Implementing gemmi-based mmcif reader (with easy extension to PDB/PDBx and mmJSON)

.github/actions/setup-deps/action.yaml

@@ -23,6 +23,8 @@ inputs:
     default: 'cython'
   fasteners:
     default: 'fasteners'
+  gemmi:
+    default: 'gemmi'
   griddataformats:
     default: 'griddataformats'
   gsd:
@@ -130,6 +132,7 @@ runs:
           ${{ inputs.dask }}
           ${{ inputs.distopia }}
           ${{ inputs.gsd }}
+          ${{ inputs.gemmi }}
           ${{ inputs.h5py }}
           ${{ inputs.hole2 }}
           ${{ inputs.joblib }}

package/MDAnalysis/coordinates/MMCIF.py

@@ -0,0 +1,85 @@
+import logging
+import warnings
+
+import numpy as np
+
+from . import base
+
+try:
+    import gemmi
+
+    HAS_GEMMI = True
+except ImportError:
+    HAS_GEMMI = False
+
+logger = logging.getLogger("MDAnalysis.coordinates.MMCIF")
+
+
+def get_coordinates(model: "gemmi.Model") -> np.ndarray:
+    """Get coordinates of all atoms in the `gemmi.Model` object.
+
+    Parameters
+    ----------
+    model
+        input `gemmi.Model`, e.g. `gemmi.read_structure('file.cif')[0]`
+
+    Returns
+    -------
+        np.ndarray, shape [n, 3], where `n` is the number of atoms in the structure.
+    """
+    return np.array(
+        [[*at.pos.tolist()] for chain in model for res in chain for at in res]
+    )
+
+
+class MMCIFReader(base.SingleFrameReaderBase):
+    """Reads from an MMCIF file using ``gemmi`` library as a backend.
+
+    Notes
+    -----
+
+    If the structure represents an ensemble, only the first structure in the ensemble
+    is read here (and a warning is thrown). Also, if the structure has a placeholder "CRYST1"
+    record (1, 1, 1, 90, 90, 90), it's set to ``None`` instead.
+
+    .. versionadded:: 2.8.0
+    """
+
+    format = ["cif", "cif.gz", "mmcif"]
+    units = {"time": None, "length": "Angstrom"}
+
+    def _read_first_frame(self):
+        structure = gemmi.read_structure(self.filename)
+        cell_dims = np.array(
+            [
+                getattr(structure.cell, name)
+                for name in ("a", "b", "c", "alpha", "beta", "gamma")
+            ]
+        )
+        if len(structure) > 1:
+            warnings.warn(
+                f"File {self.filename} has {len(structure)} models, but only the first one will be read"
+            )
+        if len(structure) > 1:
+            warnings.warn(
+                "MMCIF model {self.filename} contains {len(model)=} different models, "
+                "but only the first one will be used to assign the topology"
+            )  # TODO: if the structures represent timestamps, can parse them with :func:`get_coordinates`.
+
+        model = structure[0]
+        coords = get_coordinates(model)
+        self.n_atoms = len(coords)
+        self.ts = self._Timestep.from_coordinates(coords, **self._ts_kwargs)
+        if np.allclose(cell_dims, np.array([1.0, 1.0, 1.0, 90.0, 90.0, 90.0])):
+            warnings.warn(
+                "1 A^3 CRYST1 record,"
+                " this is usually a placeholder."
+                " Unit cell dimensions will be set to None."
+            )
+            self.ts.dimensions = None
+        else:
+            self.ts.dimensions = cell_dims
+        self.ts.frame = 0
+
+    def close(self):
+        pass

package/MDAnalysis/coordinates/__init__.py

@@ -791,3 +791,4 @@ class can choose an appropriate reader automatically.
 from . import NAMDBIN
 from . import FHIAIMS
 from . import TNG
+from . import MMCIF