Trajectory operators #16

henry-isaacson · 2024-05-03T20:25:59Z

Adds the following metrics:

0x00b1 · 2024-05-06T16:19:58Z

src/beignet/center_of_mass.py

+import torch
+
+
+def compute_center_of_mass(traj):


center_of_mass

0x00b1 · 2024-05-06T16:20:36Z

src/beignet/center_of_mass.py

+import torch
+
+
+def compute_center_of_mass(traj):


Add type annotations, e.g.,

center_of_mass(input: Tensor) -> Tensor.

0x00b1 · 2024-05-06T16:20:55Z

src/beignet/center_of_mass.py

+import torch
+
+
+def compute_center_of_mass(traj):


Rename traj to input to match PyTorch style.

0x00b1 · 2024-05-06T16:21:13Z

src/beignet/center_of_mass.py

+
+    Returns
+    -------
+    com : torch.Tensor, shape=(n_frames, 3)


Rename com to output to match PyTorch style.

0x00b1 · 2024-05-06T16:21:32Z

src/beignet/center_of_mass.py

+
+    Parameters
+    ----------
+    traj : Trajectory


Trajectory is not a type.

0x00b1 · 2024-05-06T16:21:56Z

src/beignet/center_of_mass.py

+
+
+def compute_center_of_mass(traj):
+    """Compute the center of mass for each frame.


Add the raw string prefix (r).

0x00b1 · 2024-05-06T16:22:14Z

src/beignet/center_of_mass.py

+    com = torch.empty((traj.n_frames, 3))
+
+    masses = torch.tensor([a.element.mass for a in traj.top.atoms])
+    masses /= masses.sum()


Do not use assignment ops.

0x00b1 · 2024-05-06T16:22:21Z

src/beignet/center_of_mass.py

+    com = torch.empty((traj.n_frames, 3))
+
+    masses = torch.tensor([a.element.mass for a in traj.top.atoms])
+    masses /= masses.sum()


Do not use methods.

0x00b1 · 2024-05-06T16:22:45Z

src/beignet/center_of_mass.py

+         Coordinates of the center of mass for each frame
+    """
+
+    com = torch.empty((traj.n_frames, 3))


This should be zeros. empty is random.

0x00b1 · 2024-05-06T16:23:08Z

src/beignet/center_of_mass.py

+
+    com = torch.empty((traj.n_frames, 3))
+
+    masses = torch.tensor([a.element.mass for a in traj.top.atoms])


What are a.element.mass and traj.top.atoms?

0x00b1 · 2024-05-06T16:23:31Z

src/beignet/center_of_mass.py

+    xyz = traj.xyz
+
+    for i, x in enumerate(xyz):
+        com[i, :] = torch.tensordot(masses, x.double().t(), dims=0)


tensordot?

0x00b1 · 2024-05-06T16:23:48Z

src/beignet/rmsd.py

+        rmsd_result[i] = torch.sqrt(
+            torch.sum((traj1[i] - traj2[i]) ** 2) / traj1.shape[1])
+
+    return rmsd_result


Add newline

0x00b1 · 2024-05-06T16:24:14Z

src/beignet/rmsd.py

@@ -0,0 +1,60 @@
+import torch
+from scipy.spatial.transform import Rotation as R


Use one of our rotation operators.

metrics

c019c94

0x00b1 changed the title ~~Metrics~~ Trajectory operators May 6, 2024

0x00b1 reviewed May 6, 2024

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src/beignet/center_of_mass.py Outdated

import torch

def compute_center_of_mass(traj):

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center_of_mass

0x00b1 reviewed May 6, 2024

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src/beignet/center_of_mass.py Outdated

Parameters

----------

traj : Trajectory

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Trajectory is not a type.

0x00b1 reviewed May 6, 2024

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Henry Isaacson added 2 commits May 23, 2024 10:54

com

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gyration tensor and rmsd

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Henry Isaacson added 2 commits May 23, 2024 13:55

bond angles

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bond angles

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Henry Isaacson added 2 commits May 23, 2024 17:52

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Trajectory operators #16

Trajectory operators #16

henry-isaacson commented May 3, 2024 •

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		def compute_center_of_mass(traj):
		"""Compute the center of mass for each frame.


		com = torch.empty((traj.n_frames, 3))

		masses = torch.tensor([a.element.mass for a in traj.top.atoms])

		@@ -0,0 +1,60 @@
		import torch
		from scipy.spatial.transform import Rotation as R

Trajectory operators #16

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Trajectory operators #16

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henry-isaacson commented May 3, 2024 • edited Loading

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henry-isaacson commented May 3, 2024 •

edited

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