Merge pull request #366 from Electrostatics/nathan/365

Warn about unused PROPKA options
Electrostatics · Jul 4, 2023 · 8db8d94 · 8db8d94
2 parents 1c818c0 + 04bc007
commit 8db8d94
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diff --git a/docs/source/releases.rst b/docs/source/releases.rst
@@ -6,6 +6,11 @@ Release history
 Current version
 ***************
 
+Changes
+=======
+
+* Added warnings about ignored PROPKA options (`#365 <https://github.com/Electrostatics/pdb2pqr/issues/365>`_)
+
 Fixes
 =====
 

diff --git a/docs/source/using/index.rst b/docs/source/using/index.rst
@@ -48,6 +48,13 @@ Information about additional options can be obtained by running:
 
    pdb2pqr --help
 
+.. note::
+
+   `PROPKA <https://github.com/jensengroup/propka>`_ options are exposed via the PDB2PQR command line for convenience.
+   However, not all of these options are supported in PDB2PQR.
+   We have tried to add warning or error messages when unsupported PROPKA options are passed to the code but we may have missed some.
+   Please `file an issue <https://github.com/Electrostatics/pdb2pqr/issues>`_ if you find a PROPKA option that is not working in PDB2PQR.
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Additional command-line tools
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/pdb2pqr/config.py b/pdb2pqr/config.py
@@ -5,6 +5,19 @@
 VERSION = __version__
 
 
+#: Options for PROPKA that PDB2PQR cannot handle
+IGNORED_PROPKA_OPTIONS = {
+    "thermophiles": None,
+    "chains": None,
+    "alignment": None,
+    "mutations": None,
+    "mutator": None,
+    "mutator_options": None,
+    "reuse_ligand_mol2_file": False,
+    "keep_protons": False,
+    "protonate_all": False
+}
+
 #: How to format PDB2PQR title in output
 TITLE_STR = f"PDB2PQR v{VERSION}: biomolecular structure conversion software."
 

diff --git a/pdb2pqr/main.py b/pdb2pqr/main.py
@@ -26,7 +26,7 @@
 from .ligand.mol2 import Mol2Molecule
 from .utilities import noninteger_charge
 from .config import VERSION, TITLE_STR, CITATIONS, FORCE_FIELDS
-from .config import REPAIR_LIMIT
+from .config import REPAIR_LIMIT, IGNORED_PROPKA_OPTIONS
 
 
 _LOGGER = logging.getLogger(f"PDB2PQR{VERSION}")
@@ -279,6 +279,15 @@ def check_options(args):
     :type args:  argparse.Namespace
     :raises RuntimeError:  silly option combinations were encountered.
     """
+    for option, new_value in IGNORED_PROPKA_OPTIONS.items():
+        if option in args:
+            value = getattr(args, option)
+            if value:
+                _LOGGER.warning(
+                    f"PROPKA option '{option}' {getattr(args, option)} is not "
+                    f"processed correctly by PDB2PQR. Ignoring."
+                )
+                setattr(args, option, new_value)
     if (args.ph < 0) or (args.ph > 14):
         err = (
             f"Specified pH ({args.ph}) is outside the range "