boltzkit.utils.molecular.z_matrix_factory

This file utilizes a modified version of the ZMatrixFactory from https://github.com/noegroup/bgmol.

MIT License

Copyright (c) 2020 noegroup

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

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Functions

build_fake_topology(n_atoms[, bonds, ...])

A stupid function to build an MDtraj topology with limited information.

find_rings(mdtraj_topology)

Find rings in a molecule.

is_chiral_torsion(torsions, mdtraj_topology)

True for all torsions that define HA positions.

is_methyl_torsion(torsions, mdtraj_topology)

Whether torsions are the first (proper) torsion of a methyl group.

is_proper_torsion(torsions, mdtraj_topology)

Whether torsions are proper or improper dihedrals.

is_ramachandran_torsion(torsions, ...)

Whether torsions are Ramachandran angles or not.

is_ring_torsion(torsions, mdtraj_topology)

Whether torsions are part of defining a ring.

is_type_torsion(type_torsion, torsions, ...)

Whether torsions are of the specified type.

rewire_chiral_torsions(z_matrix, mdtraj_topology)

Redefine all torsions containing HA as HA-CA-N-C torsions.

Classes

ZMatrixFactory

Factory for internal coordinate representations.
boltzkit.utils.molecular.z_matrix_factory.find_rings(mdtraj_topology: Topology)[source]

Find rings in a molecule.

Returns:

ring_atoms – Atoms constituting each ring

Return type:

List[List[int]]

Notes

Requires networkx.

boltzkit.utils.molecular.z_matrix_factory.is_ring_torsion(torsions: Sequence[Sequence[int]], mdtraj_topology: Topology)[source]

Whether torsions are part of defining a ring.

Returns:

is_ring – A boolean array which contains 1 for torsions of ring atoms and 0 for others

Return type:

np.ndarray

Notes

Requires networkx.

boltzkit.utils.molecular.z_matrix_factory.is_proper_torsion(torsions: Sequence[Sequence[int]], mdtraj_topology: Topology)[source]

Whether torsions are proper or improper dihedrals.

Parameters:

  • torsions (np.ndarray or Sequence[Sequence[int]]) – A list of torsions or a zmatrix.

  • mdtraj_topology (md.Topology)

Returns:

is_proper – A boolean array which contains 1 for proper and 0 for improper torsions.

Return type:

np.ndarray

boltzkit.utils.molecular.z_matrix_factory.is_methyl_torsion(torsions: Sequence[Sequence[int]], mdtraj_topology: Topology, general: bool = False)[source]

Whether torsions are the first (proper) torsion of a methyl group. Methyl hydrogens are placed by one proper and two improper torsions. This function only indicates the former.

Parameters:

  • torsions (np.ndarray or Sequence[Sequence[int]]) – A list of torsions or a zmatrix.

  • mdtraj_topology (md.Topology)

  • general (bool) – If true any group containing three H atoms is selected, not just methyl.

Returns:

is_methyl – A boolean array which contains 1 for proper methyl torsion and 0 otherwise

Return type:

np.ndarray

boltzkit.utils.molecular.z_matrix_factory.is_chiral_torsion(torsions: Sequence[Sequence[int]], mdtraj_topology: Topology)[source]

True for all torsions that define HA positions.

boltzkit.utils.molecular.z_matrix_factory.is_type_torsion(type_torsion: str, torsions: Sequence[Sequence[int]], mdtraj_topology: Topology)[source]

Whether torsions are of the specified type. Types supported are: ramachandran, phi, psi, omega, chi, chi1, chi2, chi3, chi4, ring, proper, methyl, chiral

Parameters:

  • type_torsion (str) – Which type of torsion among the supported ones.

  • torsions (np.ndarray or Sequence[Sequence[int]]) – A list of torsions or a zmatrix.

  • mdtraj_topology (md.Topology)

Returns:

is_type – A boolean array which contains True iff the torsion is of the specified type.

Return type:

np.ndarray

boltzkit.utils.molecular.z_matrix_factory.is_ramachandran_torsion(torsions: Sequence[Sequence[int]], mdtraj_topology: Topology)[source]

Whether torsions are Ramachandran angles or not.

Parameters:

  • torsions (np.ndarray or Sequence[Sequence[int]]) – A list of torsions or a zmatrix.

  • mdtraj_topology (md.Topology)

Returns:

is_ramachandran – A boolean array which contains True iff the torsion is Ramachandran

Return type:

np.ndarray

boltzkit.utils.molecular.z_matrix_factory.rewire_chiral_torsions(z_matrix: ndarray, mdtraj_topology: Topology, verbose=True)[source]

Redefine all torsions containing HA as HA-CA-N-C torsions. We use those to define chirality of aminoacids.

Parameters:

  • z_matrix (np.ndarray) – A matrix of atom indices defining the internal coordinate transform.

  • mdtraj_topology (md.Topology)

Returns:

z_matrix – A modified z-matrix that has all HA positions conditioned on CA, N, C

Return type:

np.ndarray

Notes

The indices do not correspond directly to indices

class boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory[source]

Bases: object

Factory for internal coordinate representations.

Parameters:

  • mdtraj_topology (mdtraj.Topology) – The system’s topology.

  • cartesian (str or sequence of ints) – The ids of atoms that are not transformed into internal coordinates. This can either be a sequence of integers or a DSL selection string for mdtraj.

z_matrix

The internal coordinate definition of shape (n_atoms - n_cartesian, 4). For each line, the placing of atom line[0] is conditioned on the atoms line[1:3]. Negative entries (-1) in a line mean that the atom is a seed for the global transform.

Type:

np.ndarray

fixed

One-dimensional array of cartesian atom indices.

Type:

np.ndarray

property z_matrix
property fixed
__init__(mdtraj_topology, cartesian=())[source]
build_naive(subset='all', render_independent=True, rewire_chiral=True, verbose=False)[source]

Place atoms relative to the closest atoms that are already placed (wrt. bond topology).

Parameters:

  • subset (str or sequence of int) – A selection string or list of atoms. The z-matrix is only build for the subset.

  • render_independent (bool) – Whether to make sure that no two positions depend on the same three other positions.

  • rewire_chiral (bool) – Whether to make sure that all HA depend on (CA, N, C).

Returns:

  • z_matrix (np.ndarray)

  • fixed_atoms (np.ndarray)

build_with_templates(*yaml_files, template_lookup_dir: str = '/home/runner/work/boltzkit/boltzkit/src/boltzkit/utils/molecular/z_matrix_templates', build_protein_backbone=True, subset='all')[source]

Build ICs from template files.

Parameters:

  • *yaml_files (str) – filenames of any other template files; if non are passed, use the bundled “z_protein.yaml”, “z_termini.yaml”

  • template_lookup_dir (str) – Directory path to look up the templates

  • build_protein_backbone (bool) – Whether to build the protein backbone first

  • subset (str or sequence of int) – A selection string or list of atoms. The z-matrix is only build for the subset.

Notes

For the formatting of template files, see data/z_protein.yaml

Returns:

  • z_matrix (np.ndarray)

  • fixed_atoms (np.ndarray)

build_with_system(system)[source]

Idea: build a lookup table of torsions and impropers; sort them by marginal entropy. Before doing the naive lookup, try to insert in the minimum-entropy torsions. Maybe: also do something regarding symmetries.

render_independent(keep=None)[source]

Rewire z matrix so that no two positions depend on the same bonded atom and angle/torsion

Parameters:

keep (Sequence[int]) – All atoms, whose placement should not be changed by any means. By default, don’t rewire CB to be able to control the chirality.

static is_independent(z)[source]
boltzkit.utils.molecular.z_matrix_factory.build_fake_topology(n_atoms, bonds=None, atoms_by_residue=None, coordinates=None)[source]

A stupid function to build an MDtraj topology with limited information.

Returns:

  • topology (md.Topology)

  • trajectory (md.Trajectory or None) – None, if no coordinates were specified.