From f0cb9eb710f87842e4bf0d6e756a49d6cccd8a25 Mon Sep 17 00:00:00 2001 From: Rocco Meli Date: Tue, 11 Aug 2020 19:05:14 +0200 Subject: [PATCH 1/2] fix documentation in rotateby --- package/MDAnalysis/transformations/rotate.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package/MDAnalysis/transformations/rotate.py b/package/MDAnalysis/transformations/rotate.py index 4e27f81012d..8e3d9cfa2c0 100644 --- a/package/MDAnalysis/transformations/rotate.py +++ b/package/MDAnalysis/transformations/rotate.py @@ -55,9 +55,9 @@ def rotateby(angle, direction, point=None, ag=None, weights=None, wrap=False): ts = u.trajectory.ts angle = 90 - ag = u.atoms() + ag = u.atoms d = [0,0,1] - rotated = MDAnalysis.transformations.rotate(angle, direction=d, ag=ag)(ts) + rotated = MDAnalysis.transformations.rotate.rotateby(angle, direction=d, ag=ag)(ts) e.g. rotate the coordinates by a custom axis: @@ -67,7 +67,7 @@ def rotateby(angle, direction, point=None, ag=None, weights=None, wrap=False): angle = 90 p = [1,2,3] d = [0,0,1] - rotated = MDAnalysis.transformations.rotate(angle, direction=d, point=point)(ts) + rotated = MDAnalysis.transformations.rotate.rotateby(angle, direction=d, point=point)(ts) Parameters ---------- From 6f6efb6b52333b6b04f5c144c8c0d8c088d38d0a Mon Sep 17 00:00:00 2001 From: Rocco Meli Date: Tue, 11 Aug 2020 21:50:23 +0200 Subject: [PATCH 2/2] fix documentation of rotateby --- package/MDAnalysis/transformations/rotate.py | 38 +++++++++++--------- 1 file changed, 21 insertions(+), 17 deletions(-) diff --git a/package/MDAnalysis/transformations/rotate.py b/package/MDAnalysis/transformations/rotate.py index 8e3d9cfa2c0..57871292ff3 100644 --- a/package/MDAnalysis/transformations/rotate.py +++ b/package/MDAnalysis/transformations/rotate.py @@ -40,35 +40,39 @@ def rotateby(angle, direction, point=None, ag=None, weights=None, wrap=False): ''' - Rotates the trajectory by a given angle on a given axis. The axis is defined by + Rotates the trajectory by a given angle on a given axis. The axis is defined by the user, combining the direction vector and a point. This point can be the center - of geometry or the center of mass of a user defined AtomGroup, or an array defining + of geometry or the center of mass of a user defined AtomGroup, or an array defining custom coordinates. - + Examples -------- - - e.g. rotate the coordinates by 90 degrees on a axis formed by the [0,0,1] vector and + + e.g. rotate the coordinates by 90 degrees on a axis formed by the [0,0,1] vector and the center of geometry of a given AtomGroup: - + .. code-block:: python - + + from MDAnalysis import transformations + ts = u.trajectory.ts angle = 90 ag = u.atoms d = [0,0,1] - rotated = MDAnalysis.transformations.rotate.rotateby(angle, direction=d, ag=ag)(ts) - + rotated = transformations.rotate.rotateby(angle, direction=d, ag=ag)(ts) + e.g. rotate the coordinates by a custom axis: - + .. code-block:: python + from MDAnalysis import transformations + ts = u.trajectory.ts angle = 90 p = [1,2,3] d = [0,0,1] - rotated = MDAnalysis.transformations.rotate.rotateby(angle, direction=d, point=point)(ts) - + rotated = transformations.rotate.rotateby(angle, direction=d, point=p)(ts) + Parameters ---------- angle: float @@ -97,7 +101,7 @@ def rotateby(angle, direction, point=None, ag=None, weights=None, wrap=False): Returns ------- MDAnalysis.coordinates.base.Timestep - + Warning ------- Wrapping/unwrapping the trajectory or performing PBC corrections may not be possible @@ -132,7 +136,7 @@ def rotateby(angle, direction, point=None, ag=None, weights=None, wrap=False): center_method = partial(atoms.center, weights, pbc=wrap) else: raise ValueError('A point or an AtomGroup must be specified') - + def wrapped(ts): if point is None: position = center_method() @@ -143,8 +147,8 @@ def wrapped(ts): translation = matrix[:3, 3] ts.positions= np.dot(ts.positions, rotation) ts.positions += translation - + return ts - + return wrapped - +