luna.MyBio.selector module

class AtomSelector(entries, **kwargs)

Bases: luna.MyBio.selector.Selector

Select atoms defined at entries.

Parameters

entries (iterable of Atom) – Sequence of atom objects.

accept_atom(atom)

Decide if the atom is valid or not.

class ChainSelector(entries, **kwargs)

Bases: luna.MyBio.selector.Selector

Select atoms from chains defined at entries.

Parameters

entries (iterable of Chain instances) – Sequence of chain objects.

accept_atom(atom)

Decide if the atom is valid or not.

accept_chain(chain)

Decide if the chain is valid or not.

accept_residue(res)

Decide if the residue is valid or not.

class ResidueSelector(entries, **kwargs)

Bases: luna.MyBio.selector.Selector

Select atoms from residues and other molecules defined at entries.

Parameters

entries (iterable of Residue) – Sequence of residue objects.

accept_atom(atom)

Decide if the atom is valid or not.

accept_residue(res)

Decide if the residue is valid or not.

class ResidueSelectorBySeqNum(entries, **kwargs)

Bases: luna.MyBio.selector.Selector

Select atoms from compounds defined at entries.

Parameters

entries (iterable of int) – Sequence of residue sequence numbers.

accept_atom(atom)

Decide if the atom is valid or not.

accept_residue(res)

Decide if the residue is valid or not.

class Selector(keep_hydrog=True, keep_altloc=True, altloc=('A', '1'))

Bases: luna.MyBio.PDB.PDBIO.Select

Select atoms for PDB output.

Parameters

• keep_hydrog (bool) – If True (default), keeps all hydrogens. Otherwise, filter them out. Hydrogens are atoms whose element is either “H” or “D” (deuterium).

• keep_altloc (bool) – If True (default), keeps all atoms. Otherwise, keeps only atoms whose alternate location is in the list altloc.

• altloc (iterable) – List of valid alternate location identifiers. The default valid values are “A” and “1”.

accept_atom(atom)

Decide if the atom is valid or not.