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Merging improvements from https://github.com/skodapetr/funpdbe-validator skodapetr@github - "fix multiple molecules issue"

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This commit is contained in:
Mihaly Varadi 2019-03-22 13:04:00 +00:00
parent 89ac85e304
commit 78b3f53a5f
2 changed files with 28 additions and 19 deletions
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16
validator/residue_index.py
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@ -2,11 +2,9 @@
"""
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,
@ -27,7 +25,6 @@ class ResidueIndexes(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 = ResidueIndexes(your_json_object)
if check_indexes.check_every_residue():
@ -119,17 +116,22 @@ class ResidueIndexes(object):
:param depositor_aa_type: Residue amino acid code provided by user
:return: True is residue numbering is valid, False if not
"""
flag = None
flag = False
for item in data:
sub_data = item[label]
if label == "chains":
flag = self._recursive_loop(sub_data, "residues", depositor_residue_number, depositor_aa_type,
flag |= self._recursive_loop(sub_data, "residues", depositor_residue_number, depositor_aa_type,
depositor_chain_id)
elif label == "residues":
return self._process_residues(sub_data, depositor_residue_number, depositor_aa_type, depositor_chain_id)
if label == "chains":
return flag
if label == "residues":
# We were checking residues and none was found, so not match found -> False.
return False
def _process_residues(self, residues, depositor_residue_number, depositor_aa_type, depositor_chain_id):
"""
This method grabs the residue information and call the comparator if the
@ -158,9 +160,9 @@ class ResidueIndexes(object):
:param depositor_residue_number: Residue number provided by the user
:return: True is residue numbering is valid, False if not
"""
if residue_name == depositor_aa_type:
if residue_name.lower() == depositor_aa_type.lower():
return True
mismatch = "residue %s_%s (%s) in data does not match residue %s (%s) in PDB" % (
depositor_chain_id, depositor_residue_number, depositor_aa_type, depositor_residue_number, residue_name)
self.mismatches.append(mismatch)
return False
return False