Source code for mmtfPyspark.interactions.interactionCenter
#!/user/bin/env python
'''interactionCenter.py:
InteractionCenter stores information about an atom involved in a molecular
interaction.
'''
__author__ = "Mars (Shih-Cheng) Huang"
__maintainer__ = "Mars (Shih-Cheng) Huang"
__email__ = "marshuang80@gmail.com"
__version__ = "0.2.0"
__status__ = "done"
from pyspark.sql.types import *
import numpy as np
[docs]class InteractionCenter(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]
'''
def __init__(self, structure=None, atomIndex=None):
if structure is not None and atomIndex is not None:
self.set_atom_name(structure.get_atom_names()[atomIndex])
self.set_element(structure.get_elements()[atomIndex])
self.set_group_name(structure.get_group_names()[atomIndex])
self.set_group_number(structure.get_group_numbers()[atomIndex])
self.set_type(structure.get_entity_types()[atomIndex])
self.set_chain_name(structure.get_chain_names()[atomIndex])
self.set_sequence_position(
structure.get_sequence_positions()[atomIndex])
self.set_coordinates(np.array([structure.get_x_coords()[atomIndex],
structure.get_y_coords()[atomIndex],
structure.get_z_coords()[atomIndex]]))
self.set_normalized_b_factors(
structure.get_normalized_b_factors()[atomIndex])
else:
self.coordinates = None
self.atomName = None
self.element = None
self.groupName = None
self.groupNumber = None
self.type = None
self.chainName = None
self.normalizedbFactor = None
[docs] def get_length():
'''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
'''
LENGTH = 7
return LENGTH
[docs] def get_atom_name(self):
'''Gets the atom name
Returns
-------
name of the atom
'''
return self.atomName
[docs] def set_atom_name(self, atomName):
'''Sets the atom name
Parameters
----------
atomName (str): name of the atom
'''
self.atomName = atomName
[docs] def get_element(self):
'''Gets the case-sensitive element symbol
Returns
-------
element symbol
'''
return self.element
[docs] def set_element(self, element):
'''Sets the case-sensitive element symbol
Parameters
----------
element (str): element symbol
'''
self.element = element
[docs] def get_group_name(self):
'''Gets the names of the group. This name is the chemical component id
of this group
Returns
-------
name of group
'''
return self.groupName
[docs] def set_group_name(self, groupName):
'''Sets the names of the group. This name is the chemical component id
of this group
Parameters
----------
groupName (str): name of group
'''
self.groupName = groupName
[docs] def get_group_number(self):
'''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
'''
return self.groupNumber
[docs] def set_group_number(self, groupNumber):
'''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
'''
self.groupNumber = groupNumber
[docs] def get_type(self):
'''Gets the type of the group.
Returns
-------
type of group
'''
return self.type
[docs] def set_type(self, gtype):
'''Sets the type of the group.
Parameters
----------
gtype (str): type of group
'''
self.type = gtype
[docs] def get_chain_name(self):
'''Gets the chainName. This corresponds to the "chain Id" in PDB files.
Returns
-------
the name of the chain
'''
return self.chainName
[docs] def set_chain_name(self, chainName):
'''Sets the chainName. This corresponds to the "chain Id" in PDB files.
Parameters
----------
chainName (str): the name of the chian
'''
self.chainName = chainName
[docs] def get_sequence_position(self):
'''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
'''
return self.sequencePosition
[docs] def set_sequence_position(self, sequencePosition):
'''Sets 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
Parameters
----------
sequencePosition (int): index into polymer sequence
'''
self.sequencePosition = sequencePosition
[docs] def get_coordinates(self):
'''Gets the position of the interaction center.
Returns
-------
the position of the interaction center
'''
return self.coordinates
[docs] def set_coordinates(self, coordinates):
'''Sets the position of the interaction center.
Parameters
----------
coordinates (list): the position of the interaction center
'''
self.coordinates = coordinates
[docs] def get_normalized_b_factors(self):
'''Gets the normalized b-factor
Returns
-------
the normalized b-factor
'''
return self.normalizedbFactor
[docs] def set_normalized_b_factors(self, normalizedbFactor):
'''Sets the normalized b-factor
Parameters
----------
normalizedbFactor (float) the normalized b-factor
'''
self.normalizedbFactor = normalizedbFactor
[docs] def get_as_object(self):
'''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
'''
return [self.atomName, self.element, self.groupName, self.groupNumber,
self.type, self.chainName, self.normalizedbFactor]
[docs] def get_struct_fields(index):
'''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
Returns
-------
schema to represent an interaction center in spark dataset.
'''
sf = []
nullable = True
index = str(index)
sf.append(StructField("atom" + index, StringType(), nullable))
sf.append(StructField("element" + index, StringType(), nullable))
sf.append(StructField("group" + index, StringType(), nullable))
sf.append(StructField("groupNum" + index, StringType(), nullable))
sf.append(StructField("type" + index, StringType(), nullable))
sf.append(StructField("chain" + index, StringType(), nullable))
sf.append(StructField("nbFactor" + index, FloatType(), nullable))
return sf
