acelleralivemoleculekit.projections.metricdihedral.AtomNotFoundException¶Bases: Exception
args¶with_traceback()¶Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
moleculekit.projections.metricdihedral.Dihedral(atom1, atom2, atom3, atom4, dihedraltype=None, check_valid=True)¶Bases: object
Class to store atoms defining a dihedral angle.
Example
>>> # Using the helper functions to construct a dihedral object
>>> d1 = Dihedral.phi(mol, 5, 6, segid='P0')
>>> d2 = Dihedral.chi1(mol, 12, segid='P0') # Defining segid
>>> d3 = Dihedral.chi1(mol, 38, chain='X') # Defining chain
>>> # Manual construction
>>> atom1 = {'name': 'N', 'resid': 5, 'segid': 'P'}
>>> atom2 = {'name': 'CA', 'resid': 3, 'segid': 'P', 'chain': 'A', 'insertion': 'B'}
>>> atom3 = {'name': 'C', 'resid': 46, 'segid': 'P', 'chain': 'X'}
>>> atom4 = {'name': 'O', 'resid': 2, 'segid': 'P'}
>>> d = Dihedral(atom1, atom2, atom3, atom4)
chi1(mol, res, segid=None, chain=None, insertion=None, ff='amber')¶Constructs a Dihedral object corresponding to the chi1 angle of a residue
dihedral – A Dihedral object
Dihedral object
chi2(mol, res, segid=None, chain=None, insertion=None, ff='amber')¶Constructs a Dihedral object corresponding to the chi2 angle of a residue
dihedral – A Dihedral object
Dihedral object
chi3(mol, res, segid=None, chain=None, insertion=None, ff='amber')¶Constructs a Dihedral object corresponding to the chi3 angle of a residue
dihedral – A Dihedral object
Dihedral object
chi4(mol, res, segid=None, chain=None, insertion=None, ff='amber')¶Constructs a Dihedral object corresponding to the chi4 angle of a residue
dihedral – A Dihedral object
Dihedral object
chi5(mol, res, segid=None, chain=None, insertion=None, ff='amber')¶Constructs a Dihedral object corresponding to the chi5 angle of a residue
dihedral – A Dihedral object
Dihedral object
dihedralsToIndexes(mol, dihedrals, sel='all')¶Converts dihedral objects to atom indexes of a given Molecule
indexes – A list containing a list of atoms that correspond to each dihedral.
list of lists
Examples
>>> dihs = []
>>> dihs.append(Dihedral.phi(mol, 1, 2))
>>> dihs.append(Dihedral.psi(mol, 2, 3))
>>> indexes = Dihedral.dihedralsToIndexes(mol, dihs)
omega(mol, res1, res2, segid=None, chain=None, insertion1=None, insertion2=None, ff='amber')¶Constructs a Dihedral object corresponding to the omega angle of res1 and res2
mol (Molecule object) – A Molecule object from which to obtain structural information
res1 (int) – The resid of the first residue containing the CA C atoms
res2 (int) – The resid of the second residue containing the N CA atoms
segid (str) – The segment id of the residues
chain (str) – The chain letter of the residues
insertion1 (str) – The insertion letter of residue 1
insertion2 (str) – The insertion letter of residue 2
dihedral – A Dihedral object
Dihedral object
phi(mol, res1, res2, segid=None, chain=None, insertion1=None, insertion2=None, ff='amber')¶Constructs a Dihedral object corresponding to the phi angle of res1 and res2
mol (Molecule object) – A Molecule object from which to obtain structural information
res1 (int) – The resid of the first residue containing the C atom
res2 (int) – The resid of the second residue containing the N CA C atoms
segid (str) – The segment id of the residues
chain (str) – The chain letter of the residues
insertion1 (str) – The insertion letter of residue 1
insertion2 (str) – The insertion letter of residue 2
dihedral – A Dihedral object
Dihedral object
proteinDihedrals(mol, sel='protein or resname ACE NME', dih=('psi', 'phi'), ff='amber')¶Returns a list of tuples containing the four resid/atom pairs for each dihedral of the protein
mol (Molecule object) – A Molecule object from which to obtain structural information
sel (str) – Atom selection string to restrict the atoms for which to calculate dihedrals (e.g. only one of many chains). See more here
dih (tuple) – A tuple of the dihedral types we want to calculate (phi, psi, omega, chi1, chi2, chi3, chi4, chi5)
dihedrals – A list of Dihedral objects
list of Dihedral objects
psi(mol, res1, res2, segid=None, chain=None, insertion1=None, insertion2=None, ff='amber')¶Constructs a Dihedral object corresponding to the psi angle of res1 and res2
mol (Molecule object) – A Molecule object from which to obtain structural information
res1 (int) – The resid of the first residue containing the N CA C atoms
res2 (int) – The resid of the second residue containing the N atom
segid (str) – The segment id of the residues
chain (str) – The chain letter of the residues
insertion1 (str) – The insertion letter of residue 1
insertion2 (str) – The insertion letter of residue 2
dihedral – A Dihedral object
Dihedral object
moleculekit.projections.metricdihedral.MetricDihedral(dih=None, sincos=True, protsel='protein or resname ACE NME')¶Bases: moleculekit.projections.projection.Projection
Calculates a set of dihedral angles from trajectories
dih (list of Dihedral object) – You can provide your own list of Dihedral objects. See example.
sincos (bool, optional) – Set to True to return the dihedral angles as their sine and cosine components. Makes them periodic.
protsel (str, optional) – Atom selection string for the protein segment for which to calculate dihedral angles. Resids should be unique within that segment. See more here
Examples
>>> mol = Molecule('3PTB')
>>> mol.filter('not insertion A')
>>> met = MetricDihedral()
>>> met.project(mol)
>>> # More complicated example
>>> dih = []
>>> dih.append(Dihedral.chi1(mol, 45))
>>> dih.append(Dihedral.psi(mol, 29, 30))
>>> met = MetricDihedral(dih, protsel='protein and segid 0')
>>> met.project(mol)
>>> met.getMapping(mol)
copy()¶Produces a deep copy of the object
getMapping(mol)¶Returns the description of each projected dimension.
mol (Molecule object) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.
map – A DataFrame containing the descriptions of each dimension
DataFrame object