schrodinger.application.matsci.maestrocmds module

Common Maestro commands.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.maestrocmds.get_colors(palette=None, seed=None, n_colors=10, normalized=False)

Return RGB color tuples.

Parameters

  • palette (str) – if not a palette in PALETTES then this is the palette kwarg passed to seaborn.color_palette

  • seed (None or int) – if given randomize the RGB color tuples using the given seed

  • n_colors (int) – the number of colors to return

  • normalized (bool) – whether to normalize the RGB tuples

Return type

list

Returns

contains RGB color tuples

schrodinger.application.matsci.maestrocmds.normalize_rgb_color(rgb)

Normalize the given color.

Parameters

rgb (tuple) – an RGB triple of integers in [0, 255]

Return type

tuple

Returns

normalized RGB triple of floats in [0, 1]

schrodinger.application.matsci.maestrocmds.get_atoms_asl(idxs)

Return the atoms ASL.

Parameters

idxs (list(int)) – atom indices

Return type

str

Returns

the atoms ASL

schrodinger.application.matsci.maestrocmds.execute_cmd(cmd)

Execute the Maestro command.

Parameters

cmd (str) – the Maestro command

schrodinger.application.matsci.maestrocmds.color_atoms(rgb, idxs)

Color atoms in the Maestro WS.

Parameters

  • rgb (tuple) – an RGB triple of integers in [0, 255]

  • idxs (list(int)) – atom indices

schrodinger.application.matsci.maestrocmds.color_atom_groups(all_idxs, rgbs=None)

Color groups of atoms in the Maestro WS.

Parameters

  • all_idxs (list(list(int))) – groups of atom indices

  • rgbs (list(tuple) or None) – RGB triples of integers in [0, 255] for coloring the different groups of atoms, if None then some defaults colors are used

schrodinger.application.matsci.maestrocmds.select_all_atoms()

Context manager to temporarily select all atoms in the Maestro WS.

schrodinger.application.matsci.maestrocmds.select_atoms(index)

Select specified atoms in Maestro WS

Parameters

index (list) – list of atom indexes

schrodinger.application.matsci.maestrocmds.color_by_element()

Color all atoms in the Maestro WS by element.

schrodinger.application.matsci.maestrocmds.set_ballnstick_repr(idxs)

Set the representation of atoms in the Maestro WS to ball-and-stick.

Parameters

idxs (list(int)) – atom indices

schrodinger.application.matsci.maestrocmds.set_included(entry_id)

Set the included entry to that of the given entry ID.

Parameters

entry_id (str) – the entry ID

schrodinger.application.matsci.maestrocmds.ensure_project_entry(struct, groupname, ptable=None, include_and_sort=False, sorting_prop=None)

Find if the structure entry exists in the project table’s group named groupname, if not create a new entry in this group. Then optionally sort the group and include/select the structure using the sorting property name.

Parameters

  • struct (structure.Structure) – The structure to ensure is in the project

  • groupname (str) – The name of the group to add the structure to

  • ptable (project.Project) – The project table

  • include_and_sort (bool) – If True, include and select the entry and sort the PT group it is in by sorting_prop. Default is False.

  • sorting_prop (str) – The structure property name used to sort the entries

Return type

project.ProjectRow

Returns

The project row for the entry

schrodinger.application.matsci.maestrocmds.sort_group_include_row(groupname, row, sorting_prop, ptable=None)

Sort the given project group by iteration number and then select/include the given row

Parameters

  • groupname (str) – The name of the group to sort

  • row (project.ProjectRow) – The project row of the entry to include

  • sorting_prop (str) – The property name used to sort the entries. If None, group sorting will be skipped.

  • ptable (project.Project) – The project table

schrodinger.application.matsci.maestrocmds.add_miller_plane(hkl, vecs, scaled_vecs=None, min_plane=0, max_plane=1, color=(255, 0, 0), opacity=75, show_arrow=True, entry_id=None, origin=None, draw_location=0, thickness=1, also_draw_planes_behind=True)

Make plane and arrow graphics of a Miller plane and lattice vectors.

Parameters

  • hkl (list[int]) – Miller triple hkl (example: [1,2,1])

  • vecs (list[float]) – Lattice vectors (A)

  • scaled_vecs (list[float]) – Scaled lattice vectors (A) that presumably fit all the planes. If not provide, vecs will be used. See related any_polygons_outside_cell function

  • min_plane (int) – Minimum plane to draw

  • max_plane (int) – Minimum plane to draw

  • color (tuple[int]) – Plane color in RGB

  • opacity (float) – Plane opacity

  • show_arrow (bool) – Whether to show plane normal as an arrow

  • entry_id (str) – Project table entry ID, plane and arrow are associated with

  • origin (list[float]) – Origin (A)

  • draw_location (float) – Shift from the origin in dHKL units

  • thickness (float) – Thickness in the dHKL units

  • also_draw_planes_behind (bool) – Whether to draw planes behind the cell

Return type

xtal.CrystalPlane, maestro.common.Group or None

Returns

Plane and graphics or None on error

schrodinger.application.matsci.maestrocmds.any_polygons_outside_cell(group)

Given a maestro graphics group, check if there are any polygons outside of it. This function is related to add_miller_plane above.

Parameters

group (maestro.common.Group) – Group to check

Return type

bool

Returns

Whether there are any polygons outside the cell