5 * wellRects[column[0]+1][2] - wellSpacing - 0.5 * columnWidth
for c in column:
delta = x - coordinates[c,0]
wellRects[c][0] += delta
coordinates[c,0] += delta
newLeft = numpy.min(coordinates[:,0])
coordinates[:,0] -= newLeft - oldLeft
# Squish columns together from the right where possible until an isomer is encountered
Nright = wells.index(network.isomers[-1])+1
columns = []
for i in range(Nright, len(wells)):
top = wellRects[i][1]
bottom = top + wellRects[i][3]
for j in range(len(columns)):
for c in columns[j]:
top0 = wellRects[c][1]
bottom0 = top0 + wellRects[c][3]
if (top >= top0 and top <= bottom0) or (top <= top0 and top0 <= bottom):
# Can't put it in this column
break
else:
# Can put it in this column
columns[j].append(i)
break
else:
# Needs a new column
columns.append([i])
for column in columns:
columnWidth = max([wellRects[c][2] for c in column])
x = coordinates[column[0]-1,0] + 0.5 * wellRects[column[0]-1][2] + wellSpacing + 0.5 * columnWidth
for c in column:
delta = x - coordinates[c,0]
wellRects[c][0] += delta
coordinates[c,0] += delta
width = max([rect[2]+rect[0] for rect in wellRects]) - min([rect[0] for rect in wellRects]) + 2 * padding
# Draw to the final surface
surface = createNewSurface(format=format, path=path, width=width, height=height)
cr = cairo.Context(surface)
# Some global settings
cr.select_font_face("sans")
cr.set_font_size(self.options['fontSizeNormal'])
# Fill the background with white
cr.set_source_rgba(1.0, 1.0, 1.0, 1.0)
cr.paint()
# # DEBUG: Draw well bounding rectangles
# cr.save()
# cr.set_line_width(1.0)
# for rect in wellRects:
# cr.rectangle(*rect)
# cr.set_source_rgba(0.0, 0.0, 1.0, 0.5)
# cr.stroke()
# cr.restore()
# Draw path reactions
for rxn in network.pathReactions:
for reac in range(len(wells)):
if wells[reac].species == rxn.reactants:
break
else:
raise Exception
for prod in range(len(wells)):
if wells[prod].species == rxn.products:
break
else:
raise Exception
E0_reac = wells[reac].E0 * 0.001 - E0_offset
E0_prod = wells[prod].E0 * 0.001 - E0_offset
E0_TS = rxn.transitionState.conformer.E0.value_si * 0.001 - E0_offset
if reac < prod:
x1, y1 = coordinates[reac,:]
x2, y2 = coordinates[prod,:]
else:
x1, y1 = coordinates[prod,:]
x2, y2 = coordinates[reac,:]
x1 += wellSpacing / 2.0; x2 -= wellSpacing / 2.0
if abs(E0_TS - E0_reac) > 0.1 and abs(E0_TS - E0_prod) > 0.1:
if len(rxn.reactants) == 2:
if reac < prod: x0 = x1 + wellSpacing * 0.5
else: x0 = x2 - wellSpacing * 0.5
elif len(rxn.products) == 2:
if reac < prod: x0 = x2 - wellSpacing * 0.5
else: x0 = x1 + wellSpacing * 0.5
else:
x0 = 0.5 * (x1 + x2)
y0 = y_E0 - (E0_TS + E0_offset) * Eslope
width1 = (x0 - x1)
width2 = (x2 - x0)
# Draw horizontal line for TS
cr.set_source_rgba(0.0, 0.0, 0.0, 1.0)
cr.set_line_width(2.0)
cr.move_to(x0 - TSwidth/2.0, y0)
cr.line_to(x0+TSwidth/2.0, y0)
cr.stroke()
# Add background and text for energy
E0 = "{0:.1f}".format(E0_TS * 1000. * Emult)
extents = cr.text_extents(E0)
x = x0 - extents[2] / 2.0; y = y0 - 6.0
cr.rectangle(x + extents[0] - 2.0, y + extents[1] - 2.0, extents[2] + 4.0, extents[3] + 4.0)
cr.set_source_rgba(1.0, 1.0, 1.0, 0.75)
cr.fill()
cr.move_to(x, y)
cr.set_source_rgba(0.0, 0.0, 0.0, 1.0)
cr.show_text(E0)
# Draw Bezier curve connecting reactants and products through TS
cr.set_source_rgba(0.0, 0.0, 0.0, 0.5)
cr.set_line_width(1.0)
cr.move_to(x1, y1)
cr.curve_to(x1 + width1/8.0, y1, x0 - width1/8.0 - TSwidth/2.0, y0, x0 - TSwidth/2.0, y0)
cr.move_to(x0 + TSwidth/2.0, y0)
cr.curve_to(x0 + width2/8.0 + TSwidth/2.0, y0, x2 - width2/8.0, y2, x2, y2)
cr.stroke()
else:
width = (x2 - x1)
# Draw Bezier curve connecting reactants and products through TS
cr.set_source_rgba(0.0, 0.0, 0.0, 0.5)
cr.set_line_width(1.0)
cr.move_to(x1, y1)
cr.curve_to(x1 + width/4.0, y1, x2 - width/4.0, y2, x2, y2)
cr.stroke()
# Draw wells (after path reactions so that they are on top)
for i, well in enumerate(wells):
x0, y0 = coordinates[i,:]
# Draw horizontal line for well
cr.set_line_width(4.0)
cr.move_to(x0 - wellWidth/2.0, y0)
cr.line_to(x0 + wellWidth/2.0, y0)
cr.set_source_rgba(0.0, 0.0, 0.0, 1.0)
cr.stroke()
# Add background and text for energy
E0 = well.E0 * 0.001 - E0_offset
E0 = "{0:.1f}".format(E0 * 1000. * Emult)
extents = cr.text_extents(E0)
x = x0 - extents[2] / 2.0; y = y0 - 6.0
cr.rectangle(x + extents[0] - 2.0, y + extents[1] - 2.0, extents[2] + 4.0, extents[3] + 4.0)
cr.set_source_rgba(1.0, 1.0, 1.0, 0.75)
cr.fill()
cr.move_to(x, y)
cr.set_source_rgba(0.0, 0.0, 0.0, 1.0)
cr.show_text(E0)
# Draw background and text for label
x = x0 - 0.5 * labelRects[i][2]
y = y0 + 6
cr.rectangle(x, y, labelRects[i][2], labelRects[i][3])
cr.set_source_rgba(1.0, 1.0, 1.0, 0.75)
cr.fill()
self.__drawLabel(well, cr, x, y, format=format)
# Finish Cairo drawing
if format == 'png':
surface.write_to_png(path)
else:
surface.finish()