Merge pull request #1296 from jamesmkrieger/pfam_fixes

pfam fixes for 4nq8
prody · Feb 5, 2021 · 639c965 · 639c965
2 parents 2be68c2 + 3c4b11c
commit 639c965
Showing 1 changed file with 15 additions and 0 deletions.
diff --git a/prody/database/pfam.py b/prody/database/pfam.py
@@ -3,6 +3,7 @@
 
 __author__ = 'Anindita Dutta, Ahmet Bakan, Cihan Kaya'
 
+from prody.dynamics.analysis import calcFracDimension
 import re
 from numbers import Integral
 
@@ -222,6 +223,7 @@ def searchPfam(query, **kwargs):
     elif xml.find(b'No valid UniProt accession or ID') > 0:
         try:
             url = prefix + 'protein/' + accession + '?output=xml'
+            LOGGER.debug('Retrieving Pfam search results: ' + url)
             xml = openURL(url, timeout=timeout).read()
         except:
             try:
@@ -230,6 +232,19 @@ def searchPfam(query, **kwargs):
                 return searchPfam(ag_seq)
             except:
                 raise ValueError('No valid UniProt accession or ID for: ' + seq)
+
+        if xml.find(b'No valid UniProt accession or ID') > 0:
+            try:
+                url = 'https://uniprot.org/uniprot/' + accession + '.xml'
+                xml = openURL(url, timeout=timeout).read()
+                root = ET.XML(xml)
+                accession = root[0][0].text
+
+                url = prefix + 'protein/' + accession + '?output=xml'
+                LOGGER.debug('Retrieving Pfam search results: ' + url)
+                xml = openURL(url, timeout=timeout).read()                
+            except:
+                raise ValueError('No valid UniProt accession or ID for: ' + seq)
 
     try:
         root = ET.XML(xml)