Move ligand_fit html generation to dlstbx

Author: rowanwalker96

src/dlstbx/util/mvs/__init__.py

@@ -0,0 +1,98 @@
+from __future__ import annotations
+
+import molviewspec as mvs
+
+
+def gen_html_ligandfit(pdb_file, map_file, outdir, acr, smiles, cc):
+    # make a story from 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=0.2).color(color="#AABDF1")
+    structure.component(selector="polymer").representation().opacity(
+        opacity=0.25
+    ).color(custom={"molstar_color_theme_name": "chain_id"})
+    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,
+    )
+
+    # SNAPSHOT2
+    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=202)
+    (
+        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_html(
+        states,
+        data={pdb_file: pdb_data, map_file: map_data},
+        ui="stories",
+    )
+
+    with open(f"{outdir}/ligand_fit.html", "w") as f:
+        f.write(html)

src/dlstbx/util/mvs/ligandfit.py

@@ -8,8 +8,8 @@
 import subprocess
 from shutil import ignore_patterns
 
-# import molviewspec as mvs
 import dlstbx.util.symlink
+from dlstbx.util.mvs.ligandfit import gen_html_ligandfit
 from dlstbx.wrapper import Wrapper
 
 
@@ -28,7 +28,7 @@ def pull_CC_from_log(self, pipeline_directory):
                 if match:
                     llist.append(match.group(1))
         file_read.close()
-        CC = llist[-1]  # take the final CC
+        CC = float(llist[-1])  # take the final CC
         return CC
 
     def send_attachments_to_ispyb(self, pipeline_directory, final_directory):
@@ -139,22 +139,20 @@ def run(self):
             self.send_attachments_to_ispyb(pipeline_directory)
             return False
 
+        os.system(
+            f"phenix.mtz2map {pipeline_directory / 'LIG_final.mtz'} {pipeline_directory / 'LIG_final.pdb'} directory={pipeline_directory} selection='resname LIG' buffer=3.5 labels=2FOFCWT,PH2FOFCWT"
+        )
+        out_map = str(pipeline_directory / "LIG_final_2mFo-DFc.ccp4")
+        out_pdb = str(pipeline_directory / "LIG_final.pdb")
+        acr = params.get("acronym", "Protein")
+        # self.generate_smiles_png(smiles, pipeline_directory)
         CC = self.pull_CC_from_log(pipeline_directory)
-
-        if CC >= min_cc_keep:
-            os.system(
-                f"phenix.mtz2map {pipeline_directory / 'LIG_final.mtz'} {pipeline_directory / 'LIG_final.pdb'} directory={pipeline_directory} selection='resname LIG' buffer=3.5 labels=2FOFCWT,PH2FOFCWT"
-            )
-            out_map = str(pipeline_directory / "LIG_final_2mFo-DFc.ccp4")
-            out_pdb = str(pipeline_directory / "LIG_final.pdb")
-            acr = params.get("acronym", "Protein")
-
-            os.system(
-                f"module load molviewspec; gen_html_ligandfit.py --pdb_file {out_pdb} --map_file {out_map} --cc {CC} --outdir {pipeline_directory} --smiles '{smiles}' --acr {acr}"
+        try:
+            gen_html_ligandfit(
+                out_pdb, out_map, pipeline_directory, cc=CC, smiles=smiles, acr=acr
             )
-
-        # self.generate_smiles_png(smiles, pipeline_directory)
-        # self.generate_html_visualisation(out_pdb, out_map, pipeline_directory, cc=CC, smiles=smiles, acr=acr)
+        except Exception as e:
+            self.log.debug(f"Exception generating mvs html: {e}")
 
         data = [
             ["Ligand_fit pipeline", "SMILES code", "Fitting CC"],
@@ -182,14 +180,7 @@ def run(self):
         self.log.info("Sending results to ISPyB")
         self.send_attachments_to_ispyb(pipeline_directory, final_directory)
 
-        if CC >= min_cc_keep:
-            self.log.info("Ligand_fitting pipeline finished successfully")
-            return True
-        else:
-            self.log.info(
-                f"Ligand_fitting pipeline finished but ligand fitting CC ({CC}) did not meet quality threshold ({min_cc_keep})"
-            )
-            return False
+        return True
 
     # def generate_smiles_png(self, smiles, outdir):
     #     mol = pybel.readstring("smi", smiles)