def construct(self):
rng = np.random.RandomState(self.seed)
moleculizer = partial(
new_molecule,
colors=lambda: rng.choice(MOLECULE_COLORS, size=3, replace=True))
proteins = molecule_universe_grid(
moleculizer, num_molecules=(5, 8)).scale(0.3).center()
proteins_frame = SurroundingRectangle(proteins,
color=WHITE).round_corners(0.5)
universe_title = Text('Known proteins').scale(0.7).next_to(
proteins_frame, UP)
framed_proteins = VGroup(universe_title, proteins_frame,
proteins).to_edge(LEFT)
self.play(FadeIn(framed_proteins))
self.wait(3)
# --- Sequence -> Number -> MLM
heavy, hcdr3 = hiv_antibody()
heavy.next_to(framed_proteins, RIGHT)
self.play(Transform(proteins[23], heavy))
self.wait(5)
mlm = MLM().next_to(framed_proteins, RIGHT)
self.play(ShrinkToCenter(heavy)) # , mlm.text
self.wait(5)
# FIXME: just to break here
if mlm.text is not None:
return
# --- Subsets
selected_proteins = [
proteins[i].copy() for i in rng.choice(
len(proteins), replace=False, size=len(proteins) // 3)
]
antibodies = VGroup(
*
[molecule_from_molecule(protein) for protein in selected_proteins])
antibodies_frame = (SurroundingRectangle(antibodies).match_color(
proteins_frame).match_width(proteins_frame).match_height(
proteins_frame)).round_corners(0.5)
framed_antibodies = VGroup(antibodies_frame, antibodies)
framed_antibodies.next_to(proteins, RIGHT, buff=MED_LARGE_BUFF)
self.play(
*[
ReplacementTransform(protein, antibody)
for protein, antibody in zip(selected_proteins, antibodies)
], Write(antibodies_frame))
self.wait(4)
def __init__(self, target: Actor, label: str, direction: np.array):
super().__init__(target)
self.target = target
self.label = "\n".join(wrap(label, 30))
self.direction = direction
block = VGroup()
title = Text(self.label, font="Helvetica").scale(0.7)
rect = Rectangle(height=title.get_height() + 0.3,
width=title.get_width() + 0.3)
title.move_to(rect)
block.add(rect, title)
block.next_to(target.get_center(), direction)
self.add(block)
def __init__(self, source: Actor, label: str):
super().__init__(source)
self.label = "\n".join(wrap(label, 30))
line_block = VGroup()
spacing = 0.4
distance = 0.8
center_x = source.get_center()[0]
line = Polygon(
[center_x, spacing, 0],
[center_x + distance, spacing, 0],
[center_x + distance, -1 * spacing, 0],
[center_x + distance / 2, -1 * spacing, 0],
[center_x + distance, -1 * spacing, 0],
[center_x + distance, spacing, 0],
[center_x, spacing, 0],
color=WHITE,
)
line.set_stroke(width=ARROW_STROKE_WIDTH)
arrow = Arrow(
start=[center_x + distance, -1 * spacing, 0],
end=[center_x, -1 * spacing, 0],
buff=0,
stroke_width=ARROW_STROKE_WIDTH,
)
line_block.add(line, arrow)
title = Text(self.label, font=self.source.font, size=0.5, slant=ITALIC)
title.next_to(line_block)
block = VGroup()
block.add(line_block, title)
block.next_to(source.get_center(), RIGHT)
self.add(block)
def __init__(self, target: Actor, label: str):
super().__init__(target)
self.target = target
self.label = "\n".join(wrap(label, 30))
line_block = VGroup()
spacing = 0.4
distance = 0.8
line = Polygon(
[target.get_center()[0], spacing, 0],
[target.get_center()[0] + distance, spacing, 0],
[target.get_center()[0] + distance, -1 * spacing, 0],
[target.get_center()[0] + distance / 2, -1 * spacing, 0],
[target.get_center()[0] + distance, -1 * spacing, 0],
[target.get_center()[0] + distance, spacing, 0],
[target.get_center()[0], spacing, 0],
color=WHITE,
)
line.set_stroke(width=ARROW_STROKE_WIDTH)
arrow = Arrow(
start=[target.get_center()[0] + distance, -1 * spacing, 0],
end=[target.get_center()[0], -1 * spacing, 0],
buff=0,
stroke_width=ARROW_STROKE_WIDTH,
)
line_block.add(line, arrow)
title = Text(self.label, font="Helvetica", size=0.7, slant=ITALIC)
title.next_to(line_block)
block = VGroup()
block.add(line_block, title)
block.next_to(target.get_center(), RIGHT)
self.add(block)
def construct(self):
a_million_forks = Text('A million forks in the road to our products'
) # to drug development
a_million_forks.to_edge(UP)
new_drugs_per_billion_RD = [('1950', 100), ('1960', 50), ('1970', 10),
('1980', 5), ('1990', 3), ('2000', 2),
('2010', 1), ('2020', 1)]
x = [x for x, _ in new_drugs_per_billion_RD]
y = [y for _, y in new_drugs_per_billion_RD]
colors = ["#003f5c", "#58508d", "#bc5090", "#ff6361", "#ffa600"]
chart = BarChart(
values=y,
max_value=max(y),
bar_colors=colors,
bar_names=x,
bar_label_scale_val=0.5,
).scale(0.8).to_edge(LEFT).shift(0.5 * DOWN)
# text_top = (
# Text('EROOM\'s Law: More expensive, slower drug discovery')
# .scale(0.9)
# .next_to(chart, UP, buff=0.1)
# )
# text_left = (
# Text('Number of drugs per billion US$ R&D spending')
# .rotate(angle=TAU / 4, axis=OUT)
# .scale(0.3)
# .next_to(chart, LEFT, buff=0.5)
# )
text_top = (
Text('Number of drugs per billion US$ R&D spending (log-scale)'
).scale(0.3).next_to(chart, UP, buff=0.5))
text_bottom = (
Text("Eroom's law: a continuous decline in Pharma R&D productivity"
).scale(0.3).next_to(chart, DOWN, buff=0.5))
# --- Examples of forks in the road
icons_text = [
(SVGMobject(SVGS.ANTIBODY).set_color(BLUE).scale(0.8),
Text('Is my antibody a potent, functional binder?')),
(SVGMobject(SVGS.CYCLIC_PEPTIDE).set_color_by_gradient(
BLUE, GREEN).scale(0.8),
Text('Can we generate peptides without liabilities?')),
(SVGMobject(SVGS.DNA).set_color_by_gradient(GREEN,
BLUE).scale(0.8),
Text(
'Can we optimize DNA to better express traits in plants or humans?'
)),
(SVGMobject(SVGS.PACMAN).set_color(RED).scale(0.8),
Text('What will an enzyme in the human gut do?')),
# (
# SVGMobject(SVGS.PACMAN).set_color_by_gradient(GREEN, BLUE, RED).scale(0.8),
# Text('Can we optimize enzymes to better manufacture bioproducts?')
# ),
(SVGMobject(SVGS.PROTEIN3D).set_color_by_gradient(
GREEN, BLUE, RED).scale(0.8),
Text('What is the 3D structure of my biomolecule?')),
(SVGMobject(SVGS.PATIENT).set_color_by_gradient(BLUE,
RED).scale(0.8),
Text('Will a patient respond to treatment in a clinical trial?')),
(SVGMobject(SVGS.MUTATION).set_color_by_gradient(BLUE, GREEN,
RED).scale(0.8),
Text('...'))
]
# icons_text = icons_text[:1]
for (icon1, _), (icon2, _) in zip(icons_text, icons_text[1:]):
icon2.next_to(icon1, DOWN, buff=0.5)
for icon, text in icons_text:
text.next_to(icon, RIGHT)
questions = VGroup(*chain.from_iterable(icons_text))
questions.scale(0.32)
questions.next_to(chart, RIGHT, buff=1).shift(0.5 * UP)
logo = LoLLogo().scale(0.7)
# logo.next_to(questions, DOWN, buff=0.5)
logo.move_to(questions)
# --- Animate
self.play(FadeIn(text_top))
self.play(Write(chart), Write(text_bottom), run_time=4)
self.wait(2)
self.play(Write(a_million_forks))
for icon, text in icons_text:
self.play(FadeIn(icon, text))
self.wait(3)
# if we have put the logo under the questions...
# self.play(FadeIn(logo))
# if we prefer the logo to morph from the questions
actionable_insights = (Text(
'Getting actionable insights from biological sequences').next_to(
logo, DOWN, buff=0.5).scale(0.4))
self.play(ReplacementTransform(questions, logo))
self.play(Write(actionable_insights))
self.wait(2)
