From e15af86d7373bb52bf2e892c7db9d410a4cf2aeb Mon Sep 17 00:00:00 2001
From: Nathan Baker <nathanbaker@microsoft.com>
Date: Mon, 3 Jul 2023 10:59:21 -0700
Subject: [PATCH 1/3] Update documentation about PROPKA options.

Warn that we ignore some PROPKA options.
---
 docs/source/releases.rst    | 5 +++++
 docs/source/using/index.rst | 7 +++++++
 2 files changed, 12 insertions(+)

diff --git a/docs/source/releases.rst b/docs/source/releases.rst
index 7d260e7..d9d00a0 100644
--- 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
index ad4a777..a54aad1 100644
--- 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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

From a02a7716a3f3c545f4161824c85f0c4416ddb61e Mon Sep 17 00:00:00 2001
From: Nathan Baker <nathanbaker@microsoft.com>
Date: Mon, 3 Jul 2023 11:34:00 -0700
Subject: [PATCH 2/3] Add warnings for unused PROPKA options.

Fixes #365.
---
 pdb2pqr/config.py | 7 +++++++
 pdb2pqr/main.py   | 9 ++++++++-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/pdb2pqr/config.py b/pdb2pqr/config.py
index f3c6094..a85e00d 100644
--- a/pdb2pqr/config.py
+++ b/pdb2pqr/config.py
@@ -5,6 +5,13 @@
 VERSION = __version__
 
 
+#: Options for PROPKA that PDB2PQR cannot handle
+IGNORED_PROPKA_OPTIONS = [
+    "thermophiles", "chains", "alignment", "mutations", "mutator",
+    "mutator_options", "reuse_ligand_mol2_file", "keep_protons",
+    "protonate_all"
+]
+
 #: 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
index e886801..17bd910 100644
--- 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 +279,13 @@ def check_options(args):
     :type args:  argparse.Namespace
     :raises RuntimeError:  silly option combinations were encountered.
     """
+    for option in IGNORED_PROPKA_OPTIONS:
+        if option in args:
+            _LOGGER.warn(
+                f"PROPKA option '{option}' is not processed correctly by "
+                f"PDB2PQR. Ignoring."
+            )
+            args.__dict__.pop(option)
     if (args.ph < 0) or (args.ph > 14):
         err = (
             f"Specified pH ({args.ph}) is outside the range "

From 04bc0071c64e4e9f30639fd6d323b32674ae16e8 Mon Sep 17 00:00:00 2001
From: Nathan Baker <nathanbaker@microsoft.com>
Date: Mon, 3 Jul 2023 13:28:19 -0700
Subject: [PATCH 3/3] Fixed dumb use of 'pop'.

Replace values instead of removing attributes.
---
 pdb2pqr/config.py | 16 +++++++++++-----
 pdb2pqr/main.py   | 14 ++++++++------
 2 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/pdb2pqr/config.py b/pdb2pqr/config.py
index a85e00d..58dacd9 100644
--- a/pdb2pqr/config.py
+++ b/pdb2pqr/config.py
@@ -6,11 +6,17 @@
 
 
 #: Options for PROPKA that PDB2PQR cannot handle
-IGNORED_PROPKA_OPTIONS = [
-    "thermophiles", "chains", "alignment", "mutations", "mutator",
-    "mutator_options", "reuse_ligand_mol2_file", "keep_protons",
-    "protonate_all"
-]
+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
index 17bd910..ffba7e0 100644
--- a/pdb2pqr/main.py
+++ b/pdb2pqr/main.py
@@ -279,13 +279,15 @@ def check_options(args):
     :type args:  argparse.Namespace
     :raises RuntimeError:  silly option combinations were encountered.
     """
-    for option in IGNORED_PROPKA_OPTIONS:
+    for option, new_value in IGNORED_PROPKA_OPTIONS.items():
         if option in args:
-            _LOGGER.warn(
-                f"PROPKA option '{option}' is not processed correctly by "
-                f"PDB2PQR. Ignoring."
-            )
-            args.__dict__.pop(option)
+            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 "