Fix unbounded coordinates in MOL/SDF files

src/biotite/structure/io/mol/ctab.py

@@ -19,6 +19,7 @@
 from biotite.structure.atoms import AtomArray, AtomArrayStack
 from biotite.structure.bonds import BondList, BondType
 from biotite.structure.error import BadStructureError
+from biotite.structure.io.util import number_of_integer_digits
 
 BOND_TYPE_MAPPING = {
     1: BondType.SINGLE,
@@ -297,6 +298,13 @@ def _write_structure_to_ctab_v2000(atoms, default_bond_type):
         "  0     0  0  0  0  0  0  1 V2000"
     )
 
+    for i, coord_name in enumerate(["x", "y", "z"]):
+        n_coord_digits = number_of_integer_digits(atoms.coord[:, i])
+        if n_coord_digits > 5:
+            raise BadStructureError(
+                f"5 pre-decimal columns for {coord_name}-coordinates are "
+                f"available, but array would require {n_coord_digits}"
+            )
     atom_lines = [
         f"{atoms.coord[i, 0]:>10.4f}"
         f"{atoms.coord[i, 1]:>10.4f}"
@@ -341,6 +349,13 @@ def _write_structure_to_ctab_v3000(atoms, default_bond_type):
 
     counts_line = f"COUNTS {atoms.array_length()} {atoms.bonds.get_bond_count()} 0 0 0"
 
+    for i, coord_name in enumerate(["x", "y", "z"]):
+        n_coord_digits = number_of_integer_digits(atoms.coord[:, i])
+        if n_coord_digits > 5:
+            raise BadStructureError(
+                f"5 pre-decimal columns for {coord_name}-coordinates are "
+                f"available, but array would require {n_coord_digits}"
+            )
     atom_lines = [
         f"{i + 1}"
         f" {_quote(atoms.element[i].capitalize())}"

src/biotite/structure/io/pdb/file.py

@@ -24,6 +24,7 @@
     encode_hybrid36,
     max_hybrid36_number,
 )
+from biotite.structure.io.util import number_of_integer_digits
 from biotite.structure.repair import infer_elements
 from biotite.structure.util import matrix_rotate
 
@@ -1248,43 +1249,31 @@ def _check_pdb_compatibility(array, hybrid36):
     if any([len(name) > 4 for name in array.atom_name]):
         raise BadStructureError("Some atom names exceed 4 characters")
     for i, coord_name in enumerate(["x", "y", "z"]):
-        n_coord_digits = _number_of_integer_digits(array.coord[..., i])
+        n_coord_digits = number_of_integer_digits(array.coord[..., i])
         if n_coord_digits > 4:
             raise BadStructureError(
                 f"4 pre-decimal columns for {coord_name}-coordinates are "
                 f"available, but array would require {n_coord_digits}"
             )
     if "b_factor" in annot_categories:
-        n_b_factor_digits = _number_of_integer_digits(array.b_factor)
+        n_b_factor_digits = number_of_integer_digits(array.b_factor)
         if n_b_factor_digits > 3:
             raise BadStructureError(
                 "3 pre-decimal columns for B-factor are available, "
                 f"but array would require {n_b_factor_digits}"
             )
     if "occupancy" in annot_categories:
-        n_occupancy_digits = _number_of_integer_digits(array.occupancy)
+        n_occupancy_digits = number_of_integer_digits(array.occupancy)
         if n_occupancy_digits > 3:
             raise BadStructureError(
                 "3 pre-decimal columns for occupancy are available, "
                 f"but array would require {n_occupancy_digits}"
             )
     if "charge" in annot_categories:
         # The sign can be omitted is it is put into the adjacent column
-        n_charge_digits = _number_of_integer_digits(np.abs(array.charge))
+        n_charge_digits = number_of_integer_digits(np.abs(array.charge))
         if n_charge_digits > 1:
             raise BadStructureError(
                 "1 column for charge is available, "
                 f"but array would require {n_charge_digits}"
             )
-
-
-def _number_of_integer_digits(values):
-    """
-    Get the maximum number of characters needed to represent the
-    pre-decimal positions of the given numeric values.
-    """
-    values = values.astype(int, copy=False)
-    n_digits = 0
-    n_digits = max(n_digits, len(str(np.min(values))))
-    n_digits = max(n_digits, len(str(np.max(values))))
-    return n_digits

src/biotite/structure/io/util.py

@@ -0,0 +1,38 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+Common functions used by a number of subpackages.
+"""
+
+__name__ = "biotite.structure.io"
+__author__ = "Patrick Kunzmann"
+__all__ = ["number_of_integer_digits"]
+
+import numpy as np
+
+
+def number_of_integer_digits(values):
+    """
+    Get the maximum number of characters needed to represent the
+    pre-decimal positions of the given numeric values.
+
+    Parameters
+    ----------
+    values : ndarray, dtype=float
+        The values to be checked.
+
+    Returns
+    -------
+    n_digits : int
+        The maximum number of characters needed to represent the
+        pre-decimal positions of the given numeric values.
+    """
+    if len(values) == 0:
+        return 0
+    values = values.astype(int, copy=False)
+    n_digits = 0
+    n_digits = max(n_digits, len(str(np.min(values))))
+    n_digits = max(n_digits, len(str(np.max(values))))
+    return n_digits