Implementation of the GEN_FF workflow

.github/workflows/python-app.yml

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-       py_version: ["3.7", "3.8", "3.9", "3.10", "3.11"] 
+       py_version: ["3.8", "3.9", "3.10", "3.11"] 
 
     steps:
     - uses: actions/checkout@v2

LICENSE

@@ -1,201 +1,4 @@
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bin/polyply

@@ -23,7 +23,7 @@ import argparse
 from pathlib import Path
 import numpy as np
 import polyply
-from polyply import (gen_itp, gen_coords, gen_seq, DATA_PATH)
+from polyply import (gen_itp, gen_coords, gen_seq, gen_ff, DATA_PATH)
 from polyply.src.load_library import load_ff_library
 from polyply.src.logging import LOGGER, LOGLEVELS
 
@@ -51,6 +51,7 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
     parser_gen_itp = subparsers.add_parser('gen_params', aliases=['gen_itp'])
     parser_gen_coords = subparsers.add_parser('gen_coords')
     parser_gen_seq = subparsers.add_parser('gen_seq')
+    parser_itp_ff = subparsers.add_parser('gen_ff')
 
     # =============================================================================
     # Input Arguments for the itp generation tool
@@ -238,6 +239,24 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
                            default=[])
     parser_gen_seq.set_defaults(func=gen_seq)
 
+    # =============================================================================
+    # Input Arguments for the itp to ff tool
+    # =============================================================================
+
+    parser_itp_ff.add_argument('-v', dest='verbosity', action='count',
+                                help='Enable debug logging output. Can be given '
+                                'multiple times.', default=0)
+
+    parser_itp_ff.add_argument('-i', dest="itppath", type=Path, required=True)
+    parser_itp_ff.add_argument('-s', dest="smile_str", required=True)
+    parser_itp_ff.add_argument('-o', dest="outpath", type=Path)
+    parser_itp_ff.add_argument('-c', dest="res_charges",  nargs='+', type=lambda s: s.split(':'),)
+    parser_itp_ff.add_argument('-f', dest='inpath', type=Path, required=False, default=[],
+                                     help='Input file (ITP|FF)', nargs='*')
+
+    parser_itp_ff.set_defaults(func=gen_ff)
+
+
     # ============================================================================
     # Deal with queries of the polyply library
     # ============================================================================