Added create_guassian_input NO_JIRA

Author: Alex-AMC

scripts/create_gaussian_input/ReadMe.md

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+# Create Gaussian Input
+
+----
+
+## Summary
+
+Allows the user to generate a Gaussian input file (.gjf) for a given CSD refcode or .mol2. If you wish to run different keywords the script will need to be changed manually. 
+
+
+## Requirements
+
+Tested with CSD Python API 3.0.9
+
+
+## Licensing Requirements
+
+CSD-Core
+
+If you wish to run Gaussian, you will need to acquire a licence for Gaussian, this is not supplied by the CCDC.
+
+## Instructions on running
+
+To create an input file for the 
+```cmd
+>python create_gaussian_input.py HXACAN
+```
+
+```cmd
+>python create_gaussian_input.py HXACAN.mol2
+```
+
+## Author
+
+_Andrew Malone_
+
+> For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](support@ccdc.cam.ac.uk)

scripts/create_gaussian_input/create_gaussian_input.py

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+#
+# 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.
+#
+# 2015-06-17: created by the Cambridge Crystallographic Data Centre
+#
+
+from __future__ import division, absolute_import, print_function
+
+"""
+This script will generate a generic Gaussian input file
+Input: CSD Identifier as a string
+Output: HTML File to working Directory
+Author: Andy Maloney 2015
+"""
+
+import sys
+import os
+import ccdc.io
+import glob
+
+
+def fatal(*args):
+    """Generates an error message if necessary to smoothly exit the program."""
+    print('ERROR:', ' '.join(map(str, args)))
+    sys.exit(1)
+
+
+def file_writer(molecule, name):
+    """Writes a standard Gaussian input file for all molecules contained in the structure files."""
+    if not mol.all_atoms_have_sites:
+        fatal(entry_id, 'has some atoms without coordinates')
+    mol.normalise_hydrogens()
+
+    for i, component in enumerate(molecule.components):
+
+        file_name = '%s_molecule%d.gjf' % (name, i)
+        f = open(file_name, 'w')
+
+        f.write('#B3LYP/6-31G**  opt\n')
+        f.write('\n')
+        f.write('Standard Gaussian Input File for %s, molecule %d\n' % (name, i))
+        f.write('\n')
+        f.write('0 1\n')
+
+        for atom in component.atoms:
+            f.write('%2s  %9.6f  %9.6f  %9.6f\n' % (atom.atomic_symbol,
+                                                    atom.coordinates.x,
+                                                    atom.coordinates.y,
+                                                    atom.coordinates.z))
+
+        f.write('\n')
+        f.write('--Link1--')
+        f.write('\n')
+        f.write('\n')
+        f.write('\n')
+
+        f.close()
+
+
+if __name__ == '__main__':
+    # Get the relevant structure typed by user
+    if len(sys.argv) != 2:
+        fatal('you must supply a structure identifier.')
+    entry_id = sys.argv[1]
+
+    # Checking the current directory for user cif file
+    filepath = '%s' % entry_id
+    if os.path.isfile(filepath):
+        reader = ccdc.io.MoleculeReader(filepath)
+        for mol in reader:
+            identifier = mol.identifier
+            file_writer(mol, identifier)
+
+    else:
+        # Read molecule from database
+        reader = ccdc.io.MoleculeReader('CSD')
+        identifier = entry_id
+        try:
+            mol = reader.molecule(entry_id)
+            file_writer(mol, identifier)
+        except RuntimeError:
+            fatal(entry_id, '- structure not found')