![]() |
Rosetta
2020.11
|
Public Member Functions | |
def | __init__ |
def | apply |
Public Attributes | |
residue_selector | |
cartoon | |
cartoon_color | |
style | |
colorscheme | |
radius | |
label | |
label_fontsize | |
label_background | |
label_fontcolor | |
command | |
Show and color cartoon, and/or show heavy atoms with provided style, color and radius for each initialized `.pdb` file, `Pose` or `PackedPose` object. If the `residue_selector` argument is provided, apply styles only to the selected residues. If the `command` argument is provided, override all other arguments and pass `py3Dmol.view.setStyle()` commands to the Viewer. Parameters ---------- first : optional `residue_selector` An instance of `pyrosetta.rosetta.core.select.residue_selector.ResidueSelector` on which to apply the style(s). Default: None second : optional `cartoon` `True` or `False` to show cartoon representation. Default: True third : optional `cartoon_color` Hexcode literal (e.g. 0xAF10AB) or `str` indicating a standard color (e.g. "grey") for the cartoon representation. If "spectrum", apply reversed color gradient based on residue numbers. The option `cartoon` must also be set to `True`. Default: "spectrum" Reference: https://3dmol.csb.pitt.edu/doc/types.html#ColorSpec fourth : optional `style` `str` indicating a representation style of heavy atoms, choosing from either "line", "cross", "stick", or "sphere". Default: "stick" fifth : optional `colorscheme` `str` indicating the color scheme for heavy atoms represented by the `style` option. Options include: A lower-case standard color followed by "Carbon" (e.g. "orangeCarbon") "ssPyMOL": PyMol secondary colorscheme "ssJmol": Jmol secondary colorscheme "Jmol": Jmol primary colorscheme "default": default colorscheme "amino": amino acid colorscheme "shapely": shapely protien colorscheme "nucleic": nucleic acid colorscheme "chain": standard chain colorscheme "chainHetatm": chain Hetatm colorscheme Default: "blackCarbon" Reference: https://3dmol.csb.pitt.edu/doc/types.html#ColorschemeSpec sixth : optional `radius` `float` or `int` indicating the radius of the heavy atoms represented by the `style` option. Default: 0.1 seventh : optional `label` `True` or `False` to show labels next to residues selected by the `residue_selector` option. Default: True eighth : optional `label_fontsize` `int` or `float` indicating the font size of labels next to residues selected by the `residue_selector` option, only if `label` is `True`. Default: 12 ninth : optional `label_background` `True` or `False` to show the background of labels next to residues selected by the `residue_selector` option, only if `label` is `True`. Default: False tenth : optional `label_fontcolor` `str` indicating a standard font color (e.g. "grey") for label text next to residues selected by the `residue_selector` option, only if `label` is `True`. Default: "black" eleventh : optional `command` `dict` or `tuple` of `dict`s of `py3Dmol.view.setStyle()` commands. If specified, this option overrides all other options. Default: None Example: command = {"hetflag": True}, {"stick": {"singleBond": False, "colorscheme": "greyCarbon", "radius": 0.15}} view = viewer.init(poses) + viewer.setStyle(command=command) view.show() Returns ------- A Viewer instance.
def pyrosetta.distributed.viewer.modules.setStyle.__init__ | ( | self, | |
residue_selector = None , |
|||
cartoon = True , |
|||
cartoon_color = "spectrum" , |
|||
style = "stick" , |
|||
colorscheme = "blackCarbon" , |
|||
radius = "0.1" , |
|||
label = True , |
|||
label_fontsize = 12 , |
|||
label_background = False , |
|||
label_fontcolor = "black" , |
|||
command = None |
|||
) |
References pyrosetta.tests.distributed.test_dask.format, and fmt.join().
Referenced by pyrosetta.distributed.tasks.taskbase.TaskBase.__setstate__().
def pyrosetta.distributed.viewer.modules.setStyle.apply | ( | self, | |
viewer, | |||
pose, | |||
pdbstring | |||
) |
References pyrosetta.distributed.viewer.modules._pdbstring_to_pose(), pyrosetta.distributed.viewer.modules._pose_to_residue_chain_tuples(), pyrosetta.distributed.viewer.modules.setStyle.cartoon, pyrosetta.distributed.viewer.modules.setStyle.cartoon_color, pyrosetta.distributed.viewer.modules.setStyle.colorscheme, pyrosetta.distributed.viewer.modules.setStyle.command, pyrosetta.distributed.viewer.modules.setStyle.label, pyrosetta.distributed.viewer.modules.setStyle.label_background, pyrosetta.distributed.viewer.modules.setStyle.label_fontcolor, pyrosetta.distributed.viewer.modules.setStyle.label_fontsize, pyrosetta.distributed.viewer.modules.setDisulfides.radius, pyrosetta.distributed.viewer.modules.setHydrogenBonds.radius, basic::sampling::orientations::QuatDBMetadata.radius, pyrosetta.distributed.viewer.modules.setHydrogens.radius, pyrosetta.distributed.viewer.modules.setStyle.radius, pyrosetta.distributed.viewer.modules.setStyle.residue_selector, and pyrosetta.distributed.viewer.modules.setStyle.style.
Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask.execute().
pyrosetta.distributed.viewer.modules.setStyle.cartoon |
Referenced by pyrosetta.distributed.viewer.modules.setStyle.apply().
pyrosetta.distributed.viewer.modules.setStyle.cartoon_color |
Referenced by pyrosetta.distributed.viewer.modules.setStyle.apply().
pyrosetta.distributed.viewer.modules.setStyle.colorscheme |
pyrosetta.distributed.viewer.modules.setStyle.command |
Referenced by pyrosetta.distributed.viewer.modules.setStyle.apply().
pyrosetta.distributed.viewer.modules.setStyle.label |
Referenced by pyrosetta.distributed.viewer.modules.setStyle.apply().
pyrosetta.distributed.viewer.modules.setStyle.label_background |
Referenced by pyrosetta.distributed.viewer.modules.setStyle.apply().
pyrosetta.distributed.viewer.modules.setStyle.label_fontcolor |
Referenced by pyrosetta.distributed.viewer.modules.setStyle.apply().
pyrosetta.distributed.viewer.modules.setStyle.label_fontsize |
Referenced by pyrosetta.distributed.viewer.modules.setStyle.apply().
pyrosetta.distributed.viewer.modules.setStyle.radius |
pyrosetta.distributed.viewer.modules.setStyle.residue_selector |
pyrosetta.distributed.viewer.modules.setStyle.style |
Referenced by pyrosetta.distributed.viewer.modules.setStyle.apply().