entities.trajectory.annotations

entities.trajectory.annotations

Classes

Name	Description
AtomInfo	Atom Info Trajectory Annotation
COM	Center-of-Mass Trajectory Annotation
COMDistance	Distance between Center-of-Masses Trajectory Annotation
CanonicalDihedrals	Canonical Dihedrals of a given residue
Label2D	Common Label2D Annotation for all entities
Label3D	Common Label3D Annotation for all entities
TrajectoryAnnotation	Base class for a Trajectory Annotation
TrajectoryAnnotationManager	Annotation Manager for Trajectory Entity
UniverseInfo	Universe Info Trajectory Annotation

AtomInfo

entities.trajectory.annotations.AtomInfo(self, trajectory)

Atom Info Trajectory Annotation

This annotation shows the atom info of a selection. This annotation can be added using the ‘add_atom_info’ method of the trajectory’s annotation manager: trajectory.annotations.add_atom_info(…)

Attributes

Name	Type	Description
selection	str	MDAnalysis selection phrase to select the atom group
show_resid	bool	Whether or not to show the res ID along with the atom name
show_segid	bool	Whether or not to show the seg ID along with the atom name

COM

entities.trajectory.annotations.COM(self, trajectory)

Center-of-Mass Trajectory Annotation

This annotation shows the center-of-mass of a selection. This annotation can be added using the ‘add_com’ method of the trajectory’s annotation manager: trajectory.annotations.add_com(…)

Attributes

Name	Type	Description
selection	str	MDAnalysis selection phrase to select the atom group
text	str	Text do display at the center-of-mass

COMDistance

entities.trajectory.annotations.COMDistance(self, trajectory)

Distance between Center-of-Masses Trajectory Annotation

This annotation shows the distance between center-of-masses of two selections. This annotation can be added using the ‘add_com_distance’ method of the trajectory’s annotation manager: trajectory.annotations.add_com_distance(…)

Attributes

Name	Type	Description
selection1	str	MDAnalysis selection phrase to select the first atom group
selection2	str	MDAnalysis selection phrase to select the second atom group
text1	str	Text do display at the first center-of-mass
text2	str	Text do display at the second center-of-mass

CanonicalDihedrals

entities.trajectory.annotations.CanonicalDihedrals(self, trajectory)

Canonical Dihedrals of a given residue

Attributes

Name	Type	Description
resid	int	The residue number
show_atom_names	bool	Whether or not to show the individual atom names in the residue
show_direction	bool	Whether or not to show the arc indicating the angle direction

Label2D

entities.trajectory.annotations.Label2D()

Common Label2D Annotation for all entities

Label3D

entities.trajectory.annotations.Label3D()

Common Label3D Annotation for all entities

TrajectoryAnnotation

entities.trajectory.annotations.TrajectoryAnnotation(self, trajectory)

Base class for a Trajectory Annotation

All trajectory annotations should derive from this base class and implement the ‘draw’ method. All derived classes will have access to the trajectory instance (self.trajectory) and all the annotation inputs and common params via self.interface.

An optional ‘defaults’ method can be provided to set default values to the annotation.

TrajectoryAnnotationManager

entities.trajectory.annotations.TrajectoryAnnotationManager(self, entity)

Annotation Manager for Trajectory Entity

UniverseInfo

entities.trajectory.annotations.UniverseInfo(self, trajectory)

Universe Info Trajectory Annotation

Attributes

Name	Type	Description
location	tuple[float, float]	Normalized coordinates (0.0 - 1.0) of the postion in viewport / render
show_frame	bool	Whether or not to show the frame number
show_topology	bool	Whether or not to show the topology filename
show_trajectory	bool	Whether or not to show the trajectory filename
show_atoms	bool	Whether or not to show the number of atoms
custom_text	str	Any custom text to add at the end of the annotation