Added concat_mol2.py NO_JIRA

Author: Alex-AMC

scripts/concat_mol2/ReadMe.md

@@ -0,0 +1,43 @@
+# Concat Mol2
+
+----
+
+## Summary
+
+Opens a set of mol2 files in the working directory and creates one concatenated multi-mol2 file.
+Optionally delete the individual mol2 files other than the new concat.mol2
+
+## Requirements
+
+CSD Python API not required.
+Mol2 files must be in the same directory.
+
+## Licensing Requirements
+
+No licence required
+
+## Instructions on running
+
+```cmd
+> python concat_mol2.py
+```
+
+Help output:
+```cmd
+> python concat_mol2.py -h
+
+usage: concat_mol2.py [-h] [-d]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -d, --delete_contributors
+                        Remove contributing individual mol2 files after
+                        concatenation
+
+```
+
+## Author
+
+_
+
+> For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](support@ccdc.cam.ac.uk)

scripts/concat_mol2/concat_mol2.py

@@ -0,0 +1,45 @@
+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+# 2014-08-11: created by Peter Galek, The Cambridge Crystallographic Data Centre
+# 2022-02-24: updated by Alex Moldovan, The Cambridge Crystallographic Data Centre
+#
+
+import glob
+import argparse
+import os
+
+
+def main(delete_separate_files):
+    mol2_files = glob.glob('*.mol2')
+    count = 0
+    with open('concat.mol2', 'w') as outfile:
+        for f in mol2_files:
+            if f == 'concat.mol2':
+                continue
+            with open(f, 'r') as infile:
+                outfile.write(infile.read())
+                count += 1
+    print(f"{count} files concatenated.")
+
+    if delete_separate_files == True:
+        count = 0
+        for f in mol2_files:
+            if f == 'concat.mol2':
+                continue
+            os.remove(f)
+            count += 1
+        print(f"{count} files removed.")
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument('-d', '--delete_contributors', action='store_true',
+                        help='Remove contributing individual mol2 files after concatenation')
+
+    args = parser.parse_args()
+    main(args.delete_contributors)