vermouth.processors.canonicalize_modifications module

Provides a Processor that identifies unexpected atoms such as PTMs and protonations, and canonicalizes their attributes based on modifications known in the forcefield.

class vermouth.processors.canonicalize_modifications.CanonicalizeModifications[source]

Bases: Processor

Identifies all modifications in a molecule and corrects their atom names.

See also

fix_ptm()

run_molecule(molecule)[source]
vermouth.processors.canonicalize_modifications.allowed_ptms(residue, res_ptms, known_ptms)[source]

Finds all PTMs in known_ptms which might be relevant for residue.

Parameters:
Yields:

tuple[networkx.Graph, networkx.isomorphism.GraphMatcher] – All graphs in known_ptms which are subgraphs of residue.

vermouth.processors.canonicalize_modifications.find_ptm_atoms(molecule)[source]

Finds all atoms in molecule that have the node attribute PTM_atom set to a value that evaluates to True. molecule will be traversed starting at these atoms until all marked atoms are visited such that they are identified per “branch”, and for every branch the anchor node is known. The anchor node is the node(s) which are not PTM atoms and share an edge with the traversed branch.

Parameters:

molecule (networkx.Graph)

Returns:

[({ptm atom indices}, {anchor indices}), ...]. Ptm atom indices are connected, and are connected to the rest of molecule via anchor indices.

Return type:

list[tuple[set, set]]

vermouth.processors.canonicalize_modifications.fix_ptm(molecule)[source]

Canonizes all PTM atoms in molecule, and labels the relevant residues with which PTMs were recognized. Modifies molecule such that atom names of PTM atoms are corrected, and the relevant residues have been labeled with which PTMs were recognized.

Parameters:

molecule (networkx.Graph) – Must not have missing atoms, and atom names must be correct. Atoms which could not be recognized must be labeled with the attribute PTM_atom=True.

vermouth.processors.canonicalize_modifications.identify_ptms(residue, residue_ptms, known_ptms)[source]

Identifies all PTMs in known_PTMs necessary to describe all PTM atoms in residue_ptms. Will take PTMs such that all PTM atoms in residue will be covered by applying PTMs from known_PTMs in order. Nodes in residue must have correct atomname attributes, and may not be missing. In addition, every PTM in must be anchored to a non-PTM atom.

Parameters:

  • residue (networkx.Graph) – The residues involved with these PTMs. Need not be connected.

  • residue_ptms (list[tuple[set, set]]) – As returned by find_PTM_atoms, but only those relevant for residue.

  • known_PTMs (collections.abc.Sequence[tuple[networkx.Graph, networkx.isomorphism.GraphMatcher]]) – The nodes in the graph must have the PTM_atom attribute (True or False). It should be True for atoms that are not part of the PTM itself, but describe where it is attached to the molecule. In addition, its nodes must have the atomname attribute, which will be used to recognize where the PTM is anchored, or to correct the atom names. Lastly, the nodes may have a replace attribute, which is a dictionary of {attribute_name: new_value} pairs. The special case here is if attribute_name is 'atomname' and new_value is None: in this case the node will be removed. Lastly, the graph (not its nodes) needs a ‘name’ attribute.

Returns:

All PTMs from known_PTMs needed to describe the PTM atoms in residue along with a dict of node correspondences. The order of known_PTMs is preserved.

Return type:

list[tuple[networkx.Graph, dict]]

Raises:

KeyError – Not all PTM atoms in residue can be covered with known_PTMs.

vermouth.processors.canonicalize_modifications.ptm_node_matcher(node1, node2)[source]

Returns True iff node1 and node2 should be considered equal. This means they are both either marked as PTM_atom, or not. If they both are PTM atoms, the elements need to match, and otherwise, the atom names must match.