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moleculekit.readers module#

moleculekit.readers.ALPHAFOLDread(filename, frame=None, topoloc=None, validateElements=True, uri='https://alphafold.ebi.ac.uk/files/AF-{uniprot}-F1-model_v3.cif')#
moleculekit.readers.BCIFread(filename, frame=None, topoloc=None, zerowarning=True, uri='https://models.rcsb.org/{pdbid}.bcif.gz', covalentonly=True)#
moleculekit.readers.BINCOORread(filename, frame=None, topoloc=None)#
moleculekit.readers.BINPOSread(filename, frame=None, topoloc=None, stride=None, atom_indices=None)#
moleculekit.readers.CIFread(filename, frame=None, topoloc=None, zerowarning=True, data=None, covalentonly=True)#
moleculekit.readers.CRDCARDread(filename, frame=None, topoloc=None)#

https://www.charmmtutorial.org/index.php/CHARMM:The_Basics title = * WATER title = * DATE: 4/10/07 4:25:51 CREATED BY USER: USER title = * Number of atoms (NATOM) = 6 Atom number (ATOMNO) = 1 (just an exmaple) Residue number (RESNO) = 1 Residue name (RESName) = TIP3 Atom type (TYPE) = OH2 Coordinate (X) = -1.30910 Coordinate (Y) = -0.25601 Coordinate (Z) = -0.24045 Segment ID (SEGID) = W Residue ID (RESID) = 1 Atom weight (Weighting) = 0.00000

now what that looks like…

  • WATER

  • DATE: 4/10/07 4:25:51 CREATED BY USER: USER

  • 6 1 1 TIP3 OH2 -1.30910 -0.25601 -0.24045 W 1 0.00000 2 1 TIP3 H1 -1.85344 0.07163 0.52275 W 1 0.00000 3 1 TIP3 H2 -1.70410 0.16529 -1.04499 W 1 0.00000 4 2 TIP3 OH2 1.37293 0.05498 0.10603 W 2 0.00000 5 2 TIP3 H1 1.65858 -0.85643 0.10318 W 2 0.00000 6 2 TIP3 H2 0.40780 -0.02508 -0.02820 W 2 0.00000

moleculekit.readers.CRDread(filename, frame=None, topoloc=None)#
moleculekit.readers.DCDread(filename, frame=None, topoloc=None, stride=None, atom_indices=None)#
exception moleculekit.readers.FormatError(value)#

Bases: Exception

moleculekit.readers.GJFread(filename, frame=None, topoloc=None)#
moleculekit.readers.GROTOPread(filename, frame=None, topoloc=None)#
moleculekit.readers.JSONread(filename, frame=None, topoloc=None, stride=None, atom_indices=None)#
moleculekit.readers.MAEread(fname, frame=None, topoloc=None)#

Reads maestro files.

Parameters:

fname (str) – .mae file

Returns:

  • topo (Topology)

  • coords (list of lists)

moleculekit.readers.MDTRAJTOPOread(filename, frame=None, topoloc=None, validateElements=True)#
moleculekit.readers.MDTRAJread(filename, frame=None, topoloc=None, validateElements=True)#
moleculekit.readers.MMTFread(filename, frame=None, topoloc=None, validateElements=True)#
moleculekit.readers.MOL2read(filename, frame=None, topoloc=None, singlemol=True, validateElements=True)#
class moleculekit.readers.MolFactory#

Bases: object

This class converts Topology and Trajectory data into Molecule objects

static construct(topos, trajs, filename, frame, validateElements=True, uniqueBonds=False)#
moleculekit.readers.NETCDFread(filename, frame=None, topoloc=None, stride=None, atom_indices=None)#
moleculekit.readers.PDBQTread(filename, frame=None, topoloc=None)#
moleculekit.readers.PDBread(filename, mode='pdb', frame=None, topoloc=None, validateElements=True, uniqueBonds=True)#
moleculekit.readers.PREPIread(filename, frame=None, topoloc=None)#
moleculekit.readers.PRMTOPread(filename, frame=None, topoloc=None, validateElements=True)#
moleculekit.readers.PSFread(filename, frame=None, topoloc=None, validateElements=True)#
moleculekit.readers.RTFread(filename, frame=None, topoloc=None)#
moleculekit.readers.SDFread(filename, frame=None, topoloc=None, mol_idx=None)#
moleculekit.readers.TRRread(filename, frame=None, topoloc=None, stride=None, atom_indices=None)#
class moleculekit.readers.Topology(pandasdata=None)#

Bases: object

property atominfo#
fromMolecule(mol)#
exception moleculekit.readers.TopologyInconsistencyError(value)#

Bases: Exception

class moleculekit.readers.Trajectory(coords=None, box=None, boxangles=None, fileloc=None, step=None, time=None)#

Bases: object

property numFrames#
moleculekit.readers.XSCread(filename, frame=None, topoloc=None)#
moleculekit.readers.XTCread(filename, frame=None, topoloc=None)#
moleculekit.readers.XYZread(filename, frame=None, topoloc=None)#
moleculekit.readers.box_vectors_to_lengths_and_angles(a, b, c)#

Convert box vectors into the lengths and angles defining the box.

Parameters:

  • a (np.ndarray) – the vector defining the first edge of the periodic box (length 3), or an array of this vector in multiple frames, where a[i,:] gives the length 3 array of vector a in each frame of a simulation

  • b (np.ndarray) – the vector defining the second edge of the periodic box (length 3), or an array of this vector in multiple frames, where b[i,:] gives the length 3 array of vector a in each frame of a simulation

  • c (np.ndarray) – the vector defining the third edge of the periodic box (length 3), or an array of this vector in multiple frames, where c[i,:] gives the length 3 array of vector a in each frame of a simulation

Examples

>>> a = np.array([2,0,0], dtype=float)
>>> b = np.array([0,1,0], dtype=float)
>>> c = np.array([0,1,1], dtype=float)
>>> l1, l2, l3, alpha, beta, gamma = box_vectors_to_lengths_and_angles(a, b, c)
>>> (l1 == 2.0) and (l2 == 1.0) and (l3 == np.sqrt(2))
True
>>> np.abs(alpha - 45) < 1e-6
True
>>> np.abs(beta - 90.0) < 1e-6
True
>>> np.abs(gamma - 90.0) < 1e-6
True
Returns:

  • a_length (scalar or np.ndarray) – length of Bravais unit vector a

  • b_length (scalar or np.ndarray) – length of Bravais unit vector b

  • c_length (scalar or np.ndarray) – length of Bravais unit vector c

  • alpha (scalar or np.ndarray) – angle between vectors b and c, in degrees.

  • beta (scalar or np.ndarray) – angle between vectors c and a, in degrees.

  • gamma (scalar or np.ndarray) – angle between vectors a and b, in degrees.

moleculekit.readers.get_raw_data_from_url(pdb_id, reduced=False)#

“ Get the msgpack unpacked data given a PDB id.

Parameters:

pdb_id – the input PDB id

:return the unpacked data (a dict)

moleculekit.readers.lengths_and_angles_to_box_vectors(a_length, b_length, c_length, alpha, beta, gamma)#

Convert from the lengths/angles of the unit cell to the box vectors (Bravais vectors). The angles should be in degrees.

Parameters:

  • a_length (scalar or np.ndarray) – length of Bravais unit vector a

  • b_length (scalar or np.ndarray) – length of Bravais unit vector b

  • c_length (scalar or np.ndarray) – length of Bravais unit vector c

  • alpha (scalar or np.ndarray) – angle between vectors b and c, in degrees.

  • beta (scalar or np.ndarray) – angle between vectors c and a, in degrees.

  • gamma (scalar or np.ndarray) – angle between vectors a and b, in degrees.

Returns:

  • a (np.ndarray) – If the inputs are scalar, the vectors will one dimesninoal (length 3). If the inputs are one dimension, shape=(n_frames, ), then the output will be (n_frames, 3)

  • b (np.ndarray) – If the inputs are scalar, the vectors will one dimesninoal (length 3). If the inputs are one dimension, shape=(n_frames, ), then the output will be (n_frames, 3)

  • c (np.ndarray) – If the inputs are scalar, the vectors will one dimesninoal (length 3). If the inputs are one dimension, shape=(n_frames, ), then the output will be (n_frames, 3)

Examples

>>> import numpy as np
>>> result = lengths_and_angles_to_box_vectors(1, 1, 1, 90.0, 90.0, 90.0)

Notes

This code is adapted from gyroid, which is licensed under the BSD http://pythonhosted.org/gyroid/_modules/gyroid/unitcell.html

moleculekit.readers.openFileOrStringIO(strData, mode=None)#
moleculekit.readers.pdbGuessElementByName(elements, names, onlymissing=True)#

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#misalignment which states that elements should be right-aligned in columns 13-14 unless it’s a 4 letter name when it would end up being left-aligned.

moleculekit.readers.sdf_generator(sdffile)#

Generates Molecule objects from an SDF file

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