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) → Iterator[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.