New command: Load trajectory

Author: dwhswenson

paths_cli/commands/load_trajectory.py

@@ -0,0 +1,51 @@
+import click
+
+import paths_cli.utils
+from paths_cli.parameters import APPEND_FILE, ENGINE, MULTI_TAG
+from paths_cli import OPSCommandPlugin
+
+
+@click.command(
+    "load-trajectory",
+    short_help="Load an external trajectory file",
+)
+@click.argument('traj_file')
+@click.option(
+    '--top',
+    help=(
+        "Topology information (typically PDB). Only for required "
+        "formats."
+    ),
+    default=None,
+)
+@APPEND_FILE.clicked(required=True)
+@MULTI_TAG.clicked()
+def load_trajectory(traj_file, top, append, tag):
+    """Load a trajectory from a file.
+
+    This uses MDTraj under the hood, and can load any file format that
+    MDTraj can. NB: This stores in a format based on OpenMM snapshots.
+    Trajectories loaded this way will work with engines compatible with
+    that input (e.g., GROMACS).
+    """
+    import mdtraj as md
+    from openpathsampling.engines.openmm.tools import ops_load_trajectory
+    traj = ops_load_trajectory(traj_file, top=top)
+    storage = append.get()
+    storage.save(traj)
+    for tag_name in tag:
+        storage.tags[tag_name] = traj
+
+
+    # tests:
+    # * check that we load PDB
+    # * check that if we load PDB with top as well works
+    # * check that we can load trr / xtc files (only with top)
+    # * maybe check for error if top doesn't match traj file? (atom numbers)
+
+PLUGIN = OPSCommandPlugin(
+    command=load_trajectory,
+    section="Miscellaneous",
+    requires_ops=(1, 6),
+    requires_cli=(0, 4),
+)