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changed the docstrings to contain args and raises headers
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Coos Baakman committed Mar 25, 2021
1 parent bb6f5d5 commit 1a77157
Showing 1 changed file with 69 additions and 47 deletions.
116 changes: 69 additions & 47 deletions deeprank/features/ResidueContacts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,10 @@ class ResidueSynonymCriteria:
def __init__(self, residue_name, atoms_present, atoms_absent):
"""Build new criteria
residue_name (string): the name of the residue
atoms_present (list of strings): the names of the atoms that should be present in the residue
atoms_absent (list of strings) the names of the atoms that should be absent in the residue
Args:
residue_name (string): the name of the residue
atoms_present (list of strings): the names of the atoms that should be present in the residue
atoms_absent (list of strings) the names of the atoms that should be absent in the residue
"""

self.residue_name = residue_name
Expand All @@ -34,8 +35,9 @@ def __init__(self, residue_name, atoms_present, atoms_absent):
def matches(self, residue_name, atom_names):
"""Check whether the given residue matches this set of criteria
residue_name (string): the name of the residue to match
atom_names (list of strings): the names of the atoms in the residue
Args:
residue_name (string): the name of the residue to match
atom_names (list of strings): the names of the atoms in the residue
"""

if self.residue_name != 'all' and residue_name != self.residue_name:
Expand All @@ -58,8 +60,9 @@ def get_squared_distance(pos1, pos2):
and should be used if one does not necessarily need
the normal distance for a large set of coordinates.
pos1 (array of 3): the xyz coords of position 1
pos2 (array of 3): the xyz coords of position 2
Args:
pos1 (array of 3): the xyz coords of position 1
pos2 (array of 3): the xyz coords of position 2
"""

return numpy.sum(numpy.square(pos1 - pos2))
Expand All @@ -69,8 +72,9 @@ def get_distance(pos1, pos2):
This is more computationally expensive than the squared distance
and should only be used when one really needs this distance.
pos1 (array of 3): the xyz coords of position 1
pos2 (array of 3): the xyz coords of position 2
Args:
pos1 (array of 3): the xyz coords of position 1
pos2 (array of 3): the xyz coords of position 2
"""

return numpy.sqrt(get_squared_distance(pos1, pos2))
Expand All @@ -79,7 +83,8 @@ def wrap_values_in_lists(dict_):
"""Wrap the dictionary's values in lists. This
appears to be necessary for the exported features to work.
dict_(dictionary): the dictionary that should be converted
Args:
dict_(dictionary): the dictionary that should be converted
"""

return {key: [value] for key,value in dict_.items()}
Expand All @@ -102,9 +107,10 @@ class _PhysicsStorage:
def _sum_up(dict_, key, value_to_add):
"""A helper function to sum the values of a dictionary.
dict_(dictionary): the dictionary to store the value in
key(hashable object): the key under which the value should be stored in dict_
value_to_add: the value to add onto the dictionary value
Args:
dict_(dictionary): the dictionary to store the value in
key(hashable object): the key under which the value should be stored in dict_
value_to_add: the value to add onto the dictionary value
"""

if key not in dict_:
Expand All @@ -116,11 +122,12 @@ def _sum_up(dict_, key, value_to_add):
def get_vanderwaals_energy(epsilon1, sigma1, epsilon2, sigma2, distance):
"""The formula to calculate the vanderwaals energy for two atoms (atom 1 and atom 2)
epsilon1 (float): the vanderwaals epsilon parameter of atom 1
sigma1 (float): the vanderwaals sigma parameter of atom 1
epsilon2 (float): the vanderwaals epsilon parameter of atom 2
sigma2 (float): the vanderwaals sigma parameter of atom 2
distance (float): the vanderwaals distance between atom 1 and atom 2
Args:
epsilon1 (float): the vanderwaals epsilon parameter of atom 1
sigma1 (float): the vanderwaals sigma parameter of atom 1
epsilon2 (float): the vanderwaals epsilon parameter of atom 2
sigma2 (float): the vanderwaals sigma parameter of atom 2
distance (float): the vanderwaals distance between atom 1 and atom 2
"""

average_epsilon = numpy.sqrt(epsilon1 * epsilon2)
Expand All @@ -143,10 +150,11 @@ def get_vanderwaals_energy(epsilon1, sigma1, epsilon2, sigma2, distance):
def get_coulomb_energy(charge1, charge2, distance, max_distance):
"""The formula to calculate the coulomb energy for two atoms (atom 1 and atom 2)
charge1 (float): the charge of atom 1
charge2 (float): the charge of atom 2
distance (float): the vanderwaals distance between atom 1 and atom 2
max_distance (float): the max distance that was used to find atoms 1 and 2
Args:
charge1 (float): the charge of atom 1
charge2 (float): the charge of atom 2
distance (float): the vanderwaals distance between atom 1 and atom 2
max_distance (float): the max distance that was used to find atoms 1 and 2
"""

return (charge1 * charge2 * _PhysicsStorage.COULOMB_CONSTANT /
Expand All @@ -155,7 +163,11 @@ def get_coulomb_energy(charge1, charge2, distance, max_distance):
def __init__(self, sqldb):
"""Build a new set of physical parameters
sqldb (pdb2sql): interface to the contents of a PDB file, with charges and vanderwaals parameters included.
Args:
sqldb (pdb2sql): interface to the contents of a PDB file, with charges and vanderwaals parameters included.
Raises:
RuntimeError: if features are missing from sqldb
"""

self._vanderwaals_parameters = sqldb.get('eps,sig')
Expand Down Expand Up @@ -185,9 +197,13 @@ def __init__(self, sqldb):
def include_pair(self, atom1, atom2, max_distance):
"""Add a pair of atoms to the sum
atom1 (int): number of atom 1
atom2 (int): number of atom 2
max_distance (float): the max distance that was used to find the atoms
Args:
atom1 (int): number of atom 1
atom2 (int): number of atom 2
max_distance (float): the max distance that was used to find the atoms
Raises:
ValueError: if atom1 and atom2 are at the same position
"""

position1 = self._positions[atom1]
Expand Down Expand Up @@ -230,8 +246,9 @@ def include_pair(self, atom1, atom2, max_distance):
def add_to_features(self, feature_data, feature_data_xyz):
"""Convert the summed interactions to deeprank features and store them in the corresponding dictionaries
feature_data (dictionary): where the per atom features should be stored
feature_data_xyz (dictionary): where the per position features should be stored
Args:
feature_data (dictionary): where the per atom features should be stored
feature_data_xyz (dictionary): where the per position features should be stored
"""

feature_data['vdwaals'] = wrap_values_in_lists(self._vanderwaals_per_atom)
Expand Down Expand Up @@ -259,8 +276,9 @@ class ResidueContacts(FeatureClass):
def get_alternative_residue_name(residue_name, atom_names):
"""Get the alternative residue name, according to the static dictionary in this class
residue_name (string): the name of the residue
atom_names (list of strings): the names of the atoms in the residue
Args:
residue_name (string): the name of the residue
atom_names (list of strings): the names of the atoms in the residue
"""

for name, crit in ResidueContacts.RESIDUE_SYNONYMS.items():
Expand All @@ -274,13 +292,14 @@ def __init__(self, pdb_path, chain_id, residue_number,
max_contact_distance=8.5):
"""Build a new residue contacts feature object
pdb_path (string): where the pdb file is located on disk
chain_id (string): identifier of the residue's protein chain within the pdb file
residue_number (int): identifier of the residue within the protein chain
top_path (string): location of the top file on disk
param_path (string): location of the param file on disk
patch_path (string): location of the patch file on disk
max_contact_distance (float): the maximum distance allowed for two atoms to be considered a contact pair
Args:
pdb_path (string): where the pdb file is located on disk
chain_id (string): identifier of the residue's protein chain within the pdb file
residue_number (int): identifier of the residue within the protein chain
top_path (string): location of the top file on disk
param_path (string): location of the param file on disk
patch_path (string): location of the patch file on disk
max_contact_distance (float): the maximum distance allowed for two atoms to be considered a contact pair
"""

super().__init__("Atomic")
Expand Down Expand Up @@ -384,9 +403,10 @@ def _extend_contact_to_residues(self):
def _get_atom_type(self, residue_name, alternative_residue_name, atom_name):
"""Find the type name of the given atom, according to top and patch data
residue_name (string): the name of the residue that the atom is in
alternative_residue_name (string): the name of the residue, outputted from 'get_alternative_residue_name'
atom_name (string): the name of the atom itself
Args:
residue_name (string): the name of the residue that the atom is in
alternative_residue_name (string): the name of the residue, outputted from 'get_alternative_residue_name'
atom_name (string): the name of the atom itself
"""

if (alternative_residue_name, atom_name) in self._patch_type:
Expand All @@ -401,9 +421,10 @@ def _get_atom_type(self, residue_name, alternative_residue_name, atom_name):
def _get_charge(self, residue_name, alternative_residue_name, atom_name):
"""Find the charge of the atom, according to top and patch data
residue_name (string): the name of the residue that the atom is in
alternative_residue_name (string): the name of the residue, outputted from 'get_alternative_residue_name'
atom_name (string): the name of the atom itself
Args:
residue_name (string): the name of the residue that the atom is in
alternative_residue_name (string): the name of the residue, outputted from 'get_alternative_residue_name'
atom_name (string): the name of the atom itself
"""

if residue_name not in self._valid_residue_names:
Expand All @@ -424,10 +445,11 @@ def _get_charge(self, residue_name, alternative_residue_name, atom_name):
def _get_vanderwaals_parameters(self, residue_name, alternative_residue_name, atom_name, atom_type):
"""Find the vanderwaals parameters of the atom, according to param data
residue_name (string): the name of the residue that the atom is in
alternative_residue_name (string): the name of the residue, outputted from 'get_alternative_residue_name'
atom_name (string): the name of the atom itself
atom_type (string): output from '_get_atom_type'
Args:
residue_name (string): the name of the residue that the atom is in
alternative_residue_name (string): the name of the residue, outputted from 'get_alternative_residue_name'
atom_name (string): the name of the atom itself
atom_type (string): output from '_get_atom_type'
"""

if residue_name not in self._valid_residue_names:
Expand Down

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