refactor/modernize md_crds legacy bundle to mdanalysis new bundle

src/bundles/Makefile

@@ -34,7 +34,7 @@ REST_SUBDIRS = add_charge addh alignment_algs alignment_headers \
 	  interfaces items_inspection io label iupac \
 	  kvfinder lighting_gui list_info log looking_glass maestro \
 	  map map_data map_eraser map_filter map_fit map_series \
-	  markers mask match_maker mcopy mcp_server md_crds \
+	  markers mask match_maker mcopy mcp_server mdanalysis \
 	  medical_toolbar meeting minimize mlp model_series \
 	  mmcif mmtf model_archive model_panel modeller \
 	  mol2 mole morph mouse_modes movie mutation_scores nmrstar \

src/bundles/md_crds/src/read_lammps.py

@@ -24,6 +24,8 @@
 
 import traceback
 
+import numpy as np
+
 from chimerax.atomic import AtomicStructure
 from chimerax.io import open_input
 from .util import determine_element_from_mass, prep_coords
@@ -140,8 +142,6 @@ def read_dump(session, path, model):
     tokens = stream.readline().split()
     print("LAMMPS dump format: ", tokens[2:])
     index_id = tokens.index('id')-2
-    index_type = tokens.index('type')-2
-    index_mol = tokens.index('mol')-2
     index_x = tokens.index('x')-2
     index_y = tokens.index('y')-2
     index_z = tokens.index('z')-2
@@ -152,24 +152,27 @@ def read_dump(session, path, model):
 
     while not done:
 
-      coords_list.append([])
+        session.logger.status(f"LAMMPS dump: {i}")
+        tmp = np.empty((num_atoms, 4), dtype=np.float64)
 
-      for j in range(num_atoms):
-        # FIXME: handle dump format other than id type mol x y z
-        tokens = stream.readline().split()
-        id = int(tokens[index_id])
-        type = int(tokens[index_type])
-        mol = int(tokens[index_mol])
-        x,y,z = float(tokens[index_x]),float(tokens[index_y]),float(tokens[index_z])
-        coords_list[i].append([id,x,y,z])
-
-      coords_list[i].sort(key=lambda atom:atom[0])
-      i += 1
-      if stream.readline():
-        for j in range(8): stream.readline()
-      else:
-        done = True
-
-    coords = array(coords_list, dtype=float64)[:,:,1:]
+        for j in range(num_atoms):
+            tokens = stream.readline().split()
+            tmp[j, 0] = int(tokens[index_id])
+            tmp[j, 1] = float(tokens[index_x])
+            tmp[j, 2] = float(tokens[index_y])
+            tmp[j, 3] = float(tokens[index_z])
+
+        idx = np.argsort(tmp[:, 0])
+        tmp[:] = tmp[idx]
+        coords_list.append(tmp[:, 1:4])
+        i += 1
+
+        if stream.readline():
+            for _ in range(8):
+                stream.readline()
+        else:
+            done = True
+
+    coords = np.array(coords_list, dtype=np.float64)
     stream.close()
     return num_atoms, coords

src/bundles/mdanalysis/Makefile

@@ -0,0 +1 @@
+include ../Makefile.bundle

src/bundles/mdanalysis/cxtest.py

@@ -0,0 +1,17 @@
+from chimerax.core.commands import run
+run(session, "open test-data/chimera_test.pdb; open test-data/chimera_test.xtc structureModel #1")
+if session.models[0].num_coordsets != 21:
+	raise SystemExit("Expected chimera_test.xtc to produce 21 coordinate sets; actually produced %s"
+		% session.models[0].num_coordsets)
+run(session, "close; open test-data/start.pdb; open test-data/test.dcd structureModel #1")
+if session.models[0].num_coordsets != 2:
+	raise SystemExit("Expected chimera_test.xtc to produce 2 coordinate sets; actually produced %s"
+		% session.models[0].num_coordsets)
+run(session, "close; open test-data/gly.psf coords test-data/gly.xtc")
+if session.models[0].num_coordsets != 4:
+	raise SystemExit("Expected gly.xtc to produce 4 coordinate sets; actually produced %s"
+		% session.models[0].num_coordsets)
+run(session, "close; open test-data/gly.data coords test-data/gly.dump")
+if session.models[0].num_coordsets != 4:
+	raise SystemExit("Expected gly.dump to produce 4 coordinate sets; actually produced %s"
+		% session.models[0].num_coordsets)

src/bundles/mdanalysis/pyproject.toml

@@ -0,0 +1,174 @@
+[build-system]
+requires = ["ChimeraX-BundleBuilder>=1.4.0", "ChimeraX-Core ~=1.0"]
+build-backend = "chimerax.bundle_builder.cx_pep517"
+
+[project]
+name = "ChimeraX-MDAnalysis"
+version = "1.0.0"
+license = { text = "Free for non-commercial use" }
+authors = [{ name = "UCSF RBVI", email = "[email protected]" }]
+description = "Molecular dynamics support using MDAnalysis"
+dependencies = [
+  "ChimeraX-Core ~=1.0",
+  "ChimeraX-Atomic ~=1.22",
+  "ChimeraX-DataFormats ~=1.0",
+  "ChimeraX-OpenCommand ~=1.0",
+  "ChimeraX-SaveCommand ~=1.0",
+  "ChimeraX-UI ~=1.47",
+  "MDAnalysis>=2.0.0",
+]
+dynamic = ["classifiers", "requires-python"]
+
+[project.readme]
+content-type = "text"
+text = """This bundle provides parsers for various molecular dynamics file formats using MDAnalysis."""
+
+[project.urls]
+Home = "https://www.rbvi.ucsf.edu/chimerax/"
+
+[tool.chimerax]
+min-session-version = 1
+max-session-version = 1
+module-name-override = "mdanalysis"
+categories = ["Molecular Dynamics"]
+classifiers = ["Development Status :: 4 - Beta"]
+
+[tool.chimerax.manager."MD plotting"]
+autostart = false
+
+# --- Open Commands ---
+[[tool.chimerax.provider."open command"]]
+name = "psf"
+want-path = true
+
+[[tool.chimerax.provider."open command"]]
+name = "gro"
+want-path = true
+
+[[tool.chimerax.provider."open command"]]
+name = "data"
+want-path = true
+
+[[tool.chimerax.provider."open command"]]
+name = "dcd"
+want-path = true
+
+[[tool.chimerax.provider."open command"]]
+name = "xtc"
+want-path = true
+
+[[tool.chimerax.provider."open command"]]
+name = "trr"
+want-path = true
+
+[[tool.chimerax.provider."open command"]]
+name = "amber"
+want-path = true
+
+[[tool.chimerax.provider."open command"]]
+name = "dump"
+want-path = true
+
+# --- Data Formats ---
+[[tool.chimerax.provider."data formats"]]
+name = "Protein structure file"
+category = "Molecular structure"
+nicknames = "psf"
+suffixes = ".psf"
+synopsis = "PSF topology"
+
+[[tool.chimerax.provider."data formats"]]
+name = "Gromacs structure"
+category = "Molecular structure"
+nicknames = "gro"
+suffixes = ".gro"
+synopsis = "Gromos87 structure"
+
+[[tool.chimerax.provider."data formats"]]
+name = "LAMMPS data"
+category = "Molecular structure"
+nicknames = "data"
+suffixes = ".data"
+default-for = ".data"
+synopsis = "LAMMPS data format"
+
+[[tool.chimerax.provider."data formats"]]
+name = "DCD trajectory"
+category = "Molecular trajectory"
+nicknames = "dcd"
+suffixes = ".dcd"
+synopsis = "DCD trajectory"
+
+[[tool.chimerax.provider."data formats"]]
+name = "Gromacs XTC"
+category = "Molecular trajectory"
+nicknames = "xtc"
+suffixes = ".xtc"
+synopsis = "Gromacs compressed trajectory"
+
+[[tool.chimerax.provider."data formats"]]
+name = "Gromacs TRR"
+category = "Molecular trajectory"
+nicknames = "trr"
+suffixes = ".trr"
+synopsis = "Gromacs full-precision trajectory"
+
+[[tool.chimerax.provider."data formats"]]
+name = "Amber NetCDF"
+category = "Molecular trajectory"
+nicknames = "amber"
+suffixes = ".nc"
+synopsis = "Amber NetCDF trajectory"
+
+[[tool.chimerax.provider."data formats"]]
+name = "LAMMPS dump"
+category = "Molecular trajectory"
+nicknames = "dump"
+suffixes = ".dump"
+default-for = ".dump"
+synopsis = "LAMMPS dump trajectory"
+
+# --- Save Commands (Legacy support maintained) ---
+[[tool.chimerax.provider."save command"]]
+name = "dcd"
+
+# --- MD Plotting ---
+[[tool.chimerax.provider."MD plotting"]]
+name = "distance"
+num-atoms = "2"
+text-format = "distance"
+
+[[tool.chimerax.provider."MD plotting"]]
+name = "angle"
+num-atoms = "3"
+text-format = "angle"
+min-val = "0"
+max-val = "180"
+
+[[tool.chimerax.provider."MD plotting"]]
+name = "torsion"
+num-atoms = "4"
+text-format = "angle"
+min-val = "-180"
+max-val = "180"
+
+[[tool.chimerax.provider."MD plotting"]]
+name = "surface"
+ui-name = "SASA"
+num-atoms = "0"
+text-format = "%.1f"
+exclude = "solution=true,ligands=true,metals=alkali"
+
+[[tool.chimerax.provider."MD plotting"]]
+name = "rmsd"
+ui-name = "RMSD"
+num-atoms = "0"
+text-format = "%.2f"
+need-ref-frame = true
+exclude = "solution=true,hydrogens=true,ligands=false,metals=alkali"
+
+[[tool.chimerax.provider."MD plotting"]]
+name = "hbonds"
+ui-name = "H-Bonds"
+num-atoms = "0"
+text-format = "%d"