modules

class pyrosetta.distributed.viewer.modules.setBackgroundColor(color=4294967295)

Bases: object

Set Viewer background color with either Hexcode or standard colors.

firstoptional

color

Hexcode literal (e.g. 0xffffffff) or str indicating a standard color (e.g. “black”). Default: 0xffffffff

A Viewer instance.

__init__(color=4294967295)

apply(viewer, pose, pdbstring)

class pyrosetta.distributed.viewer.modules.setDisulfides(color='gold', radius=0.5)

Bases: object

Display disulfide bonds according to pyrosetta.rosetta.core.conformation.is_disulfide_bond() for all combinations of cysteine residues in each initialized .pdb file, Pose or PackedPose object.

firstoptional

color

str indicating a standard color (e.g. “black”). Default: “gold”

secondoptional

radius

float or int indicating the radius of the stick connecting the atoms participating in each disulfide bond. Default: 0.5

A Viewer instance.

__init__(color='gold', radius=0.5)

apply(viewer, pose, pdbstring)

class pyrosetta.distributed.viewer.modules.setHydrogenBonds(color='black', dashed=True, radius=None)

Bases: object

Display hydrogen bonds according to pyrosetta.rosetta.core.pose.Pose.get_hbonds() in each initialized .pdb file, Pose or PackedPose object.

firstoptional

color

str indicating a standard color (e.g. “yellow”). Default: “black”

secondoptional

dashed

True or False to show hydrogen bonds as dashed lines. If True, then option radius must be None. If False, then option radius must be specified. Default: True

thirdoptional

radius

float or int indicating the radius of the solid (non-dashed) stick connecting the atoms participating in each hydrogen bond. If set, this automatically sets the option dashed to False. Default: None

A Viewer instance.

__init__(color='black', dashed=True, radius=None)

apply(viewer, pose, pdbstring)

class pyrosetta.distributed.viewer.modules.setHydrogens(color='white', radius=0.05, polar_only=False)

Bases: object

Show all or only polar hydrogen atoms in each initialized .pdb file, Pose or PackedPose object.

firstoptional

color

str indicating a standard color (e.g. “grey”). Default: “white”

secondoptional

radius

float or int indicating the radius of the hydrogen atom stick represnetations. Default: 0.05

thirdoptional

polar_only

True or False. True to show only polar hydrogen atoms, and False to show all hydrogen atoms. Default: False

A Viewer instance.

__init__(color='white', radius=0.05, polar_only=False)

apply(viewer, pose, pdbstring)

class pyrosetta.distributed.viewer.modules.setStyle(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)

Bases: object

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.

firstoptional

residue_selector

An instance of pyrosetta.rosetta.core.select.residue_selector.ResidueSelector on which to apply the style(s). Default: None

secondoptional

cartoon

True or False to show cartoon representation. Default: True

thirdoptional

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

fourthoptional

style

str indicating a representation style of heavy atoms, choosing from either “line”, “cross”, “stick”, or “sphere”. Default: “stick”

fifthoptional

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

sixthoptional

radius

float or int indicating the radius of the heavy atoms represented by the style option. Default: 0.1

seventhoptional

label

True or False to show labels next to residues selected by the residue_selector option. Default: True

eighthoptional

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

ninthoptional

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

tenthoptional

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”

eleventhoptional

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()

A Viewer instance.

__init__(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)

apply(viewer, pose, pdbstring)

class pyrosetta.distributed.viewer.modules.setSurface(residue_selector=None, surface_type='VDW', opacity=0.5, color=None, colorscheme=None)

Bases: object

Show the specified surface for each initialized .pdb file, Pose or PackedPose object.

firstoptional

residue_selector

An instance of pyrosetta.rosetta.core.select.residue_selector.ResidueSelector to select residues on which to apply the surface. Default: None

secondoptional

surface_type

str indicating surface type to be displayed. py3Dmol supports the following options:

“VDW”: Van der Waals surface “MS”: Molecular surface “SES”: Solvent excluded surface “SAS”: Solvent accessible surface

Default: “VDW”

thirdoptional

opacity

float or int between 0 and 1 for opacity of the displayed surface. Default: 0.5

fourthoptional

color

str indicating a standard color (e.g. “grey”) of the surface to be displayed. Either color or colorscheme may be specified, where colorscheme overrides color. Default: None

fifthoptional

colorscheme

str indicating the color scheme of the surface to be displayed. Either color or colorscheme may be specified, where colorscheme overrides color. Options include:

A lower-case standard color followed by “Carbon” (e.g. “yellowCarbon”) “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: None Reference: https://3dmol.csb.pitt.edu/doc/types.html#ColorschemeSpec

A Viewer instance.

__init__(residue_selector=None, surface_type='VDW', opacity=0.5, color=None, colorscheme=None)

apply(viewer, pose, pdbstring)

class pyrosetta.distributed.viewer.modules.setZoom(factor=2)

Bases: object

Set the zoom magnification factor of each initialized .pdb file, Pose or PackedPose object. Values >1 zoom in, and values <1 zoom out.

firstoptional

factor

float or int indicating the zoom magnification factor. Default: 2

A Viewer instance.

__init__(factor=2)

apply(viewer, pose, pdbstring)

class pyrosetta.distributed.viewer.modules.setZoomTo(residue_selector=None)

Bases: object

Zoom to a ResidueSelector in each initialized .pdb file, Pose or PackedPose object.

firstoptional

residue_selector

An instance of pyrosetta.rosetta.core.select.residue_selector.ResidueSelector into which to zoom. Default: None

A Viewer instance.

__init__(residue_selector=None)

apply(viewer, pose, pdbstring)

exception pyrosetta.distributed.viewer.modules.ViewerInputError(obj)

Bases: Exception

Exception raised for errors with the input argument residue_selector.

__init__(obj)

add_note()

Exception.add_note(note) – add a note to the exception

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

pyrosetta.distributed.viewer.modules._pose_to_residue_chain_tuples(pose, residue_selector, logger=<Logger pyrosetta.distributed.viewer (WARNING)>)

Given a Pose object and ResidueSelector object, return a tuple of `list`s containing PDB residue numbers and chain IDs for the selection.

pyrosetta.distributed.viewer.modules._pdbstring_to_pose(pdbstring, class_name, logger=<Logger pyrosetta.distributed.viewer (WARNING)>)

Convert pdbstring to a Pose with logging.