schrodinger.utils.pymol module

Utilities to load Maestro projects into PyMOL.

Example:

>>> cmd = PymolInstance(["/path/to/pymol"])
>>> pt = maestro.project_table_get()
>>> process_prj(cmd, pt)

Copyright Schrodinger LLC, All rights reserved.

Author: Thomas Holder

class schrodinger.utils.pymol.Mapping

Bases: object

Mappings from Maestro codes to PyMOL representations and settings

surface_cmd = {0: 'isosurface', 1: 'isomesh', 2: 'isodot'}
ramp_colors = {'rainbow': '[red, yellow, green, cyan, blue, magenta]', 'redwhiteblue': '[red, white, blue]', 'whiteblue': '[white, blue]', 'whitered': '[white, red]'}
stereomethods = {'anaglyph': 'anaglyph', 'chromadepth': 'off', 'crosseyed': 'crosseye', 'hardware': 'quadbuffer', 'interlaced': 'byrow', 'walleyed': 'walleye'}
class schrodinger.utils.pymol.PymolInstance(pymol_command=('pymol',))

Bases: object

Represents a remote PyMOL instance (controlled via a one-way pipe)

Acts like a proxy to the cmd module, without return values on function calls (which would actually be very usefull).

See also: PyMOL XMLRPC server (pymol -R)

__init__(pymol_command=('pymol',))
Parameters

pymol_command (list or tuple) – path to pymol executable

Replacement for cmd.get_legal_name

Parameters

name (str) – name candidate

Returns

legal PyMOL object name

Return type

str

get_unused_name(name, alwaysnumber=1)

Replacement for cmd.get_unused_name, does not talk back to PyMOL but maintains it’s own set of already used names.

This is only necessary because the the pipe cannot return values.

Parameters

  • name (str) – name candidate

  • alwaysnumber (bool) – if False, only append a number if name already exists

Returns

unused legal PyMOL object name

Return type

str

sendVersionCheck()

Print a warning on the PyMOL log window if PyMOL version is too old.

do(cmmd)

Send command to PyMOL

Parameters

cmmd (str) – PyMOL command

Returns

True on success and False on error

Return type

bool

close()

Quit PyMOL

class schrodinger.utils.pymol.PymolScriptInstance(pymol_command=('pymol',))

Bases: schrodinger.utils.pymol.PymolInstance

Represents a PyMOL script for deferred execution.

close(args=('-cqk',))

Close file handle and execute script in PyMOL

Parameters

args (list or tuple) – extra command line arguments for pymol

class schrodinger.utils.pymol.VisRecord(row, idx)

Bases: object

Represents a surface entry in a “vis_list” file

Variables

  • name_pymol (str) – PyMOL object name

  • visfile (str) – filename of vis file

__init__(row, idx)
Parameters

  • row (RowProxy) – project table row

  • idx (int) – zero-based index in “m_surface” table

class schrodinger.utils.pymol.VisRecordVol(row, idx)

Bases: schrodinger.utils.pymol.VisRecord

Represents a volume entry in a “vis_list” file

Volume gets auto-loaded when accessing name_pymol.

class schrodinger.utils.pymol.RowProxy(row, cmd)

Bases: schrodinger.project.project.ProjectRow

Proxy for project table row to attach additional data.

__init__(row, cmd)
Parameters

  • row (schrodinger.project.ProjectRow) – project table row

  • cmd (PymolInstance) – PyMOL API proxy

doGroup(name)

Put name in PyMOL group, if row is in a Maestro group.

Parameters

name (str) – PyMOL object name

schrodinger.utils.pymol.select_surf_asl(row, surf_handle, name='')

Make a PyMOL selection for surface ASL.

Returns

PyMOL selection name

class schrodinger.utils.pymol.WorkspaceIdMapper(prj_handle)

Bases: object

Maps workspace atom indices to (row.index, ID)

__init__(prj_handle)
Parameters

prj_handle (schrodinger.project.Project) – project handle

schrodinger.utils.pymol.get_measurement_items(key, mmprojadmin)

Get workspace atom ids from the measurements table. If not running from Maestro, read the .tab files from the .mmproj-admin directory.

Parameters

key (str) – one of distance, angle or dihedral

Return type

list(int)

Returns

List of lists of atom ids (workspace)

schrodinger.utils.pymol.create_selection(cmd, idmapper, atom_ids)

Create selection list of strings from atom ids. Like this [‘1fjs & id 345’, ‘1fjs & id 571’]

Parameters
Returns

selection list of strings

schrodinger.utils.pymol.get_interaction_data()

Get interactions data

Returns

interactions data

schrodinger.utils.pymol.create_interactions_group(cmd, interaction_name, object_names)

Create interactions group

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • interaction_name (string) – interaction’s name

  • object_names (string) – space separated string of object names which will be added to the group

schrodinger.utils.pymol.create_pi_pi_interaction_distance(cmd, idmapper, interaction_data_list, interaction_name, color)

Create workspace Pi Pi interaction as a distance object in PyMOL

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • idmapper (WorkspaceIdMapper) – id mapper

  • interaction_data_list (list) – list of interactions

  • interaction_name (string) – interaction’s name

  • name (string) – rgb color

schrodinger.utils.pymol.create_pi_cation_interaction_distance(cmd, idmapper, interaction_data_list, interaction_name, color)

Create workspace Pi Cation interaction as a distance object in PyMOL

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • idmapper (WorkspaceIdMapper) – id mapper

  • interaction_data_list (list) – list of interactions

  • interaction_name (string) – interaction’s name

  • name (string) – rgb color

schrodinger.utils.pymol.create_interaction_distance(cmd, idmapper, interaction_data_list, interaction_name, color)

Create workspace interaction as a distance object in PyMOL

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • idmapper (WorkspaceIdMapper) – id mapper

  • interaction_data_list (list) – list of interactions

  • interaction_name (string) – interaction’s name

  • name (string) – rgb color

schrodinger.utils.pymol.process_interactions(cmd, prj_handle)

Send workspace interactions to PyMOL

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • prj_handle (schrodinger.project.Project) – project handle

schrodinger.utils.pymol.process_measurements(cmd, prj_handle)

Send workspace measurements to PyMOL

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • prj_handle (schrodinger.project.Project) – project handle

schrodinger.utils.pymol.get_font_id(font_name, font_style)

Get the PyMOL label_font_id which best matches the given font name and style.

Return type

int

schrodinger.utils.pymol.process_highlights(cmd, prj_handle)

Send “highlights” (label+arrow annotation) to PyMOL

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • prj_handle (schrodinger.project.Project) – project handle

schrodinger.utils.pymol.process_prj(cmd, prj_handle, limit='all', with_surf=True, mimic=True, include_trajectories=False)

Send maestro project to PyMOL. By default send everything, optional filters may apply.

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • prj_handle (schrodinger.project.Project) – project handle

  • limit (str) – all, included or selected. The latter will not send workspace items like measurements and text highlights.

  • with_surf (bool) – send surfaces and maps (volumes)

  • mimic (bool) – use PyMOL settings to match style as close as possible

  • include_trajectories (bool) – include trajectories

schrodinger.utils.pymol.process_watermap(cmd: schrodinger.utils.pymol.PymolInstance, row: schrodinger.project.project.ProjectRow)

Process watermaps. Get watermap sites from structure and send them to PyMOL as colored spheres

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • row (schrodinger.project.ProjectRow) – project table row

schrodinger.utils.pymol.process_hypothesis(cmd, row, mae)

Import Phase pharmacophores as CGOs into PyMOL.

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • row (schrodinger.project.ProjectRow) – project table row

  • mae (str) – reference mae filename

schrodinger.utils.pymol.process_row(cmd, proj, row, limit_included=False, with_surf=True, mimic=True, include_trajectories=False)

Send a row from the project table to PyMOL.

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • proj (schrodinger.project.Project) – project

  • row (schrodinger.project.ProjectRow) – project table row

  • limit_included (bool) – limit surface export to workspace

  • with_surf (bool) – send surfaces

  • mimic (bool) – use PyMOL settings to match style as close as possible

  • include_trajectories (bool) – include trajectories

schrodinger.utils.pymol.process_trajectory(cmd, proj, row, mae_file_name, mimic=True)

Send trajectory to PyMOL

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • proj (schrodinger.project.Project) – project

  • row (RowProxy - proxy for project table with additional data) – project table row

  • mae_file_name (str) – mae file name to send to PyMOL

  • mimic (bool) – use PyMOL settings to match style as close as possible

schrodinger.utils.pymol.process_surface(cmd, row, e_surf)

Send a surface to PyMOL

Parameters

  • cmd (PymolInstance) – PyMOL API proxy

  • row (RowProxy) – project table row

  • e_surf (schrodinger.project.EntrySurface) – surface

schrodinger.utils.pymol.send_maestro_settings(cmd)

Map Maestro settings to closest matching PyMOL settings.

Parameters

cmd (PymolInstance) – PyMOL API proxy

Return type

bool

Returns

True on success and False if Maestro is not available