--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_top.py	Mon Oct 24 22:12:01 2022 +0000
@@ -0,0 +1,65 @@
+import argparse
+
+import parmed as pmd
+
+
+def merge_gro_files(prot_gro, lig_gro, cmplx_gro):
+    prot = pmd.load_file(prot_gro)
+    lig = pmd.load_file(lig_gro)
+    cmplx = prot + lig
+    cmplx.save(cmplx_gro)
+
+
+def merge_top_files(prot_top, lig_top, cmplx_top):
+    with open(lig_top, 'r') as f:
+        lig_top_sections = f.read().split('\n[')
+
+    # open ligand topology
+    for n in range(len(lig_top_sections)):
+        if 'atomtypes' in lig_top_sections[n][:10]:
+            lig_atomtypes = lig_top_sections[n]
+            del lig_top_sections[n]
+            break
+    else:
+        lig_atomtypes = None
+    lig_top_updated = '\n['.join(lig_top_sections)
+
+    # open protein topology
+    with open(prot_top, 'r') as f:
+        prot_top_combined = f.read()
+    if lig_atomtypes:
+        prot_top_sections = prot_top_combined.split('[ moleculetype ]\n')
+        prot_top_combined = (prot_top_sections[0] +
+                             '; Include ligand atomtypes\n[' +
+                             lig_atomtypes +
+                             '\n[ moleculetype ]\n' +
+                             prot_top_sections[1])
+    prot_top_sections = prot_top_combined.split('; Include water topology')
+    prot_top_combined = (prot_top_sections[0] +
+                         '; Include ligand topology\n' +
+                         lig_top_updated +
+                         '\n; Include water topology' +
+                         prot_top_sections[1])
+    prot_top_combined += 'base     1\n'
+
+    # save complex topology
+    with open(cmplx_top, 'w') as f:
+        f.write(prot_top_combined)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Perform SMD runs for dynamic undocking')
+    parser.add_argument('--lig-top', help='Ligand TOP file.')
+    parser.add_argument('--prot-top', help='Protein TOP file.')
+    parser.add_argument('--lig-gro', help='Ligand GRO file.')
+    parser.add_argument('--prot-gro', help='Protein GRO file.')
+    parser.add_argument('--complex-top', help='Complex TOP file.')
+    parser.add_argument('--complex-gro', help='Complex GRO file.')
+    args = parser.parse_args()
+    merge_gro_files(args.prot_gro, args.lig_gro, args.complex_gro)
+    merge_top_files(args.prot_top, args.lig_top, args.complex_top)
+
+
+if __name__ == "__main__":
+    main()