def _get_text_size(self, text, padding=2, file_format='pdf'):
try:
import cairocffi as cairo
except ImportError:
import cairo
# Use dummy surface to determine text extents
surface = create_new_surface(file_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, reaction, file_format, path=None):
"""
Draw the potential energy surface for the given `network` as a Cairo
surface of the given `file_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.reaction = reaction
self.wells = [
Well(self.reaction.reactants),
Well(self.reaction.products)
]
# Generate the bounding rectangles for each configuration label
label_rects = []
for well in self.wells:
label_rects.append(
self._get_label_size(well, file_format=file_format))
# Get energy range (use kJ/mol internally)
e0_min, e0_max = self._get_energy_range()
e0_min *= 0.001
e0_max *= 0.001
# Drawing parameters
padding = self.options['padding']
well_width = self.options['wellWidth']
well_spacing = self.options['wellSpacing']
e_slope = self.options['Eslope']
ts_width = self.options['TSwidth']
e0_offset = self.options['E0offset'] * 0.001
# Choose multiplier to convert energies to desired units (on figure only)
e_units = self.options['Eunits']
try:
e_mult = {
'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
}[e_units]
except KeyError:
raise InputError(
'Invalid value "{0}" for Eunits parameter.'.format(e_units))
# Determine height required for drawing
e_height = self._get_text_size('0.0', file_format=file_format)[3] + 6
y_e0 = (e0_max - 0.0) * e_slope + padding + e_height
height = (e0_max - e0_min) * e_slope + 2 * padding + e_height + 6
for i in range(len(self.wells)):
if 0.001 * self.wells[i].E0 == e0_min:
height += label_rects[i][3]
break
# Determine naive position of each well (one per column)
coordinates = np.zeros((len(self.wells), 2), np.float64)
x = padding
for i in range(len(self.wells)):
well = self.wells[i]
rect = label_rects[i]
this_well_width = max(well_width, rect[2])
e0 = 0.001 * well.E0
y = y_e0 - e0 * e_slope
coordinates[i] = [x + 0.5 * this_well_width, y]
x += this_well_width + well_spacing
width = x + padding - well_spacing
# Determine the rectangles taken up by each well
# We'll use this to merge columns safely so that wells don't overlap
well_rects = []
for i in range(len(self.wells)):
l, t, w, h = label_rects[i]
x, y = coordinates[i, :]
if w < well_width:
w = well_width
t -= 6 + e_height
h += 6 + e_height
well_rects.append([l + x - 0.5 * w, t + y + 6, w, h])
# Squish columns together from the left where possible until an isomer is encountered
old_left = np.min(coordinates[:, 0])
n_left = -1
columns = []
for i in range(n_left, -1, -1):
top = well_rects[i][1]
bottom = top + well_rects[i][3]
for column in columns:
for c in column:
top0 = well_rects[c][1]
bottom0 = top + well_rects[c][3]
if (top0 <= top <= bottom0) or (top <= top0 <= bottom):
# Can't put it in this column
break
else:
# Can put it in this column
column.append(i)
break
else:
# Needs a new column
columns.append([i])
for column in columns:
column_width = max([well_rects[c][2] for c in column])
x = coordinates[column[0] + 1, 0] - 0.5 * well_rects[
column[0] + 1][2] - well_spacing - 0.5 * column_width
for c in column:
delta = x - coordinates[c, 0]
well_rects[c][0] += delta
coordinates[c, 0] += delta
new_left = np.min(coordinates[:, 0])
coordinates[:, 0] -= new_left - old_left
# Squish columns together from the right where possible until an isomer is encountered
n_right = 3
columns = []
for i in range(n_right, len(self.wells)):
top = well_rects[i][1]
bottom = top + well_rects[i][3]
for column in columns:
for c in column:
top0 = well_rects[c][1]
bottom0 = top0 + well_rects[c][3]
if (top0 <= top <= bottom0) or (top <= top0 <= bottom):
# Can't put it in this column
break
else:
# Can put it in this column
column.append(i)
break
else:
# Needs a new column
columns.append([i])
for column in columns:
column_width = max([well_rects[c][2] for c in column])
x = coordinates[column[0] - 1, 0] + 0.5 * well_rects[
column[0] - 1][2] + well_spacing + 0.5 * column_width
for c in column:
delta = x - coordinates[c, 0]
well_rects[c][0] += delta
coordinates[c, 0] += delta
width = max([rect[2] + rect[0] for rect in well_rects]) - min(
[rect[0] for rect in well_rects]) + 2 * padding
# Draw to the final surface
surface = create_new_surface(file_format=file_format,
target=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()
self._draw_text('E0 ({0})'.format(e_units), cr, 15, 10,
padding=2) # write units
# Draw reactions
e0_reac = self.wells[0].E0 * 0.001 - e0_offset
e0_prod = self.wells[1].E0 * 0.001 - e0_offset
e0_ts = self.reaction.transition_state.conformer.E0.value_si * 0.001 - e0_offset
x1, y1 = coordinates[0, :]
x2, y2 = coordinates[1, :]
x1 += well_spacing / 2.0
x2 -= well_spacing / 2.0
if abs(e0_ts - e0_reac) > 0.1 and abs(e0_ts - e0_prod) > 0.1:
if len(self.reaction.reactants) == 2:
if e0_reac < e0_prod:
x0 = x1 + well_spacing * 0.5
else:
x0 = x2 - well_spacing * 0.5
elif len(self.reaction.products) == 2:
if e0_reac < e0_prod:
x0 = x2 - well_spacing * 0.5
else:
x0 = x1 + well_spacing * 0.5
else:
x0 = 0.5 * (x1 + x2)
y0 = y_e0 - (e0_ts + e0_offset) * e_slope
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 - ts_width / 2.0, y0)
cr.line_to(x0 + ts_width / 2.0, y0)
cr.stroke()
# Add background and text for energy
e0 = "{0:.1f}".format(e0_ts * 1000. * e_mult)
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 - ts_width / 2.0, y0,
x0 - ts_width / 2.0, y0)
cr.move_to(x0 + ts_width / 2.0, y0)
cr.curve_to(x0 + width2 / 8.0 + ts_width / 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(self.wells):
x0, y0 = coordinates[i, :]
# Draw horizontal line for well
cr.set_line_width(4.0)
cr.move_to(x0 - well_width / 2.0, y0)
cr.line_to(x0 + well_width / 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. * e_mult)
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 * label_rects[i][2]
y = y0 + 6
cr.rectangle(x, y, label_rects[i][2], label_rects[i][3])
cr.set_source_rgba(1.0, 1.0, 1.0, 0.75)
cr.fill()
self._draw_label(well, cr, x, y, file_format=file_format)
# Finish Cairo drawing
if file_format == 'png':
surface.write_to_png(path)
else:
surface.finish()