def demo_boxes(scene: CodeScene):
scene.add_background(f"{example_dir}/resources/blackboard.jpg")
title = Text("examples/boxes.py", font=DEFAULT_FONT)
title.to_edge(UP)
scene.add(title)
comp1 = TextBox("Component A", shadow=False)
comp2 = TextBox("Component B", shadow=False)
comp3 = TextBox("Component C", shadow=False)
comp1.next_to(title, DOWN, buff=2)
comp1.to_edge(LEFT)
comp2.next_to(comp1, DOWN, buff=1)
comp3.next_to(comp1, RIGHT, buff=4)
arrow1 = Connection(comp2, comp1, "Do something")
arrow2 = Connection(comp1, comp3, "Do another thing")
scene.play(FadeIn(comp2))
scene.wait_until_beat(1)
scene.play(Create(arrow1))
scene.play(FadeIn(comp1))
scene.wait_until_beat(1)
scene.play(Create(arrow2))
scene.play(FadeIn(comp3))
scene.wait_until_beat(4)
scene.clear()
def add_to_scene(self,
scene,
initial_blank_seconds=0.,
end_blank_seconds=0.):
scene.wait(initial_blank_seconds)
scene.play(FadeIn(self.lol))
scene.wait()
scene.play(Write(self.commons), FadeIn(self.commons_left),
FadeIn(self.commons_right))
scene.wait(end_blank_seconds)
def construct(self):
# Atom level
adenine = Text(ADENINE_SMILES)
# Nucleotide level
dna = Text('ACTGAATATAGACTATA',
t2c={
'A': RED,
'C': BLUE,
'T': GREEN,
'G': PURPLE
})
# Amino acid level
aas = 'VQGGAAVQQEVLA'
aas = Text(aas, t2c=get_aa_hex_color_dict('skylign_protein'))
# Logo level
logo = LoLLogo()
# Animate... from nucleotide to LoL Commons
self.wait()
self.play(Write(adenine))
self.wait()
if self.add_vector_transform:
# FIXME: This is not quite pretty / useful at the moment
numbers = Text(
'[0.12 0.32 0.01 0.88 0.99 0.22 0.55 0.42 0.13 0.07]')
replacements = [adenine, dna, aas, numbers, logo.lol]
else:
replacements = [adenine, dna, aas, logo.lol]
for source, target in zip(replacements, replacements[1:]):
self.play(ReplacementTransform(source, target))
self.wait()
self.play(Write(logo.commons), FadeIn(logo.commons_left),
FadeIn(logo.commons_right))
self.wait()
for replacer in self.replacers:
logo.replace_left_right(self, replacer, run_time_s=0.8)
self.wait(0.3)
# Move logo to left lower corner
if self.logo_down:
mini_logo = logo.copy()
mini_logo.scale(0.5)
mini_logo.to_corner()
self.play(Transform(logo, mini_logo))
# And keep the scene
# self.play(Write(Text('Corporate info follows...')))
self.wait(5)
def test_scene_time():
with tempconfig({"dry_run": True}):
scene = Scene()
assert scene.renderer.time == 0
scene.wait(2)
assert scene.renderer.time == 2
scene.play(FadeIn(Circle()), run_time=0.5)
assert pytest.approx(scene.renderer.time) == 2.5
scene.renderer._original_skipping_status = True
scene.play(FadeIn(Square()), run_time=5) # this animation gets skipped.
assert pytest.approx(scene.renderer.time) == 7.5
def insert(self,
bt_node,
side_offset_multiply: float = 2.5,
down_offset_multiply: float = 2.5,
direction=LEFT,
start_from_root=True) -> BinaryTreeNode:
if self.is_full():
raise AttributeError("This node %s is completed" %
str(self.node_id))
bt_node.parent = self
if start_from_root:
parents = [self]
while parents[-1].parent is not None:
parents.append(parents[-1].parent)
self.scene.add(bt_node)
bt_node.next_to(parents[-1], buff=0, direction=UP)
parents.pop()
self.scene.play(FadeIn(bt_node.value),
run_time=bt_node.animation_duration)
while len(parents) > 0:
elem = parents[-1]
self.scene.play(bt_node.value.animate.next_to(elem, buff=0),
run_time=bt_node.animation_duration)
parents.pop()
else:
bt_node.next_to(self.value, buff=0)
self.scene.play(Write(bt_node.value),
run_time=bt_node.animation_duration)
if direction is LEFT and self.has_left():
direction = RIGHT
self.right = bt_node
else:
self.left = bt_node
child_location = self.value.get_center() + \
side_offset_multiply * self.radius * direction + \
down_offset_multiply * self.radius * DOWN
parent_child_vector = normalize(child_location -
self.value.get_center())
edge_start = (self.value.get_center() +
parent_child_vector * self.radius)
edge_end = child_location - parent_child_vector * self.radius
edge = Line(edge_start, edge_end)
self.scene.play(bt_node.value.animate.move_to(child_location),
FadeIn(edge),
run_time=bt_node.animation_duration)
return bt_node
def play_encode_decode(self, scene):
scene.play(FadeIn(self.text))
scene.wait(1)
scene.play(ReplacementTransform(self.text, self.masked_text))
scene.wait(1)
scene.play(FadeIn(self.encoder), FadeIn(self.decoder))
scene.wait(1)
scene.play(
ReplacementTransform(self.text.copy(), self.encoder),
ReplacementTransform(self.encoder.copy(), self.embedding),
ReplacementTransform(self.embedding.copy(), self.decoder),
ReplacementTransform(self.decoder.copy(), self.masked_decoded))
scene.wait(1)
scene.play(ReplacementTransform(self.masked_decoded, self.decoded))
scene.wait(1)
def construct(self):
comp1 = TextBox("Component A", shadow=False)
comp2 = TextBox("Component B", shadow=False)
comp3 = TextBox("Component C", shadow=False)
comp1.to_edge(LEFT)
comp2.next_to(comp1, DOWN, buff=1)
comp3.next_to(comp1, RIGHT, buff=4)
arrow1 = Connection(comp2, comp1, "Do something")
arrow2 = Connection(comp1, comp3, "Another thing")
self.play(FadeIn(comp2))
self.play(Create(arrow1))
self.play(FadeIn(comp1))
self.play(Create(arrow2))
self.play(FadeIn(comp3))
self.wait(5)
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 construct(self):
lib = Library()
comp1 = lib.text_box("Component A", shadow=False)
comp2 = lib.text_box("Component B", shadow=False)
comp3 = lib.text_box("Component C", shadow=False)
comp1.to_edge(LEFT)
comp2.next_to(comp1, DOWN, buff=1)
comp3.next_to(comp1, RIGHT, buff=4)
arrow1 = lib.connect(comp2, comp1, "Do something")
arrow2 = lib.connect(comp1, comp3, "Do another thing")
self.play(FadeIn(comp2))
self.play(ShowCreation(arrow1))
self.play(FadeIn(comp1))
self.play(ShowCreation(arrow2))
self.play(FadeIn(comp3))
self.wait(5)
def title_scene(scene):
scene.add_background(f"{example_dir}/resources/blackboard.jpg")
title = PangoText("How to use Code Video Generator", font="Helvetica")
scene.play(ShowCreation(title))
scene.play(
FadeIn(
PangoText("A code walkthrough",
font="Helvetica").scale(0.6).next_to(title,
direction=DOWN,
buff=LARGE_BUFF)))
scene.wait(3)
scene.clear()
def title_scene(scene):
scene.add_background(f"{example_dir}/resources/blackboard.jpg")
title = Text("How to use Code Video Generator", font="Helvetica")
scene.play(Create(title))
scene.play(
FadeIn(
Text(f"Code and examples from version {__version__}",
font="Helvetica").scale(0.6).next_to(title,
direction=DOWN,
buff=LARGE_BUFF)))
scene.wait(3)
scene.clear()
def highlight_lines(self,
code: Code,
start: int = 1,
end: int = -1,
caption: Optional[str] = None):
"""
Convenience method for animating a code object.
Args:
code: The code object, must be wrapped in `AutoScaled`
start: The start line number
end: The end line number, defaults to the end of the file
caption: The text to display with the highlight
"""
if end == -1:
end = len(code.line_numbers) + code.line_no_from
layout = ColumnLayout(columns=3)
actions = []
if caption and not self.caption:
self.play(
ApplyMethod(
code.fill_between_x,
layout.get_x(1, span=2, direction=LEFT),
layout.get_x(1, span=2, direction=RIGHT),
))
if self.caption:
actions.append(FadeOut(self.caption))
self.caption = None
if not caption:
self.play(ApplyMethod(code.full_size))
else:
callout = TextBox(caption,
text_attrs=dict(size=0.4, font=DEFAULT_FONT))
callout.align_to(code.line_numbers[start - code.line_no_from], UP)
callout.set_x(layout.get_x(3), LEFT)
actions += [HighlightLines(code, start, end), FadeIn(callout)]
self.caption = callout
self.play(*actions)
if not self.caption:
self.play(ApplyMethod(code.full_size))
else:
wait_time = len(self.caption.text) / (200 * 5 / 60)
self.wait_until_measure(wait_time, -1.5)
def demo_boxes(scene: CodeScene):
scene.add_background(f"{example_dir}/resources/blackboard.jpg")
lib = Library()
comp1 = lib.text_box("Component A", shadow=False)
comp2 = lib.text_box("Component B", shadow=False)
comp3 = lib.text_box("Component C", shadow=False)
comp1.to_edge(LEFT)
comp2.next_to(comp1, DOWN, buff=1)
comp3.next_to(comp1, RIGHT, buff=4)
arrow1 = lib.connect(comp2, comp1, "Do something")
arrow2 = lib.connect(comp1, comp3, "Do another thing")
scene.play(FadeIn(comp2))
scene.wait_until_beat(1)
scene.play(ShowCreation(arrow1))
scene.play(FadeIn(comp1))
scene.wait_until_beat(1)
scene.play(ShowCreation(arrow2))
scene.play(FadeIn(comp3))
scene.wait_until_beat(4)
scene.clear()
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)