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:
- 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.calculateAnglesAndDihedrals(bonds, cyclicdih=False)#
Calculate all angles and dihedrals from a set of bonds.
- moleculekit.util.check_port(port, host='127.0.0.1', timeout=120)#
- 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.file_diff(file, reference)#
- moleculekit.util.find_executable(execname)#
- moleculekit.util.folder_diff(folder, reference, ignore_ftypes=('.log', '.txt'))#
- moleculekit.util.guessAnglesAndDihedrals(bonds, cyclicdih=False)#
Calculate all angles and dihedrals from a set of bonds.
- moleculekit.util.maxDistance(mol, sel='all', origin=None)#
Calculates the max distance of a set of atoms from an origin
- Parameters:
- Returns:
maxd – The maximum distance in Angstrom
- Return type:
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
- moleculekit.util.natsorted(items)#
- moleculekit.util.opm(pdbid, keep=False, keepaltloc='A', validateElements=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:
Examples
>>> mol = Molecule("1kdx") >>> mol = orientOnAxes(mol,"chain B")
- moleculekit.util.readCube(fname)#
Read 3D numpy array from CUBE file
- Parameters:
fname (str) – CUBE file path
- Returns:
data (np.ndarray) – 3D numpy array with the volumetric data
meta (dict) – Dictionary with the metadata of the CUBE file
- 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:
- 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, step=1)#
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
step (int) – The step size for incremeting the ID
- 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.string_to_tempfile(content, ext)#
- 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_measurefunction.Apparently this code can randomly provide flipped molecules (chirality-wise), so a fix found in tmadl/sklearn-random-rotation-ensembles was applied.
- Returns:
M – A uniformly distributed rotation 3 x 3 matrix
- Return type:
np.ndarray
- moleculekit.util.wait_for_port(port, host='127.0.0.1', timeout=240.0, _logger=False)#
Wait until a port starts accepting TCP connections. :param port: Port number. :type port: int :param host: Host address on which the port should exist. :type host: str :param timeout: In seconds. How long to wait before raising errors. :type timeout: float
- Raises:
TimeoutError – The port isn’t accepting connection after time specified in timeout.
- moleculekit.util.writeCube(arr, filename, vecMin, vecRes)#
Writes 3D array 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 in Angstrom
- moleculekit.util.writeVoxels(arr, filename, vecMin, vecRes)#
DEPRECACTED: Use writeCube instead