Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/rosettacommons/pyrosetta_viewer3d

Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab
https://github.com/rosettacommons/pyrosetta_viewer3d

Last synced: 5 days ago
JSON representation

Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab

Awesome Lists containing this project

README 

        
# viewer3d

Display `PackedPose` objects, `Pose` objects, or `.pdb` files within a Jupyter notebook and Google Colab.



# Description

The `viewer3d` macromolecular viewer quickly renders `.pdb` files, dynamically instantiating `Pose` objects if required for certain visualization modules (matching the name `viewer3d.set*`). So when adding visualization modules to the viewer or using presets, passing `Pose` or `PackedPose` objects to the viewer is suggested for quicker rendering. If a `Pose` object or `list`, `tuple`, or `set` of `Pose` objects are provided to the viewer, the `Pose`(s) pointer location(s) in memory remain fixed, and so the viewer can dynamically update upon `Pose` conformational changes by calling the following methods:



```

update_viewer(index=None, model=None, add_objects=True, remove_objects=True)

```



```

add_pose(pose, index=None, update_viewer=True)

```



```

add_pdbstring(pdbstring, index=None, update_viewer=True)

```



```

remove_pose(index=None, model=None, update_viewer=True)

```



```

remove_pdbstring(index=None, model=None, update_viewer=True)

```



```

update_pose(pose, index=None, model=None, update_viewer=True)

```



```

update_pdbstring(pdbstring, index=None, model=None, update_viewer=True)

```



```

update_poses(poses, index=None, update_viewer=True)

```



```

update_pdbstrings(pdbstrings, index=None, update_viewer=True)

```



For adding/removing visualization modules in the widget update function, either initialize the viewer with `viewer3d.init(modules=[...])` or call the `set_modules()` method to overwrite the current list of modules. Otherwise, call the `clear()` method then add the new modules. After pose conformational changes and setting the viewer modules, call the `update_viewer()` method if the pose's pointer in memory remains the same, otherwise call the `update_pose(pose)` method to update the pose and viewer.



See docstrings for more information. The viewer applies visualization modules in the same order they are added (from left to right), so layering different styles (and `ResidueSelector`s) on top of one another becomes possible. The user must have already initialized PyRosetta providing `.params` files for any ligands and non-canonical residues in the input molecule(s), otherwise `pyrosetta.distributed` automatically initializes PyRosetta with default command line options.



# Contributing

Please open a pull request with an updated unit test from a custom branch.



# Unit Tests

`python -m unittest`



# Installation

`conda env create -f environment.yml`



# PyPI Releases

1. Update version number in `setup.py`

2. `pip install --user --upgrade setuptools wheel twine`

3. `rm -rf dist/*`

4. `python setup.py sdist bdist_wheel`

5. `python -m twine upload dist/*`



# Usage Examples:

```

import viewer3d

```



Example Jupyter notebook commands:



```

v = viewer3d.init("path/to/pdbfile.pdb")

v.show()

```



```

import logging

logging.basicConfig(level=logging.WARNING)

import pyrosetta

pyrosetta.init("-mute all")



pose = pyrosetta.toolbox.rcsb.pose_from_rcsb("5BVL")



view = viewer3d.init(pose, window_size=(800, 600), backend="nglview")

view() # Equivalent to view.show()

```



```

poses = [pyrosetta.toolbox.rcsb.pose_from_rcsb(pdbid) for pdbid in ["5BVL", "6MSR", "1QCQ"]]



view = viewer3d.init(poses) \

+ viewer3d.setStyle(colorscheme="lightgreyCarbon") \

+ viewer3d.setHydrogenBonds()

view()

```



```

import pyrosetta.distributed.io as io

packed_pose = io.to_packed(pyrosetta.toolbox.pose_from_rcsb("2FD7"))

polar_residue_selector = pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector(

    pyrosetta.rosetta.core.chemical.ResidueProperty(52)

)



view = viewer3d.init(packed_pose)

view.add(viewer3d.setStyle(radius=0.1))

view.add(viewer3d.setStyle(residue_selector=polar_residue_selector, colorscheme="whiteCarbon", radius=0.25, label=False))

view.add(viewer3d.setHydrogens(color="white", polar_only=True, radius=0.1))

view.add(viewer3d.setHydrogenBonds(color="black"))

view.add(viewer3d.setDisulfides(radius=0.1))

view()

```



```

view = sum(

    [

        viewer3d.init(packed_pose),

        viewer3d.setStyle(cartoon=False, style="sphere", radius=1.5, colorscheme="darkgreyCarbon"),

        viewer3d.setZoom(factor=1.5)

    ]

)

view.show()

```



```

from pyrosetta.rosetta.core.select.residue_selector import ChainSelector

pose = pyrosetta.toolbox.rcsb.pose_from_rcsb("6MSR")

chA = ChainSelector("A")

chB = ChainSelector("B")



view = sum(

    [

        viewer3d.init(pose, backend=1, gui=True),

        viewer3d.setStyle(cartoon_color="lightgrey", radius=0.25),

        viewer3d.setSurface(residue_selector=chA, colorscheme="greenCarbon", opacity=0.65, surface_type="VDW"),

        viewer3d.setSurface(residue_selector=chB, color="blue", opacity=1.0, surface_type="SAS"),

        viewer3d.setDisulfides(radius=0.25),

        viewer3d.setZoom(factor=1.5)

    ]

)

view()

```



```

import pyrosetta.distributed.io as io

import viewer3d

from pyrosetta.rosetta.core.select.residue_selector import (

    LayerSelector,

    ChainSelector,

)



poses = [io.pose_from_sequence("TEST" * i) for i in range(1, 6)]

core_selector = LayerSelector()

core_selector.set_layers(True, False, False)

boundary_selector = LayerSelector()

boundary_selector.set_layers(False, True, False)

surface_selector = LayerSelector()

surface_selector.set_layers(False, False, True)

view = (

    viewer3d.init(poses, (1200, 800.01), delay=0, backend=1) \

    + viewer3d.setStyle()  #residue_selector=surface_selector, style="stick", colorscheme="element", label=False) #+ viewer3d.setSurface(opacity=0.5)

    + viewer3d.setDisulfides() \

    + viewer3d.setBackgroundColor(color="lightgray")

    + viewer3d.setHydrogenBonds()

    + viewer3d.setHydrogens(polar_only=True, color="white")

    + viewer3d.setZoomTo(ChainSelector("A")) \

    + viewer3d.setZoom(-1) \

)

view.show()

```



```

from pyrosetta.rosetta.core.select.residue_selector import SecondaryStructureSelector

helix_selector = SecondaryStructureSelector("H")

sheet_selector = SecondaryStructureSelector("E")

loop_selector = SecondaryStructureSelector("L")



modules = [

    viewer3d.setBackgroundColor(color="grey"),

    viewer3d.setStyle(residue_selector=helix_selector, cartoon_color="blue", label=False, radius=0),

    viewer3d.setStyle(residue_selector=sheet_selector, cartoon_color="red", label=False, radius=0),

    viewer3d.setStyle(residue_selector=loop_selector, cartoon_color="white", label=False, radius=0)

]



view = viewer3d.init(poses, window_size=(1200, 600), modules=modules, continuous_update=True)

view()

```



```

view.clear() # Subtract all visualization modules previously added to the Viewer

view()

```



View a live trajectory:

```

pose = pyrosetta.toolbox.pose_from_rcsb("2FD7")

v = viewer3d.init(pose, delay=0.1) + viewer3d.setStyle(radius=0.1) + viewer3d.setDisulfides(radius=0.1)

backrub = pyrosetta.rosetta.protocols.backrub.BackrubMover()

minimize = pyrosetta.rosetta.protocols.minimization_packing.MinMover()



for _ in range(100):

    backrub.apply(pose)

    minimize.apply(pose)

    v.update_pose(pose)

```



Display preset custom viewers for routine visualizations:

```

viewer3d.presets.coreBoundarySurface(poses, window_size=(800, 600), continuous_update=True)

```



```

view = viewer3d.presets.makeBundle(backend=1)

view.show()

```



Visualize the residue 1 psi-space of a 20-residue polyvaline extended peptide:

```

from bokeh.palettes import Viridis

n = 11 # 256

v = viewer3d.init(backend=1)

pose = pyrosetta.io.pose_from_sequence("V" * 20)

for i, hex_str in enumerate(Viridis[n]):

    v.set_modules(viewer3d.setStyle(cartoon_color=hex_str, radius=0))

    pose.set_psi(1, i * 360 / n)

    v.add_pose(pose)

```



Overlay multiple poses:

```

pose1 = pyrosetta.toolbox.rcsb.pose_from_rcsb("6V67")

pose2 = pyrosetta.toolbox.rcsb.pose_from_rcsb("1ATP")

v = viewer3d.init()

v += viewer3d.setStyle(colorscheme='redCarbon')

v += viewer3d.setSurface()

v.add_pose(pose1) # Automatically updates the viewer with the currently set modules

v.reset() # Subtract all modules

v += viewer3d.setStyle(colorscheme='blueCarbon')

v.add_pose(pose2)

```



View different sets of different overlaid poses:

```

pose = pyrosetta.toolbox.pose_from_rcsb("2FD7")

v = viewer3d.init(pose, delay=0, backend=1)

backrub = pyrosetta.rosetta.protocols.backrub.BackrubMover()

minimize = pyrosetta.rosetta.protocols.minimization_packing.MinMover()

v.set_modules([viewer3d.setStyle(), viewer3d.setDisulfides()])



for h in range(5):

    for i in range(5):

        for j in range(5):

            backrub.apply(pose)

            minimize.apply(pose)

        v.add_pose(pose.clone(), index=h, update_viewer=False)

v.show()

```



Overlay all poses or PDB strings:

```

v.overlay()

```



Color residues by `PerResidueRealMetric`s:

```

scorefxn = pyrosetta.create_score_function("ref2015")

minimize = pyrosetta.rosetta.protocols.minimization_packing.MinMover()

e = (

    pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric()

)

e.set_scorefunction(scorefxn)

v = viewer3d.init(backend=backend, gui=True)

palette = list(bokeh.palettes.Greens256) + list(

    reversed(bokeh.palettes.Reds256)

)

v += viewer3d.setStyle(radius=0)

v += viewer3d.setPerResidueRealMetric(

    scoretype="res_energy", vmin=-10, vmax=10, radius=0.2, log=10, palette=palette

)

v += viewer3d.setHydrogens(polar_only=True, color="lightgray")

v += viewer3d.setHydrogenBonds()

v += viewer3d.setDisulfides()

for h in range(10):

    _pose = pose.clone()

    _pose.scores.clear()

    for i in range(20):

        minimize.apply(_pose)

    e.apply(_pose)

    v.add_pose(_pose, index=h, update_viewer=False)

v.show()

```



Color residues by per-residue total score:

```

v = viewer3d.presets.perResidueEnergyMetric(pose)

v.show()

```



Color residues by per-residue clash score:

```

v = viewer3d.presets.perResidueClashMetric(poses, backend=0)

v.show()

```



Color residues by per-residue SASA score:

```

v = viewer3d.presets.perResidueSasaMetric(pose, backend=1)

v.show()

```



Color residues by per-residue satisfied backbone hydrogen bonds:

```

v = viewer3d.presets.unsatSelector(pose)

v.show()

```



Visualize multiple Rosetta analyses:

```

v = viewer3d.presets.rosettaViewer(poses, backend=1)

v.show()

```