Metadata

class hippo.metadata.MetaData(_MetaData__dict: Mapping[str, str] | None)[source]

Metadata dictionary linked to a compound or pose in a HIPPO Database

Attention

Metadata objects should not be created directly. Instead use the methods Compound.metadata() and Pose.metadata()

Metadata initialisation

del self[key: str] → None[source]: Set a dictionary key

self[key: str] = item → None[source]: Set the value associated to a specific dictionary key

append(key: str, value, commit: bool = True) → None[source]

Create or append to a list-like value with given key

Parameters:

key – metadata dictionary key to be modified
value – value to be appended to list-like metadata[key]
commit – commit the changes (Default value = True)

property db: Database: associated Database

property id: int: entry ID in the associated Database table

property table: str: name of the associated Database table

update(data: dict, commit: bool = True) → None[source]

Wrapper for dict.update()

Parameters:

data – data with which to update the metadata
commit – commit the changes (Default value = True)

class hippo.tags.TagTable(db: Database)[source]

Object representing the ‘tag’ table in the Database.

Attention

TagTable objects should not be created directly. Instead use the HIPPO.tags() property.

TagTable initialisation

repr(self) → str[source]: ANSI Formatted string representation

str(self) → str[source]: Unformatted representation of this object

property db: Database: Returns a pointer to the parent database

delete(tag: str) → None[source]: Delete all assignments for the given tag

rename(old: str, new: str) → None[source]: Rename all instances of a tag across the database

summary(return_df: bool = False) → pd.DataFrame[source]: Print a summary table of tags with compound and pose counts

property table: str: Returns the name of the Database table

property unique: set[str]: Returns a set of unique tag names contained in the table

class hippo.tags.TagSet(parent: Compound | Pose, tags: list | tuple | None = None, immutable: bool = False, commit: bool = True)[source]

Object representing a subset of the ‘tag’ table in the Database belonging to a certain Compound or Pose.

Attention

TagSet objects should not be created directly. Instead use the Compound.tags() or Pose.tags() property.

TagSet initialisation

self + other[source]: Attention

Adding sets together is not supported

tag: str in self → bool[source]: Is this tag in the set?

self[key: int][source]: Get a specific element in the set by index

iter(self)[source]: Iterate through this set

len(self) → int[source]: Number of tags in this set

repr(self) → str[source]: ANSI Formatted string representation

str(self) → str[source]: Unformatted representation of this object

add(tag: str, commit: bool = True) → None[source]

Add a tag to the set

Parameters:

tag – tag to add
commit – commit the change? (Default value = True)

clear()[source]: Clear all tags

property db: Database: Returns a pointer to the parent database

discard(tag: str) → None[source]

Discard an element

Parameters:: tag – tag to discard

glob(pattern: str) → list[str][source]

Construct a list from tags in the set names that match a given UNIX-style pattern.

Parameters:: pattern – unix style pattern with shell-style wildcards
Returns:: list of tags

property immutable: bool: Is this set is immutable?

property parent: Returns this set of tags parent Compound or Pose.

pop() → str[source]: Pop the last element

remove(tag: str) → None[source]

Remove an element

Parameters:: tag – tag to remove
Raises:: ValueError – if tag is not in set

property tags: list: Returns the elements in this set

class hippo.target.Target(db: Database, id: int, name: str)[source]

Object representing a protein target

Attention

Target objects should not be created directly. Instead use HIPPO.register_target() or Pose.target().

Target initialisation

repr(self) → str[source]: ANSI Formatted string representation

str(self) → str[source]: Unformatted string representation

calculate_features(protein: mp.System, reference_id: int | None = None, force: bool = False) → list[Feature][source]

Calculate features from a protein system

Parameters:: protein – molparse.System object, likely from Pose.protein_system()
Returns:: a list of Feature objects

property db: Database: Returns a pointer to the parent database

property feature_ids: list[int]: Returns the target’s feature ID’s

property features: list[Feature]: Returns the target’s features

property id: int: Returns the target’s ID

property name: str: Returns the target’s name

property subsites: list[Subsite]: List of Subsite objects on this target