Merge pull request #732 from haddocking/haddock3_restraints

Haddock3 restraints

requirements.txt

@@ -10,3 +10,4 @@ tox==3.24.5
 pandas==1.5.1
 plotly==5.11.0
 kaleido==0.2.1
+freesasa==2.2.0.post3

setup.py

@@ -90,6 +90,7 @@ def read(*names, **kwargs) -> str:
             'haddock3-unpack = haddock.clis.cli_unpack:maincli',
             'haddock3-analyse = haddock.clis.cli_analyse:maincli',
             'haddock3-traceback = haddock.clis.cli_traceback:maincli',
+	    'haddock3-restraints = haddock.clis.cli_restraints:maincli'
             ]
         },
     # cmdclass={'build_ext': optional_build_ext},

src/haddock/clis/cli_restraints.py

@@ -0,0 +1,79 @@
+"""
+HADDOCK3 CLI for restraints-related tasks.
+
+DISCLAIMER: these scripts have been ported from old code and are not
+optimized for code quality and performance. They are provided as a convenience
+ for the user.
+
+USAGE::
+
+    haddock3-restraints <TASK_NAME> <TASK_ARGS>
+
+For the list of available tasks, run::
+
+    haddock3-restraints -h
+
+For the list of arguments for a given task, run::
+
+    haddock3-restraints <TASK_NAME> -h
+"""
+import argparse
+import sys
+
+from haddock.restraints.restrain_bodies import add_restrain_bodies_arguments, restrain_bodies
+from haddock.restraints.passive_from_active import add_pass_from_act_arguments, passive_from_active
+from haddock.restraints.validate_tbl import add_validate_tbl_arguments, validate_tbl
+from haddock.restraints.active_passive_to_ambig import add_actpass_to_ambig_arguments, actpass_to_ambig
+
+
+# Command line interface parser
+ap = argparse.ArgumentParser(
+    prog="haddock3-restraints",
+    description=__doc__,
+    formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+subparsers = ap.add_subparsers(title='subcommands',
+                               description='valid subcommands',
+                               help='additional help')
+
+# restrain_bodies subcommand
+restrain_bodies_subcommand = subparsers.add_parser('restrain_bodies')
+restrain_bodies_subcommand.set_defaults(func=restrain_bodies)
+restrain_bodies_subcommand = add_restrain_bodies_arguments(restrain_bodies_subcommand)
+
+# passive_from_active subcommand
+pass_from_act_subcommand = subparsers.add_parser('passive_from_active')
+pass_from_act_subcommand.set_defaults(func=passive_from_active)
+pass_from_act_subcommand = add_pass_from_act_arguments(pass_from_act_subcommand)
+
+# validate_tbl subcommand
+validate_tbl_subcommand = subparsers.add_parser('validate_tbl')
+validate_tbl_subcommand.set_defaults(func=validate_tbl)
+validate_tbl_subcommand = add_validate_tbl_arguments(validate_tbl_subcommand)
+
+# active_passive_to_ambig subcommand
+actpass_to_ambig_subcommand = subparsers.add_parser('active_passive_to_ambig')
+actpass_to_ambig_subcommand.set_defaults(func=actpass_to_ambig)
+actpass_to_ambig_subcommand = add_actpass_to_ambig_arguments(actpass_to_ambig_subcommand)
+
+
+def _ap():
+    return ap
+
+
+def load_args(ap):
+    """Load argument parser args."""
+    return ap.parse_args()
+
+
+def maincli():
+    """Execute main client."""
+    args = ap.parse_args()
+    cmd = vars(load_args(ap))
+    cmd.pop("func")
+    args.func(**cmd)
+
+
+if __name__ == "__main__":
+    sys.exit(maincli())