move delta-ml beaker files to this git repo

molecules-delta-ml/copy_from_docker

+container=ae5fbce12ee3
+docker cp $container:/home/beaker/notebooks/ex1-molecules/molkrr/ml_chemical_space.bkr python-modules/molkrr/

molecules-delta-ml/copy_to_docker

+container=ae5fbce12ee3
+docker cp python-modules/molkrr $container:/home/beaker/notebooks/ex1-molecules/
+docker exec $container chown -R beaker.beaker /home/beaker/notebooks/ex1-molecules/molkrr
+

molecules-delta-ml/python-modules/molkrr/readxyz.py

+# ----- Experimental code taken from ASE -----
+from ase import Atoms
+
+
+class XYZError(IOError):
+    pass
+
+
+def iterchunks(fd):
+    """Yield unprocessed chunks (header, lines) for each xyz image."""
+    while True:
+        line = next(fd).strip()  # Raises StopIteration on empty file
+        try:
+            natoms = int(line)
+        except ValueError:
+            raise XYZError('Expected integer, found "{0}"'.format(line))
+        try:
+            header = next(fd)
+            lines = [next(fd) for _ in range(natoms)]
+        except StopIteration:
+            raise XYZError('Incomplete XYZ chunk')
+        yield header, lines
+
+
+def chunk2atoms(header, lines):
+    """Convert unprocessed chunk into Atoms."""
+    symbols = []
+    positions = []
+
+    for line in lines:
+        tokens = line.split()
+        symbols.append(tokens[0])
+        positions.append([float(x) for x in tokens[1:]])
+
+    if len(symbols) > 0 and symbols[0].isdigit():
+        numbers = symbols
+        symbols = None
+    else:
+        numbers = None
+    return Atoms(symbols=symbols, numbers=numbers, positions=positions)
+
+
+def iread_xyz(fd):
+    """Yield all images from file."""
+    for header, lines in iterchunks(fd):
+        yield chunk2atoms(header, lines)