Trajectories¶

CreateCoordGroup(atoms)¶

Parameters:

atoms (AtomHandleList) – List of atoms. All atoms must be from the same entity.

Return type:

CoordGroupHandle

Returns:

A coord group with zero frames

class CoordGroupHandle¶

A collection of coordinate frames, e.g. an MD trajectory. Create with CreateCoordGroup().

entity¶

The attached entity.

Type:

EntityHandle

atoms¶

The atoms of this coord group. The order of atoms is the same as the positions in the coord frames. All atoms are from the same entity.

Type:

AtomHandleList

AddFrames(frames)¶

Combine two trajectories by appending the frames of the second to the first :param frames: a valid coord group :type frames: CoordGroupHandle

Capture()¶

Record the atom positions of the entity attached to this coord group in a new coordinate frame. Note that the atom positions transformed by the entity transform will be stored. Only available for mutable coord groups.

See:

AtomHandle.pos

CaptureInto(frame_index)¶

Same as Capture(), but doesn’t create a new frame and stores the coordinates directly into frame with index frame_index. Only available for mutable coord groups.

Parameters:

frame_index (int) – index of the frame

CopyFrame(frame_index)¶

Copies the coordinates of frame with index frame_index to the attached entity.

Parameters:

frame_index (int) – index of the frame

Filter(view)¶

Returns a new trajectory containing only coordinates of the atoms in view. Useful to remove water and other solvent molecules from a trajectory to save memory.

Parameters:

view (EntityView) – a valid entity view

Return type:

CoordGroupHandle

GetAtomCount()¶

Returns the number of atoms in the coord group

Return type:

int

GetAtomList()¶

Returns the atoms of the coord group in the same order they appear in the coordinate frames.

Return type:

AtomHandleList

GetAtomPos(frame_index, atom)¶

Get position of atom in frame with index frame_index.

Parameters:

• frame_index (int) – frame index

• atom (AtomHandle) – A valid atom

Return type:

Vec3

GetEntity()¶

Returns the attached entity

Return type:

EntityHandle

GetFrameCount()¶

Returns the number of frames of this coord group

Return type:

int

IsValid()¶

Whether this coord group is valid

Return type:

bool

SetAtomPos(frame_index, atom, pos)¶

Set position of atom in frame with index frame_index to pos

Parameters:

• frame_index (int) – index of the frame

• atom (AtomHandle) – a valid atom

• pos (Vec3) – new position of the atom

SetFramePositions(frame_index, positions)¶

Set the frame positions of frame with index frame_index. Order and count of positions must match atoms.

Parameters:

• frame_index (int) – index of frame

• positions (Vec3List) – list of positions

class CoordFrame¶

A single frame of coordinates in a CoordGroupHandle.

GetAngle(atom1, atom2, atom3)¶

Parameters:

• atom1 (AtomHandle) – first atom

• atom2 (AtomHandle) – second (central) atom

• atom3 (AtomHandle) – third atom

Returns:

the angle in radians between the 3 atoms

Return type:

float

GetAtomPos(atom)¶

Returns the position of the atom in the coord frame

Parameters:

atom (AtomHandle) – A valid atom handle

Return type:

Vec3

GetCenterOfMassPos(view)¶

Parameters:

view (EntityView) – A valid entity view

Return type:

Vec3

GetDihedralAngle(atom1, atom2, atom3, atom4)¶

Get dihedral angle of the four atoms.

Parameters:

• atom1 (AtomHandle) – First atom. Must be valid

• atom2 (AtomHandle) – Second atom. Must be valid

• atom3 (AtomHandle) – Third atom. Must be valid

• atom3 – Fourth atom. Must be valid

Return type:

float

GetDistanceBetwAtoms(atom1, atom2)¶

Get distance in (Angstroem) between atom1 and atom2 in coord frame.

Parameters:

• atom1 (AtomHandle) – First atom. Must be valid

• atom2 (AtomHandle) – Second atom. Must be valid

Return type:

float

GetDistanceBetwCenterOfMass(view1, view2)¶

Get distance between center of mass of the first selection and the second.

Parameters:

• view1 (EntityView) – First view. Must be valid

• view2 (EntityView) – Second view. Must be valid

Return type:

float

GetRMSD(view1, view2)¶

Get RMSD between two views in the coord frame. The coordinates of the views are taken as is without superposition. The two views must have the same number of atoms. Atoms are matches as they appear in EntityView.atoms.

Parameters:

• view1 (EntityView) – First view. Must be valid

• view2 (EntityView) – Second view. Must be valid

Return type:

float