Added new names for systems and configurations

HISTORY.rst

@@ -1,6 +1,12 @@
 =======
 History
 =======
+2024.7.28 -- Added new names for systems and configurations
+  * Made the naming of systems and configurations consistent with the standard
+    parameters for them in the GUI.
+  * Removed all "from file" options, replacing them with "title", which means the title
+    from the file, if it exists, or the filename if it doesn't.
+
 2023.11.16 -- Bugfix: titles in SDF files
   * Crashed reading some SDF files write by SEAMM due to the system and configuration
     names encoded in the title having multiple slashes (/).

read_structure_step/formats/cif/cif.py

@@ -135,9 +135,7 @@ def load_cif(
     with (
         gzip.open(path, mode="rt")
         if path.suffix == ".gz"
-        else bz2.open(path, mode="rt")
-        if path.suffix == ".bz2"
-        else open(path, "r")
+        else bz2.open(path, mode="rt") if path.suffix == ".bz2" else open(path, "r")
     ) as fd:
         for line in fd:
             if line[0:5] == "data_":
@@ -166,9 +164,7 @@ def load_cif(
     with (
         gzip.open(path, mode="rt")
         if path.suffix == ".gz"
-        else bz2.open(path, mode="rt")
-        if path.suffix == ".bz2"
-        else open(path, "r")
+        else bz2.open(path, mode="rt") if path.suffix == ".bz2" else open(path, "r")
     ) as fd:
         for line in fd:
             if line[0:5] == "data_":
@@ -378,9 +374,7 @@ def write_cif(
     with (
         gzip.open(path, mode="wb")
         if path.suffix == ".gz"
-        else bz2.open(path, mode="wb")
-        if path.suffix == ".bz2"
-        else open(path, "w")
+        else bz2.open(path, mode="wb") if path.suffix == ".bz2" else open(path, "w")
     ) as fd:
         for configuration in configurations:
             text = configuration.to_cif_text()

read_structure_step/formats/cif/mmcif.py

@@ -295,9 +295,7 @@ def write_mmcif(
     with (
         gzip.open(path, mode="wb")
         if path.suffix == ".gz"
-        else bz2.open(path, mode="wb")
-        if path.suffix == ".bz2"
-        else open(path, "w")
+        else bz2.open(path, mode="wb") if path.suffix == ".bz2" else open(path, "w")
     ) as fd:
         for configuration in configurations:
             text = configuration.to_mmcif_text()

read_structure_step/formats/mol2/mol2.py

@@ -101,7 +101,7 @@ def load_mol2(
         Normally and subsequent structures are loaded into new systems; however,
         if this option is True, they will be added as configurations.
 
-    system_name : str = "from file"
+    system_name : str = "title"
         The name for systems. Can be directives like "SMILES" or
         "Canonical SMILES". If None, no name is given.
 
@@ -174,24 +174,44 @@ def load_mol2(
         # Set the system name
         if system_name is not None and system_name != "":
             lower_name = system_name.lower()
-            if "from file" in lower_name:
-                system.name = obMol.GetTitle()
+            if lower_name == "title":
+                tmp = obMol.GetTitle()
+                if tmp != "":
+                    system.name = tmp
+                else:
+                    system.name = f"{path.stem} {structure_no}"
             elif "canonical smiles" in lower_name:
                 system.name = configuration.canonical_smiles
             elif "smiles" in lower_name:
                 system.name = configuration.smiles
+            elif "iupac" in lower_name:
+                system.name = configuration.PC_iupac_name
+            elif "inchikey" in lower_name:
+                system.name = configuration.inchikey
+            elif "inchi" in lower_name:
+                system.name = configuration.inchi
             else:
                 system.name = system_name
 
         # And the configuration name
         if configuration_name is not None and configuration_name != "":
             lower_name = configuration_name.lower()
-            if "from file" in lower_name:
-                configuration.name = obMol.GetTitle()
+            if lower_name == "title":
+                tmp = obMol.GetTitle()
+                if tmp != "":
+                    configuration.name = tmp
+                else:
+                    configuration.name = f"{path.stem} {structure_no}"
             elif "canonical smiles" in lower_name:
                 configuration.name = configuration.canonical_smiles
             elif "smiles" in lower_name:
                 configuration.name = configuration.smiles
+            elif "iupac" in lower_name:
+                configuration.name = configuration.PC_iupac_name
+            elif "inchikey" in lower_name:
+                configuration.name = configuration.inchikey
+            elif "inchi" in lower_name:
+                configuration.name = configuration.inchi
             elif lower_name == "sequential":
                 configuration.name = str(structure_no)
             else:

read_structure_step/formats/mop/obabel.py

@@ -497,9 +497,7 @@ def load_mop(
     # Set the system name
     if system_name is not None and system_name != "":
         lower_name = system_name.lower()
-        if "from file" in lower_name:
-            system.name = str(path)
-        elif lower_name == "title":
+        if lower_name == "title":
             if len(description_lines) > 0:
                 system.name = description_lines[0]
             else:
@@ -508,18 +506,30 @@ def load_mop(
             system.name = configuration.canonical_smiles
         elif "smiles" in lower_name:
             system.name = configuration.smiles
+        elif "iupac" in lower_name:
+            system.name = configuration.PC_iupac_name
+        elif "inchikey" in lower_name:
+            system.name = configuration.inchikey
+        elif "inchi" in lower_name:
+            system.name = configuration.inchi
         else:
             system.name = system_name
 
     # And the configuration name
     if configuration_name is not None and configuration_name != "":
         lower_name = configuration_name.lower()
-        if "from file" in lower_name:
+        if lower_name == "title":
             configuration.name = obMol.GetTitle()
         elif "canonical smiles" in lower_name:
             configuration.name = configuration.canonical_smiles
         elif "smiles" in lower_name:
             configuration.name = configuration.smiles
+        elif "iupac" in lower_name:
+            configuration.name = configuration.PC_iupac_name
+        elif "inchikey" in lower_name:
+            configuration.name = configuration.inchikey
+        elif "inchi" in lower_name:
+            configuration.name = configuration.inchi
         elif lower_name == "sequential":
             configuration.name = "1"
         else:

read_structure_step/formats/openbabel_io/obabel.py

@@ -22,7 +22,7 @@ def load_file(
     path,
     configuration,
     extension=".sdf",
-    add_hydrogens=True,
+    add_hydrogens=False,
     system_db=None,
     system=None,
     indices="1:end",
@@ -111,24 +111,44 @@ def load_file(
     # Set the system name
     if system_name is not None and system_name != "":
         lower_name = system_name.lower()
-        if "from file" in lower_name:
-            system.name = obMol.GetTitle()
+        if lower_name == "title":
+            tmp = obMol.GetTitle()
+            if tmp != "":
+                system.name = tmp
+            else:
+                system.name = path.stem
         elif "canonical smiles" in lower_name:
             system.name = configuration.canonical_smiles
         elif "smiles" in lower_name:
             system.name = configuration.smiles
+        elif "iupac" in lower_name:
+            system.name = configuration.PC_iupac_name
+        elif "inchikey" in lower_name:
+            system.name = configuration.inchikey
+        elif "inchi" in lower_name:
+            system.name = configuration.inchi
         else:
             system.name = system_name
 
     # And the configuration name
     if configuration_name is not None and configuration_name != "":
         lower_name = configuration_name.lower()
-        if "from file" in lower_name:
-            configuration.name = obMol.GetTitle()
+        if lower_name == "title":
+            tmp = obMol.GetTitle()
+            if tmp != "":
+                configuration.name = tmp
+            else:
+                configuration.name = path.stem
         elif "canonical smiles" in lower_name:
             configuration.name = configuration.canonical_smiles
         elif "smiles" in lower_name:
             configuration.name = configuration.smiles
+        elif "iupac" in lower_name:
+            configuration.name = configuration.PC_iupac_name
+        elif "inchikey" in lower_name:
+            configuration.name = configuration.inchikey
+        elif "inchi" in lower_name:
+            configuration.name = configuration.inchi
         elif lower_name == "sequential":
             configuration.name = "1"
         else:

read_structure_step/formats/sdf/sdf.py

@@ -64,7 +64,7 @@ def load_sdf(
     system=None,
     indices="1-end",
     subsequent_as_configurations=False,
-    system_name="Canonical SMILES",
+    system_name="title",
     configuration_name="sequential",
     printer=None,
     references=None,
@@ -105,7 +105,7 @@ def load_sdf(
         Normally and subsequent structures are loaded into new systems; however,
         if this option is True, they will be added as configurations.
 
-    system_name : str = "from file"
+    system_name : str = "title"
         The name for systems. Can be directives like "SMILES" or
         "Canonical SMILES". If None, no name is given.
 
@@ -139,9 +139,7 @@ def load_sdf(
     with (
         gzip.open(path, mode="rt")
         if path.suffix == ".gz"
-        else bz2.open(path, mode="rt")
-        if path.suffix == ".bz2"
-        else open(path, "r")
+        else bz2.open(path, mode="rt") if path.suffix == ".bz2" else open(path, "r")
     ) as fd:
         for line in fd:
             if line[0:4] == "$$$$":
@@ -172,9 +170,7 @@ def load_sdf(
     with (
         gzip.open(path, mode="rt")
         if path.suffix == ".gz"
-        else bz2.open(path, mode="rt")
-        if path.suffix == ".bz2"
-        else open(path, "r")
+        else bz2.open(path, mode="rt") if path.suffix == ".bz2" else open(path, "r")
     ) as fd:
         for line in fd:
             text += line
@@ -213,7 +209,7 @@ def load_sdf(
                 if subsequent_as_configurations:
                     configuration = system.create_configuration()
                 else:
-                    if have_sysname and "from file" in system_name.lower():
+                    if have_sysname and "title" in system_name.lower():
                         # Reuse the system if it exists
                         if system_db.system_exists(sysname):
                             system = system_db.get_system(sysname)
@@ -245,24 +241,42 @@ def load_sdf(
             # Set the system name
             if system_name is not None and system_name != "":
                 lower_name = system_name.lower()
-                if "from file" in lower_name:
-                    system.name = sysname
+                if lower_name == "title":
+                    if sysname != "":
+                        system.name = sysname
+                    else:
+                        system.name = f"{path.stem}_{record_no}"
                 elif "canonical smiles" in lower_name:
                     system.name = configuration.canonical_smiles
                 elif "smiles" in lower_name:
                     system.name = configuration.smiles
+                elif "iupac" in lower_name:
+                    system.name = configuration.PC_iupac_name
+                elif "inchikey" in lower_name:
+                    system.name = configuration.inchikey
+                elif "inchi" in lower_name:
+                    system.name = configuration.inchi
                 else:
                     system.name = system_name
 
             # And the configuration name
             if configuration_name is not None and configuration_name != "":
                 lower_name = configuration_name.lower()
-                if "from file" in lower_name:
-                    configuration.name = confname
+                if lower_name == "title":
+                    if confname != "":
+                        configuration.name = confname
+                    else:
+                        configuration.name = f"{path.stem}_{record_no}"
                 elif "canonical smiles" in lower_name:
                     configuration.name = configuration.canonical_smiles
                 elif "smiles" in lower_name:
                     configuration.name = configuration.smiles
+                elif "iupac" in lower_name:
+                    configuration.name = configuration.PC_iupac_name
+                elif "inchikey" in lower_name:
+                    configuration.name = configuration.inchikey
+                elif "inchi" in lower_name:
+                    configuration.name = configuration.inchi
                 elif lower_name == "sequential":
                     configuration.name = str(record_no)
                 else:

read_structure_step/formats/smi/smi.py

@@ -188,24 +188,44 @@ def load_mol2(
         # Set the system name
         if system_name is not None and system_name != "":
             lower_name = system_name.lower()
-            if "from file" in lower_name:
-                system.name = obMol.GetTitle()
+            if lower_name == "title":
+                tmp = obMol.GetTitle()
+                if tmp != "":
+                    system.name = tmp
+                else:
+                    system.name = f"{path.stem}_{structure_no}"
             elif "canonical smiles" in lower_name:
                 system.name = configuration.canonical_smiles
             elif "smiles" in lower_name:
                 system.name = configuration.smiles
+            elif "iupac" in lower_name:
+                system.name = configuration.PC_iupac_name
+            elif "inchikey" in lower_name:
+                system.name = configuration.inchikey
+            elif "inchi" in lower_name:
+                system.name = configuration.inchi
             else:
                 system.name = system_name
 
         # And the configuration name
         if configuration_name is not None and configuration_name != "":
             lower_name = configuration_name.lower()
-            if "from file" in lower_name:
-                configuration.name = obMol.GetTitle()
+            if lower_name == "title":
+                tmp = obMol.GetTitle()
+                if tmp != "":
+                    configuration.name = tmp
+                else:
+                    configuration.name = f"{path.stem}_{structure_no}"
             elif "canonical smiles" in lower_name:
                 configuration.name = configuration.canonical_smiles
             elif "smiles" in lower_name:
                 configuration.name = configuration.smiles
+            elif "iupac" in lower_name:
+                configuration.name = configuration.PC_iupac_name
+            elif "inchikey" in lower_name:
+                configuration.name = configuration.inchikey
+            elif "inchi" in lower_name:
+                configuration.name = configuration.inchi
             elif lower_name == "sequential":
                 configuration.name = str(structure_no)
             else: