stjames 0.0.57__py3-none-any.whl → 0.0.59__py3-none-any.whl

stjames/atomium_stjames/mmcif.py

@@ -399,12 +399,12 @@ def update_models_list(mmcif_dict: dict[str, Any], data_dict: dict[str, Any]) ->
     # sequences = make_sequences(mmcif_dict)
     secondary_structure = make_secondary_structure(mmcif_dict)
     aniso = make_aniso(mmcif_dict)
-    model: dict[str, Any] = {"polymer": {}, "non-polymer": {}, "water": {}, "branched": {}}
+    model: dict[str, Any] = {"polymer": {}, "non_polymer": {}, "water": {}, "branched": {}}
     model_num = mmcif_dict["atom_site"][0]["pdbx_PDB_model_num"]
     for atom in mmcif_dict["atom_site"]:
         if atom["pdbx_PDB_model_num"] != model_num:
             data_dict["models"].append(model)
-            model = {"polymer": {}, "non-polymer": {}, "water": {}, "branched": {}}
+            model = {"polymer": {}, "non_polymer": {}, "water": {}, "branched": {}}
             model_num = atom["pdbx_PDB_model_num"]
         mol_type = types[entities[atom["label_asym_id"]]]
         if mol_type == "polymer" or mol_type == "branched":
@@ -501,13 +501,13 @@ def add_atom_to_polymer(atom: dict[str, Any], aniso: dict[int, Any], model: dict
 
 
 def add_atom_to_non_polymer(atom: dict[str, Any], aniso: dict[int, Any], model: dict[str, Any], mol_type: str, names: dict[str, Any]) -> None:
-    """Takes an MMCIF atom dictionary, converts it, and adds it to a non-polymer
+    """Takes an MMCIF atom dictionary, converts it, and adds it to a non_polymer
     dictionary.
 
     :param dict atom: the .mmcif dictionary to read.
     :param dict aniso: lookup dictionary for anisotropy information.
     :param dict model: the model to update.
-    :param str mol_type: non-polymer or water.
+    :param str mol_type: non_polymer or water.
     :param dict names: the lookup dictionary for full name information."""
 
     mol_id = make_residue_id(atom)
@@ -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/atomium_stjames/pdb.py

@@ -145,7 +145,7 @@ def update_models_list(pdb_dict: dict[str, Any], data_dict: dict[str, Any]) -> N
     for model_lines in pdb_dict["MODEL"]:
         aniso = make_aniso(model_lines)
         last_ter = get_last_ter_line(model_lines)
-        model: dict[str, Any] = {"polymer": {}, "non-polymer": {}, "water": {}}
+        model: dict[str, Any] = {"polymer": {}, "non_polymer": {}, "water": {}}
         for index, line in enumerate(model_lines):
             if line[:6] in ["ATOM  ", "HETATM"]:
                 chain_id = line[21] if index < last_ter else id_from_line(line)
@@ -512,7 +512,7 @@ def add_atom_to_non_polymer(line: str, model: dict[Any, Any], res_id: str, aniso
     :param str res_id: the molecule ID to add to.
     :param dict aniso_dict: lookup dictionary for anisotropy information."""
 
-    key = "water" if line[17:20] in ["HOH", "DOD"] else "non-polymer"
+    key = "water" if line[17:20] in ["HOH", "DOD"] else "non_polymer"
     try:
         model[key][res_id]["atoms"][int(line[6:11])] = atom_line_to_dict(line, aniso_dict)
     except Exception:
@@ -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/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
@@ -84,7 +84,7 @@ class PDBModel(BaseModel):
     model_config = ConfigDict(extra=EXTRA)
 
     polymer: dict[str, PDBPolymer] = {}
-    non_polymer: dict[str, PDBNonPolymer] = Field(alias="non-polymer", default_factory=dict)
+    non_polymer: dict[str, PDBNonPolymer] = {}
     branched: dict[str, Any] = {}
     water: dict[str, PDBWater] = {}
 
@@ -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-0.0.57.dist-info → stjames-0.0.59.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.57
+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-0.0.57.dist-info → stjames-0.0.59.dist-info}/RECORD

@@ -15,7 +15,7 @@ stjames/method.py,sha256=5hBHk2xQLpxZ52LwJ9FHWaqQMdFKnsbQEOxaVe6O4Go,2321
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=DeNYmFdvbuKeXvLqlu-UxHMyZVK6y4j-Lw3HITGMnHw,12406
 stjames/opt_settings.py,sha256=gxXGtjy9l-Q5Wen9eO6T6HHRCuS8rfOofdVQIJj0JcI,550
-stjames/pdb.py,sha256=u2DHcKER2igG0Tn94lSSFuwNRCEtk3ye8C1k6nzW6ew,25274
+stjames/pdb.py,sha256=UxbgtIbc28L9O74AESYQiLBeiWZhdEbrBUT3mlyqRt8,25411
 stjames/periodic_cell.py,sha256=eV_mArsY_MPEFSrFEsTC-CyCc6V8ITAXdk7yhjjNI7M,1080
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/scf_settings.py,sha256=WotVgVrayQ_8PUHP39zVtG7iLT9PV41lpzruttFACP8,2356
@@ -27,8 +27,8 @@ stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856Kffx
 stjames/types.py,sha256=hw-3UBikESvN3DzfK5doZB030kIEfx9gC3yBkIbebsI,3764
 stjames/atomium_stjames/__init__.py,sha256=gZkzC7i9D_fmWUTN55gtygITo3-qvJUda5CXLR0jyCQ,306
 stjames/atomium_stjames/data.py,sha256=-hzwBpTHq5JetsOVyopUJswKnKAkMtJ_XkONxjXVupU,5675
-stjames/atomium_stjames/mmcif.py,sha256=16LNhQW7GkwEmRAG2lDEnhQaeBabtzIiEbzjjBnLhNg,27108
-stjames/atomium_stjames/pdb.py,sha256=nkCqdc6fy6rKNcIZZDysDLTdlPJWWRmTYBYEFr1wcAQ,22365
+stjames/atomium_stjames/mmcif.py,sha256=SjyWd1Zg_Pd0zM9OhaZ3rWGg3TDUuRJS88Zsvdbi-5M,27420
+stjames/atomium_stjames/pdb.py,sha256=C2mEcBDDrnoXD9ZCMIH2uJpjiWPJy6ktXq8IFZsrQKM,22482
 stjames/atomium_stjames/utilities.py,sha256=PSrOGn6MED4sXvbTLb65Jv20Ylptz4slZtjWEDzeRrI,4776
 stjames/data/__init__.py,sha256=O59Ksp7AIqwOELCWymfCx7YeBzwNOGCMlGQi7tNLqiE,24
 stjames/data/bragg_radii.json,sha256=hhbn-xyZNSdmnULIjN2Cvq-_BGIZIqG243Ls_mey61w,1350
@@ -57,8 +57,8 @@ stjames/workflows/scan.py,sha256=uNSuUmVMAV4exNvcv1viVe7930i7GZMn7RtEimnwEE8,100
 stjames/workflows/spin_states.py,sha256=b-uCf-pHjF_JHbExeb5GdRToE0pIxP0JTd50U130ckI,4693
 stjames/workflows/tautomer.py,sha256=x3TC8hkMs87ZUodLyhce5EUzYoV276ePfPMi7ISWyNU,651
 stjames/workflows/workflow.py,sha256=tIu5naADYgYS7kdW8quvGEWHWosBcrIdcD7L86v-uMQ,976
-stjames-0.0.57.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.57.dist-info/METADATA,sha256=FNtbr8EoBU0v70X_3-1GaQtu1MniVytVf3g9vgHSarI,1713
-stjames-0.0.57.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-stjames-0.0.57.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.57.dist-info/RECORD,,
+stjames-0.0.59.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.59.dist-info/METADATA,sha256=SDY-2LM12v5-wk8e25U1-U6L9ylteTXnMbm1FLkdohc,1713
+stjames-0.0.59.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+stjames-0.0.59.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.59.dist-info/RECORD,,