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Minor refactoring and adding more docs

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This commit is contained in:
mvaradi 2018-10-14 10:37:14 +01:00
parent 7d89f1131b
commit 33b484085f
2 changed files with 66 additions and 44 deletions
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38
tests/test_residue_index.py
View file

@ -49,56 +49,56 @@ class TestCheckResidueIndices(TestCase):
self.cri = CheckResidueIndices(mock_data)
def test_loop_chains(self):
self.cri.get_residue_numbering = mock_get_residue_numbering_false
result = self.cri.loop_chains()
self.cri._get_residue_numbering = mock_get_residue_numbering_false
result = self.cri.check_every_residue()
self.assertFalse(result)
self.cri.get_residue_numbering = mock_get_residue_numbering_true
result = self.cri.loop_chains()
self.cri._get_residue_numbering = mock_get_residue_numbering_true
result = self.cri.check_every_residue()
self.assertTrue(result)
self.cri.pdb_id = None
self.assertFalse(self.cri.loop_chains())
self.assertFalse(self.cri.check_every_residue())
def test_set_pdb_id(self):
self.assertIsNotNone(self.cri.set_pdb_id())
self.assertIsNotNone(self.cri._set_pdb_id())
bad_cri = CheckResidueIndices(mock_data_no_pdb_id)
self.assertIsNone(bad_cri.set_pdb_id())
self.assertIsNone(bad_cri._set_pdb_id())
def test_check_numbering(self):
result = self.cri.check_numbering({}, {})
result = self.cri._check_numbering({}, {})
self.assertFalse(result)
self.cri.compare_residue_number = mock_compare_residue_number
result = self.cri.check_numbering({}, {"residues": [{"pdb_res_label": 0, "aa_type": "ALA"}]})
self.cri._compare_residue_number = mock_compare_residue_number
result = self.cri._check_numbering({}, {"residues": [{"pdb_res_label": 0, "aa_type": "ALA"}]})
self.assertFalse(result)
def test_get_residue_numbering(self):
mock_data = {"chain_label": "A"}
self.cri.pdb_id = "1CBS"
self.cri.check_numbering = lambda x, y : True
result = self.cri.get_residue_numbering(mock_data)
self.cri._check_numbering = lambda x, y : True
result = self.cri._get_residue_numbering(mock_data)
self.assertTrue(result)
self.cri.pdb_id = "2H58"
result = self.cri.get_residue_numbering(mock_data)
result = self.cri._get_residue_numbering(mock_data)
self.assertFalse(result)
def test_recursive_loop(self):
result = self.cri.recursive_loop([{"foo": "bar"}], "foo", None, None)
result = self.cri._recursive_loop([{"foo": "bar"}], "foo", None, None)
self.assertFalse(result)
def test_with_bad_numbering(self):
cri_with_bad_numbering = CheckResidueIndices(mock_data_bad_numbering)
result = cri_with_bad_numbering.loop_chains()
result = cri_with_bad_numbering.check_every_residue()
self.assertFalse(result)
def test_process_residues(self):
result = self.cri.process_residues(
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
self.assertTrue(result)
result = self.cri.process_residues(
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": "C"}], "1C", "ALA")
self.assertTrue(result)
result = self.cri.process_residues(
result = self.cri._process_residues(
[{"author_residue_number": 2, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
self.assertFalse(result)
result = self.cri.process_residues(
result = self.cri._process_residues(
[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "HIS")
self.assertFalse(result)

72
validator/residue_index.py
View file

@ -1,3 +1,20 @@
#!/usr/bin/env python3
"""
Copyright 2018 EMBL - European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
either express or implied. See the License for the specific
language governing permissions and limitations under the
License.
"""
import json
import requests
@ -10,25 +27,21 @@ class CheckResidueIndices(object):
and each has to match the indices in the official PDB entry
This class relies on the PDBe API to get the current residue
indices
Example usage:
check_indexes = CheckResidueIndices(your_json_object)
if check_indexes.check_every_residue():
# all residues in every chain are correctly indexed
"""
def __init__(self, data):
self.api_url = "https://www.ebi.ac.uk/pdbe/api/pdb/entry/residue_listing/"
self.data = data
self.pdb_id = self.set_pdb_id()
self.pdb_id = self._set_pdb_id()
self.mismatches = []
self.labels = ["residues", "chains", "molecules"]
def set_pdb_id(self):
"""
Sets the PDB id based on the JSON data
:return: String, PDB id or None
"""
if "pdb_id" in self.data.keys():
return self.data["pdb_id"].lower()
return None
def loop_chains(self):
def check_every_residue(self):
"""
Looping through all the chains that are present
in the JSON data
@ -37,11 +50,20 @@ class CheckResidueIndices(object):
if not self.pdb_id:
return False
for chain_data in self.data["chains"]:
if not self.get_residue_numbering(chain_data):
if not self._get_residue_numbering(chain_data):
return False
return True
def get_residue_numbering(self, chain_data):
def _set_pdb_id(self):
"""
Sets the PDB id based on the JSON data
:return: String, PDB id or None
"""
if "pdb_id" in self.data.keys():
return self.data["pdb_id"].lower()
return None
def _get_residue_numbering(self, chain_data):
"""
Gets the residue numbering from the PDBe API and
checks all residues
@ -55,9 +77,9 @@ class CheckResidueIndices(object):
if not residue_numbering.keys():
self.mismatches.append("No residues in PDB for this entry - probably obsoleted entry")
return False
return self.check_numbering(residue_numbering, chain_data)
return self._check_numbering(residue_numbering, chain_data)
def check_numbering(self, residue_numbering, chain_data):
def _check_numbering(self, residue_numbering, chain_data):
"""
This method loops through all the residues in a chain
and call the residue index comparator method
@ -70,11 +92,11 @@ class CheckResidueIndices(object):
for residue in chain_data["residues"]:
depositor_residue_number = residue["pdb_res_label"]
depositor_aa_type = residue["aa_type"]
if not self.compare_residue_number(depositor_residue_number, depositor_aa_type, residue_numbering):
if not self._compare_residue_number(depositor_residue_number, depositor_aa_type, residue_numbering):
return False
return True
def compare_residue_number(self, depositor_residue_number, depositor_aa_type, residue_numbering):
def _compare_residue_number(self, depositor_residue_number, depositor_aa_type, residue_numbering):
"""
This method starts looping through the substructure of the PDBe API data
:param depositor_residue_number: Residue number provided by the user
@ -83,9 +105,9 @@ class CheckResidueIndices(object):
:return: True is residue numbering is valid, False if not
"""
molecules = residue_numbering[self.pdb_id]["molecules"]
return self.recursive_loop(molecules, "chains", depositor_residue_number, depositor_aa_type)
return self._recursive_loop(molecules, "chains", depositor_residue_number, depositor_aa_type)
def recursive_loop(self, data, label, depositor_residue_number, depositor_aa_type):
def _recursive_loop(self, data, label, depositor_residue_number, depositor_aa_type):
"""
A recursive loop that goes down to residue level and processes all residues
:param data: JSON data
@ -97,12 +119,12 @@ class CheckResidueIndices(object):
for item in data:
sub_data = item[label]
if label == "chains":
return self.recursive_loop(sub_data, "residues", depositor_residue_number, depositor_aa_type)
return self._recursive_loop(sub_data, "residues", depositor_residue_number, depositor_aa_type)
elif label == "residues":
return self.process_residues(sub_data, depositor_residue_number, depositor_aa_type)
return self._process_residues(sub_data, depositor_residue_number, depositor_aa_type)
return False
def process_residues(self, residues, depositor_residue_number, depositor_aa_type):
def _process_residues(self, residues, depositor_residue_number, depositor_aa_type):
"""
This method grabs the residue information and call the comparator if the
residue number of PDBe is the same as the user input
@ -113,11 +135,11 @@ class CheckResidueIndices(object):
"""
for residue in residues:
if "%i%s" % (residue["author_residue_number"], residue["author_insertion_code"]) == depositor_residue_number:
return self.make_comparison(residue["residue_name"], depositor_aa_type, depositor_residue_number)
return self._make_comparison(residue["residue_name"], depositor_aa_type, depositor_residue_number)
self.mismatches.append("residue numbering is completely mismatched between data and PDB entry")
return False
def make_comparison(self, residue_name, depositor_aa_type, depositor_residue_number):
def _make_comparison(self, residue_name, depositor_aa_type, depositor_residue_number):
"""
This method does the comparison between two residues that have the same index number
The comparison is between amino acid code
@ -131,4 +153,4 @@ class CheckResidueIndices(object):
mismatch = "residue %s (%s) in data does not match residue %s (%s) in PDB" % (
depositor_residue_number, depositor_aa_type, depositor_residue_number, residue_name)
self.mismatches.append(mismatch)
return False
return False