MoleculeSelector

MoleculeSelector(self, mol=None)

A helper to create selections for Molecules and AtomArrays.

The selection (self.mask) is not computed or returned until the evaluate_on_array method is called. Until then methods are stored for later evaluation.

Parameters

Name	Type	Description	Default
mol	Molecule	The molecule object to select from.	None

Attributes

Name	Type	Description
mol	Molecule	The molecule object to select from.
mask	ndarray or None	Boolean array for the selection on the most recently evaluated array.
pending_selections	list	List of selection operations to be applied once evaluate_on_array is called.

Methods

Name	Description
atom_name	Select atoms by their name.
chain_id	Select atoms by chain identifier.
element	Select atoms by element symbol.
evaluate_on_array	Evaluate this selection on the AtomArray.
is_amino_acid	Select amino acid residues.
is_backbone	Select backbone atoms for peptide and nucleotide.
is_canonical_amino_acid	Select canonical amino acid residues.
is_canonical_nucleotide	Select canonical nucleotide residues.
is_carbohydrate	Select carbohydrate residues.
is_hetero	Select hetero atoms.
is_ligand	Select ligand atoms.
is_monoatomic_ion	Select monoatomic ions.
is_nucleotide	Select nucleotide residues.
is_peptide_backbone	Select peptide backbone atoms.
is_phosphate_backbone	Select phosphate backbone atoms.
is_polymer	Select polymer atoms.
is_solvent	Select solvent atoms.
linear_bond_continuity	Select atoms with linear bond continuity.
not_amino_acids	Select non-amino acid residues.
not_atom_names	Select atoms not matching the specified atom names.
not_canonical_amino_acids	Select non-canonical amino acid residues.
not_canonical_nucleotides	Select non-canonical nucleotide residues.
not_carbohydrates	Select non-carbohydrate residues.
not_chain_id	Select atoms not in the specified chains.
not_element	Select atoms not matching the specified elements.
not_hetero	Select non-hetero atoms.
not_monoatomic_ions	Select non-monoatomic ion atoms.
not_nucleotides	Select non-nucleotide residues.
not_peptide_backbone	Select non-peptide backbone atoms.
not_phosphate_backbone	Select non-phosphate backbone atoms.
not_polymer	Select non-polymer atoms.
not_res_id	Select atoms not matching the specified residue IDs.
not_res_name	Select atoms not matching the specified residue names.
not_solvent	Select non-solvent atoms.
res_id	Select atoms by residue ID.
res_name	Select atoms by residue name.
reset	Reset all pending selections and the mask
store_selection	Evaluate and store the current selection as a named attribute on the Molecule

atom_name

MoleculeSelector.atom_name(atom_name)

Select atoms by their name.

Parameters

Name	Type	Description	Default
atom_name	str or list of str or tuple of str or ndarray	The atom name(s) to select.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

chain_id

MoleculeSelector.chain_id(chain_id)

Select atoms by chain identifier.

Parameters

Name	Type	Description	Default
chain_id	list of str or tuple of str or ndarray	The chain identifier(s) to select.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

element

MoleculeSelector.element(element)

Select atoms by element symbol.

Parameters

Name	Type	Description	Default
element	list of str or tuple of str or ndarray	The element symbol(s) to select.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

evaluate_on_array

MoleculeSelector.evaluate_on_array(array)

Evaluate this selection on the AtomArray.

Parameters

Name	Type	Description	Default
array	AtomArray or AtomArrayStack	The atomic structure to evaluate the selection on.	required

Returns

Name	Type	Description
	ndarray	Boolean mask array indicating which atoms match the selection criteria.

Notes

All of the selection operations that have been staged for this Selector are evaluated and combined with a logical AND, using the AtomArray as input.

is_amino_acid

MoleculeSelector.is_amino_acid()

Select amino acid residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_backbone

MoleculeSelector.is_backbone()

Select backbone atoms for peptide and nucleotide.

is_canonical_amino_acid

MoleculeSelector.is_canonical_amino_acid()

Select canonical amino acid residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_canonical_nucleotide

MoleculeSelector.is_canonical_nucleotide()

Select canonical nucleotide residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_carbohydrate

MoleculeSelector.is_carbohydrate()

Select carbohydrate residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_hetero

MoleculeSelector.is_hetero()

Select hetero atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_ligand

MoleculeSelector.is_ligand()

Select ligand atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_monoatomic_ion

MoleculeSelector.is_monoatomic_ion()

Select monoatomic ions.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_nucleotide

MoleculeSelector.is_nucleotide()

Select nucleotide residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_peptide_backbone

MoleculeSelector.is_peptide_backbone()

Select peptide backbone atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_phosphate_backbone

MoleculeSelector.is_phosphate_backbone()

Select phosphate backbone atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_polymer

MoleculeSelector.is_polymer()

Select polymer atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

is_solvent

MoleculeSelector.is_solvent()

Select solvent atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

linear_bond_continuity

MoleculeSelector.linear_bond_continuity()

Select atoms with linear bond continuity.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_amino_acids

MoleculeSelector.not_amino_acids()

Select non-amino acid residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_atom_names

MoleculeSelector.not_atom_names(atomname)

Select atoms not matching the specified atom names.

Parameters

Name	Type	Description	Default
atomname	str or list of str	The atom name(s) to exclude.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_canonical_amino_acids

MoleculeSelector.not_canonical_amino_acids()

Select non-canonical amino acid residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_canonical_nucleotides

MoleculeSelector.not_canonical_nucleotides()

Select non-canonical nucleotide residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_carbohydrates

MoleculeSelector.not_carbohydrates()

Select non-carbohydrate residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_chain_id

MoleculeSelector.not_chain_id(chain_id)

Select atoms not in the specified chains.

Parameters

Name	Type	Description	Default
chain_id	str or list of str	The chain identifier(s) to exclude.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_element

MoleculeSelector.not_element(element)

Select atoms not matching the specified elements.

Parameters

Name	Type	Description	Default
element	str or list of str	The element symbol(s) to exclude.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_hetero

MoleculeSelector.not_hetero()

Select non-hetero atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_monoatomic_ions

MoleculeSelector.not_monoatomic_ions()

Select non-monoatomic ion atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_nucleotides

MoleculeSelector.not_nucleotides()

Select non-nucleotide residues.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_peptide_backbone

MoleculeSelector.not_peptide_backbone()

Select non-peptide backbone atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_phosphate_backbone

MoleculeSelector.not_phosphate_backbone()

Select non-phosphate backbone atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_polymer

MoleculeSelector.not_polymer()

Select non-polymer atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_res_id

MoleculeSelector.not_res_id(num)

Select atoms not matching the specified residue IDs.

Parameters

Name	Type	Description	Default
num	int or list of int	The residue ID(s) to exclude.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_res_name

MoleculeSelector.not_res_name(res_name)

Select atoms not matching the specified residue names.

Parameters

Name	Type	Description	Default
res_name	str or list of str	The residue name(s) to exclude.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

not_solvent

MoleculeSelector.not_solvent()

Select non-solvent atoms.

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

res_id

MoleculeSelector.res_id(num)

Select atoms by residue ID.

Parameters

Name	Type	Description	Default
num	int or list of int	The residue ID(s) to select.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

res_name

MoleculeSelector.res_name(res_name)

Select atoms by residue name.

Parameters

Name	Type	Description	Default
res_name	str or list of str	The residue name(s) to select.	required

Returns

Name	Type	Description
	Selector	Returns self for method chaining.

reset

MoleculeSelector.reset()

Reset all pending selections and the mask

Returns

Name	Type	Description
self	Selector	Returns self for method chaining

store_selection

MoleculeSelector.store_selection(name)

Evaluate and store the current selection as a named attribute on the Molecule

Parameters

Name	Type	Description	Default
name	str	The name to store the selection under.	required

Returns

Name	Type	Description
	None

Raises

Name	Type	Description
	ValueError	If no selection has been made.