Scripts to generate template coords, fix pdb4amber

Add two scripts used in RESISTOR for the star-protocol.

- gen-templ-coords.sh is for generating template coordinates.
- p4a-undo.py is for fixing the numbering and chain ID of a structure
  after pdb4amber has "fixed" deficiencies.

src/main/julia/resistor/gen-templ-coords.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# Generates template coordinates from a PDB file's atom records.
+# Can be used to generate template coordinates for, e.g., a small molecule ligand.
+#
+# ./gen-templ-coords.sh sch7.pdb 38Z
+# (script) (structure) (residue ID in structure)
+
+if [[ $# -ne 2 ]]; then
+	echo "Expecting 2 parameters: <structure-file> and <residue ID>" >&2
+	exit 1
+fi
+
+echo $2 $(wc --lines < $1)
+tr --squeeze-repeats ' ' < $1 | cut --delimiter=' ' --fields=3,7,8,9

src/main/julia/resistor/p4a-undo.py

@@ -0,0 +1,38 @@
+import sys
+
+# This script "fixes" residue numbers and chain IDs after using Ambertool's
+# pdb4amber program to ensure an input structure PDB file can be used with
+# ambertools. One of the things pdb4amber does is change all residue numbering
+# to start at 1, and gives every chain the same chain ID. This script undoes
+# those two changes.
+
+# python p4a-undo.py structure.pdb renumfile.txt
+
+def main(args):
+    if len(args) != 2:
+        print('expected two arguments: <pdb file> <renum file>', file=sys.stderr)
+        exit(1)
+
+    with open(args[1]) as renum_lines:
+        renum_dict = { 
+              line.split()[4] : (line.split()[2], line.split()[1])
+          for line in renum_lines
+        }
+
+    with open(args[0]) as pdb_lines:
+        for line in pdb_lines:
+            if not line.strip():
+                continue
+            if line[:4] != 'ATOM' and line[:4] != 'HETA' and line[:3] != 'TER':
+                print(line, end='')
+                continue
+
+            res_name = line[17:20].strip()
+            res_num = line[22:26].strip()
+            old_num = renum_dict[res_num][0].rjust(4)
+            chain = renum_dict[res_num][1]
+            print(f'{line[:21]}{chain}{old_num}{line[26:]}'.strip())
+
+if __name__ == '__main__':
+    main(sys.argv[1:])
+