biotite 0.41.1__cp312-cp312-macosx_10_16_x86_64.whl

biotite/structure/info/bonds.py

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+# 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.
+
+__name__ = "biotite.structure.info"
+__author__ = "Patrick Kunzmann"
+__all__ = ["bond_type", "bonds_in_residue"]
+
+from ..bonds import BondType
+from .ccd import get_from_ccd
+
+
+BOND_TYPES = {
+    ("SING", "N") : BondType.SINGLE,
+    ("DOUB", "N") : BondType.DOUBLE,
+    ("TRIP", "N") : BondType.TRIPLE,
+    ("QUAD", "N") : BondType.QUADRUPLE,
+    ("SING", "Y") : BondType.AROMATIC_SINGLE,
+    ("DOUB", "Y") : BondType.AROMATIC_DOUBLE,
+    ("TRIP", "Y") : BondType.AROMATIC_TRIPLE,
+}
+
+_intra_bonds = {}
+
+
+def bond_type(res_name, atom_name1, atom_name2):
+    """
+    Get the :class:`BondType` for two atoms of the same residue, based
+    on the PDB chemical components dictionary.
+
+    Parameters
+    ----------
+    res_name : str
+        The up to 3-letter name of the residue
+        `atom_name1` and `atom_name2` belong to.
+    atom_name1, atom_name2 : str
+        The names of the two atoms to get the bond order from.
+
+    Returns
+    -------
+    order : BondType or None
+        The :class:`BondType` of the bond between `atom_name1` and
+        `atom_name2`.
+        If the atoms form no bond, if any of the two atoms does not
+        exist in the context of the residue or if the residue is unknown
+        to the chemical components dictionary, `None` is returned.
+
+    Examples
+    --------
+
+    >>> print(bond_type("PHE", "CA", "CB"))
+    BondType.SINGLE
+    >>> print(bond_type("PHE", "CG", "CD1"))
+    BondType.AROMATIC_DOUBLE
+    >>> print(bond_type("PHE", "CA", "CG"))
+    None
+    >>> print(bond_type("PHE", "FOO", "BAR"))
+    None
+    """
+    bonds_for_residue = bonds_in_residue(res_name)
+    if bonds_for_residue is None:
+        return None
+    # Try both atom orders
+    bond_type_int = bonds_for_residue.get(
+        (atom_name1, atom_name2),
+        bonds_for_residue.get((atom_name2, atom_name1))
+    )
+    if bond_type_int is not None:
+        return BondType(bond_type_int)
+    else:
+        return None
+
+
+def bonds_in_residue(res_name):
+    """
+    Get a dictionary containing all atoms inside a given residue
+    that form a bond.
+
+    Parameters
+    ----------
+    res_name : str
+        The up to 3-letter name of the residue to get the bonds for.
+
+    Returns
+    -------
+    bonds : dict ((str, str) -> int)
+        A dictionary that maps tuples of two atom names to their
+        respective bond types (represented as integer).
+        Empty, if the residue is unknown to the
+        chemical components dictionary.
+
+    Warnings
+    --------
+    Treat the returned dictionary as immutable.
+    Modifying the dictionary may lead to unexpected behavior.
+    In other functionalities throughout *Biotite* that uses this
+    function.
+
+    Examples
+    --------
+    >>> bonds = bonds_in_residue("PHE")
+    >>> for atoms, bond_type_int in sorted(bonds.items()):
+    ...     atom1, atom2 = sorted(atoms)
+    ...     print(f"{atom1:3} + {atom2:3} -> {str(BondType(bond_type_int))}")
+    C   + O   -> BondType.DOUBLE
+    C   + OXT -> BondType.SINGLE
+    C   + CA  -> BondType.SINGLE
+    CA  + CB  -> BondType.SINGLE
+    CA  + HA  -> BondType.SINGLE
+    CB  + CG  -> BondType.SINGLE
+    CB  + HB2 -> BondType.SINGLE
+    CB  + HB3 -> BondType.SINGLE
+    CD1 + CE1 -> BondType.AROMATIC_SINGLE
+    CD1 + HD1 -> BondType.SINGLE
+    CD2 + CE2 -> BondType.AROMATIC_DOUBLE
+    CD2 + HD2 -> BondType.SINGLE
+    CE1 + CZ  -> BondType.AROMATIC_DOUBLE
+    CE1 + HE1 -> BondType.SINGLE
+    CE2 + CZ  -> BondType.AROMATIC_SINGLE
+    CE2 + HE2 -> BondType.SINGLE
+    CD1 + CG  -> BondType.AROMATIC_DOUBLE
+    CD2 + CG  -> BondType.AROMATIC_SINGLE
+    CZ  + HZ  -> BondType.SINGLE
+    CA  + N   -> BondType.SINGLE
+    H   + N   -> BondType.SINGLE
+    H2  + N   -> BondType.SINGLE
+    HXT + OXT -> BondType.SINGLE
+    """
+    global _intra_bonds
+    if res_name not in _intra_bonds:
+        chem_comp_bond_dict = get_from_ccd("chem_comp_bond", res_name)
+        if chem_comp_bond_dict is None:
+            _intra_bonds[res_name] = {}
+        else:
+            bonds_for_residue = {}
+            for atom1, atom2, order, aromatic_flag in zip(
+                chem_comp_bond_dict["atom_id_1"],
+                chem_comp_bond_dict["atom_id_2"],
+                chem_comp_bond_dict["value_order"],
+                chem_comp_bond_dict["pdbx_aromatic_flag"]
+            ):
+                bond_type = BOND_TYPES[order, aromatic_flag]
+                bonds_for_residue[atom1.item(), atom2.item()] = bond_type
+            _intra_bonds[res_name] = bonds_for_residue
+    return _intra_bonds[res_name]

biotite/structure/info/ccd/README.rst

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+These files are based on the
+`Chemical Component Dictionary <https://www.wwpdb.org/data/ccd>`_
+and were created using ``setup_ccd.py``.
+
+To keep the size of the repository small, the original commit should be
+rewritten, if the formats of the affected files are compatible with the
+original ones.
+The name of the commit is ``Add CCD dataset``.