added constriction site generation to the registry

kdtree_approach.py

@@ -54,7 +54,6 @@ def transform_points_to_C0(points: np.ndarray, base_point: np.ndarray, axis_poin
 
     return points_transformed
 
-
 def transform_points_from_C0(points: np.ndarray, base_point: np.ndarray, axis_point: np.ndarray) -> np.ndarray:
     translation, rotation = get_transformation_to_C0(base_point, axis_point)
     points_unrotated = points @ rotation
@@ -63,9 +62,9 @@ def transform_points_from_C0(points: np.ndarray, base_point: np.ndarray, axis_po
     return points_untranslated
 def main():
     # Load your points and transform them as before
-    RCSB_ID    = '4UG0'
+    RCSB_ID    = '8QSJ'
     R          = 40
-    H          = 120
+    H          = 100
     Vsize      = 1
     ATOM_SIZE  = 2
     base_point = np.array(PTC_location(RCSB_ID).location)

ribctl/asset_manager/asset_manager.py

@@ -24,6 +24,7 @@ def get_asset_path(self, pdb_id: str, asset_type: AssetType) -> Path:
               AssetType.MMCIF                : "{asset_dir}/{pdb_id}.cif",
               AssetType.STRUCTURE_PROFILE    : "{asset_dir}/{pdb_id}.json",
               AssetType.PTC                  : "{asset_dir}/{pdb_id}_PTC.json",
+              AssetType.CONSTRICTION_SITE                  : "{asset_dir}/{pdb_id}_CONSTRICTION_SITE.json",
             #   AssetType.THUMBNAIL            : "{asset_dir}/{pdb_id}.png",
             #   AssetType.CLASSIFICATION_REPORT: "{asset_dir}/classification_report_{pdb_id}.json",
             #   AssetType.NPET_MESH            : "{asset_dir}/TUNNELS/{pdb_id}_NPET_MESH.ply",

ribctl/asset_manager/asset_registry.py

@@ -8,8 +8,9 @@
 from ribctl import RIBETL_DATA
 from ribctl.asset_manager.asset_manager import RibosomeAssetManager
 from ribctl.etl.etl_collector import ETLCollector
+from ribctl.lib.landmarks.constriction import get_constriction
 from ribctl.lib.landmarks.ptc_via_trna import PTC_location
-from ribctl.lib.schema.types_ribosome import PTCInfo, RibosomeStructure
+from ribctl.lib.schema.types_ribosome import ConstrictionSite, PTCInfo, RibosomeStructure
 from .asset_types import AssetType
 
 ModelT = TypeVar("ModelT", bound=BaseModel)
@@ -83,7 +84,6 @@ async def generate_multiple(
         for asset_type in asset_types:
             await self.generate_asset(rcsb_id, asset_type, force)
 
-
 main_registry = AssetRegistry(RibosomeAssetManager(RIBETL_DATA))
 
 
@@ -92,7 +92,10 @@ async def generate_profile(rcsb_id: str) -> RibosomeStructure:
     profile = await ETLCollector(rcsb_id).generate_profile()
     return profile
 
-
 @main_registry.register(AssetType.PTC)
 async def generate_ptc(rcsb_id: str) -> PTCInfo:
     return PTC_location(rcsb_id)
+
+@main_registry.register(AssetType.CONSTRICTION_SITE)
+async def generate_constriction(rcsb_id: str) -> ConstrictionSite:
+    return ConstrictionSite(location=get_constriction(rcsb_id).tolist())

ribctl/asset_manager/asset_types.py

@@ -6,7 +6,7 @@
 from typing import TypeVar, Generic, Optional, Type, Tuple
 from pydantic import BaseModel
 
-from ribctl.lib.schema.types_ribosome import PTCInfo, RibosomeStructure
+from ribctl.lib.schema.types_ribosome import ConstrictionSite, PTCInfo, RibosomeStructure
 
 # Type for any pydantic model
 ModelT = TypeVar('ModelT', bound=BaseModel)
@@ -33,6 +33,7 @@ class AssetType(Enum):
     # Model Based assets
     STRUCTURE_PROFILE = AssetInfo("profile", model=RibosomeStructure)
     PTC               = AssetInfo("ptc", model=PTCInfo, dependencies={"STRUCTURE_PROFILE", "MMCIF"});
+    CONSTRICTION_SITE = AssetInfo("constriction_site", model=ConstrictionSite, dependencies={"STRUCTURE_PROFILE", "MMCIF"});
 
     @property
     def model_type(self) -> Optional[Type[BaseModel]]:

ribctl/lib/landmarks/constriction.py

@@ -15,7 +15,8 @@ def get_constriction(rcsb_id: str)->np.ndarray:
     if uL4 is None or uL22 is None:
         raise ValueError("Could not find uL4 or uL22 in {}".format(rcsb_id))
     structure = ro.assets.biopython_structure()
-    uL4_c :Chain  = structure[0][uL4.auth_asym_id]
+
+    uL4_c  :Chain = structure[0][uL4.auth_asym_id]
     uL22_c :Chain = structure[0][uL22.auth_asym_id]
 
     uL4_coords  = [(r.center_of_mass() ) for r in uL4_c.child_list]

ribctl/lib/schema/types_ribosome.py

@@ -585,6 +585,9 @@ class PTCInfo(BaseModel):
     location: list[float]
     residues: list[ResidueSummary]
 
+class ConstrictionSite(BaseModel):
+    location: list[float]
+
 class RibosomeStructureMetadata(BaseModel):
 
     def get_polymers_by_assembly(self)->dict[str,list[str]]: