Core Views

A quick overview of all possible views within qcio.

from qcio import ProgramOutput, view

# Defaults changed just to fit the examples within the narrow documentation layout
view.DEFAULT_WIDTH = 400
view.DEFAULT_HEIGHT = 300

xtb_opt = ProgramOutput.open("U1-_180_mmff94s-opt-xtb.json")
terachem_opt = ProgramOutput.open("U1-_mmff94s_180-opt-terachem-thf.json")
crest_confsearch = ProgramOutput.open("U1-_confsearch-crest.json")

Structure Views

Basic Structure

Pass in a structure to visualize it. If structure.ids.name or structure.ids.smiles is set this will be used automatically for a title. Subtitles can be passed manually.

view.view(
    xtb_opt.input_data.structure, 
    subtitles=["My Awesome Subtitle"]
)

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Pass view_2d=True for a 2D image of the molecule.

view.view(
    xtb_opt.input_data.structure, 
    view_2d=True, 
    subtitles=["My Awesome Subtitle"]
)

U1- 180

My Awesome Subtitle

Multi-Structure

Pass multiple Structure objects to view.view(...) and it will create a grid of Structure objects. Pass titles and subtitles as desired. show_indices=True will display the indices for each atom.

view.view(
    xtb_opt.input_data.structure, xtb_opt.results.final_structure, 
    titles=['Initial Structure', 'Final Structure'], 
    subtitles=["First Subtitle", "Second Subtitle"],
    show_indices=True,
)

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Overlay Structures

Set same_viewer=True to overlay two (or more) Structure objects in the same viewer.

view.view(
    xtb_opt.input_data.structure, xtb_opt.results.final_structure, 
    same_viewer=True,
    subtitles=["First and Last Structure"],
)

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Animation

Pass one or more list of Structure objects to view.view(...) and each list will be animated. The .results.structures objects passed belows are lists of Structure.

view.view(
    xtb_opt.results.structures, terachem_opt.results.structures, 
    titles=['xtb Opt', 'TeraChem Opt'],
    subtitles=['Successful Trajectory', 'Failed Opt Trajectory'],
)

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Program Output Views

Simply pass any ProgramOutput object to view.view(...) to see a visualization of the results.

Single Point Calculation

view.view(
    xtb_opt.results.trajectory[0], 
    subtitles=["A Subtitle for the Structure"]
)

Structure	Success	Wall Time	Calculation Type	Program	Model	Keywords
charge -1 multiplicity 1 name U1- 180	True	00.09s	gradient	xtb 22.1	method GFN2xTB basis None	solvent 13

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Result	Value
energy	-107.07214860598548
gradient	[[5.94e-02 -6.73e-04 -1.02e-02] [1.54e-02 -1.44e-03 -1.14e-02] [2.13e-02 8.42e-04 1.78e-03] ... [-1.21e-03 7.30e-04 6.00e-03] [5.60e-03 -4.61e-04 -3.16e-03] [-2.50e-03 -7.75e-04 -5.17e-03]]
wavefunction	scf_eigenvalues_a=array([-8.78e-01, -8.76e-01, -8.76e-01, ..., 5.85e-01, 6.02e-01, 7.60e-01])
scf_dipole_moment	[1.8777798514342063, -0.021687969861866857, -0.4637756180825757]

Optimization

May pass animate=False if the animations are slowing down the browser.

view.view(
    xtb_opt, 
    animate=True, 
    subtitles=["Some nice subtitle"], 
    titles_extra=["Optimization Trajectory"]
)

Structure	Success	Wall Time	Calculation Type	Program	Model	Keywords	Subprogram	Subprogram Model	Subprogram Keywords
charge -1 multiplicity 1 name U1- 180	True	33.29s	optimization	geometric 1.0.2		transition False	xtb	method='GFN2xTB'	solvent 13

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If you have too many molecule viewers or animations running and your browser is slowing down, pass view_2d=True to any view to substitute a static 2D molecule image.

view.view(
    xtb_opt, 
    animate=False, 
    view_2d=True,
)

Structure	Success	Wall Time	Calculation Type	Program	Model	Keywords	Subprogram	Subprogram Model	Subprogram Keywords
charge -1 multiplicity 1 name U1- 180	True	33.29s	optimization	geometric 1.0.2		transition False	xtb	method='GFN2xTB'	solvent 13

U1- 180 (Final Structure)

Conformer Search

view.view(crest_confsearch)

Structure	Success	Wall Time	Calculation Type	Program	Model	Keywords
charge -1 multiplicity 1 name	True	15m:23.10s	conformer_search	crest 3.0.1	method gfn2 basis None

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