bla_chromophor#

Functions#

get_max_chromophor_BLA(…)

Calculate bond length alternation value (BLA) for the maximum chromophor

Module Contents#

get_max_chromophor_BLA(atXYZ_source: shnitsel.data.tree.node.TreeNode[Any, shnitsel.data.dataset_containers.trajectory.Trajectory | shnitsel.data.dataset_containers.frames.Frames | xarray.Dataset | xarray.DataArray], structure_selection: shnitsel.filtering.structure_selection.StructureSelection | shnitsel.filtering.structure_selection.StructureSelectionDescriptor | None = None, SMARTS: str | None = None, num_double_bonds: int | None = None, allowed_chain_elements: str = '#6,#7,#8,#15,#16', max_considered_BLA_double_bonds: int = 50) → shnitsel.data.tree.node.TreeNode[Any, xarray.DataArray]#
get_max_chromophor_BLA(atXYZ_source: shnitsel.data.dataset_containers.trajectory.Trajectory | shnitsel.data.dataset_containers.frames.Frames | xarray.Dataset | xarray.DataArray, structure_selection: shnitsel.filtering.structure_selection.StructureSelection | shnitsel.filtering.structure_selection.StructureSelectionDescriptor | None = None, SMARTS: str | None = None, num_double_bonds: int | None = None, allowed_chain_elements: str = '#6,#7,#8,#15,#16', max_considered_BLA_double_bonds: int = 50) → xarray.DataArray

Calculate bond length alternation value (BLA) for the maximum chromophor in the provided structure_selection or the maximum chromophor in the structure represented by atXYZ.

Parameters:

  • atXYZ_source (TreeNode[Any, Trajectory | Frames | xr.Dataset | xr.DataArray] | Trajectory | Frames | xr.Dataset | xr.DataArray) – An xarray.DataArray of molecular coordinates, with dimensions atom and direction or another source of positional data like a trajectory, a frameset, a dataset representing either of those or a tree structure holding such data.

  • StructureSelectionDescriptor (structure_selection |) – Object encapsulating feature selection on the structure whose positional information is provided in atXYZ. If this argument is omitted altogether, a default selection for all bonds and atoms within the structure is created.

  • optional – Object encapsulating feature selection on the structure whose positional information is provided in atXYZ. If this argument is omitted altogether, a default selection for all bonds and atoms within the structure is created.

  • SMARTS (str, optional) – SMARTS string to match for the maximum chromophor.

  • num_double_bonds (int, optional) – The specified number of double bonds for the maximum chromophor.

  • allowed_chain_elements (str, default="#6,#7,#8,#15,#16") – SMARTS atomic specification, i.e. comma-separated list of element descriptors (default: C,N,O,P,S represented as ‘#6,#7,#8,#15,#16’).

  • max_considered_BLA_double_bonds (int, optional) – Maximum number of double bonds in a BLA chromophor if automatic maximum size detection is performed. Defaults to 50.

Return type:

An xarray.DataArray of the BLA for the maximum-length chromophor (alternating double bonds)

Raises:

ValueError – If the maximum chromophor within the provided selection or the entire molecule is not unique.