Bump version: 2.9.0 → 2.9.2

 - added support to use sites with fixed protonation states (fixed_sites) from the CLI
 - small bug fix for CpHMD

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.9.0
+current_version = 2.9.2
 commit = True
 tag = True
 

pypka/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Pedro B. P. S. Reis"
 __email__ = "pdreis@fc.ul.pt"
-__version__ = "2.9.0"
+__version__ = "2.9.2"
 
 from .main import Titration, getTitrableSites

pypka/clean/checksites.py

@@ -338,12 +338,17 @@ def correct_res_names(molecule, chain, resnumb, resname, aname):
         ):
             aname = molecule.correct_atoms[resnumb][aname]
 
-        if (
-            Config.pypka_params["ff_family"] == "CHARMM"
-            and resname == "HIS"
-            # and ((fixed_sites and chain in fixed_sites and resnumb not in fixed_sites[chain]) or (fixed_sites and chain not in fixed_sites))
-        ):
-            resname = "HSP"
+        if Config.pypka_params["ff_family"] == "CHARMM" and resname == "HIS":
+            if (
+                not fixed_sites
+                or (
+                    fixed_sites
+                    and chain in fixed_sites
+                    and resnumb not in fixed_sites[chain]
+                )
+                or (fixed_sites and chain not in fixed_sites)
+            ):
+                resname = "HSP"
 
         return resnumb, resname, aname
 

pypka/cli.py

@@ -43,15 +43,19 @@ def read_settings(filename):
                     parameters[param_name] = param_value
     # Search for all titrable sites in different chains
     sites = {}
+    fixed_sites = {}
     for param_name in parameters:
+        if "_" in param_name:
+            chain = param_name.split("_")[-1]
+        else:
+            chain = " "
         if param_name.startswith("site"):
-            if "_" in param_name:
-                chain = param_name.split("_")[1]
-            else:
-                chain = " "
             sites_str = parameters[param_name]
             chain_sites = [i.strip() for i in sites_str.split(",")]
             sites[chain] = chain_sites
+        elif param_name.startswith("fixed_site"):
+            fixed_sites_str = parameters[param_name]
+            fixed_sites[chain] = eval(fixed_sites_str)
 
     if " " in sites and sites[" "] == ["all"]:
         if len(sites) != 1:
@@ -69,7 +73,7 @@ def read_settings(filename):
             'Missing mandatory "sites" parameter\nTitratate all sites: sites = all\nTitrate all sites only from chain A: sites_A = all'
         )
 
-    return sites, parameters
+    return sites, fixed_sites, parameters
 
 
 def check_cli_args():
@@ -110,14 +114,15 @@ def check_cli_args():
         raise IOError("File {0} does not exist.".format(args.settings))
 
     # Read Settings File
-    sites, parameters = read_settings(args.settings)
+    sites, fixed_sites, parameters = read_settings(args.settings)
 
-    return sites, parameters, args.debug
+    return sites, fixed_sites, parameters, args.debug
 
 
 def CLI():
     # Read command line arguments
-    sites, parameters, debug = check_cli_args()
+    sites, fixed_sites, parameters, debug = check_cli_args()
 
-    Titration(parameters, sites=sites, debug=debug)
+
+    Titration(parameters, sites=sites, fixed_sites=fixed_sites, debug=debug)
     print("CLI exited successfully")

pypka/config.py

@@ -54,7 +54,11 @@ def filter_params(cls, parameters):
         """
         # Define all parameters
         for param_name, param_value in parameters.items():
-            if param_name.startswith("sites") or param_name in IGNORED_PARAMS:
+            if (
+                param_name.startswith("sites")
+                or param_name.startswith("fixed_sites")
+                or param_name in IGNORED_PARAMS
+            ):
                 continue
             config_obj = cls.getConfigObj(param_name)
             if config_obj:

pyproject.toml

@@ -25,7 +25,7 @@ commands=
 """
 [tool.poetry]
 name = "pypka"
-version = "2.9.0"
+version = "2.9.2"
 description = "A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism"
 authors = ["Pedro Reis <pdreis@fc.ul.pt>"]
 license = "LGPLv3"
@@ -48,7 +48,7 @@ numpy = [
 ]
 pytest = ">=6.2.5"
 delphi4py = "==1.2.0"
-pdbmender = "==0.5.0"
+pdbmender = "==0.5.3"
 
 [tool.poetry.dev-dependencies]
 recommonmark = "*"