Integrate PyMOL rendering into examples

doc/conf.py

@@ -195,7 +195,7 @@
     "within_subsection_order": FileNameSortKey,
     # Do not run example scripts with a trailing '_noexec'
     "filename_pattern": "^((?!_noexec).)*$",
-    "ignore_pattern": r"(.*ignore\.py)|(.*pymol\.py)",
+    "ignore_pattern": r"(.*ignore\.py)",
     "download_all_examples": False,
     # Never report run time
     "min_reported_time": sys.maxsize,

doc/examples/scripts/structure/alphabet/structure_search.py

@@ -24,6 +24,7 @@
 import numpy as np
 import biotite
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.sequence as seq
 import biotite.sequence.align as align
 import biotite.sequence.graphics as graphics
@@ -374,8 +375,20 @@ def filter_undefined_spans(sequence, min_length):
 _, transform = struc.superimpose(query_anchors, target_anchors)
 # Apply this transformation to full structure
 target_chain = transform.apply(target_chain)
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "structure_search_pymol.py"
+
+# Visualization with PyMOL
+pymol_interface.cmd.set("cartoon_rect_length", 1.0)
+pymol_interface.cmd.set("depth_cue", 0)
+pymol_interface.cmd.set("cartoon_cylindrical_helices", 1)
+pymol_interface.cmd.set("cartoon_helix_radius", 1.5)
+pymol_query = pymol_interface.PyMOLObject.from_structure(query_chain)
+pymol_target = pymol_interface.PyMOLObject.from_structure(target_chain)
+pymol_query.show_as("cartoon")
+pymol_target.show_as("cartoon")
+pymol_query.color("biotite_lightgreen")
+pymol_target.color("biotite_lightorange")
+pymol_query.orient()
+pymol_interface.show((1500, 1000))
 # sphinx_gallery_thumbnail_number = 3
 
 ########################################################################################

doc/examples/scripts/structure/contacts/contact_sites.py

@@ -15,6 +15,7 @@
 
 import numpy as np
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
 import biotite.structure.io.pdbx as pdbx
 
@@ -25,7 +26,8 @@
 
 # Fetch and load structure
 pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("2or1", "bcif"))
-structure = pdbx.get_structure(pdbx_file, model=1)
+structure = pdbx.get_structure(pdbx_file, model=1, include_bonds=True)
+structure = structure[~struc.filter_solvent(structure)]
 
 
 # Separate structure into the DNA and the two identical protein chains
@@ -70,5 +72,41 @@
     res_name = protein_l.res_name[protein_l.res_id == res_id][0]
     print(res_name.capitalize() + str(res_id))
 
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "contact_sites_pymol.py"
+
+# Visualization with PyMOL
+pymol_obj = pymol_interface.PyMOLObject.from_structure(structure)
+pymol_obj.color("gray", np.isin(structure.chain_id, ["A", "B"]))
+pymol_obj.color("biotite_brightorange", structure.chain_id == "L")
+pymol_obj.color("biotite_lightgreen", structure.chain_id == "R")
+# Set view
+pymol_interface.cmd.set_view(
+    (
+        -0.044524662,
+        0.767611504,
+        0.639355302,
+        0.998693943,
+        0.018437184,
+        0.047413416,
+        0.024606399,
+        0.640637815,
+        -0.767439663,
+        0.000000000,
+        0.000000000,
+        -115.614288330,
+        56.031833649,
+        23.317802429,
+        3.761308193,
+        73.517341614,
+        157.711288452,
+        -20.000000000,
+    )
+)
+# Highlight contacts
+residue_mask = np.isin(structure.res_id, common_ids)
+pymol_obj.show("sticks", np.isin(structure.chain_id, ["L", "R"]) & residue_mask)
+for chain, color in zip(("L", "R"), ("biotite_dimorange", "biotite_darkgreen")):
+    pymol_obj.color(
+        color,
+        (structure.chain_id == chain) & (structure.atom_name != "CA") & residue_mask,
+    )
+pymol_interface.show((1500, 800))

doc/examples/scripts/structure/contacts/leaflet.py

@@ -25,6 +25,7 @@
 from tempfile import NamedTemporaryFile
 import networkx as nx
 import numpy as np
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
 import biotite.structure.io as strucio
 
@@ -111,7 +112,32 @@ def find_leaflets(structure, head_atom_mask, cutoff_distance=15.0, periodic=Fals
 # Save marked lipids to structure file
 temp = NamedTemporaryFile(suffix=".pdb")
 strucio.save_structure(temp.name, structure)
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "leaflet_pymol.py"
-
 temp.close()
+
+
+# Visualization with PyMOL
+pymol_interface.cmd.set("sphere_scale", 1.5)
+# Remove hydrogen and water
+structure = structure[(structure.element != "H") & (structure.res_name != "TIP")]
+structure.bonds = struc.connect_via_distances(structure)
+pymol_obj = pymol_interface.PyMOLObject.from_structure(structure)
+# Configure lipid tails
+pymol_obj.color("biotite_lightgreen", structure.chain_id == "A")
+pymol_obj.color("biotite_brightorange", structure.chain_id == "B")
+pymol_obj.show("sticks", np.isin(structure.chain_id, ("A", "B")))
+# Configure lipid heads
+pymol_obj.color(
+    "biotite_darkgreen", (structure.chain_id == "A") & (structure.atom_name == "P")
+)
+pymol_obj.color(
+    "biotite_dimorange", (structure.chain_id == "B") & (structure.atom_name == "P")
+)
+pymol_obj.show(
+    "spheres", np.isin(structure.chain_id, ("A", "B")) & (structure.atom_name == "P")
+)
+# Adjust camera
+pymol_obj.orient()
+pymol_interface.cmd.turn("x", 90)
+pymol_obj.zoom(buffer=-10)
+# Display
+pymol_interface.show((1500, 1000))

doc/examples/scripts/structure/misc/biological_assembly.py

@@ -28,22 +28,23 @@
 `this page <https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies>`_.
 
 In this example, we will create the complete biological assembly of the
-capsid from the *Sulfolobus turreted icosahedral virus*
-- a hetero 1080-mer!
+capsid from the lambda phage.
 
 At first we will check, which assemblies are available to us.
 """
 
 # Code source: Patrick Kunzmann
 # License: BSD 3 clause
 
-from tempfile import NamedTemporaryFile
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
-import biotite.structure.io as strucio
 import biotite.structure.io.pdbx as pdbx
 
-pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("3J31", "bcif"))
+PDB_ID = "7VII"
+
+
+pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif"))
 
 assemblies = pdbx.list_assemblies(pdbx_file)
 print("ID    name")
@@ -61,19 +62,38 @@
 # It returns the chosen assembly as :class:`AtomArray`.
 # Note that the assembly ID is a string, not an integer.
 
-biological_unit = pdbx.get_assembly(pdbx_file, assembly_id="1", model=1)
-print("Number of protein chains:", struc.get_chain_count(biological_unit))
+assembly = pdbx.get_assembly(
+    pdbx_file,
+    assembly_id="1",
+    model=1,
+    # To identify later which atoms belong to which protein type
+    extra_fields=["label_entity_id"],
+)
+
+print("Number of protein chains:", struc.get_chain_count(assembly))
 
 ########################################################################
-# Now we could do some analysis on the biological unit.
-# But for this example we will simply save the entire assembly as *PDB*
-# file for later visualization.
+# The assembly consists of two different protein types, so called entities.
+# Each entity may be represented by multiple chain IDs.
 
-# For brevity, save only CA atoms to file for visualization
-biological_unit = biological_unit[biological_unit.atom_name == "CA"]
-temp = NamedTemporaryFile(suffix=".cif")
-strucio.save_structure(temp.name, biological_unit)
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "biological_assembly_pymol.py"
+entity_info = pdbx_file.block["entity"]
+print("ID    description")
+print()
+for entity_id, description in zip(
+    entity_info["id"].as_array(), entity_info["pdbx_description"].as_array()
+):
+    print(f"{entity_id:2}    {description}")
+
+########################################################################
+# Now we could do some analysis on the biological unit.
+# But for this example we will visualize the entire assembly.
 
-temp.close()
+# Show capsid structure as CA spheres to increase rendering speed
+assembly = assembly[assembly.atom_name == "CA"]
+pymol_object = pymol_interface.PyMOLObject.from_structure(assembly)
+pymol_object.color("biotite_dimgreen", assembly.label_entity_id == "1")
+pymol_object.color("biotite_lightorange", assembly.label_entity_id == "2")
+pymol_object.set("sphere_scale", 2.0)
+pymol_object.show_as("spheres")
+pymol_object.zoom(buffer=25)
+pymol_interface.show((1500, 1500))