interactionCenter.py:
InteractionCenter stores information about an atom involved in a molecular interaction.
InteractionCenter(structure=None, atomIndex=None)[source]¶Bases: object
Class that stores information about an atom involved in a molecular interaction.
Attributes
| structure | (mmtfStructure) structure to be used as interaction center [None] |
| atomIndex | (int) the index of the atom at center [None] |
Methods
get_as_object() |
Returns a list of objects representing this interaction center. |
get_atom_name() |
Gets the atom name |
get_chain_name() |
Gets the chainName. |
get_coordinates() |
Gets the position of the interaction center. |
get_element() |
Gets the case-sensitive element symbol |
get_group_name() |
Gets the names of the group. |
get_group_number() |
Gets the group number for the interaction center. |
get_length() |
Returns the number of data items in an interaction center. |
get_normalized_b_factors() |
Gets the normalized b-factor |
get_sequence_position() |
Gets an index into the one-letter polymer sequence. |
get_struct_fields() |
Returns a schema to create Spark Datasets. |
get_type() |
Gets the type of the group. |
set_atom_name(atomName) |
Sets the atom name |
set_chain_name(chainName) |
Sets the chainName. |
set_coordinates(coordinates) |
Sets the position of the interaction center. |
set_element(element) |
Sets the case-sensitive element symbol |
set_group_name(groupName) |
Sets the names of the group. |
set_group_number(groupNumber) |
Sets the group number for the interaction center. |
set_normalized_b_factors(normalizedbFactor) |
Sets the normalized b-factor |
set_sequence_position(sequencePosition) |
Sets an index into the one-letter polymer sequence. |
set_type(gtype) |
Sets the type of the group. |
get_as_object()[source]¶Returns a list of objects representing this interaction center. Note, not all data are currently included. This method is ucsed to create Spark datasets.
| Returns: | list of objects representing this interaction center |
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get_chain_name()[source]¶Gets the chainName. This corresponds to the “chain Id” in PDB files.
| Returns: | the name of the chain |
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get_coordinates()[source]¶Gets the position of the interaction center.
| Returns: | the position of the interaction center |
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get_group_name()[source]¶Gets the names of the group. This name is the chemical component id of this group
| Returns: | name of group |
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get_group_number()[source]¶Gets the group number for the interaction center. A group number consists of the residue number (e.g. 101) plus an optional insertion code (e.g. A): 101A.
| Returns: | group number |
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get_length()[source]¶Returns the number of data items in an interaction center. Note, not all data are currently included
| Returns: | the number of data items in an interaction center |
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get_sequence_position()[source]¶Gets an index into the one-letter polymer sequence. this index is zero-based. If the interaction center is not a polymer atom, this index is -1
| Returns: | index into polymer sequence |
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get_struct_fields()[source]¶Returns a schema to create Spark Datasets. This schema must match the order in which the data are return by the getAsObject() method.
| Parameters: | index (int): an integer to label an interaction center |
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| Returns: | schema to represent an interaction center in spark dataset. |
set_chain_name(chainName)[source]¶Sets the chainName. This corresponds to the “chain Id” in PDB files.
| Parameters: | chainName (str): the name of the chian |
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set_coordinates(coordinates)[source]¶Sets the position of the interaction center.
| Parameters: | coordinates (list): the position of the interaction center |
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set_element(element)[source]¶Sets the case-sensitive element symbol
| Parameters: | element (str): element symbol |
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set_group_name(groupName)[source]¶Sets the names of the group. This name is the chemical component id of this group
| Parameters: | groupName (str): name of group |
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set_group_number(groupNumber)[source]¶Sets the group number for the interaction center. A group number consists of the residue number (e.g. 101) plus an optional insertion code (e.g. A): 101A.
| Parameters: | groupNumber (str): group number |
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set_normalized_b_factors(normalizedbFactor)[source]¶Sets the normalized b-factor
| Parameters: | normalizedbFactor (float) the normalized b-factor |
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