schrodinger.project.utils module

schrodinger.project.utils.get_PT()

Safe getter for the project instance that swallows exceptions that occur if the project has been closed.

Using this function avoids unnecessary tracebacks that occur if the project is requested in the brief period after the project has been closed before a new one is created.

Returns

a project instance, if a project is available in Maestro

Return type

project.Project or NoneType

schrodinger.project.utils.set_entries_pinned(entry_ids, pin)

Pin or unpin entries from the workspace.

Parameters

  • entry_ids (list(str)) – a list of entry IDs

  • pin (bool) – whether to pin or unpin the specified entries to the workspace

schrodinger.project.utils.set_entry_pinned(entry_id, pin)

Pin or unpin an entry from the workspace.

Parameters

  • entry_id (str) – an entry ID

  • pin (bool) – whether to pin or unpin the specified entry to the workspace

schrodinger.project.utils.set_entries_included(entry_ids, include, override_pin=False)

For the specified entries, either include them in or exclude them from the workspace.

Parameters

  • entry_ids (list(str)) – a list of entry IDs

  • include (bool) – whether to include (True) or exclude (False)

  • override_pin (bool) – if False, ignore pinned entries. If True, exclude entries that are set to be excluded even if they are pinned. If pinned entries are set to be included, leave them as pinned (because they are also included as pinned entries)

schrodinger.project.utils.set_entry_included(entry_id, include, override_pin=False)

For the specified entry, either include it in or exclude it from the workspace.

Parameters

  • entry_id (str) – an entry ID

  • include (bool) – whether to include (True) or exclude (False)

  • override_pin (bool) – if False, ignore pinned entries. If True, exclude entries that are set to be excluded even if they are pinned. If pinned entries are set to be included, leave them as pinned (because they are also included as pinned entries)

schrodinger.project.utils.include_entries(entry_ids)

Include the given entries and exclude any previously included entries.

Parameters

entry_ids (list(str)) – a list of entry IDs

schrodinger.project.utils.entry_is_pinned(entry_id)

Return whether the specified entry is pinned in the workspace.

Parameters

entry_id (str) – the entry ID of a row in the project

Returns

whether the entry is pinned in the workspace

Return type

bool

schrodinger.project.utils.entry_is_included(entry_id)

Return whether the specified entry is included in the workspace.

Parameters

entry_id (str) – the entry ID of a row in the project

Returns

whether the entry is included in the workspace

Return type

bool

schrodinger.project.utils.entry_is_selected(entry_id)

Return whether the specified entry is selected in the project.

Parameters

entry_id (str) – the entry ID of a row in the project

Returns

whether the entry is selected in the project

Return type

bool

schrodinger.project.utils.set_entry_locked(entry_id, lock)

Set the supplied project table entry to be “locked” or “unlocked.”

These operations are grouped because they are both performed when locking an entry in the visual interface.

Parameters

  • entry_id (str) – the entry ID of a row in the project

  • lock (bool) – whether to lock or unlock the specified entry

schrodinger.project.utils.entry_is_locked(entry_id)

Return whether the supplied project entry is read-only and not deletable.

These properties are both tested because both values are set when locking an entry in the visual interface.

Parameters

entry_id (str) – the entry ID of a row in the project

Returns

whether the entry is locked

Return type

bool

schrodinger.project.utils.remove_entries(entry_ids)

Cleanly remove the specified entries from the project. If an entry cannot be found, do not raise an exception.

Parameters

entry_id (list(str)) – a list of entry IDs

schrodinger.project.utils.create_subgroup(entry_ids, group_name, subgroup_title)

Create a subgroup of the specified project group, and place the supplied entries into it.

Parameters

  • entry_ids (list(str)) – entry IDs for project entries to be placed into the new subgroup

  • group_name (str) – name of the group to which this new subgroup will belong

  • subgroup_title (str) – the title of the new subgroup

Returns

the new group object

Return type

project.EntryGroup

schrodinger.project.utils.move_group(group, row_number)

Move all of the entries in the specified group to be below a specified row number in the project, while still retaining their group identity.

Parameters

  • group (project.EntryGroup) – a non-empty entry group

  • row_number (int) – the number of a row in the project: one that designates order within the project, not an entry ID

schrodinger.project.utils.get_rows(entry_ids)
Parameters

entry_id (list(str)) – a list of entry IDs

Returns

a list of either project rows corresponding to the provided entry IDs, if they exist, or None otherwise

Return type

list(project.ProjectRow or None)

schrodinger.project.utils.get_row(entry_id)
Parameters

entry_id (str) – an entry ID

Returns

row corresponding to the entry ID, if it exists

Return type

project.ProjectRow or None

schrodinger.project.utils.get_structures_for_entry_ids(entry_ids, copy=True, props=True, pt=None)

Iterate over structures for the given entry IDs.

schrodinger.project.utils.get_included_structures(copy=True, props=True, pt=None, sort_by_row_number: bool = False) → collections.abc.Iterator[schrodinger.structure._structure.Structure]

Iterate over structures for entries that are included in the Workspace. :param sort_by_row_number: Whether to sort the rows by the row number (current Project Table order)

schrodinger.project.utils.get_included_entry_ids(pt=None)

Iterate over entry IDs for entries that are included in the Workspace.

Return type

Iterator[str]

Returns

Each iteration yields the entry id of an included project entry

schrodinger.project.utils.get_selected_structures(copy=True, props=True, pt=None)

Iterate over structures for entries that are selected in the Project Table.

schrodinger.project.utils.get_selected_entry_ids(pt=None)

Iterate over entry IDs for entries that are selected in the Project Table.

Return type

Iterator[str]

Returns

Each iteration yields the entry id of an included project entry

schrodinger.project.utils.get_structure(entry_id)
Parameters

entry_ids (str) – an entry ID

Returns

a structure from the specified entry, if available

Return type

structure.Structure or None

schrodinger.project.utils.preserve_selection(pt=None)

Save the selection state of the project, then restore it on exit.

Parameters

pt (project.Project or NoneType) – optionally, a project instance

schrodinger.project.utils.unlock_entries(entry_ids, update_pt=True)

Temporarily unlock the specified entries, if they are locked. Otherwise, do not modify their lock state. Suppress signals from the project model during this process.

Parameters

  • entry_ids (list(str)) – a list of entry IDs

  • update_pt (bool) – whether to update the project table on exiting the context environment

schrodinger.project.utils.create_child_group(entry_ids, parent_group_name, group_name=None, before_entry_id=None)

Create a new group using the supplied entry IDs as a child group of the specified parent group.

Raises

ValueError – if no entry IDs are provided

Parameters

  • entry_ids (list(str)) – a list of entry IDs to put into the new group

  • parent_group_name (str) – the name of the group that should be the parent of the group created by this function

  • group_name (str or None) – the name of the group to be created; if not supplied, a unique name will be randomly generated

  • before_entry_id (str or NoneType) – optionally, the entry ID of a project entry above which the new subgroup should be created

Returns

the new group

Return type

project.EntryGroup

schrodinger.project.utils.get_entry_group(group_name)

Return the group in the project with the specified name.

Parameters

group_name (str) – the name of the desired group

Returns

the group with the specified name, if available

Return type

str or None

schrodinger.project.utils.generate_unique_group_name()
Returns

a unique entry group name

Return type

str

schrodinger.project.utils.get_top_entry(entry_ids)

Given a list of project entry IDs, return the one that appears in the highest visual row in the project.

Parameters

entry_ids (list(str)) – a list of project entry IDs

Returns

the entry ID corresponding to the “highest” entry in entry_ids

Return type

str

schrodinger.project.utils.entry_is_marked(entry_id)

Return whether the specified entry is “marked” with the Maestro property b_m_Mark.

Parameters

entry_id (str) – a project entry ID

Returns

whether the specified entry has the Mark property, and that the value of that property is True

Return type

bool

schrodinger.project.utils.set_entries_marked(entry_ids)

Programmatically mimic the behavior of the Maestro command “entrymarkincluded”, but for an arbitrary group of entries. If all entries are marked, unmark all entries. Otherwise, mark all entries.

Parameters

entry_ids (list(str)) – a list of entry IDs

schrodinger.project.utils.get_base_entry_group(entry_id)

For the specified entry, return the highest-level parent group to which it belongs, if possible.

Parameters

entry_id (str) – a project entry ID

Returns

the top-level entry group that contains the entry, if the entry belongs to any group

Return type

project.EntryGroup or NoneType

schrodinger.project.utils.move_row(entry_id, row_number)

Move the specified entry row to the specified position in the project.

Parameters

  • entry_id (str) – an entry ID

  • row_number (int) – the position to which the specified entry should be moved

schrodinger.project.utils.modify_row_structure(entry_id=None, row=None)

Context which returns a structure from the row corresponding to the given entry id and sets the structure back to the row afterwards. Also preserves the structure’s trajectory property.

Parameters

  • entry_id (str) – entry id of rows to modify

  • row (project.ProjectRow) – The project row for this entry. Either row or entry_id must be supplied

Returns

a structure in a context manager that will set the structure back onto the project row when control is returned to this function

Return type

structure.Structure or NoneType

schrodinger.project.utils.has_valid_wscore_block(row)

Given a ProjectRow instance, return True if the entry has associated WScore data and a valid receptor; False otherwise.

class schrodinger.project.utils.ProjectStructure(row=None, eid=None, modify=True)

Bases: object

A Context manager that gets the structure for an entry from the project table and then optionally puts it back in the PT upon exit

__init__(row=None, eid=None, modify=True)

Create a ProjectStructure instance

Parameters

  • row (project.ProjectRow) – The project row for this entry. Either row or eid must be supplied

  • eid (str) – The entry ID for this entry. Either row or eid must be suppled. If the eid is not found in the project, the self.row attribute will be None.

  • modify (bool) – If True (default), set the structure back in the project on exit. If False, do not modify the structure in the project.

Raises

AttributeError – If neither row nor eid are supplied

schrodinger.project.utils.get_trajectory_path(proj, eid)

Method will return None if passed a falsey entry ID. Return trajectory file path if any, or None.

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

schrodinger.project.utils.has_watermap(proj, eid)

If entry has watermap

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

Returns

True if entry has watermap, False otherwise

Return type

boolean

schrodinger.project.utils.has_trajectory(proj, eid)

Whether the entry with given entry id has a trajectory associated with it

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

schrodinger.project.utils.has_desmond_trajectory(proj, eid)

Whether the entry with given entry id has desmond trajectory

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

schrodinger.project.utils.has_materials_trajectory(proj, eid)

Whether the entry with given entry id has materials trajectory

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

schrodinger.project.utils.entry_excluded(entry_id: str)

Exclude the given entry temporarily.

Parameters

entry_id – Entry id to be excluded temporarily.

schrodinger.project.utils.restore_included_entries()

Store and restore any included entries.