pyviblib.gui.windows

Windows of PyVib2

Classes

BaseWindow

base class of all windows

WorkspaceWindow

window that can be saved in a PyVib2 workspace

MoleculeWindow

exploring molecules

CorrelateVibrationsWindow

correlating vibrations

CorrelationResultsWindow

representing results of a correlation

SingleVibrationWindow

exploring a single vibration

VibrationPairWindow

exploring two vibrations simultaneously

AbstractFigureWindow

abstract class for windows with figures

RamanROADegcircCalcWindow

exploring Raman/ROA spectra

RamanROAGenerationWindow

Raman/ROA generation interface

AbstractCalcMixtureWindow

abstract class for mixture spectra

RamanROADegcircCalcMixtureWindow

exploring spectra of several molecules

IRVCDCalcMixtureWindow

exploring spectra of several molecules

BoltzmannMixtureSpectraWindow

spectra of a mixture of molecules

IRVCDCalcWindow

exploring IR/VCD spectra

IRVCDGenerationWindow

IR/VCD generation interface

ImportRamanROAExpSpectraWindow

importing exp. Raman/ROA spectra

ImportIRExpSpectraWindow

importing exp. infrared abs. spectra

RamanROADegcircExpWindow

exploring exp. Raman/ROA spectra

IRExpWindow

exploring exp. infrared abs. spectra

DCMSumsWindow

sums of internuclear distances

ArrangeExpSpectraWindow

select experimental spectra for one plot

AbstractMultipleExpWindow

abstract class for mult. exp. spectra

RamanROADegcircMultipleExpWindow

exploring sev. exp. Raman/ROA spectra

IRMultipleExpWindow

exploring sev. exp. infrared spectra

CorrelateExpExpSpectraWindow

correlating two experimental spectra

CorrelateCalcExpSpectraWindow

correlating calc. and exp. spectra

CorrelateCalcCalcSpectraWindow

correlating two calculated spectra

CompareMoleculesWindow

comparing molecule

CompareRamanROAACPWindow

comparing Raman/ROA ACPs

CompareIRVCDACPWindow

comparing IR/VCD ACPs

AnalyzeClusterWindow

analyzing clusters

GroupsInfoWindow

mark group(s) of atoms in a molecule

GroupsLocalizationWindow

show groups and localizations

VOASimilarityCurvesWindow

Raman/ROA similarity curves window

VibLocalizationsWindow

localizations of vibs on a fragment

CumulatedNormalizedVibSumsWindow

window with cumulated normalized vibrational sums for VROA

ExpROACumulatedNormalizedSumsWindow

window with experimental cumulated normalized sums of ROA

Author:Maxim Fedorovsky

class pyviblib.gui.windows.BaseWindow(mainApp, **kw)

Base class for all windows of PyVib2.

The following public methods are exported:

destroyme()

destroy the window

maximize()

maximize the window

clone()

clone the window (should be overridden in subclases)

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• destroy_command – function to be called before the window is destroyed
• geom – window geometry

clone()

Clone the window (must be implemented).

destroyme(unregister=True)

Destroy the window.

Parameter:unregister – whether to unregister oneself from the Windows menu of the main window of PyVib2

maximize()

Maximize oneself.

class pyviblib.gui.windows.WorkspaceWindow(mainApp, **kw)

Window that can be saved in a PyVib2 workspace.

The following public methods are declared in this class:

get_type_id()

get a string uniquely identifying the window type

get_pickle_dict()

get a dictionary to be pickled in the workspace

get_molecules()

get a list of molecules if appropriate

Initializer of the class (kw are passed to BaseWindow).

get_molecules()

Get a list of molecules if appropriate (otherwise return None).

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.MoleculeWindow(mainApp, thumbnail, datasrc, camera=None, geom='500x500', atoms=None)

Window for exploring molecules.

The following properties are exposed:

filename

file name from which the molecule was read

molecule_name

name of the molecule

molecule

molecule (pyviblib.molecule.Molecule)

vib_toolbar

vibrational toolbar

renderWidget

3D render widget

settings

dictionary with the settings of the window

status

text to be set to the message bar of the window

The following methods are exported:

apply_settings()

callback for the buttons of the settings dialog

save_vibrations()

save vibrations

save_animation()

save an animation of the current vibration

clone()

clone the molecule window

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• thumbnail – thumbnail
• datasrc – molecule, string(file name), parser object
• camera – initial camera
• geom – window geometry
• atoms – list of atoms to be picked

apply_settings(close_dialog=False)

Callback for the Apply/Ok buttons of the settings dialog.

Parameter:close_dialog – whether the dialog is to be closed

clone()

Clone the molecule window.

get_molecules()

Get a list of molecules if appropriate (otherwise return None).

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

save_animation(filename, nFrames, resolution, speed, format_='Animated GIF', transparent_bg=False, openfile=False)

Save an animation of the current vibration.

The gifsicle and ppm2fli programs must be installed.

Parameters:

• filename – file name for the animation
• nFrames – number of frames per each direction
• resolution – VTK resolution for rendering
• speed – speed of animation delay between frames in hundredths of a second http://www.lcdf.org/gifsicle/man.html http://vento.pi.tu-berlin.de/ppm2fli/ppm2fli.1.html
• format – format, one of (‘Animated GIF’, ‘FLI’)
• transparent_bg – whether the background should be made transparent
• openfile – whether to open the animation after the saving, this feature must be supported by Python

save_vibrations(**params)

Save vibrations.

Parameters:

• filepattern – pattern to generating file names for the vibrations
• image_format – image format, one of (‘jpeg’, ‘tiff’, ‘png’, ‘eps’, ‘ppm’)
• magnify_factor – integer magnification factor for the render widget
• vibs_list – list of vibrations to be saved vibration numbers are one-based
• create_archive – whether to create a zip-archive

All the keyword arguments must be supplied.

class pyviblib.gui.windows.CorrelateVibrationsWindow(mainApp, ref_mol=None, tr_mol=None, molecules=None, startpage=None, ref_camera=None)

Window for correlating vibrations.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• ref_mol – start reference molecule must be instance of pyviblib.molecule.Molecule, if None, the choice is made automatically
• tr_mol – start trial molecule must be instance of pyviblib.molecule.Molecule, if None, the choice is made automatically
• molecules – list of molecule whose vibrations are to be correlated if None, use the molecules listed in the thumbnail pane of the main window of PyVib2
• startpage – tab name of RamanROADegcircCalcMixtureWindow to be shown at startup
• ref_camera – camera to be installed to the reference widget

clone()

Does nothing.

class pyviblib.gui.windows.CorrelationResultsWindow(mainApp, correlation_results, goback_window=None, startpage=None)

Window for representing results of a correlation of vibrations.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• correlation_results – results of the correlation (dictionary)

correlation_results must have the following keys:

• start_time - formatted start time

• t0 - start time as a tuple returned by os.times()

• t1 - end time as a tuple returned by os.times()

• ref_mol - reference molecule (pyviblib.molecule.Molecule)

• tr_mol - trial molecule (pyviblib.molecule.Molecule)

• atom_pairs - atom_pairs of the fit fragment (null-based ndarray),

  shape: (Natoms_F, 2) with Natoms_F being the number of atoms in the fragment atom numbers are one-based

• alignment - type of the orientationsl alignment

  must be one of (‘Orientational’, ‘Inertia axes’,None)

• include_tr_rot - if translations / rotations were included

• overlaps - overlaps matrix (one-based ndarray)

  shape: (1 + NFreq_ref, 1 + NFreq_tr) with NFreq_ref and NFreq_tr being the number of the vibrations being correlated

• similarities - overlaps matrix (one-based ndarray),

  shape: (1 + NFreq_ref, 1 + NFreq_tr)

• camera - camera to be installed to the reference widget

  if the orientational alignment has been performed:

  • rms - RMS value

  • q - quaternion (null-based ndarray), shape: (4,)

  • U - left rotation matrix (one-based ndarray), shape: (4, 4)

  • ref_center - center of the reference molecule

    (one-based ndarray), shape: (4,)

  • fit_center - center of the fitted molecule

    (one-based ndarray), shape: (4,)

Parameters:

• goback_window – window to switch to
• startpage – tab name of RamanROADegcircCalcMixtureWindow to be shown at startup

clone()

Does nothing.

class pyviblib.gui.windows.SingleVibrationWindow(mainApp, mol, **kw)

Window for exploring a single vibration.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• molecule_name – molecule name shown in the title of the window if given, override the value of molecule.name
• vib_no – number of vibration to show
• roa_gen – whether the ROA ACP button is to be shown
• invert_roa – whether to invert the sign of ROA
• vcd_gen – whether the VCD acp button is to be shown
• invert_vcd – whether to invert the sign of VCD
• camera – initial camera position
• marked_vib_atoms – atoms to be marked

clone()

Does nothing.

set_infotext(info)

Set an information text.

class pyviblib.gui.windows.VibrationPairWindow(mainApp, ref_mol, tr_mol, **kw)

Window for exploring two vibrations simultaneously.

The following property is exposed:

ref_camera()

camera installed in the reference render widget

No public methods are exported.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• ref_mol – reference molecule which is shown at the left
• tr_mol – trial molecule which is shown at the right
• atom_pairs – atom pairs of the fragment to be marked (null-based ndarray), shape: (Natoms_F, 2) with Natoms_F being the number of atoms in the fragment atom numbers are one-based
• overlap – overlap
• similarity – similarity
• ref_no – reference number of vibration
• tr_no – trial number of vibration
• U – left rotation matrix for the trial frame (one-based ndarray), shape: (4, 4)
• ref_camera – camera to be installed to the reference widget
• startpage – tab name of RamanROADegcircCalcMixtureWindow to be shown at startup

clone()

Does nothing.

class pyviblib.gui.windows.AbstractFigureWindow(mainApp, **kw)

Abstract class for widnows having spectra figures.

The canvas of the spectra is saved by resizing and there is a function for saving a figure.

The following read-only property is exposed:

figure

figure embeded in the window

Initializer of the class.

Parameter:mainApp – reference to the main window of PyVib2

get_molecules()

Return self._mol,

class pyviblib.gui.windows.RamanROADegcircCalcWindow(mainApp, mol, **kw)

Window for exploring Raman/ROA spectra.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• camera – camera to be set in secondary windows
• groups_AB – unless None, plot additionally a second spectrum with either AA, AB or BB contribution. Format : [group_A, group_B, t]
• label_AB – if groups_AB is set, this string is used as title2
• geom – window geometry
• parallel – whether to use parallel calculation

clone()

Clone the molecule window.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.AbstractCalcMixtureWindow(mainApp, mols, names, prefices, composition=None, molecule_labels=None, mark_vibs=None, lim_wavenumbers=None, startpage=None, scattering=None, render_spectra_labels=True, add_corr_spectra=False, geom=None)

Abstract class for exploring spectra of several molecules.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mols – list of molecules to be opened
• names – names of the tabs
• prefices – prefices to identify the spectra
• composition – composition of the mixture (null-based ndarray). If None, do not render the Mixture tab
• molecule_labels – labels for the molecules
• mark_vibs – list of vibrations to be marked on the spectra
• startpage – start tab to activate
• scattering – start value of the scattering
• render_spectra_labels – whether to render the spectra labels, appearing to the left side of the spectra canvas
• geom – window geometry

get_molecules()

Return self._mols,

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

class pyviblib.gui.windows.RamanROADegcircCalcMixtureWindow(mainApp, mols, composition=None, molecule_labels=None, mark_vibs=None, lim_wavenumbers=None, startpage=None, scattering=None, render_spectra_labels=True, geom=None)

Window for exploring Raman/ROA/Degree of circularity spectra of several molecules.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mols – list of molecules to be opened
• names – names of the tabs
• prefices – prefices to identify the spectra
• composition – composition of the mixture (null-based ndarray) if None, do not render the Mixture tab
• molecule_labels – labels for the molecules
• mark_vibs – list of vibrations to be marked on the spectra
• startpage – start tab to activate
• scattering – start value of the scattering
• render_spectra_labels – whether to render the spectra labels, appearing to the left side of the spectra canvas
• geom – window geometry

clone()

Clone the molecule window.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.IRVCDCalcMixtureWindow(mainApp, mols, composition=None, molecule_labels=None, mark_vibs=None, lim_wavenumbers=None, startpage=None, render_spectra_labels=True, geom=None)

Window for exploring IR/VCD/g spectra of several molecules.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mols – list of molecules to be opened
• names – names of the tabs
• prefices – prefices to identify the spectra
• composition – composition of the mixture (null-based ndarray), if None, do not render the Mixture tab
• molecule_labels – labels for the molecules
• mark_vibs – list of vibrations to be marked on the spectra
• startpage – start tab to activate
• render_spectra_labels – whether to render the spectra labels, appearing to the left side of the spectra canvas
• geom – window geometry

clone()

Clone the molecule window.

get_pickle_dict()

Remove the scattering keyword from the base class implementation.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.RamanROAGenerationWindow(mainApp, mol, **kw)

Raman/ROA generation interface.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• vib_no – start vibration number
• camera – camera to be set in secondary windows
• tabname – start tab name
• molinv – molecular invariant to show
• group_mode – ‘single atoms’ or ‘groups’
• invert_roa – whether to invert the sign of ROA
• geom – window geometry

clone()

Clone the molecule window.

get_molecules()

Get a list of molecules if appropriate (otherwise return None).

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.IRVCDCalcWindow(mainApp, mol, **kw)

Window for exploring IR/VCD spectra.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• camera – camera to be set in secondary windows
• groups_AB – unless None, plot additionally a second spectrum with either AA, AB or BB contribution. Format : [group_A, group_B, t]
• label_AB – if groups_AB is set, this string is used as title2
• geom – window geometry

clone()

Clone the molecule window.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.IRVCDGenerationWindow(mainApp, mol, **kw)

IR/VCD generation interface.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• vib_no – start vibration number
• camera – camera to be set in secondary windows
• tabname – start tab name
• intensity – molecular invariant to show
• group_mode – ‘single atoms’ or ‘groups’
• invert_vcd – whether to invert the sign of VCD
• geom – window geometry

clone()

Clone the molecule window.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.BoltzmannMixtureSpectraWindow(mainApp, mols, check_all=False, raman_roa=True)

Window for plotting spectra of a mixture of molecules.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mols – list of molecules to be opened
• check_all – whether to check all molecules at startup
• raman_roa – if True, plot Raman/ROA/Degree of circularity spectra, otherwise IR/VCD/g

clone()

Does nothing.

class pyviblib.gui.windows.ImportRamanROAExpSpectraWindow(mainApp)

Window for importing experimetnal Raman/ROA spectra.

Initializer of the class.

Parameter:mainApp – reference to the main window of PyVib2

clone()

Does nothing.

class pyviblib.gui.windows.ImportIRExpSpectraWindow(mainApp)

Window for importing experimental infrared absorption spectra.

Initializer of the class.

Parameter:mainApp – reference to the main window of PyVib2

clone()

Does nothing.

class pyviblib.gui.windows.RamanROADegcircExpWindow(mainApp, exp_data, compound_name=None, parser=None, spectrumID=None, geom=None)

Window for exploring experimental Raman/ROA/Degree of circularity spectra.

The following read-only properties are exposed:

exp_data

experimental data

raw_data

laser_energy, X, raman, roa, degcirc

spectrumID

a unique string identifying the spectra

scattering

scattering

info

information about the experimental spectra

roa_invert

whether ROA is to be inverted

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• exp_data – list with the experimental data
• compound_name – compound name
• parser – unless None, it is RamanROAExpSpectraFileParser and suppose to be used instead of exp_data
• spectrumID – spectrumID
• geom – window geometry

clone()

Clone the molecule window.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.IRExpWindow(mainApp, X, Y, datatype, filename, compound_name=None, spectrumID=None, geom=None)

Window for exploring experimental infrared absorption spectra.

The following read-only properties are exposed:

raw_data

X, Y

spectrumID

a unique string identifying the spectra

datatype

datatype, see resources.STRINGS_EXP_IR_SPECTRA_TYPES

info

information about the experimental spectra

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• X – array with wavenumbers in cm**(-1)
• Y – spectrum, see the datatype keyword
• datatype – see resources.STRINGS_EXP_IR_SPECTRA_TYPES
• filename – file name
• compound_name – compound name
• spectrumID – spectrumID
• geom – window geometry

clone()

Clone the molecule window.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.DCMSumsWindow(mainApp, mol, geom=None)

Representing the sums of internuclear distances.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• geom – window geometry

clone()

Clone oneself.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.ArrangeExpSpectraWindow(mainApp, spectratype=None, scattering=None)

Arrange several experimental spectra to be put on one plot.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• spectratype – spectra type, see resources.STRING_EXP_SPECTRA_TYPES
• scattering – start value of the scattering, see resources.STRINGS_SCATTERING_TYPES

clone()

Does nothing.

class pyviblib.gui.windows.AbstractMultipleExpWindow(mainApp, names, prefices, spectrumIDs, ar_raw_data, geom=None)

Abstract class for exploring experimental spectra of several molecules.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• names – names of the tabs
• prefices – prefices to identify the spectra
• spectrumIDs – list of spectrumIDs to be plotted
• ar_raw_data – list of raw data for the spectra
• geom – window geometry

get_pickle_dict()

Return spectrumIDs, ar_raw_data and geom.

class pyviblib.gui.windows.RamanROADegcircMultipleExpWindow(mainApp, spectrumIDs, ar_raw_data, scattering, geom=None)

Exploring experimental Raman/ROA/Degcree of circularity spectra of several molecules.

Initializer of the class.

Parameters:

• spectrumIDs – list of spectrumIDs to be plotted
• ar_raw_data – list of raw data for the spectra
• scattering – string identifying the scattering
• geom – window geometry

clone()

Does nothing.

get_pickle_dict()

Add the scattering keyword to the base class implementation.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.IRMultipleExpWindow(mainApp, spectrumIDs, ar_raw_data, ar_datatype, geom=None)

Exploring experimental infrared spectra of several molecules.

Initializer of the class.

Parameters:

• spectrumIDs – list of spectrumIDs to be plotted
• ar_raw_data – list of raw data for the spectra
• ar_datatype – list of datatypes
• geom – window geometry

clone()

Does nothing.

get_pickle_dict()

Add the ar_datatype keyword to the base class implementation.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.CorrelateExpExpSpectraWindow(mainApp, spectra_type, spectrumIDs, XY, start=None, end=None)

Window for correlating two experimental spectra.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• spectra_type – type of the spectra to be correlated
• spectrumIDs – list of spectrumIDs to be plotted
• XY – list of [[X0, Y0], [X1, Y1], ...]

clone()

Does nothing.

class pyviblib.gui.windows.CorrelateCalcExpSpectraWindow(mainApp, mols, spectrumIDs, composition=None, start=None, end=None, N_G=6, FWHM_is=3.5, FWHM_anis=10.0, FWHM_inst=7.0)

Window for correlating a calculated and experimental spectrum.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mols – list or tuple of molecules
• spectrumIDs – available experimental spectrumIDs
• startx – start wavenumber
• endx – end wavenumber
• composition – composition of the mixture (null-based ndarray)
• N_G – number of Gauss functions
• FWHM_is – full width at half maximum for the isotropic invariants a2 and b2
• FWHM_anis – full width at half maximum for the anisotropic invariants b2, b2G, b2A
• FWHM_inst – full width at half maximum for the Gaussian instrument profile

clone()

Does nothing.

class pyviblib.gui.windows.CorrelateCalcCalcSpectraWindow(mainApp, mols, **kw)

Window for correlating two calculated Raman/ROA or IR/VCD spectra.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mols – molecules with Raman/ROA
• ramanroa – True for Raman/ROA, otherwise IR/VCD
• N_G – number of Gauss functions
• FWHM_is – full width at half maximum for the isotropic invariants a2 and b2
• FWHM_anis – full width at half maximum for the anisotropic invariants b2, b2G, b2A
• FWHM_inst – full width at half maximum for the Gaussian instrument profile
• FWHM_irvcd – full width at half maximum of the Lorentz bands for IR/VCD (used if ramanroa = False)

clone()

Does nothing.

class pyviblib.gui.windows.CompareMoleculesWindow(mainApp, ref_mol=None, tr_mol=None, molecules=None, ref_camera=None, groups_mode=False, finish_command=None, pairs=None, npairs_min=2)

Window for comparing molecules.

One can superimpose the molecules, subtract ACPs if the data are available.

The following read-only property is exposed

pairs

ndarray with selected one-based atom pairs

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• ref_mol – start reference molecule must be instance of pyviblib.molecule.Molecule if None, the choice is made automatically
• tr_mol – start trial molecule, must be instance of pyviblib.molecule.Molecule if None, the choice is made automatically
• molecules – list of molecule whose vibrations are to be correlated. if None, use the molecules listed in the thumbnail pane of the main window of PyVib2
• ref_camera – start camera for the reference widget
• groups_mode – True for the group selection mode
• finish_command – callback for the Finish selection button should be a callable which accepts one argument, being the pairs selected
• pairs – start pairs to be set (ndarray), contains one-based number of atoms
• npairs_min – minimal number of pairs which can be selected

clone()

Does nothing.

class pyviblib.gui.windows.CompareRamanROAACPWindow(mainApp, ref_mol, tr_mol, ans_fit, geom=None)

Comparing Raman/ROA ACPs.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• ref_mol – reference molecule
• tr_mol – trial molecule
• ans_fit – results of the superimposing of ref_mol and tr_mol
• geom – window geometry

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.CompareIRVCDACPWindow(mainApp, ref_mol, tr_mol, ans_fit, geom=None)

Comparing IR/VCD ACPs.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• ref_mol – reference molecule
• tr_mol – trial molecule
• ans_fit – results of the superimposing of ref_mol and tr_mol
• geom – window geometry

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.AnalyzeClusterWindow(mainApp, molecules)

Analyzing clusters.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• molecules – molecules to be analyzed

clone()

Does nothing.

class pyviblib.gui.windows.GroupsInfoWindow(mainApp, mol, group1, group1_color, group2=None, group2_color=None, label1=None, label2=None, ramanroa=True)

Mark one or two groups of atoms in a molecule.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• group1 – list of atoms in a first group
• group1_color – color in HTML format to be used for the first group
• group2 – list of atoms in a second group
• group2_color – color in HTML format to be used for the second group
• label1 – label of the first group
• label2 – label of the second group
• ramanroa – True for Raman/ROA, otherwise IR/VCD

clone()

Does nothing.

class pyviblib.gui.windows.GroupsLocalizationWindow(mainApp, mol, geom=None)

Show available groups for a molecule and localizations on them.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• geom – window geometry

clone()

Clone oneself.

get_molecules()

Return self._mols,

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.VOASimilarityCurvesWindow(mainApp, mols, X, sim_y1, sim_y2, ab=None, show_hint=True, interp=True, lim_wavenumbers=None, ramanroa=True, geom=None)

Raman/ROA similarity curves window.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mols – list of molecules
• X – wavenumbers
• sim_raman – Raman similarity curve
• sim_roa – ROA similarity curve
• ab – experimental correction
• show_hint – show hints
• interp – increase the number of points
• lim_wavenumbers – (startx, endx)
• ramanroa – True for Raman/ROA, otherwise IR/VCD
• geom – window geometry

clone()

Does nothing.

get_molecules()

Return self._mols,

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.VibLocalizationsWindow(mainApp, mol, fragment, geom=None)

Representing the localizations of vibrations on a fragment.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• fragment – fragment to show the localizations on
• geom – window geometry

clone()

Clone oneself.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.CumulatedNormalizedVibSumsWindow(mainApp, mol, voa=0, from_=None, to_=None, geom=None)

Window with cumulated normalized vibrational sums for VROA.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• mol – molecule
• voa – 0 for roa and 1 for vcd
• from – initial value of the from field
• to – initial value of the to field
• geom – window geometry

clone()

Clone the molecule window.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.

class pyviblib.gui.windows.ExpROACumulatedNormalizedSumsWindow(mainApp, raw_data, from_=None, to_=None, geom=None)

Window with experimental cumulated normalized sums of ROA.

Initializer of the class.

Parameters:

• mainApp – reference to the main window of PyVib2
• raw_data – laser_energy, X, raman, roa, degcirc
• from – initial value of the from field
• to – initial value of the to field
• geom – window geometry

clone()

Clone the molecule window.

get_pickle_dict()

Get a dictionary to be pickled in the workspace.

static get_type_id()

Get a string uniquely identifying the window type.