moleculekit.util module

moleculekit.util.assertSameAsReferenceDir(compareDir, outdir='.')

Check if files in refdir are present in the directory given as second argument AND their content matches.

Raise an exception if not.

moleculekit.util.boundingBox(mol, sel='all')

Calculates the bounding box of a selection of atoms.

Parameters

  • mol (Molecule object) – The molecule containing the atoms

  • sel (str) – Atom selection string of atoms. See more here

Returns

bbox – The bounding box around the atoms selected in sel.

Return type

np.ndarray

Example

>>> boundingBox(mol, sel='chain A')
array([[-17.3390007 , -10.43700027,  -1.43900001],
       [ 25.40600014,  27.03800011,  46.46300125]], dtype=float32)
moleculekit.util.ensurelist(tocheck, tomod=None)

Convert np.ndarray and scalars to lists.

Lists and tuples are left as is. If a second argument is given, the type check is performed on the first argument, and the second argument is converted.

moleculekit.util.guessAnglesAndDihedrals(bonds, cyclicdih=False)

Generate a guess of angle and dihedral N-body terms based on a list of bond index pairs.

moleculekit.util.maxDistance(mol, sel='all', origin=None)

Calculates the max distance of a set of atoms from an origin

Parameters

  • mol (Molecule object) – The molecule containing the atoms

  • sel (str) – Atom selection string for atoms for which to calculate distances. See more here

  • origin (list) – The origin x,y,z coordinates

Returns

maxd – The maximum distance in Angstrom

Return type

float

Example

>>> y = maxDistance(mol, sel='protein', origin=[0, 0, 0])
>>> print(round(y,2))
48.39
moleculekit.util.molRMSD(mol, refmol, rmsdsel1, rmsdsel2)

Calculates the RMSD between two Molecules

Parameters

  • mol (Molecule object) –

  • refmol –

  • rmsdsel1 –

  • rmsdsel2 –

Returns

rmsd – The RMSD between the two structures

Return type

float

moleculekit.util.molTMscore(mol, ref, selCAmol, selCAref)

Calculates the TMscore between two Molecules

Parameters

  • mol (Molecule object) – A Molecule containing a single or multiple frames

  • ref (Molecule object) – A reference Molecule containing a single frame. Will automatically keep only ref.frame.

  • selCAmol (numpy.ndarray) – An atomselection array of booleans or indexes of the CA atoms for mol

  • selCAref (numpy.ndarray) – An atomselection array of booleans or indexes of the CA atoms for ref

Returns

  • tmscoreRef (numpy.ndarray) – TMscore normalized by length of ref

  • rmsd (numpy.ndarray) – RMSD only OF COMMON RESIDUES for all frames. This is not the same as a full protein RMSD!!!

Examples

tmscore, rmsd = molTMscore(mol, ref, mol.atomselect(‘protein’), ref.atomselect(‘protein’))

moleculekit.util.opm(pdb, keep=False, keepaltloc='A')

Download a molecule from the OPM.

Parameters

  • pdb (str) – The 4-letter PDB code

  • keep (bool) – If False, removes the DUM atoms. If True, it keeps them.

Returns

  • mol (Molecule) – The oriented molecule

  • thickness (float or None) – The bilayer thickness (both layers)

Examples

>>> mol, thickness = opm("1z98")
>>> mol.numAtoms
7902
>>> thickness
28.2
>>> _, thickness = opm('4u15')
>>> thickness is None
True
moleculekit.util.orientOnAxes(mol, sel='all')

Rotate a molecule so that its main axes are oriented along XYZ.

The calculation is based on the axes of inertia of the given selection, but masses will be ignored. After the operation, the main axis will be parallel to the Z axis, followed by Y and X (the shortest axis). Only the first frame is oriented. The reoriented molecule is returned.

Parameters

  • mol – The Molecule to be rotated

  • sel (str) – Atom selection string on which the rotation is computed. See more here

Examples

>>> mol = Molecule("1kdx")
>>> mol = orientOnAxes(mol,"chain B")
moleculekit.util.rotationMatrix(axis, theta)

Produces a rotation matrix given an axis and radians

Return the rotation matrix associated with counterclockwise rotation about the given axis by theta radians.

Parameters

  • axis (list) – The axis around which to rotate

  • theta (float) – The rotation angle in radians

Returns

M – The rotation matrix.

Return type

numpy.ndarray

Examples

>>> M = rotationMatrix([0, 0, 1], 1.5708)
>>> M.round(4)
array([[-0., -1.,  0.],
       [ 1., -0.,  0.],
       [ 0.,  0.,  1.]])

>>> axis = [4.0, 4., 1.]
>>> theta = 1.2
>>> v = [3.0, 5., 0.]
>>> np.dot(rotationMatrix(axis, theta), v).round(2)
array([ 2.75,  4.77,  1.92])
moleculekit.util.sequenceID(field, prepend=None)

Array of integers which increments at value change of another array

Parameters

  • field (np.ndarray or tuple) – An array of values. Once a change in value happens, a new ID will be created in seq. If a tuple of ndarrays is passed, a change in any of them will cause an increase in seq.

  • prepend (str) – A string to prepend to the incremental sequence

Returns

seq – An array of equal size to field containing integers which increment every time there is a change in field

Return type

np.ndarray

Examples

>>> # A change in resid, insertion, chain or segid will cause an increase in the sequence
>>> sequenceID((mol.resid, mol.insertion, mol.chain, mol.segid))
array([  1,   1,   1, ..., 285, 286, 287])
>>> # it is typically used to renumber resids as follows
>>> mol.set('resid', sequenceID((mol.resid, mol.insertion, mol.chain, mol.segid)))
moleculekit.util.tempname(suffix='', create=False)
moleculekit.util.uniformRandomRotation()

Return a uniformly distributed rotation 3 x 3 matrix

The initial description of the calculation can be found in the section 5 of “How to generate random matrices from the classical compact groups” of Mezzadri (PDF: https://arxiv.org/pdf/math-ph/0609050.pdf; arXiv:math-ph/0609050; and NOTICES of the AMS, Vol. 54 (2007), 592-604). Sample code is provided in that section as the haar_measure function.

Apparently this code can randomly provide flipped molecules (chirality-wise), so a fix found in https://github.com/tmadl/sklearn-random-rotation-ensembles/blob/5346f29855eb87241e616f6599f360eba12437dc/randomrotation.py was applied.

Returns

M – A uniformly distributed rotation 3 x 3 matrix

Return type

np.ndarray

moleculekit.util.writeVoxels(arr, filename, vecMin, vecRes)

Writes grid free energy to cube file

Parameters

  • arr (np.ndarray) – 3D array with volumetric data.

  • filename (str) – string with the filename of the cubefile

  • vecMin (np.ndarray) – 3D vector denoting the minimal corner of the grid

  • vecRes (np.ndarray) – 3D vector denoting the resolution of the grid in each dimension