--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_model_all.py	Fri Jan 22 15:50:27 2021 +0000
@@ -0,0 +1,84 @@
+#! /usr/bin/env python3
+import argparse
+from os import mkdir, remove
+from os.path import isdir, isfile
+
+from spring_package.DBKit import DBKit
+from spring_package.Modeller import createModel
+
+
+class ModelArguments:
+    def __init__(self, args):
+        self.log = args.log
+        self.index = args.index
+        self.database = args.database
+        self.cross = args.cross
+        self.wenergy = args.wenergy
+        self.minscore = args.minscore
+        self.maxtries = args.maxtries
+        self.maxclashes = args.maxclashes
+        self.showtemplate = args.showtemplate
+
+    def set(self, a_hhr, b_hhr, output):
+        self.a_hhr = a_hhr
+        self.b_hhr = b_hhr
+        self.output = output
+
+
+def main(args):
+    modelArgs = ModelArguments(args)
+    outPath = args.outputpath.rstrip("/")
+    if not isdir(outPath):
+        mkdir(outPath)
+    if not isdir("temp"):
+        mkdir("temp")
+    dbkit = DBKit(args.hhr_index, args.hhr_database)
+    logFile = open(args.log, "w")
+    logFile.write("#namea\t nameb\t springscore\t tmscore\t energy\t clashes\n")
+    with open(args.pairs, "r") as file:
+        for line in file:
+            param = line.split()
+            aIdentifier = param[0]
+            bIdentifier = param[1]
+            aFile = "temp/%s" % aIdentifier
+            bFile = "temp/%s" % bIdentifier
+            if not dbkit.createFile(aIdentifier, aFile):
+                print("Failed to retrieve entry %s." % aIdentifier)
+                continue
+            if not dbkit.createFile(bIdentifier, bFile):
+                print("Failed to retrieve entry %s." % bIdentifier)
+                continue
+            output = "%s/%s.%s.pdb" % (outPath, aIdentifier, bIdentifier)
+            modelArgs.set(a_hhr=aFile, b_hhr=bFile, output=output)
+            modelData = createModel(modelArgs)
+            if modelData:
+                infoStr = "%s\t %s\t %5.2f\t %5.2f\t %5.2f\t %5.2f\n" % (aIdentifier, bIdentifier,
+                                                                         modelData["springscore"],
+                                                                         modelData["tmscore"],
+                                                                         modelData["energy"],
+                                                                         modelData["clashes"])
+                logFile.write(infoStr)
+            if isfile(aFile):
+                remove(aFile)
+            if isfile(bFile):
+                remove(bFile)
+    logFile.close()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Create 3D models from HH-search results.')
+    parser.add_argument('-p', '--pairs', help='Interaction table e.g. from min-Z evaluation (2-columns)', required=True)
+    parser.add_argument('-ih', '--hhr_index', help='HHR Index database file (ffindex)', required=True)
+    parser.add_argument('-dh', '--hhr_database', help='HHR Database file (ffdata)', required=True)
+    parser.add_argument('-i', '--index', help='PDB Database Index file (ffindex)', required=True)
+    parser.add_argument('-d', '--database', help='PDB Database file (ffdata)', required=True)
+    parser.add_argument('-c', '--cross', help='PDB Cross Reference', required=True)
+    parser.add_argument('-g', '--log', help='Log file', required=True)
+    parser.add_argument('-o', '--outputpath', help='Path to output directory', required=True)
+    parser.add_argument('-we', '--wenergy', help='Weight Energy term', type=float, default=-0.01, required=False)
+    parser.add_argument('-ms', '--minscore', help='Minimum min-Z score threshold', type=float, default=10.0, required=False)
+    parser.add_argument('-mt', '--maxtries', help='Maximum number of templates', type=int, default=20, required=False)
+    parser.add_argument('-mc', '--maxclashes', help='Maximum fraction of clashes', type=float, default=0.1, required=False)
+    parser.add_argument('-sr', '--showtemplate', help='Add reference template to model structure', required=False, default="true")
+    args = parser.parse_args()
+    main(args)