mdciao.utils.bonds

Simple operations with bonds between the residues of an mdtraj.Topology

Functions

bonded_neighborlist_from_top(top[, n, ...])

Bonded neighbors of all the residues in the topology file.

connected_sets(mat)

Return the connected components/sets of an adjacency matrix

neighborlists_from_adjacency_matrix(mat, n)

Return neighborlists from an adjacency matrix.

top2residue_bond_matrix(top[, ...])

Return a symmetric residue-residue bond matrix from a Topology.

top2residue_bond_matrix_naive(top[, ...])

Creates a naive (=linear) residue-residue bond-matrix, where a bond is assumed between the n-th and the n+1-th residue

top2residuebonds(top, ...)

mdciao.utils.bonds.bonded_neighborlist_from_top(top, n=1, residue_indices=None, verbose=False)

Bonded neighbors of all the residues in the topology file.

Parameters:

  • top (Topology)

  • n (int, default is 1) – Number of bonded neighbors considered, i.e. A-B-C has only [B] as neighbors if n = 1, but [B,C] if n = 2

  • residue_indices (iterable, default is None) – Compute the neighborlists only for these indices. None computes neighbors all indices. The returned neighborlist will have empty-lists for items not present in residue_indices.

Returns:

neighbor_list – List of len top.n_residues. The i-th list contains the n -bonded neighbors of the i-th residue, in ascending order

Return type:

list of lists

mdciao.utils.bonds.connected_sets(mat)

Return the connected components/sets of an adjacency matrix

Uses connected_components under the hood with directed=False

Parameters:

mat (2D _np.array, square matrix (M,M)) – Adjacency matrix, can be symmetric or not. Nodes are always self-adjacent, i.e. the diagonal of mat is ignored

Returns:

sets – The connected components as 1D _np.ndarrays

Return type:

list

mdciao.utils.bonds.neighborlists_from_adjacency_matrix(mat, n, indices=None)

Return neighborlists from an adjacency matrix.

The diagonal of mat is ignored, i.e. it can be 0 or 1

Parameters:

  • mat (2D _np.array, square matrix (M,M)) – Adjacency matrix, can be symmetric or not

  • n (int) – Connectedness. The special case of n=0 returns no neighbors (not even the index with itself)

  • indices (iterable, default is None) – Compute the neighborlists only for these indices. None computes neighbors all indices. The returned neighborlist will have empty-lists for items not present in indices.

Returns:

neighbors – A list of len M where the i-th entry contains the indices of the nodes separated from the i-ith node by a maximum of n jumps. The indices are always in ascending order. For items not present in indices, empty lists will be returned.

Return type:

list

mdciao.utils.bonds.top2residue_bond_matrix(top, force_resSeq_breaks=False, verbose=True, create_standard_bonds=False, bond_titrable_residues=True)

Return a symmetric residue-residue bond matrix from a Topology.

The bonds used are those found in bonds

Parameters:

  • top (mdtraj.Topology)

  • force_resSeq_breaks (boolean, default is False) – Delete bonds if there is a resSeq jump between residues.

  • verbose (boolean, default is True) – Print a statement if residue index has no bonds

  • create_standard_bonds (boolean, default is False) – Advanced users only, can easily lead to wrong results in case of .gro files, because create_standard_bonds needs chain information to avoid creating bonds between residues that follow one another

  • bond_titrable_residues (bool, default is True.) – Handle the gromacs-type constant-ph, titratable, residues ‘ARGT’, ‘ASPT’, ‘GLUT’, ‘HSPT’, ‘LYST’, since they don’t get all bonds in mdtraj.core.Topology.create_standard_bonds Note that this is only for the purposes of the returned residue_bond_matrix, s.t. the top.bonds attribute itself is unaltered, i.e. this operation leaves no trace and does not change the topology. Also note that standard protonated residues, e.g. “GLH”, are accepted by mdtraj as standard .

Returns:

residue_bond_matrix – Returns a symmetric adjacency matrix with entries ij=1 and ji=1, if there is a bond between residue i and residue j.

Return type:

2D np.ndarray

mdciao.utils.bonds.top2residue_bond_matrix_naive(top, only_protein=True, fragments=None)

Creates a naive (=linear) residue-residue bond-matrix, where a bond is assumed between the n-th and the n+1-th residue

Usually, one would resort to this method if the topology’s own create_standard_bonds() method does not work, e.g. because there’s only alpha Carbons

Parameters:

  • top (Topology)

  • only_protein (bool, default is True) – Only create bonds when both residues satisfy are protein residues. The check is done using the attribute mdtraj.core.topology.Residue.is_protein

  • fragments (iterable of ints, default is None) – Use fragment/chain definition to avoid bonds between fragments/chains. These definitions need to cover the entire Topology, i.e. each residue index must appear once (an and only once) in the :obj`fragments`. Note that breaks introduced via the only_protein argument will always be present, whether these residues are in the same fragment or not

Returns:

mat – Symmetric residue-residue bond-matrix. The diagonal is filled with ones as well.

Return type:

2D np.ndarray