Merge branch 'main' into documentation

Author: rclune

doc/source/overview.md

@@ -12,4 +12,4 @@ RFdiffusion2 addresses these limitations by:
 
 To learn how to run RFdiffusion2 using an [Apptainer](https://apptainer.org/) image, see the [READEME](readme_link.html). 
 
-> **NOTE:** The current rendition of RFdiffusion2 makes it particularly useful for enzyme scaffolding, but for many other applications RFdiffusion (the original) will be easier to use and may provide comparable or better results. 
+> **NOTE:** The current rendition of RFdiffusion2 makes it particularly useful for enzyme scaffolding, but for many other applications RFdiffusion (the original) will be easier to use and may provide comparable or better results. 

rf_diffusion/dev/analyze.py

@@ -21,6 +21,7 @@
 REPO_DIR = os.path.dirname(PKG_DIR)
 
 from rf_diffusion.dev.pymol import cmd
+from rf_diffusion.dev.pymol import mass_paper_rainbow_sel
 
 import rf_diffusion.estimate_likelihood as el
 from rf_diffusion.inference import utils
@@ -1189,7 +1190,7 @@ def show_paper_pocket(row, des=True, ligand=False):
         #cmd.align(des.name, af2_scaffold.name)
         cmd.align(f'{des.motif_sele()} and name ca', f'{native.motif_sele()} and name ca')
         cmd.show('cartoon', f'{des.name}')
-        cmd.do(f'mass_paper_rainbow_sel {des.name}')
+        mass_paper_rainbow_sel(des.name)
 
     # AF2 sidechains
     cmd.show('licorice', f'({af2.motif_sele()}) and not (name o)')
@@ -1268,7 +1269,7 @@ def show_paper_pocket_af2(row, b=None, des=True, ligand=False, traj_types=None,
         if has_motif:
             cmd.align(f'{des.motif_sele()} and name ca', f'{native.motif_sele()} and name ca')
         cmd.show('cartoon', f'{des.name}')
-        cmd.do(f'mass_paper_rainbow_sel {des.name}')
+        mass_paper_rainbow_sel(des.name)
 
     if show_af2 and has_motif:
         # AF2 sidechains

rf_diffusion/dev/paper_vis.py

@@ -9,6 +9,7 @@
 from rf_diffusion.dev import show_bench
 from rf_diffusion.dev import analyze
 from rf_diffusion.dev import pymol_atom_colors
+from rf_diffusion.dev.pymol import mass_paper_rainbow_sel
 
 cmd = analyze.cmd
 
@@ -80,7 +81,7 @@ def make_transparent_rainbow(
     diffused_transparency = 0.45):
     cmd.set('cartoon_transparency', diffused_transparency)
     cmd.set('stick_transparency', diffused_transparency, e['sidechains_diffused'])
-    cmd.do(f'mass_paper_rainbow {e["protein"]}')
+    mass_paper_rainbow_sel(f'{e["protein"]}')
 
 def show_backbone_cartoon(e):
     cmd.show_as('cartoon', f"({e['protein']}) and not (({e['sidechains_motif']}) or ({e['sidechains_diffused']}))")

rf_diffusion/dev/pymol.py

@@ -24,7 +24,7 @@ def __call__(self, *args, **kw):
             raise Exception(f"cmd.{self.name}('{','.join(all_args)})'") from e
 
 def get_cmd(pymol_url='http://localhost:9123'):
-    cmd = xmlrpclib.ServerProxy(pymol_url)
+    cmd = xmlrpclib.ServerProxy(pymol_url, allow_none=True)
     if not  ('ipd' in pymol_url or 'localhost' in pymol_url):
         make_network_cmd(cmd)
     return cmd
@@ -41,7 +41,14 @@ def init(pymol_url='http://localhost:9123', init_colors=False):
 
     if init_colors:
         set_colors()
+        cmd.set('sphere_scale', 0.3)
 
+def mass_paper_rainbow_sel(name):
+    """
+    Colors the given selection with a pastel gradient according to residue index.
+    """
+    cmd.spectrum("count", "paper_navaho paper_melon paper_pink paper_purple paper_lightblue paper_blue paper_darkblue", name, None, None, 0, 1)
+
 def set_colors():
     """
     Creates extra colors in pymol 

rf_diffusion/dev/show_bench.py

@@ -17,6 +17,7 @@
 from rf_diffusion.dev import show_tip_pa
 from rf_diffusion.dev import analyze
 from rf_diffusion.parsers import parse_pdb_lines_target
+from rf_diffusion.dev.pymol import mass_paper_rainbow_sel
 
 logger = logging.getLogger(__name__)
 
@@ -458,7 +459,7 @@ def format_ppi(all_entities):
                 continue
             e.selectors['target'] = "chain B and not hetatm"
             cmd.color('paper_teal', e['target'])
-            cmd.do(f"mass_paper_rainbow_sel ({e.NOT('target')} and not hetatm)")
+            mass_paper_rainbow_sel(f"({e.NOT('target')} and not hetatm)")
 
 def pseudoatom(
         cmd,

rf_diffusion/dev/show_tip_row.py

@@ -5,6 +5,7 @@
 import functools
 
 from rf_diffusion.dev import analyze
+from rf_diffusion.dev.pymol import mass_paper_rainbow_sel
 cmd = analyze.cmd
 
 class PymolPalette:
@@ -176,7 +177,7 @@ def color_selectors(selectors, carbon=True, verbose=False, des_color=None, hetat
             print(f'{color} --> {sel}')
         if des_color and j==0:
             if des_color == 'rainbow':
-                cmd.do(f'mass_paper_rainbow_sel {sel}')
+                mass_paper_rainbow_sel(sel)
             else:
                 cmd.color(des_color, sel)
         else: