OpenBind processing update

setup.py

@@ -79,7 +79,6 @@
     "mrbump = dlstbx.wrapper.mrbump:MrBUMPWrapper",
     "pandda_xchem = dlstbx.wrapper.pandda_xchem:PanDDAWrapper",
     "pandda_post = dlstbx.wrapper.pandda_post:PanDDApostWrapper",
-    "pandda_rhofit = dlstbx.wrapper.pandda_rhofit:PanDDARhofitWrapper",
     "pipedream_xchem = dlstbx.wrapper.pipedream_xchem:PipedreamWrapper",
     "phaser_ellg  = dlstbx.wrapper.phaser_ellg:PhasereLLGWrapper",
     "rlv = dlstbx.wrapper.rlv:RLVWrapper",

src/dlstbx/util/mvs/helpers.py

@@ -0,0 +1,55 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import gemmi
+
+
+def find_residue_by_name(structure, name):
+    for model in structure:
+        for chain in model:
+            for res in chain:
+                if res.name == name:
+                    return chain, res
+    raise ValueError(f"Residue {name} not found")
+
+
+def residue_centroid(residue):
+    n = 0
+    x = y = z = 0.0
+    for at in residue:
+        p = at.pos
+        x += p.x
+        y += p.y
+        z += p.z
+        n += 1
+    if n == 0:
+        raise ValueError("Residue has no atoms")
+    return gemmi.Position(x / n, y / n, z / n)
+
+
+def save_cropped_map(pdb_file, map_file, resname, radius):
+    st = gemmi.read_structure(pdb_file)
+    cell = st.cell
+    m = gemmi.read_ccp4_map(map_file, setup=True)
+    grid = m.grid
+
+    chain, res = find_residue_by_name(st, resname)
+    center = residue_centroid(res)  # ligand center
+
+    mask = grid.clone()
+    mask.fill(0.0)
+
+    mask.set_points_around(center, radius, 1.0, use_pbc=True)  # spherical mask in Å
+
+    dl = gemmi.Position(radius, radius, radius)  # box d/2
+    box = gemmi.FractionalBox()
+    box.extend(cell.fractionalize(center - dl))
+    box.extend(cell.fractionalize(center + dl))
+
+    grid.array[:] *= mask.array
+    m.set_extent(box)
+    path = Path(map_file)
+    map_out = str(path.parents[0] / f"{path.stem}_cropped.ccp4")
+    m.write_ccp4_map(map_out)
+    return map_out

src/dlstbx/util/mvs/ligandfit.py → src/dlstbx/util/mvs/viewer_ligandfit.py

@@ -1,10 +1,17 @@
 from __future__ import annotations
 
+import gemmi
 import molviewspec as mvs
 
+from dlstbx.util.mvs.helpers import find_residue_by_name
+
+
+def gen_html_ligandfit(pdb_file, map_file, resname, outdir, acr, smiles, cc):
+    # make an mvs story from snapshots
+    st = gemmi.read_structure(pdb_file)
+    chain, res = find_residue_by_name(st, resname)
+    residue = mvs.ComponentExpression(label_seq_id=res.seqid.num)
 
-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(
@@ -30,21 +37,28 @@ def gen_html_ligandfit(pdb_file, map_file, outdir, acr, smiles, cc):
 
     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,
+        description=f"## Ligand_Fit Results: \n ### {acr} with ligand & electron density map \n - SMILES: {smiles} \n - 2FO-FC map at 1.5σ, blue \n - Fitting CC = {cc}",
+        transition_duration_ms=700,
+        linger_duration_ms=4000,
     )
 
     # 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"
+    ).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").focus().representation(
+    structure.component(selector="ligand").representation(type="surface").opacity(
+        opacity=0.1
+    ).color(custom={"molstar_color_theme_name": "element-symbol"})
+
+    structure.component(selector=residue).focus().representation(
         type="ball_and_stick"
     ).color(custom={"molstar_color_theme_name": "element-symbol"})
 
@@ -56,25 +70,19 @@ def gen_html_ligandfit(pdb_file, map_file, outdir, acr, smiles, cc):
         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}")
+    structure.component(
+        selector=residue,
+        custom={
+            "molstar_show_non_covalent_interactions": True,
+            "molstar_non_covalent_interactions_radius_ang": 5,
+        },
     )
 
     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,
+        transition_duration_ms=700,
+        linger_duration_ms=4000,
     )
 
     states = mvs.States(

src/dlstbx/util/mvs/viewer_pandda.py

@@ -0,0 +1,120 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import gemmi
+import molviewspec as mvs
+
+from dlstbx.util.mvs.helpers import find_residue_by_name
+
+
+def gen_html_pandda(pdb_file, event_map, z_map, resname, outdir, dtag, smiles, score):
+    # make an mvs story from snapshots
+    st = gemmi.read_structure(pdb_file)
+    chain, res = find_residue_by_name(st, resname)
+    residue = mvs.ComponentExpression(label_seq_id=res.seqid.num)
+
+    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="surface", size_factor=0.7
+    ).opacity(opacity=0.1).color(custom={"molstar_color_theme_name": "element-symbol"})
+
+    structure.component(selector=residue).focus().representation(
+        type="ball_and_stick"
+    ).color(custom={"molstar_color_theme_name": "element-symbol"})
+
+    ccp4 = builder.download(url=event_map).parse(format="map")
+    ccp4.volume().representation(
+        type="isosurface",
+        relative_isovalue=3,
+        show_wireframe=True,
+        show_faces=False,
+    ).color(color="blue").opacity(opacity=0.25)
+
+    structure.component(
+        selector=residue,
+        custom={
+            "molstar_show_non_covalent_interactions": True,
+            "molstar_non_covalent_interactions_radius_ang": 5,
+        },
+    )
+
+    snapshot1 = builder.get_snapshot(
+        title="Event_map",
+        description=f"## PanDDA2 Results: \n ### {dtag} \n - Ligand score: {score} \n - SMILES: {smiles} \n - Event map at 3σ, blue",
+        transition_duration_ms=700,
+        linger_duration_ms=4000,
+    )
+
+    # 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=0.2).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="surface", size_factor=0.7
+    ).opacity(opacity=0.1).color(custom={"molstar_color_theme_name": "element-symbol"})
+
+    structure.component(selector=residue).focus().representation(
+        type="ball_and_stick"
+    ).color(custom={"molstar_color_theme_name": "element-symbol"})
+
+    ccp4 = builder.download(url=z_map).parse(format="map")
+    ccp4.volume().representation(
+        type="isosurface",
+        relative_isovalue=3,
+        show_wireframe=True,
+        show_faces=False,
+    ).color(color="green").opacity(opacity=0.25)
+
+    structure.component(
+        selector=residue,
+        custom={
+            "molstar_show_non_covalent_interactions": True,
+            "molstar_non_covalent_interactions_radius_ang": 5,
+        },
+    )
+
+    snapshot2 = builder.get_snapshot(
+        title="Z_map",
+        description=f"## PanDDA2 Results: \n ### {dtag} \n - Ligand score: {score} \n - SMILES: {smiles} \n - Z_map at 3σ, green",
+        transition_duration_ms=700,
+        linger_duration_ms=4000,
+    )
+
+    states = mvs.States(
+        snapshots=[snapshot1, snapshot2],  # [snapshot1, snapshot2]
+        metadata=mvs.GlobalMetadata(description="PanDDA2 Results"),
+    )
+
+    with open(pdb_file) as f:
+        pdb_data = f.read()
+
+    # with open(event_map, mode="rb") as f:
+    #     map_data1 = f.read()
+
+    with open(z_map, mode="rb") as f:
+        map_data2 = f.read()
+
+    html = mvs.molstar_html(
+        states,
+        data={pdb_file: pdb_data, z_map: map_data2},  # event_map: map_data1,
+        ui="stories",
+    )
+
+    out_file = Path(f"{outdir}/pandda2_mvs.html")
+    with open(out_file, "w") as f:
+        f.write(html)
+
+    return out_file

src/dlstbx/util/mvs/viewer_pipedream.py

@@ -0,0 +1,74 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import gemmi
+import molviewspec as mvs
+
+from dlstbx.util.mvs.helpers import find_residue_by_name
+
+
+def gen_html_pipedream(pdb_file, map_file, resname, outdir, dtag, smiles):
+    # make an mvs story from snapshots
+    st = gemmi.read_structure(pdb_file)
+    chain, res = find_residue_by_name(st, resname)
+    residue = mvs.ComponentExpression(label_seq_id=res.seqid.num)
+
+    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=residue).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)
+
+    structure.component(
+        selector=residue,
+        custom={
+            "molstar_show_non_covalent_interactions": True,
+            "molstar_non_covalent_interactions_radius_ang": 5,
+        },
+    )
+
+    snapshot1 = builder.get_snapshot(
+        title="Main View",
+        description=f"## Pipedream Results: \n ### {dtag} \n - SMILES: {smiles} \n - 2FO-FC map map at 1.5σ, blue",
+        transition_duration_ms=700,
+        linger_duration_ms=4000,
+    )
+
+    states = mvs.States(
+        snapshots=[snapshot1],
+        metadata=mvs.GlobalMetadata(description="Pipedream 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",
+    )
+
+    out_file = Path(f"{outdir}/pipedream_mvs.html")
+    with open(out_file, "w") as f:
+        f.write(html)
+
+    return out_file

src/dlstbx/wrapper/ligand_fit.py

@@ -9,7 +9,7 @@
 from shutil import ignore_patterns
 
 import dlstbx.util.symlink
-from dlstbx.util.mvs.ligandfit import gen_html_ligandfit
+from dlstbx.util.mvs.viewer_ligandfit import gen_html_ligandfit
 from dlstbx.wrapper import Wrapper
 
 
@@ -149,7 +149,13 @@ def run(self):
         CC = self.pull_CC_from_log(pipeline_directory)
         try:
             gen_html_ligandfit(
-                out_pdb, out_map, pipeline_directory, cc=CC, smiles=smiles, acr=acr
+                out_pdb,
+                out_map,
+                resname="LIG",
+                outdir=pipeline_directory,
+                cc=CC,
+                smiles=smiles,
+                acr=acr,
             )
         except Exception as e:
             self.log.debug(f"Exception generating mvs html: {e}")