Upload ligand_fit files despite fitting quality

Author: rowanwalker96

src/dlstbx/wrapper/ligand_fit.py

@@ -8,8 +8,6 @@
 import subprocess
 from shutil import ignore_patterns
 
-from iotbx import pdb
-
 # import molviewspec as mvs
 import dlstbx.util.symlink
 from dlstbx.wrapper import Wrapper
@@ -26,10 +24,11 @@ def pull_CC_from_log(self, pipeline_directory):
         llist = []
         for line in lines:
             if text in line:
-                llist.append(line)
+                match = re.search(r"CC\s*=\s*([0-9.]+)", line)
+                if match:
+                    llist.append(match.group(1))
         file_read.close()
-        match = re.search(r"CC\s*=\s*([0-9.]+)", llist[-1])
-        CC = float(match.group(1))
+        CC = llist[-1]  # take the final CC
         return CC
 
     def send_attachments_to_ispyb(self, pipeline_directory, final_directory):
@@ -54,7 +53,7 @@ def send_attachments_to_ispyb(self, pipeline_directory, final_directory):
             try:
                 shutil.copy(pipeline_directory / f.name, final_directory)
                 result_dict = {
-                    "file_path": str(pipeline_directory),
+                    "file_path": str(final_directory),
                     "file_name": f.name,
                     "file_type": file_type,
                     "importance_rank": importance_rank,
@@ -140,9 +139,6 @@ def run(self):
             self.send_attachments_to_ispyb(pipeline_directory)
             return False
 
-        with open(working_directory / "ligand_fit.log", "w") as log_file:
-            log_file.write(result.stdout)
-
         CC = self.pull_CC_from_log(pipeline_directory)
 
         if CC >= min_cc_keep:
@@ -199,114 +195,3 @@ def run(self):
     #     mol = pybel.readstring("smi", smiles)
     #     mol.make2D()
     #     mol.draw(show=False, filename=(f"{outdir}/SMILES.png"))
-
-
-# def generate_html_visualisation(pdb_file, map_file, outdir, acr, smiles, cc):
-#     # generate html with multiple snapshots
-#     builder = mvs.create_builder()
-#     structure = builder.download(url=pdb_file).parse(format="pdb").model_structure()
-#     structure.component(selector="polymer").representation(
-#         type="surface", size_factor=0.7
-#     ).opacity(opacity=0.6).color(color="#EEC4EE")
-#     structure.component(selector="polymer").representation().opacity(opacity=0.6).color(
-#         color="grey"
-#     )
-#     structure.component(selector="ligand").representation(type="ball_and_stick").color(
-#         custom={"molstar_color_theme_name": "element-symbol"}
-#     )
-#     structure.component(selector="ligand").representation(type="surface").opacity(
-#         opacity=0.1
-#     ).color(custom={"molstar_color_theme_name": "element-symbol"})
-
-#     ccp4 = builder.download(url=map_file).parse(format="map")
-#     ccp4.volume().representation(
-#         type="isosurface",
-#         relative_isovalue=1.5,
-#         show_wireframe=True,
-#         show_faces=False,
-#     ).color(color="blue").opacity(opacity=0.25)
-
-#     snapshot1 = builder.get_snapshot(
-#         title="Main View",
-#         description=f"## Ligand_Fit Results: \n ### {acr} with ligand & electron density map \n - SMILES: {smiles} \n - 2FO-FC at 1.5σ, blue \n - Fitting CC = {cc}",
-#         transition_duration_ms=2000,
-#         linger_duration_ms=5000,
-#     )
-
-#     # snapshot 2
-#     builder = mvs.create_builder()
-#     structure = builder.download(url=pdb_file).parse(format="pdb").model_structure()
-#     structure.component(selector="polymer").representation(
-#         type="surface", size_factor=0.7
-#     ).opacity(opacity=0.5).color(color="#D8BFD8")
-#     structure.component(selector="polymer").representation().opacity(opacity=0.6).color(
-#         color="grey"
-#     )
-#     structure.component(selector="ligand").focus().representation(
-#         type="ball_and_stick"
-#     ).color(custom={"molstar_color_theme_name": "element-symbol"})
-
-#     ccp4 = builder.download(url=map_file).parse(format="map")
-#     ccp4.volume().representation(
-#         type="isosurface",
-#         relative_isovalue=1.5,
-#         show_wireframe=True,
-#         show_faces=False,
-#     ).color(color="blue").opacity(opacity=0.25)
-
-#     # add a label
-#     info = get_chain_and_residue_numbers(pdb_file, "LIG")
-#     resid = info[0][1]
-#     residue = mvs.ComponentExpression(label_seq_id=resid)
-#     (
-#         structure.component(
-#             selector=residue,
-#             custom={
-#                 "molstar_show_non_covalent_interactions": True,
-#                 "molstar_non_covalent_interactions_radius_ang": 5.0,
-#             },
-#         ).label(text=f"CC = {cc}")
-#     )
-
-#     snapshot2 = builder.get_snapshot(
-#         title="Focus View",
-#         description=f"## Ligand_Fit Results: \n ### {acr} with ligand & electron density map \n - SMILES: {smiles} \n - 2FO-FC at 1.5σ, blue \n - Fitting CC = {cc}",
-#         transition_duration_ms=2000,
-#         linger_duration_ms=5000,
-#     )
-
-#     states = mvs.States(
-#         snapshots=[snapshot1, snapshot2],
-#         metadata=mvs.GlobalMetadata(description="Ligand_fit Results"),
-#     )
-
-#     with open(pdb_file) as f:
-#         pdb_data = f.read()
-
-#     with open(map_file, mode="rb") as f:
-#         map_data = f.read()
-
-#     html = mvs.molstar_widgets.molstar_html(
-#         states,
-#         data={pdb_file: pdb_data, map_file: map_data},
-#         ui="stories",
-#     )
-
-#     with open(outdir / "ligand_fit.html", "w") as f:
-#         f.write(html)
-
-
-def get_chain_and_residue_numbers(pdb_file_path, target_residue_name):
-    """
-    Finds (chain ID, residue number) for a given residue name in a PDB file.
-    """
-    pdb_hierarchy = pdb.input(file_name=pdb_file_path).construct_hierarchy()
-
-    results = [
-        (res.parent().id.strip(), f"{res.resseq.strip()}{res.icode.strip() or ''}")
-        for res in pdb_hierarchy.residue_groups()
-        for ag in res.atom_groups()
-        if ag.resname.strip() == target_residue_name
-    ]
-
-    return results