stjames 0.0.58__tar.gz → 0.0.59__tar.gz

{stjames-0.0.58/stjames.egg-info → stjames-0.0.59}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.58
+Version: 0.0.59
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.58 → stjames-0.0.59}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.58"
+version = "0.0.59"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.58 → stjames-0.0.59}/stjames/atomium_stjames/mmcif.py

@@ -606,6 +606,16 @@ def atom_dict_to_atom_dict(d: dict[str, Any], aniso_dict: dict[int, Any]) -> dic
     for key in ["x", "y", "z", "charge", "bvalue", "occupancy"]:
         if atom[key] is not None:
             atom[key] = float(atom[key])
+    if atom["charge"] == 0:
+        atom["charge"] = None
+    if not atom["is_hetatm"]:
+        atom["is_hetatm"] = None
+    if not atom["alt_loc"]:
+        atom["alt_loc"] = None
+    if atom["occupancy"] == 1:
+        atom["occupancy"] = None
+    if atom["name"] == atom["element"]:
+        atom["name"] = None
     return atom
 
 

{stjames-0.0.58 → stjames-0.0.59}/stjames/atomium_stjames/pdb.py

@@ -557,6 +557,10 @@ def atom_line_to_dict(line: str, aniso_dict: dict[Any, Any]) -> dict[str, Any]:
         a["is_hetatm"] = None
     if not a["alt_loc"]:
         a["alt_loc"] = None
+    if a["occupancy"] == 1:
+        a["occupancy"] = None
+    if a["name"] == a["element"]:
+        a["name"] = None
     return a
 
 

{stjames-0.0.58 → stjames-0.0.59}/stjames/pdb.py

@@ -22,7 +22,7 @@ class PDBAtom(BaseModel):
     y: float
     z: float
     element: str
-    name: str
+    name: str | None = None
     charge: float | None = None
     occupancy: float | None = None
     alt_loc: str | None = None
@@ -413,12 +413,15 @@ def _format_atom_line(
     else:
         chg = "  "
 
+    atom_name = atom.name if atom.name else atom.element
+    occupancy = atom.occupancy if atom.occupancy else 1.0
+
     # Construct the line.
     # Use exact spacing & field widths to match PDB guidelines.
     line = (
         f"{record_type}"
         f"{serial:5d} "  # atom serial number (columns 7-11)
-        f"{atom.name:<4}"  # atom name (columns 13-16, left-justified in this snippet)
+        f"{atom_name:<4}"  # atom name (columns 13-16, left-justified in this snippet)
         f"{alt_loc_char}"  # altLoc (column 17)
         f"{residue_name:>3}"  # residue name (columns 18-20)
         f" {chain_char}"  # chain ID (column 22)
@@ -427,7 +430,7 @@ def _format_atom_line(
         f"{atom.x:8.3f}"  # x (columns 31-38)
         f"{atom.y:8.3f}"  # y (columns 39-46)
         f"{atom.z:8.3f}"  # z (columns 47-54)
-        f"{atom.occupancy:6.2f}"  # occupancy (columns 55-60)
+        f"{occupancy:6.2f}"  # occupancy (columns 55-60)
         f"{atom.bvalue:6.2f}"  # temp factor (columns 61-66)
         f"          "  # columns 67-76 (padding)
         f"{atom.element:>2}"  # element (columns 77-78)
@@ -468,6 +471,8 @@ def _format_anisou_line(
     else:
         chg = "  "
 
+    atom_name = atom.name if atom.name else atom.element
+
     if atom.anisotropy:
         aniso_lines = (
             f"{_float_to_pdb_string(atom.anisotropy[0]):>7}"  # x (columns 29-35)
@@ -493,7 +498,7 @@ def _format_anisou_line(
     line = (
         f"{record_type}"
         f"{serial:5d} "  # atom serial number (columns 7-11)
-        f"{atom.name:<4}"  # atom name (columns 13-16, left-justified in this snippet)
+        f"{atom_name:<4}"  # atom name (columns 13-16, left-justified in this snippet)
         f"{alt_loc_char}"  # altLoc (column 17)
         f"{residue_name:>3}"  # residue name (columns 18-20)
         f" {chain_char}"  # chain ID (column 22)

{stjames-0.0.58 → stjames-0.0.59/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.58
+Version: 0.0.59
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames