schrodinger.application.matsci.swap_fragments_utils module

Utilities for swapping fragments to create a structure built from specified parts of two other structures.

Copyright Schrodinger, LLC. All rights reserved.

exception schrodinger.application.matsci.swap_fragments_utils.SwapFragmentsException

Bases: Exception

schrodinger.application.matsci.swap_fragments_utils.get_idx_groups_str(idx_groups)

Get a string representation of the given index groups.

Parameters:

idx_groups (list) – contains lists of indices

Return type:

str

Returns:

the string

schrodinger.application.matsci.swap_fragments_utils.get_idxs_marked_atoms(st, prop)

Return a list of indices of atoms in the given structure that have the given property defined.

Parameters:
Return type:

list

Returns:

contains indices of atoms

schrodinger.application.matsci.swap_fragments_utils.get_idx_groups(text)

Get index groups from the given string.

Parameters:

text (str) – the string

Raises:

SwapFragmentsException – if there is an issue

Return type:

list

Returns:

contains list of indices

schrodinger.application.matsci.swap_fragments_utils.get_keep_idxs(st)

Return a list of indices of keep atoms in the given structure.

Parameters:

st (schrodinger.structure.Structure) – the structure

Return type:

list

Returns:

contains indices of keep atoms

schrodinger.application.matsci.swap_fragments_utils.get_superposition_idxs(st)

Return a list of indices of superposition atoms in the given structure.

Parameters:

st (schrodinger.structure.Structure) – the structure

Return type:

list

Returns:

contains indices of superposition atoms

schrodinger.application.matsci.swap_fragments_utils.get_extracted_and_maps(st, idxs)

Extract and return a structure from the given indices as well as old-to-new and new-to-old atom index maps.

Parameters:
Return type:

schrodinger.structure.Structure, dict, dict

Returns:

the extracted structure and old-to-new and new-to-old index maps

schrodinger.application.matsci.swap_fragments_utils.get_cut_bonds(st, keep_idxs)

Return a list of (keep, replace, order) tuples, where keep is an index that will be kept, replace is an index that will be replaced, and order is the bond order, for bonds involving atoms specified in the given keep indices.

Parameters:
Return type:

list

Returns:

contains (keep, replace, order) tuples

schrodinger.application.matsci.swap_fragments_utils.get_closest_atom(ref_st, ref_idx, nov_cell)

Return the novel atom index closest to the given reference atom index.

Parameters:

  • ref_st (schrodinger.structure.Structure) – second structure, called reference

  • ref_idx (int) – the reference index

  • nov_cell (infrastructure.DistanceCell) – distance cell for the novel structure

Return type:

int or None

Returns:

the novel index if there is one

schrodinger.application.matsci.swap_fragments_utils.get_ref_nov_close_pairs(nov_st, ref_st)

Return a map of reference to novel close atoms.

Parameters:
Return type:

dict

Returns:

a map of reference to novel close atoms

schrodinger.application.matsci.swap_fragments_utils.get_assembled_structure(nov_st, ref_st, nov_superposition_idxs, ref_superposition_idxs, nov_keep_idxs, ref_keep_idxs, title=None, require_identical_bonds=True)

Return an assembled structure from the given structures using superposition followed by extraction.

Parameters:

  • nov_st (schrodinger.structure.Structure) – first structure, called novel

  • ref_st (schrodinger.structure.Structure) – second structure, called reference

  • nov_superposition_idxs (list) – novel superposition indices

  • ref_superposition_idxs (list) – reference superposition indices

  • nov_keep_idxs (list) – novel keep indices

  • ref_keep_idxs (list) – reference keep indices

  • title (str) – the title to be given to the assembled structure

  • require_identical_bonds (bool) – whether to require that bonds to be created must exist in both novel and reference structures and be of the same bond order

Raises:

SwapFragmentsException – if there is an issue

Return type:

schrodinger.structure.Structure

Returns:

the assembled structure

schrodinger.application.matsci.swap_fragments_utils.get_idxs_str(idxs, sort=True)

Get a string representation of the given indices.

Parameters:

  • idxs (list) – the idxs

  • sort (bool) – whether to sort

Return type:

str

Returns:

the string

schrodinger.application.matsci.swap_fragments_utils.get_idxs(le)

Get indices from the given QLineEdit.

Parameters:

le (QtWidgets.QLineEdit) – the line edit

Return type:

list

Returns:

the indices