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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.utils.pymol', '__doc__': '\n Mappings from Maestro codes to PyMOL representations and settings\n ', 'surface_cmd': {0: 'isosurface', 1: 'isomesh', 2: 'isodot'}, 'ramp_colors': {'redwhiteblue': '[red, white, blue]', 'whiteblue': '[white, blue]', 'whitered': '[white, red]', 'rainbow': '[red, yellow, green, cyan, blue, magenta]'}, 'stereomethods': {'hardware': 'quadbuffer', 'crosseyed': 'crosseye', 'walleyed': 'walleye', 'interlaced': 'byrow', 'anaglyph': 'anaglyph', 'chromadepth': 'off'}, '__dict__': <attribute '__dict__' of 'Mapping' objects>, '__weakref__': <attribute '__weakref__' of 'Mapping' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.utils.pymol'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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 (str) – path to pymol executable
__getattr__(name)

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.utils.pymol', '__doc__': '\n Represents a remote PyMOL instance (controlled via a one-way pipe)\n\n Acts like a proxy to the cmd module, without return values on function\n calls (which would actually be very usefull).\n\n See also: PyMOL XMLRPC server (pymol -R)\n ', '__init__': <function PymolInstance.__init__>, '_initPipe': <function PymolInstance._initPipe>, '_hangingStdinWorkaround': <function PymolInstance._hangingStdinWorkaround>, '_getEnviron': <function PymolInstance._getEnviron>, '__getattr__': <function PymolInstance.__getattr__>, '_re_illegal': re.compile('[^-.\\w]'), 'get_legal_name': <function PymolInstance.get_legal_name>, 'get_unused_name': <function PymolInstance.get_unused_name>, '_get_unused_group_name': <function PymolInstance._get_unused_group_name>, 'sendVersionCheck': <function PymolInstance.sendVersionCheck>, 'do': <function PymolInstance.do>, 'close': <function PymolInstance.close>, '__dict__': <attribute '__dict__' of 'PymolInstance' objects>, '__weakref__': <attribute '__weakref__' of 'PymolInstance' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.utils.pymol'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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 (str) – extra command line arguments for pymol
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.utils.pymol', '__doc__': '\n Represents a PyMOL script for deferred execution.\n ', '_initPipe': <function PymolScriptInstance._initPipe>, 'close': <function PymolScriptInstance.close>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(name)
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(pymol_command='pymol')
Parameters:pymol_command (str) – path to pymol executable
__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.utils.pymol'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

do(cmmd)

Send command to PyMOL

Parameters:cmmd (str) – PyMOL command
Returns:True on success and False on error
Return type:bool

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.

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
__getattr__(key)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.utils.pymol', '__doc__': '\n Represents a surface entry in a "vis_list" file\n\n :vartype name_pymol: str\n :ivar name_pymol: PyMOL object name\n\n :vartype visfile: str\n :ivar visfile: filename of vis file\n ', '_prefix': 'surf', '__init__': <function VisRecord.__init__>, '__getattr__': <function VisRecord.__getattr__>, '_load': <function VisRecord._load>, '__dict__': <attribute '__dict__' of 'VisRecord' objects>, '__weakref__': <attribute '__weakref__' of 'VisRecord' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.utils.pymol'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.utils.pymol', '__doc__': '\n Represents a volume entry in a "vis_list" file\n\n Volume gets auto-loaded when accessing *name_pymol*.\n ', '_prefix': 'vol', '_load': <function VisRecordVol._load>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(key)
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(row, idx)
Parameters:
  • row (RowProxy) – project table row
  • idx (int) – zero-based index in “m_surface” table
__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.utils.pymol'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

Bases: schrodinger.project.ProjectRow

Proxy for project table row to attach additional data.

__init__(row, cmd)
Parameters:
__del__()
doGroup(name)

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

Parameters:name (str) – PyMOL object name
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__delitem__(prop)
Deprecated, instead use:
del ProjectRow.property[prop]
__dict__ = mappingproxy({'__module__': 'schrodinger.utils.pymol', '__doc__': '\n Proxy for project table row to attach additional data.\n ', '__init__': <function RowProxy.__init__>, '__del__': <function RowProxy.__del__>, 'doGroup': <function RowProxy.doGroup>})
__dir__() → list

default dir() implementation

__eq__(other)

Test ProjectRow equality by project handle and entry index.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(prop)
Deprecated, instead use:
value = ProjectRow.property[prop]
__gt__

Return self>value.

__hash__ = None
__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.utils.pymol'
__ne__(other)

Test ProjectRow inequality by project handle and entry index.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()

Return string representation

__setattr__

Implement setattr(self, name, value).

__setitem__(prop, value)
Deprecated, instead use:
ProjectRow.property[prop] = value
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

cms_file

Return associated CMS file or None if there is no associated file

cms_structure_reader

Return StructureReader for associated CMS file or EmptyIterator if there is no associated file

deletable

Whether the entry is deletable or not

delete()

Delete this row/entry from the project.

doc = 'Inclusion state of the entry (NOT_IN_WORKSPACE/IN_WORKSPACE/LOCKED_IN_WORKSPACE)\nWARNING: This property should NOT be treated as a boolean.'
entry_id

Entry ID of the row

getStructure(props=True, copy=True)
Returns:

The entry’s structure
Return type:

structure.Structure
Parameters:
  • props (bool) – Whether the accociated PT properties are included in the returned structure (default).
  • copy – Whether to return a copy of the PT structure (default). If set to False, returns the original CT for the entry. Such use should in general be avoided, except as an optimization. NOTE: With copy=False, when the returned CT is modified, the changes are instantly propagated to the PT, but not the Workspace, and changes to properties do not propagate. Unless it’s certain that properties didn’t change, and that the structure is not included in the Workspace, any changes to it should be followed up by a call to setStructure().

WARNING: The current default (copy=True) is to make a duplicate of the entry’s structure. These will be marked for garbage collection once they go out of scope in the calling code, but if, for example, you are in a loop your memory usage will grow until the loop is exited (and it may even take a while for it to drop since garbage collection is not necessarily immediate). This can cause large memory usage if, for example, you are iterating over a large number entries. In some cases you may want to explicitly delete the returned Structure. For example, in a loop iterating over a large number of entries you may want to delete the Structure while still in the loop (after you’re done processing the Structure) to prevent memory bloat.

group

EntryGroup for the row

inWorkspace()

Obsolete. Use ProjectRow.in_workspace property instead.

in_workspace

Inclusion state of the entry (NOT_IN_WORKSPACE/IN_WORKSPACE/LOCKED_IN_WORKSPACE) WARNING: This property should NOT be treated as a boolean.

includeOnly()

Include this entry in the workspace and exclude all other entries.

index

Internal Project index of the row. This is different from Project Table row number or from entry ID.

is_selected

Whether the entry is selected

moveToGroup(group_name)

Move this entry to group. If group does not exist it will be created.

Parameters:group_name – Name of group to which to move this entry. If such

group doesn’t exist, it will be created. Note, this is different from the user-visible group title. :type group_name: string

newMolecularSurface(*args, **kwargs)

Create a new molecular surface for this row

Parameters:
  • name (str) – The name of the surface. Note that project rows require all surfaces to be named uniquely. See overwrite.
  • asl (str or NoneType) – If given, the surface will only be created for atoms in the structure that match the provided ASL. Note that only one of asl and atoms may be given. If neither are given, then the surface will be created for all atoms in the structure.
  • atoms (list or NoneType) – An optional list of atom numbers. If given, the surface will only be created for the specified atoms. Note that only one of asl and atoms may be given. If neither are given, then the surface will be created for all atoms in the structure.
  • resolution (float) – The resolution of the surface, generally between 0 and 1. Smaller numbers lead to a more highly detailed surface.
  • probe_radius (float) – The radius of the rolling sphere used to calculate the surface. Defaults to 1.4 if mol_surf_type is surface.MolSurfType.Molecular or surface.MolSurfType.Extended. May not be given if mol_surf_type is surface.MolSurfType.vdw.
  • vdw_scaling (float) – If given, all atomic radii will be scaled by the provided value before the surface is calculated.
  • mol_surf_type (surface.MolSurfType) – The type of surface to create.
  • overwrite (bool) – What to do if the new surface has the same name as an existing surface for this project row. If True, the existing surface will be overwritten. In False, a ValueError will be raised.
Returns:

The new surface
Return type:

project_surface.Surface
property

Dictionary-like container of entry properties. Keys are strings of the form type_family_name as described in structure.PropertyName documentation.

read_only

Whether the entry is read only or not

row_number

This is the Project Table row number, as it appears to the user in Maestro. It is different from the internal row index.

selectOnly()

Select this entry and de-select all other entries in the Project Table.

setStructure(struct, props=True, copy=True, sync_workspace=True)

Set the structure of the entry to the specified structure. If the entry is included in the Workspace, the Workspace CT will be updated accordingly.

Parameters:
  • struct (schrodinger.structure.Structure) – Set the entry to this Structure object
  • copy (bool) – If True, a copy of the Structure (CT) is made and that copy is used to set the entry. If False, the original Structure, struct, is placed into the project table. Doing this hands off control of struct and you should no longer use struct.
  • props (bool) – If True, update properties in the entry. If False, properties are ignored.
  • sync_workspace (bool) – Whether to update the maestro workspace
structure

This attribute is deprecated. Please use ProjectRow.getStructure() and ProjectRow.setStructure() instead.

surface

A dictionary of all surfaces for this row. Keys are surface names and values are project_surface.Surface objects. :type: project_surface.SurfaceDict

surfaces

Return an interator to the surface objects available for this entry

title

The title of the entry

ungroup()

Remove this entry from its current group.

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
__getitem__(i)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.utils.pymol', '__doc__': '\n Maps workspace atom indices to (row.index, ID)\n ', '__init__': <function WorkspaceIdMapper.__init__>, '__getitem__': <function WorkspaceIdMapper.__getitem__>, '__dict__': <attribute '__dict__' of 'WorkspaceIdMapper' objects>, '__weakref__': <attribute '__weakref__' of 'WorkspaceIdMapper' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.utils.pymol'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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.process_measurements(cmd, prj_handle)

Send workspace measurements to PyMOL

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

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

Import Phase pharmacophores as CGOs into PyMOL.

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

Send a row from the project table to PyMOL.

Parameters:
  • cmd (PymolInstance) – PyMOL API proxy
  • 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
schrodinger.utils.pymol.process_surface(cmd, row, e_surf)

Send a surface to PyMOL

Parameters:
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