Name	Description
Animateclass	Build a fluent protein or camera animation through the .animate property.
Animationclass	Base class for animations evaluated by the scene timeline.
AnimationGroupclass	Compose actions with independent durations and start offsets in seconds. Animation.during(seconds, delay=...) is shorthand.
Annotationclass	Base class for text and lines drawn over the image.
AnnotationAnimateclass	Build position, offset, and opacity animations for annotations.
BackboneMorphclass	Move matched backbone residues in order and fade unmatched residues.
BaseStyleclass	Crossfade nucleotide bases between slabs, rings, sticks, ladder, or none.
Calloutclass	Connect an image label to a selected region with a line.
Cameraclass	A perspective camera with orbit, zoom, framing, depth cueing, and EEVEE lens focus.
charges_from_pqr()function	Match PQR charges to the protein’s atom identities.
ColorByPropertyclass	Animate property-based residue colors and optional cartoon thickness.
Colorizeclass	Animate a tint on a whole protein or a selected region.
ColorLegendclass	A horizontal color bar with numeric limits and measurement units.
ColorScaleclass	A fixed linear scale mapping scalar values to RGB colors.
Concealclass	Close the open cutaway.
ContactMapclass	A live binary backbone contact map with linked residue markers.
ContactMatchclass	Store an ordered residue correspondence and its search report.
Deformclass	Interpolate coordinates toward the result of a user-supplied function.
DensityMapclass	An immutable scalar grid with physical coordinates and optional periodic boundaries.
DensitySliceclass	A trilinearly sampled map plane with a fixed color scale and animated position.
DensitySurfaceclass	A cached contour mesh with animated level, opacity, and transforms.
Distanceclass	Draw a distance line between two atom or residue selections.
domain_motion()function	How a domain turns and shifts between two structures, after superposing on a fixed part.
DomainMotionclass	Rigid motion of a domain between two structures, as a screw in the source's model frame.
ease_in_out_sine()function	Apply sinusoidal easing that starts and ends slowly.
EEVEEclass	Keep one Blender process alive while rendering multiple frames.
EEVEEOptionsclass	Configure the optional EEVEE renderer. Blender 4.5+ is installed separately.
Electrostaticsclass	Compute screened Coulomb pair energies and electrostatic potential.
FadeInclass	Fade a protein or annotation from transparent to its current opacity.
FadeOutclass	Fade a protein or annotation to zero opacity.
find_blender()function	Locate the Blender executable and explain how to install it if absent.
Focusclass	Animate the camera to a protein or selected region.
FocusPullclass	Animate lens focus to a protein, residue selection or world point.
Heatmapclass	A matrix of colored cells with a color bar; rows and columns can be residues.
HideAtomsclass	Fade ball-and-stick detail atoms back into the cartoon, ribbon, or surface.
HideSideChainsclass	Fade amino acid side chains back into the cartoon.
HydrogenBondsclass	Detect hydrogen bonds from donor–acceptor distance and hydrogen geometry.
Interactionclass	An immutable record for one detected molecular interaction.
InteractionHighlightclass	Draw selected hydrogen-bond or electrostatic contact lines.
linear()function	Return progress unchanged.
match_backbones()function	Find the largest ordered residue match under a contact-error limit.
match_structures()function	Pair chains, residues, ligands, and atoms of two structures of the same protein.
MolecularStyleclass	Reusable representation name and keyword options for Protein.set_style() and Representation().
Morphclass	Interpolate matching atoms to a protein or coordinate array.
NucleicAcidclass	A DNA/RNA structure with base colors, nucleotide cartoons, surfaces and the Protein animation API.
PlayTrajectoryclass	Interpolate through coordinate states in a trajectory.
Proteinclass	A molecular structure with fixed atom identities, coordinates, and display settings.
ProteinSceneclass	Define a protein animation as a sequence of play() and wait() calls.
RamachandranPlotclass	A live φ/ψ plot: one point per residue over favored and allowed regions.
Regionclass	A selection of atoms that follows its parent protein’s coordinates.
RegionAnimateclass	Create styling animations through region.animate.
RegionHighlightclass	Draw a sphere, wire box, or atom halos around a region.
Rendererclass	Render protein and annotation objects with a reusable GPU renderer.
Representationclass	Transition between cartoon, ribbon, ball-and-stick and surface, with optional nucleotide base styles.
ResidueLabelclass	Label one amino acid at its projected Cα position.
ResidueLabelsclass	Label several residues and adjust their positions to reduce overlap.
ResidueValuesclass	One measurement per topology residue, with identity checks and optional units.
Revealclass	Open a view-dependent cutaway onto a region: geometry in front of it fades inside a window that follows the camera.
Rotateclass	Rotate a protein around its molecular centroid.
RotateTorsionsclass	Turn torsions by amounts in degrees, for example a full side-chain rotation.
Scenealias	Alias for ProteinScene.
SecondaryStructureclass	Blend the cartoon to new helix, strand, and coil states.
SequenceTrackclass	A sequence with a thin strip of current structure colors or a fixed numerical property.
SetOpacityclass	Animate transparency on a whole protein or a selected region.
SetTorsionsclass	Animate backbone and side-chain torsions to new values in degrees; atoms rotate about bonds, so bond lengths and angles stay fixed.
ShowAtomsclass	Grow atoms in as ball-and-stick detail over a cartoon, ribbon, or surface.
ShowSideChainsclass	Grow amino acid side chains from the cartoon as ball-and-stick detail.
smooth()function	Apply quintic easing with zero endpoint speed and acceleration.
StructureMatchclass	Atom correspondence between two structures, with the residue and chain pairs behind it and the rigid core they share.
StructureMorphclass	Morph between two experimental structures of the same protein, moving residues along screw paths.
StudioLookclass	Studio lighting, material, and global effects presets with explicit per-setting overrides.
Textclass	Draw shaped vector text over the protein image.
TextGroupclass	Vertically arrange Text objects and animate a caption as one object. Child positions are ignored.
TextStyleclass	Reusable typography for Text(style=...). Sizes use 1080p design pixels.
there_and_back()function	Move smoothly from 0 to 1 and back to 0 over one clip.
Threadclass	Thread the actual cartoon or atoms and bonds into view with eased travel over the full clip.
TimeSeriesPlotclass	A vector trace with a cursor linked to scene time or a protein trajectory.
TorsionAnglesclass	φ, ψ, ω, and χ1–χ5 in degrees for a set of residues; NaN where a residue lacks a torsion.
TorsionMarkerclass	A live protractor for one torsion: its bond, an arc around the bond, and the current angle.
Trajectoryclass	A random-access sequence of coordinate frames in ångströms.
Unthreadclass	Reverse Thread, pulling actual molecular geometry out of view along curved paths.
Unwriteclass	Erase glyph fills and then their outlines.
Writeclass	Draw text outlines and then fill the glyphs.