diff spring_cross.py @ 37:0be0af9e695d draft

"planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_cross.py	Wed Nov 25 14:35:35 2020 +0000
@@ -0,0 +1,70 @@
+#! /usr/bin/env python3
+import argparse
+from os import system
+
+from spring_package.DBKit import createFile
+from spring_package.Molecule import Molecule
+
+
+def getId(line):
+    line = line.split()[0]
+    return line[:4].upper() + line[4:6]
+
+
+def main(args):
+    logFile = open(args.log, "w")
+    system("mkdir -p %s" % args.temp)
+    pdbCount = 0
+    partnerList = set()
+    entries = list()
+    with open(args.list) as file:
+        for line in file:
+            entries.append(getId(line))
+    logFile.write("Found %s template entries.\n" % len(entries))
+    for entryId in entries:
+        pdb = entryId[:4].lower()
+        pdbChain = entryId[5:6]
+        pdbFile = "%s/temp.pdb" % args.temp
+        pdbDatabaseId = "%s.pdb" % pdb
+        createFile(pdbDatabaseId, args.index, args.database, pdbFile)
+        try:
+            mol = Molecule(pdbFile)
+        except Exception:
+            logFile.write("Warning: File '%s' not found.\n" % pdbDatabaseId)
+            continue
+        pdbCount = pdbCount + 1
+        logFile.write("Processing %s, chain %s.\n" % (pdb, pdbChain))
+        logFile.write("Found %d biomolecule(s).\n" % len(mol.biomol.keys()))
+        for biomolNumber in mol.biomol:
+            if biomolNumber == 0:
+                logFile.write("Processing biomolecule.\n")
+                bioMolecule = mol
+            else:
+                logFile.write("Processing biomolecule %d.\n" % biomolNumber)
+                bioMolecule = mol.createUnit(biomolNumber)
+            nChains = len(bioMolecule.calpha.keys())
+            print("Found %d chain(s)." % nChains)
+            if nChains > 1 and pdbChain in bioMolecule.calpha:
+                for bioChain in bioMolecule.calpha:
+                    if bioChain == pdbChain:
+                        continue
+                    partnerPdbChain = "%s_%s" % (pdb.upper(), bioChain[:1])
+                    partnerList.add("%s\t%s" % (entryId, partnerPdbChain))
+            else:
+                logFile.write("Skipping: Chain not found or single chain [%s].\n" % pdbChain)
+        logFile.flush()
+    with open(args.output, 'w') as output_file:
+        for entry in sorted(partnerList):
+            output_file.write("%s\n" % entry)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='List filtering.')
+    parser.add_argument('-l', '--list', help='List of PDB chains [PDB_CHAIN]', required=True)
+    parser.add_argument('-i', '--index', help='PDB Database Index file (dbkit_index)', required=True)
+    parser.add_argument('-d', '--database', help='PDB Database files (dbkit)', required=True)
+    parser.add_argument('-o', '--output', help='Output file', required=True)
+    parser.add_argument('-t', '--temp', help='Temporary Directory', required=True)
+    parser.add_argument('-g', '--log', help='Log File', required=True)
+    args = parser.parse_args()
+    main(args)