Bugfix/rdf bugfix

PQAnalysis/analysis/rdf/rdf.py

@@ -31,7 +31,6 @@
 from .exceptions import RDFError
 
 
-
 class RDF:
 
     """
@@ -75,8 +74,8 @@ def __init__(
         traj: Trajectory | TrajectoryReader,
         reference_species: SelectionCompatible,
         target_species: SelectionCompatible,
-        use_full_atom_info: bool = False,
-        no_intra_molecular: bool = False,
+        use_full_atom_info: bool | None = False ,
+        no_intra_molecular: bool | None = False,
         n_bins: PositiveInt | None = None,
         delta_r: PositiveReal | None = None,
         r_max: PositiveReal | None = None,
@@ -92,10 +91,10 @@ def __init__(
             The reference species of the RDF analysis.
         target_species : SelectionCompatible
             The target species of the RDF analysis.
-        use_full_atom_info : bool, optional
+        use_full_atom_info : bool | None, optional
             Whether to use the full atom information of the trajectory
             or not, by default None (False).
-        no_intra_molecular : bool, optional
+        no_intra_molecular : bool | None, optional
             Whether to exclude intra-molecular distances or not, by default None (False).
         n_bins : PositiveInt | None, optional
             number of bins, by default None
@@ -193,7 +192,7 @@ def __init__(
         ############################################
         # Initialize Trajectory iterator/generator #
         ############################################
-
+        
         self.cells = traj.cells
 
         if isinstance(traj, TrajectoryReader):
@@ -209,6 +208,7 @@ def __init__(
             )
 
         self.first_frame = next(self.frame_generator)
+
         self.topology = traj.topology
 
         self._setup_bins(
@@ -526,8 +526,11 @@ def _finalize_run(
         differential_bins : Np1DNumberArray
             The differential bins of the RDF analysis based on the spherical shell model.
         """
-
-        target_density = len(self.target_index_combinations[0])
+        if self.no_intra_molecular:
+            target_density = len(self.target_index_combinations[0])
+        else:
+            target_density = len(self.target_indices)
+
         target_density /= self._average_volume
 
         norm = self._norm(

PQAnalysis/analysis/rdf/rdf_input_file_reader.py

@@ -76,7 +76,8 @@ def read(self):
         super().read()
         super().check_required_keys(self.required_keys)
         super().check_known_keys(self.required_keys + self.optional_keys)
-
+        super().not_defined_optional_keys(self.optional_keys)
+
         if (self.no_intra_molecular is not None and
             (self.restart_file is None or self.moldescriptor_file is None)):
             self.logger.error(
@@ -96,6 +97,16 @@ def read(self):
                 exception=InputFileError,
             )
 
+        if self.restart_file is None and self.moldescriptor_file is None:
+            self.logger.error(
+                (
+                "The restart_file key or the moldescriptor_file key with restart_file key "
+                "have to be set in order to use the RDF analysis." 
+                "It is needed for the selection of the target and reference residues."
+                ),
+                exception=InputFileError,
+            )
+
 
 
 input_keys_documentation = f"""

PQAnalysis/io/input_file_reader/pq_analysis/_parse.py

@@ -87,7 +87,7 @@ def _parse_real(input_dict: InputDictionary, key: str) -> Real | None:
     except PQKeyError:
         return None
 
-    if data[1] not in ["float", "int"]:
+    if data[1] not in ["float", "int", "None"]:
         logger.error(
             f"The \"{key}\" value has to be of float type - actually it is parsed as a {data[1]}",
             exception=InputFileError
@@ -132,7 +132,10 @@ def _parse_files(input_dict: InputDictionary, key: str) -> List[str] | None:
 
     if data_type in {"glob", "list(str)"}:
         return data[0]
-
+
+    if data_type == "None":
+        return None
+
     logger.error(
         (
         f"The \"{key}\" value has to be either a "
@@ -170,7 +173,7 @@ def _parse_int(input_dict: InputDictionary, key: str) -> int | None:
     except PQKeyError:
         return None
 
-    if data[1] != "int":
+    if data[1] not in ["int", "None"]:
         logger.error(
             f"The \"{key}\" value has to be of int type - actually it is parsed as a {data[1]}",
             exception=InputFileError
@@ -245,7 +248,7 @@ def _parse_string(input_dict: InputDictionary, key: str) -> str | None:
     except PQKeyError:
         return None
 
-    if data[1] != "str":
+    if data[1] not in ["str", "None"]:
         logger.error(
             (
             f"The \"{key}\" value has to be of "
@@ -266,7 +269,7 @@ def _parse_bool(input_dict: InputDictionary, key: str) -> bool | None:
     ----------
     dict : InputDictionary
         the input dictionary
-    key : str
+    key : str 
         the key to get the value from
 
     Returns
@@ -283,8 +286,8 @@ def _parse_bool(input_dict: InputDictionary, key: str) -> bool | None:
         data = input_dict[key]
     except PQKeyError:
         return None
-
-    if data[1] != "bool":
+    
+    if data[1] not in["bool", "None"]:
         logger.error(
             f"The \"{key}\" value has to be of bool type - actually it is parsed as a {data[1]}",
             exception=InputFileError

PQAnalysis/io/input_file_reader/pq_analysis/pqanalysis_input_file_reader.py

@@ -129,3 +129,17 @@ def check_known_keys(self, known_keys: List[str] | None = None):
                 "Unknown keys were set in the input file! "
                 f"The known keys are: {known_keys}. They will be ignored!"
             )
+
+    def not_defined_optional_keys(self, optional_keys: List[str]):
+        """
+        Checks if optional keys are set in the input file.
+        If not set, it sets them to None.
+
+        Parameters
+        ----------
+        optional_keys : List[str]
+            the optional keys
+        """
+        for key in optional_keys:
+            if key not in self.dictionary.keys():
+                self.dictionary.__setitem__(key=key,value=(None,"None","None"))

PQAnalysis/io/traj_file/trajectory_reader.py

@@ -56,7 +56,7 @@ def __init__(
             The format is inferred from the file extension.
         md_format : MDEngineFormat | str, optional
             The format of the trajectory. Default is MDEngineFormat.PQ.
-        topology : Topology, optional
+        topology : Topology | None, optional
             The topology of the trajectory. Default is None.
         constant_topology : bool, optional
             Whether the topology is constant over the trajectory or does change. Default is True.