--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_package/Utilities.py	Fri Jan 22 15:50:27 2021 +0000
@@ -0,0 +1,65 @@
+from os.path import isfile
+
+
+def validateIdentifier(identifier):
+    if len(identifier) < 6 or identifier[4:5] != "_":
+        raise Exception("Invalid list entry (`PDB_CHAIN`): %s." % identifier)
+
+
+def getId(identifier):
+    identifier = identifier.strip()
+    validateIdentifier(identifier)
+    return identifier[:4].upper() + identifier[4:6]
+
+
+def getChain(identifier):
+    validateIdentifier(identifier)
+    pdbChain = identifier[5:6]
+    return pdbChain
+
+
+def getName(identifier):
+    pdb = identifier[:4].lower()
+    return pdb
+
+
+def getCrossReference(crossReferenceFile, allPartners=False):
+    crossReference = dict()
+    crossCount = 0
+    with open(crossReferenceFile) as file:
+        for line in file:
+            columns = line.split()
+            if len(columns) < 2:
+                raise Exception("Invalid Cross Reference Entry %s." % line)
+            core = columns[0]
+            partner = columns[1]
+            if len(columns) < 4:
+                templates = [core, partner]
+            else:
+                templates = [columns[2], columns[3]]
+            if core not in crossReference:
+                crossReference[core] = dict(partners=list(), templates=list())
+            if allPartners or partner not in crossReference[core]["partners"]:
+                crossReference[core]["partners"].append(partner)
+                crossReference[core]["templates"].append(templates)
+                crossCount = crossCount + 1
+    print("Identified %s reference interactions." % crossCount)
+    return crossReference
+
+
+def getTemplates(hhrFile, minScore=10):
+    result = dict()
+    topTemplate = None
+    if isfile(hhrFile):
+        with open(hhrFile) as file:
+            for index, line in enumerate(file):
+                if index > 8:
+                    if not line.strip():
+                        break
+                    templateId = line[4:10]
+                    templateScore = float(line[57:63])
+                    if templateScore > minScore:
+                        if topTemplate is None:
+                            topTemplate = templateId
+                        result[templateId] = templateScore
+    return topTemplate, result