acelleralivemoleculekit.molecule.Molecule(filename=None, name=None, **kwargs)¶Bases: object
Class to manipulate molecular structures.
Molecule contains all the fields of a PDB and it is independent of any force field. It can contain multiple conformations and trajectories, however all operations are done on the current frame. The following PDB fields are accessible as attributes (record, serial, name, altloc, resname, chain, resid, insertion, coords, occupancy, beta, segid, element, charge). The coordinates are accessible via the coords attribute ([number of atoms x 3 x number of frames] where [x,y,z] are the second dimension.
filename (str or list of str) – Optionally load a PDB file from the specified file. If there’s no file and the value is four characters long assume it is a PDB accession code and try to download from the RCSB web server.
name (str) – Give a name to the Molecule that will be used for visualization
kwargs – Accepts any further arguments that should be passed to the Molecule.read method.
Examples
>>> mol = Molecule( './test/data/dhfr/dhfr.pdb' )
>>> mol = Molecule( '3PTB', name='Trypsin' )
>>> print(mol)
Molecule with 1701 atoms and 1 frames
Atom field - altloc shape: (1701,)
Atom field - atomtype shape: (1701,)
...
Methods
Attributes
record¶The record field of a PDB file if the topology was read from a PDB.
np.ndarray
serial¶The serial number of each atom.
np.ndarray
name¶The name of each atom.
np.ndarray
altloc¶The alternative location flag of the atoms if read from a PDB.
np.ndarray
resname¶The residue name of each atom.
np.ndarray
chain¶The chain name of each atom.
np.ndarray
resid¶The residue ID of each atom.
np.ndarray
insertion¶The insertion flag of the atoms if read from a PDB.
np.ndarray
occupancy¶The occupancy value of each atom if read from a PDB.
np.ndarray
beta¶The beta factor value of each atom if read from a PDB.
np.ndarray
segid¶The segment ID of each atom.
np.ndarray
element¶The element of each atom.
np.ndarray
charge¶The charge of each atom.
np.ndarray
masses¶The mass of each atom.
np.ndarray
atomtype¶The atom type of each atom.
np.ndarray
coords¶A float32 array with shape (natoms, 3, nframes) containing the coordinates of the Molecule.
np.ndarray
box¶A float32 array with shape (3, nframes) containing the periodic box dimensions of an MD trajectory.
np.ndarray
boxangles¶The angles of the box. If none are set they are assumed to be 90 degrees.
np.ndarray
bonds¶Atom pairs corresponding to bond terms.
np.ndarray
bondtype¶The type of each bond in Molecule.bonds if available.
np.ndarray
angles¶Atom triplets corresponding to angle terms.
np.ndarray
dihedrals¶Atom quadruplets corresponding to dihedral terms.
np.ndarray
impropers¶Atom quadruplets corresponding to improper dihedral terms.
np.ndarray
crystalinfo¶A dictionary containing crystallographic information. It has fields [‘sGroup’, ‘numcopies’, ‘rotations’, ‘translations’]
reps¶A list of representations that is used when visualizing the molecule
Representations object
align(sel, refmol=None, refsel=None, frames=None, matchingframes=False)¶Align conformations.
Align a given set of frames of this molecule to either the current active frame of this molecule (mol.frame) or the current frame of a different reference molecule. To align to any frame other than the current active one modify the refmol.frame property before calling this method.
sel (str) – Atom selection string for aligning. See more here
refmol (Molecule, optional) – Optionally pass a reference Molecule on which to align. If None is given, it will align on the first frame
of the same Molecule
refsel (str, optional) – Atom selection for the refmol if one is given. Default: same as sel. See more here
frames (list or range) – A list of frames which to align. By default it will align all frames of the Molecule
matchingframes (bool) – If set to True it will align the selected frames of this molecule to the corresponding frames of the refmol. This requires both molecules to have the same number of frames.
Examples
>>> mol=tryp.copy()
>>> mol.align('protein')
>>> mol.align('name CA', refmol=Molecule('3PTB'))
alignBySequence(ref, molseg=None, refseg=None, nalignfragment=1, returnAlignments=False, maxalignments=1)¶Aligns the Molecule to a reference Molecule by their longest sequence alignment
ref (Molecule object) – The reference Molecule to which we want to align
molseg (str) – The segment of this Molecule we want to align
refseg (str) – The segment of ref we want to align to
nalignfragments (int) – The number of fragments used for the alignment.
returnAlignments (bool) – Return all alignments as a list of Molecules
maxalignments (int) – The maximum number of alignments we want to produce
mols – If returnAlignments is True it returns a list of Molecules each containing a different alignment. Otherwise it modifies the current Molecule with the best single alignment.
append(mol, collisions=False, coldist=1.3)¶Append a molecule at the end of the current molecule
mol (Molecule) – Target Molecule which to append to the end of the current Molecule
collisions (bool) – If set to True it will remove residues of mol which collide with atoms of this Molecule object.
coldist (float) – Collision distance in Angstrom between atoms of the two molecules. Anything closer will be considered a collision.
Example
>>> mol=tryp.copy()
>>> mol.filter("not resname BEN")
>>> lig=tryp.copy()
>>> lig.filter("resname BEN")
>>> mol.append(lig)
appendFrames(mol)¶Appends the frames of another Molecule object to this object.
mol (Molecule) – A Molecule object.
atomselect(sel, indexes=False, strict=False, fileBonds=True, guessBonds=True)¶Get a boolean mask or the indexes of a set of selected atoms
asel – Either a boolean mask of selected atoms or their indexes
np.ndarray
Examples
>>> mol=tryp.copy()
>>> mol.atomselect('resname MOL')
array([False, False, False, ..., False, False, False], dtype=bool)
center(loc=(0, 0, 0), sel='all')¶Moves the geometric center of the Molecule to a given location
Examples
>>> mol=tryp.copy()
>>> mol.center()
>>> mol.center([10, 10, 10], 'name CA')
copy()¶Create a copy of the Molecule object
newmol – A copy of the object
deleteBonds(sel, inter=True)¶Deletes all bonds that contain atoms in sel or between atoms in sel.
dropFrames(keep='all', drop=None)¶Removes trajectory frames from the Molecule
Examples
>>> mol = Molecule('1sb0')
>>> mol.dropFrames(keep=[1,2])
>>> mol.numFrames == 2
>>> mol.dropFrames(drop=[0])
>>> mol.numFrames == 1
empty(numAtoms)¶Creates an empty molecule of numAtoms atoms.
numAtoms (int) – Number of atoms to create in the molecule.
Example
>>> newmol = Molecule().empty(100)
filter(sel, _logger=True)¶Removes all atoms not included in the selection
Examples
>>> mol=tryp.copy()
>>> mol.filter('protein')
frameThe currently active frame of the Molecule on which methods will be applied
fstepThe frame-step of the trajectory
get(field, sel=None)¶Retrieve a specific PDB field based on the selection
vals – Array of values of field for all atoms in the selection.
np.ndarray
Examples
>>> mol=tryp.copy()
>>> mol.get('resname')
array(['ILE', 'ILE', 'ILE', ..., 'HOH', 'HOH', 'HOH'], dtype=object)
>>> mol.get('resname', sel='resid 158')
array(['LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU'], dtype=object)
getDihedral(atom_quad)¶Get the value of a dihedral angle.
atom_quad (list) – Four atom indexes corresponding to the atoms defining the dihedral
angle – The angle in radians
Examples
>>> mol.getDihedral([0, 5, 8, 12])
insert(mol, index, collisions=0, coldist=1.3)¶Insert the atoms of one molecule into another at a specific index.
mol (Molecule) – Molecule to be inserted
index (integer) – The atom index at which the passed molecule will be inserted
collisions (bool) – If set to True it will remove residues of mol which collide with atoms of this Molecule object.
coldist (float) – Collision distance in Angstrom between atoms of the two molecules. Anything closer will be considered a collision.
Example
>>> mol=tryp.copy()
>>> mol.numAtoms
1701
>>> mol.insert(tryp, 0)
>>> mol.numAtoms
3402
moveBy(vector, sel=None)¶Move a selection of atoms by a given vector
Examples
>>> mol=tryp.copy()
>>> mol.moveBy([3, 45 , -8])
mutateResidue(sel, newres)¶Mutates a residue by deleting its sidechain and renaming it
Examples
>>> mol=tryp.copy()
>>> mol.mutateResidue('resid 158', 'ARG')
numAtomsNumber of atoms in the molecule
numFramesNumber of coordinate frames in the molecule
numResiduesThe number of residues in the Molecule
read(filename, type=None, skip=None, frames=None, append=False, overwrite='all', keepaltloc='A', guess=None, guessNE=None, _logger=True, **kwargs)¶Read topology, coordinates and trajectory files in multiple formats.
Detects from the extension the file type and loads it into Molecule
filename (str) – Name of the file we want to read
type (str, optional) – File type of the file. If None, it’s automatically determined by the extension
skip (int, optional) – If the file is a trajectory, skip every skip frames
frames (list, optional) – If the file is a trajectory, read only the given frames
append (bool, optional) – If the file is a trajectory or coor file, append the coordinates to the previous coordinates. Note append is slow.
overwrite (str, list of str) – A list of the existing fields in Molecule that we wish to overwrite when reading this file. Set to None if you don’t want to overwrite any existing fields.
keepaltloc (str) – Set to any string to only keep that specific altloc. Set to ‘all’ if you want to keep all alternative atom positions.
guess (list of str) – Properties of the molecule to guess. Can be any combination of (‘bonds’, ‘angles’, ‘dihedrals’)
guessNE (list of str) – Properties of the molecule to guess if it’s Non-Existent. Can be any combination of (‘bonds’, ‘angles’, ‘dihedrals’)
remove(selection, _logger=True)¶Remove atoms from the Molecule
selection (str) – Atom selection string of the atoms we want to remove. See more here
removed – The list of atoms removed
np.array
Example
>>> mol=tryp.copy()
>>> mol.remove('name CA')
array([ 1, 9, 16, 20, 24, 36, 43, 49, 53, 58,...
renumberResidues(returnMapping=False)¶Renumbers protein residues incrementally.
It checks for changes in either of the resid, insertion, chain or segid fields and in case of a change it creates a new residue number.
returnMapping (bool) – If set to True, the method will also return the mapping between the old and new residues
Examples
>>> mapping = mol.renumberResidues(returnMapping=True)
reorderAtoms(order)¶Reorder atoms in Molecule
Changes the order of atoms in the Molecule to the defined order.
order (list) – A list containing the new order of atoms
Examples
>>> mol = Molecule()
>>> mol.empty(4)
>>> mol.name[:] = ['N', 'C', 'H', 'S']
>>> neworder = [1, 3, 2, 0]
>>> mol.reorderAtoms(neworder)
>>> print(mol.name)
array(['C', 'S', 'H', 'N'], dtype=object)
rotateBy(M, center=(0, 0, 0), sel='all')¶Rotate a selection of atoms by a given rotation matrix around a center
Examples
>>> mol = tryp.copy()
>>> mol.rotateBy(rotationMatrix([0, 1, 0], 1.57))
sequence(oneletter=True, noseg=False)¶Return the aminoacid sequence of the Molecule.
sequence – The primary sequence as a dictionary segid - string (if oneletter is True) or segid - list of strings (otherwise).
Examples
>>> mol=tryp.copy()
>>> mol.sequence()
{'0': 'IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN'}
>>> sh2 = Molecule("1LKK")
>>> pYseq = sh2.sequence(oneletter=False)
>>> pYseq['1']
['PTR', 'GLU', 'GLU', 'ILE']
>>> pYseq = sh2.sequence(oneletter=True)
>>> pYseq['1']
'XEEI'
set(field, value, sel=None)¶Set the values of a Molecule field based on the selection
field (str) – The field we want to set. To see a list of all available fields do print(Molecule._atom_and_coord_fields).
value (string or integer) – All atoms that match the atom selection will have the field field set to this scalar value (or 3-vector if setting the coordinates)
sel (str) – Atom selection string for atom which to set. See more here
Examples
>>> mol=tryp.copy()
>>> mol.set('segid', 'P', sel='protein')
setDihedral(atom_quad, radians, bonds=None)¶Sets the angle of a dihedral.
atom_quad (list) – Four atom indexes corresponding to the atoms defining the dihedral
radians (float) – The angle in radians to which we want to set the dihedral
bonds (np.ndarray) – An array containing all bonds of the molecule. This is needed if multiple modifications are done as the bond guessing can get messed up if atoms come very close after the rotation.
Examples
>>> mol.setDihedral([0, 5, 8, 12], 0.16)
>>> # If we perform multiple modifications, calculate bonds first and pass them as argument to be safe
>>> bonds = mol._getBonds()
>>> mol.setDihedral([0, 5, 8, 12], 0.16, bonds=bonds)
>>> mol.setDihedral([18, 20, 24, 30], -1.8, bonds=bonds)
view(sel=None, style=None, color=None, guessBonds=True, viewer=None, hold=False, name=None, viewerhandle=None, gui=False)¶Visualizes the molecule in a molecular viewer
sel (str) – Atom selection string for the representation. See more here
color (str or int) – Coloring mode (str) or ColorID (int). See more here.
guessBonds (bool) – Allow VMD to guess bonds for the molecule
viewer (str ('vmd', 'webgl')) – Choose viewer backend. Default is taken from either moleculekit.config or if it doesn’t exist from moleculekit.config
hold (bool) – If set to True, it will not visualize the molecule but instead collect representations until set back to False.
name (str, optional) – A name to give to the molecule in VMD
viewerhandle (VMD object, optional) – A specific viewer in which to visualize the molecule. If None it will use the current default viewer.
wrap(wrapsel=None, fileBonds=True, guessBonds=False)¶Wraps the coordinates of the molecule into the simulation box
wrapsel (str) – Atom selection string of atoms on which to center the wrapping box. See more here
Examples
>>> mol=tryp.copy()
>>> mol.wrap()
>>> mol.wrap('protein')
write(filename, sel=None, type=None, **kwargs)¶Writes the topology and coordinates of the Molecule in any of the supported formats.
x¶Get the x coordinates at the current frame
y¶Get the y coordinates at the current frame
z¶Get the z coordinates at the current frame
moleculekit.molecule.Representations(mol)¶Bases: object
Class that stores representations for Molecule.
Examples
>>> from moleculekit.molecule import Molecule
>>> mol = tryp.copy()
>>> mol.reps.add('protein', 'NewCartoon')
>>> print(mol.reps)
rep 0: sel='protein', style='NewCartoon', color='Name'
>>> mol.view()
>>> mol.reps.remove()
add(sel=None, style=None, color=None)¶Adds a new representation for Molecule.
append(reps)¶list()¶Lists all representations. Equivalent to using print.
moleculekit.molecule.TopologyInconsistencyError(value)¶Bases: Exception
args¶with_traceback()¶Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
moleculekit.molecule.UniqueAtomID(**kwargs)¶Bases: object
fromMolecule(mol, sel=None, idx=None)¶selectAtom(mol, indexes=True, ignore=None)¶moleculekit.molecule.UniqueResidueID(**kwargs)¶Bases: object
fromMolecule(mol, sel=None, idx=None)¶selectAtoms(mol, indexes=True, ignore=None)¶moleculekit.molecule.calculateUniqueBonds(bonds, bondtype)¶Given bonds and bondtypes calculates unique bonds dropping any duplicates
bonds (np.ndarray) – The bonds of a molecule
bondtype (np.ndarray) – The bond type of each bond in the bonds array
uqbonds (np.ndarray) – The unique bonds of the molecule
uqbondtype (np.ndarray) – The corresponding bond types for uqbonds
Examples
>>> from moleculekit.molecule import Molecule
>>> mol = Molecule('3PTB')
>>> mol.bonds, mol.bondtype = calculateUniqueBonds(mol.bonds, mol.bondtype) # Overwrite the bonds and bondtypes with the unique ones
moleculekit.molecule.mol_equal(mol1, mol2, checkFields=('record', 'serial', 'name', 'altloc', 'resname', 'chain', 'resid', 'insertion', 'occupancy', 'beta', 'segid', 'element', 'charge', 'masses', 'atomtype', 'coords'), exceptFields=None, fieldPrecision=None, _logger=True)¶Compare two Molecules for equality.
mol1 (Molecule) – The first molecule to compare
mol2 (Molecule) – The second molecule to compare to the first
checkFields (list) – A list of fields to compare. By default compares all atom information and coordinates in the molecule
exceptFields (list) – A list of fields to not compare.
fieldPrecision (dict) – A dictionary of field, precision key-value pairs which defines the numerical precision of the value comparisons of two arrays
_logger (bool) – Set to False to disable the printing of the differences in the two Molecules
equal – Returns True if the molecules are equal or False if they are not.
Examples
>>> mol_equal(mol1, mol2, checkFields=['resname', 'resid', 'segid'])
>>> mol_equal(mol1, mol2, exceptFields=['record', 'name'])
>>> mol_equal(mol1, mol2, fieldPrecision={'coords': 1e-5})