Support V3000 CTAB

src/biotite/structure/io/ctab.py

@@ -2,46 +2,20 @@
 # under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
 # information.
 
-"""
-Functions for parsing and writing an :class:`AtomArray` from/to
-*MDL* connection tables (Ctab).
-"""
-
 __name__ = "biotite.structure.io"
 __author__ = "Patrick Kunzmann"
 __all__ = ["read_structure_from_ctab", "write_structure_to_ctab"]
 
 import warnings
-import numpy as np
-from ..error import BadStructureError
-from ..atoms import AtomArray, AtomArrayStack
-from ..bonds import BondList, BondType
-
-BOND_TYPE_MAPPING = {
-    1: BondType.SINGLE,
-    2: BondType.DOUBLE,
-    3: BondType.TRIPLE,
-    6: BondType.SINGLE,
-    7: BondType.DOUBLE,
-    8: BondType.ANY,
-}
-BOND_TYPE_MAPPING_REV = {
-    BondType.SINGLE: 1,
-    BondType.DOUBLE: 2,
-    BondType.TRIPLE: 3,
-    BondType.AROMATIC_SINGLE: 1,
-    BondType.AROMATIC_DOUBLE: 2,
-    BondType.ANY: 8,
-}
-
-CHARGE_MAPPING = {0: 0, 1: 3, 2: 2, 3: 1, 5: -1, 6: -2, 7: -3}
-CHARGE_MAPPING_REV = {val: key for key, val in CHARGE_MAPPING.items()}
+from ..bonds import BondType
 
 
 def read_structure_from_ctab(ctab_lines):
     """
     Parse a *MDL* connection table (Ctab) to obtain an
-    :class:`AtomArray`. :footcite:`Dalby1992`
+    :class:`AtomArray`. :footcite:`Dalby1992`.
+
+    DEPRECATED: Moved to :mod:`biotite.structure.io.mol.ctab`.
 
     Parameters
     ----------
@@ -60,48 +34,18 @@ def read_structure_from_ctab(ctab_lines):
 
     .. footbibliography::
     """
-    n_atoms, n_bonds = _get_counts(ctab_lines[0])
-    atom_lines = ctab_lines[1 : 1 + n_atoms]
-    bond_lines = ctab_lines[1 + n_atoms : 1 + n_atoms + n_bonds]
-
-    atoms = AtomArray(n_atoms)
-    atoms.add_annotation("charge", int)
-    for i, line in enumerate(atom_lines):
-        atoms.coord[i, 0] = float(line[0:10])
-        atoms.coord[i, 1] = float(line[10:20])
-        atoms.coord[i, 2] = float(line[20:30])
-        atoms.element[i] = line[31:34].strip().upper()
-        charge = CHARGE_MAPPING.get(int(line[36:39]))
-        if charge is None:
-            warnings.warn(
-                f"Cannot handle MDL charge type {int(line[36 : 39])}, "
-                f"0 is used instead"
-            )
-            charge = 0
-        atoms.charge[i] = charge
-
-    bond_array = np.zeros((n_bonds, 3), dtype=np.uint32)
-    for i, line in enumerate(bond_lines):
-        bond_type = BOND_TYPE_MAPPING.get(int(line[6:9]))
-        if bond_type is None:
-            warnings.warn(
-                f"Cannot handle MDL bond type {int(line[6 : 9])}, "
-                f"BondType.ANY is used instead"
-            )
-            bond_type = BondType.ANY
-        bond_array[i, 0] = int(line[0:3]) - 1
-        bond_array[i, 1] = int(line[3:6]) - 1
-        bond_array[i, 2] = bond_type
-    atoms.bonds = BondList(n_atoms, bond_array)
-
-    return atoms
+    warnings.warn("Moved to biotite.structure.io.mol.ctab", DeprecationWarning)
+    from biotite.structure.io.mol.ctab import read_structure_from_ctab
+    return read_structure_from_ctab(ctab_lines)
 
 
 def write_structure_to_ctab(atoms, default_bond_type=BondType.ANY):
     """
     Convert an :class:`AtomArray` into a
     *MDL* connection table (Ctab). :footcite:`Dalby1992`
 
+    DEPRECATED: Moved to :mod:`biotite.structure.io.mol.ctab`.
+
     Parameters
     ----------
     atoms : AtomArray
@@ -123,44 +67,6 @@ def write_structure_to_ctab(atoms, default_bond_type=BondType.ANY):
 
     .. footbibliography::
     """
-    if isinstance(atoms, AtomArrayStack):
-        raise TypeError(
-            "An 'AtomArrayStack' was given, "
-            "but only a single model can be written"
-        )
-    if atoms.bonds is None:
-        raise BadStructureError("Input AtomArray has no associated BondList")
-
-    try:
-        charge = atoms.charge
-    except AttributeError:
-        charge = np.zeros(atoms.array_length(), dtype=int)
-
-    atom_lines = [
-        f"{atoms.coord[i,0]:>10.5f}"
-        f"{atoms.coord[i,1]:>10.5f}"
-        f"{atoms.coord[i,2]:>10.5f}"
-        f" {atoms.element[i]:>3}"
-        f"  {CHARGE_MAPPING_REV.get(charge[i], 0):>3d}" + f"{0:>3d}" * 10
-        for i in range(atoms.array_length())
-    ]
-
-    default_bond_value = BOND_TYPE_MAPPING_REV[default_bond_type]
-
-    bond_lines = [
-        f"{i+1:>3d}{j+1:>3d}"
-        f"{BOND_TYPE_MAPPING_REV.get(bond_type, default_bond_value):>3d}"
-        + f"{0:>3d}" * 4
-        for i, j, bond_type in atoms.bonds.as_array()
-    ]
-
-    counts_line = (
-        f"{len(atom_lines):>3d}{len(bond_lines):>3d}"
-        "  0     0  0  0  0  0  0  1 V2000"
-    )
-
-    return [counts_line] + atom_lines + bond_lines + ["M  END"]
-
-
-def _get_counts(counts_line):
-    return int(counts_line[0:3]), int(counts_line[3:6])
+    warnings.warn("Moved to biotite.structure.io.mol.ctab", DeprecationWarning)
+    from biotite.structure.io.mol.ctab import write_structure_to_ctab
+    return write_structure_to_ctab(atoms, default_bond_type)

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

@@ -32,7 +32,8 @@ def get_structure(mol_file):
     return mol_file.get_structure()
 
 
-def set_structure(mol_file, atoms, default_bond_type=BondType.ANY):
+def set_structure(mol_file, atoms, default_bond_type=BondType.ANY,
+                  version=None):
     """
     Set the :class:`AtomArray` for the MOL file.
 
@@ -46,6 +47,12 @@ def set_structure(mol_file, atoms, default_bond_type=BondType.ANY):
     array : AtomArray
         The array to be saved into this file.
         Must have an associated :class:`BondList`.
-
+    version : {"V2000", "V3000"}, optional
+        The version of the CTAB format.
+        ``"V2000"`` uses the *Atom* and *Bond* block, while ``"V3000"``
+        uses the *Properties* block.
+        By default, ``"V2000"`` is used unless the number of atoms or
+        bonds exceed the fixed size columns in the table, in which case
+        ``"V3000"`` is used.
     """
-    mol_file.set_structure(atoms, default_bond_type)
+    mol_file.set_structure(atoms, default_bond_type, version)