sith.visualize package

Submodules

class sith.visualize.ngl.EnergiesNGL(sith_info, idef='all', alignment=None, axis=False, background='#FFFFFF', **kwargs)[source]

Bases: MoleculeNGL

Set of tools to show a molecule and the distribution of energies in the different DOF.

Parameters:

  • sith_info – sith object or sith.utilities.ReadSummary object

  • idef (int. Default='all') – number of the deformation to be analized. Default=None, that means, all the structures are displayed as a trajectory.

  • alignment (list. Default=None) – 3 indexes to fix the correspondig atoms in the xy plane. The first atom is placed in the negative side of the x axis, the second atom is placed in the positive side of the x axis, and the third atom is placed in the positive side of the y axis.

  • axis (bool) – add xyz axis

  • background (color) – background color. Default: ‘#ffc’

  • kwargs – kwargs of MoleculeNGL

change_def(def_dict: dict, **kwargs) → tuple[source]

This functions change the values stored in a dictionary and removes each one of the arguments from the kwargs.

Parameters:

  • def_dict (dict) – dictionary with the default values.

  • kwargs – all the arguments you want to change.

Returns:

  • (dict, dict) modified dictionary withe the default values and set of

  • kwargs without the used keys.

energies_all_dof(**kwargs)[source]

Add all DOF with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

kwargs – of internal method energies_some_dof.

Return type:

(plt.figure) fig of energies_some_dof.

energies_angles(**kwargs)[source]

Add the angles with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

kwargs – of internal method energies_some_dof.

Return type:

(plt.figure) fig of energies_some_dof.

energies_bonds(**kwargs)[source]

Add the bonds with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

kwargs – of internal method energies_some_dof.

Return type:

(plt.figure) fig of energies_some_dof.

energies_dihedrals(**kwargs)[source]

Add the dihedral angles with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

kwargs – of internal method energies_some_dof.

Return type:

(plt.figure) fig of energies_some_dof.

energies_some_dof(dofs, **kwargs)[source]

Add the bonds with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

  • dofs (list of tuples.) – list of degrees of freedom defined using 1-based indexing.

  • kwargs – optional kwargs of internal method change_def

Return type:

(plt.figure) figure of the colorbar.

show_bonds(**kwargs)[source]

Show the bonds in the molecule.

Parameters:

show_dof (kwargs for)

Return type:

(None)

Notes

The color is not related with the JEDI method. It could be changed with the kwarg color=rgb list.

show_bonds_of_DOF(dof, unique=False, color=None)[source]

Show an specific dof.

Parameters:

  • dof (int.) – index in sith object that corresponds to the dof you want to show.

  • unique (Bool. default False.. Default=False) – True if you want to remove all the other bonds and only keeping these ones.

  • color (list[3(int)]. default R G B for angles, distances, dihedrals.) – color that you want to use in this dof.

Return type:

(list) Bonds in the system.

show_dof(dofs, **kwargs)[source]

Show specific degrees of freedom.

Parameters:

  • dofs (list of tuples.) – list of degrees of freedom defined using 1-based indexing.

  • add_dof (kwargs for)

Return type:

(None)

Notes

The color is not related with the JEDI method. It could be changed with the kwarg color=rgb list.

update_frame()[source]

Function that is called when the frame is changed. Set the internal atribute self.kwargs_edofs to keep fixed the parameters to update the visualization of dofs.

Return type:

(bool) True

class sith.visualize.ngl.MoleculeNGL(atoms, alignment=None, axis=False, xsize: int = 500, ysize: int = 500, n=5)[source]

Bases: object

Set of graphic tools to see the distribution of energies in the different degrees of freedom (lengths, angles, dihedrals). Wrap to NGLview.

Parameters:

  • atoms (ase.Atoms) – Atoms object to be visualized

  • alignment (list[int]. Default=None) – list of three indexes corresponding to the indexes of the atoms in the xy plane. the first two atoms are set to the x axis.

  • axis (bool. Default=False) – Show xyz axis.

  • xsize (int. Default=500.) – Horizontal size of the visualization windows.

  • ysize (int. Default=500.) – Vertical size of the visualization windows.

add_angle(atom1index, atom2index, atom3index, color=None, n=None)[source]

Add an angle to between three atoms: atom1, atom2 and atom3 - with the vertex in the atom2

Parameters:

  • atom1index (int) – Indexes of the first atom that defines the angle.

  • atom2index (int) – Indexes of the second atom that defines the angle.

  • atom3index (int) – Indexes of the third atom that defines the angle.

  • color (color list. Default all gray([0.5, 0.5, 0.5])) – RGB triplet.

  • n (int. Default=internal defined n) – number of intermedia points to add in the arc of the angle.

Return type:

(list) list of meshes forming the angle.

add_arc(vertex, arcdots, color)[source]

Add an arc using triangles.

Parameters:

  • vertex (array) – center of the arc

  • arcdots (list of arrays) – vectors that define the points of the arc. These vectors must be defined respect the vertex.

  • color (color format.) – color if the arc to be added

Return type:

(list) list of meshes forming the arc.

add_axis(length=1, radius=0.1)[source]

Add xyz axis.

Parameters:

  • length (float. Default=1) – indicates the length of the axis in the visualization. Default=1

  • radius (float. Default=0.1) – thickness of the xyz axis

Return type:

(dict) axis as dict with cylinder shapes of nglview.

add_bond(atom1index, atom2index, color=None, radius=0.1)[source]

Add a bond between two atoms: atom1 and atom2

Parameters:

  • atom1index (int) – Indexes of the atoms to be connected using 1-based indexing.

  • atom2index (int) – Indexes of the atoms to be connected using 1-based indexing.

  • color (list. Default=gray([0.5, 0.5, 0.5])) – RGB triplet.

  • radius (float. Default=0.1) – Radius of the bond.

Return type:

(Vpython object) Cylinder representing the just added bond.

add_bonds(atoms1indexes, atoms2indexes, colors=None, radii=None)[source]

Add a bond between each pair of atoms corresponding to two lists of atoms: atom1indexes and atom2indexes.

Parameters:

  • atoms1indexes (int) – Indexes of the atoms to be connected using 1-based indexing.

  • atoms2indexes (int) – Indexes of the atoms to be connected using 1-based indexing.

  • colors (list of color lists. Default all gray([0.5, 0.5, 0.5])) – RGB triplets for each of the bonds. It can be one a triplet in case of just one color in all bonds.

  • radii (float or list of floats. Default 0.1) – radius of each bond.

Return type:

(list) Bonds in the system

add_dihedral(atom1index, atom2index, atom3index, atom4index, color=None, n=None)[source]

Add an dihedral angle between four atoms: atom1, atom2, atom3 and atom4 - with the vertex in the midle of the atom 2 and 3

Parameters:

  • atom1index (int) – Indexes of the first atom that defines the angle.

  • atom2index (int) – Indexes of the second atom that defines the angle.

  • atom3index (int) – Indexes of the third atom that defines the angle.

  • atom4index (int) – Indexes of the fourth atom that defines the angle.

  • color (color list. Default all gray([0.5, 0.5, 0.5])) – RGB triplet.

  • n (int. Default 10) – number of intermedia points to add in the arc of the angle.

Return type:

(list) All the displayed dihedral angles.

add_dof(dof, color=None, **kwargs)[source]

Add the degree of freedom to the molecule image

Parameters:

  • dof (tuple) – label of the degree of freedom using 1-based indexing.

  • color (color format. Default=[0.5, 0.5, 0.5]) – Color of the DOF in the visual representation.

  • kwargs – arguments for the function add_bond, add_angle or add_dihedral, according to the case.

Return type:

(list) list of DOFs of the same kind.

Example

dof=(1, 2) means a bond between atoms 1 and 2 dof=(1, 2, 3) means an angle between atoms 1, 2 and 3 dof=(1, 2, 3, 4) means a dihedral angle between atoms 1, 2, 3 and 4

align_axis(vector)[source]

Apply the necessary rotations to set a vector aligned with positive x axis.

Parameters:

vector (np.array) – vector to to be aligned.

Returns:

  • (np.array) 3x3 transformation matrix to align the vector with the x

  • axis.

align_plane(vector)[source]

Rotation around x axis to set a vector in the xy plane

Parameters:

vector (np.array) – vector to be aligned.

Returns:

  • (np.array) 3x3 transformation matrix to align the vector with the x

  • axis.

apply_trans(atoms, trans, indexes=None)[source]

Apply a transformation to all vector positions of the atoms object

Parameters:

  • atoms (ase.Atoms) – Atoms object to be transformed.

  • trans – 3x3 matrix containing the transformation.

  • indexes (Default=None (namely, all atoms)) – indexes of atoms to apply the transformation.

Return type:

(np.array) array of new positions.

download_image(*args, **kwargs)[source]

Download image.

Parameters:

  • args – args for the function nglview.view.download_image.

  • kwargs – kwargs for the function nglview.view.download_image.

Return type:

(bool) True.

intermedia_vectors(a, b, n)[source]

Define the intermedia arc dots between two vectors

Parameters:

  • a (array) – Vector of side a of the angle.

  • b (array) – Vector of side b of the angle.

  • n (int) – number of intermedia dots.

Return type:

(list) Return the intermedia vectors between two side vectors.

picked()[source]

Call the function picked of nglview that checks the last clicked object and shows the information related to it.

Return type:

output of function nglview.view.picked

remove_all_angles()[source]

Remove all angles.

Return type:

(list) Return all the angles in the display.

remove_all_bonds()[source]

Remove all bonds

Return type:

(list) Return the bonds in the system.

remove_all_dihedrals()[source]

Remove all dihedral angles.

Return type:

(list) all the dihedral angles

remove_angle(atom1index, atom2index, atom3index)[source]

Remove an angle if it exists

Parameters:

  • atom1index (int) – Indexes of the first atom that defines the angle.

  • atom2index (int) – Indexes of the second atom that defines the angle.

  • atom3index (int) – Indexes of the third atom that defines the angle.

Return type:

(list) Return all the angles in the display.

remove_axis()[source]

remove xyz axis

Return type:

(dict) axis as dict with cylinder shapes of nglview.

remove_bond(atom1index, atom2index)[source]

Remove a bond between two atoms: atoms1 and atoms2.

Parameters:

  • atom1index (int) – Indexes of the atoms that are connected. This bond will be removed.

  • atom2index (int) – Indexes of the atoms that are connected. This bond will be removed.

Return type:

(list) Return the bonds in the system.

remove_bonds(atoms1indexes=None, atoms2indexes=None)[source]

Remove several bonds in the plot between two list of atoms: atoms1 and atoms2.

Parameters:

  • atoms1indexes (list[int]. Default=None) – Indexes of the atoms that are connected.

  • atoms2indexes (list[int]. Default=None) – Indexes of the atoms that are connected.

Returns:

  • (list) Return the bonds in the system.

  • Note (if atoms2 is None, all bonds with atoms1 will me removed.)

  • If atoms1 and atoms2 are None, all bonds in the structure are

  • removed.

remove_dihedral(atom1index, atom2index, atom3index, atom4index)[source]

Remove the dihedral angle between 4 atoms:

Parameters:

  • atom1index (int) – Indexes of the first atom that defines the angle.

  • atom2index (int) – Indexes of the second atom that defines the angle.

  • atom3index (int) – Indexes of the third atom that defines the angle.

  • atom4index (int) – Indexes of the fourth atom that defines the angle.

Return type:

(list) Return the dihedral angles.

rot_x(angle)[source]

Returns the rotation matrix around x axis.

Parameters:

angle (float) – angle to rotate in radians.

Return type:

(np.array) 3x3 rotation matrix.

rot_y(angle)[source]

Returns the rotation matrix around y axis.

Parameters:

angle (float) – angle to rotate in radians.

Return type:

(np.array) 3x3 rotation matrix.

rot_z(angle)[source]

Returns the rotation matrix around z axis.

Parameters:

angle (float) – angle to rotate in radians.

Return type:

(np.array) 3x3 rotation matrix.

show()[source]

Show the molecule.

Return type:

(box)

xy_alignment(atoms, index1, index2, index3)[source]

Transforme the positions of the atoms such that the atoms of indexes 1 and 2 are aligned in the x axis

Parameters:

  • atoms (ase.Atoms) – Atoms to be transformed.

  • index1 (int) – first atom to go in the x axis.

  • index2 (int) – second atom to go to the x axis.

  • index3 (int) – atom to go in the xy plane.

Return type:

(np.array) numpy array with new positions.

class sith.visualize.vmol.EnergiesVMol(sith_info: SITH, dofs: list = None, idef: int = 0, alignment: list | tuple | ndarray = None, show_axis: bool = False, background: list | color = vector(1, 1, 1), respect_to_total_energy: bool = False, **kwargs)[source]

Bases: VMolecule

Set of graphic tools to visualize the distribution of energies in the different degrees of freedom (lengths, angles, dihedrals). Wrap to VMol.

Parameters:

  • sith_info (SITH object.) – SITH object with the information of the system.

  • dofs (list. Default=None) – list of degrees of freedom defined according with 1-based indexing. It could also be ‘all’, ‘bonds’, ‘angles’ or ‘dihedrals’ to display all the corresponding DOFs.

  • idef (int. Default=0) – index of the stretching to be displayed.

  • alignment (list, tuple or np.ndarray. Default=None.) – indexes for the alignment of the molecule. See VMolecule.xy_alignment for more details.

  • show_axis (bool. Default=False.) – True if you want to show the axis in the scene.

  • background (list or vp.color. Default=vp.color.white.) – color of the background of the scene.

  • respect_to_total_energy (Default=False) – if true, the maximum of energies will be calculated with respect to the total energy of all the DOFs, not only the selected ones.

  • kwargs – other arguments for VMolecule.

change_def(def_dict: dict, **kwargs) → tuple[source]

This functions change the values stored in a dictionary and removes each one of the arguments from the kwargs.

Parameters:

  • def_dict (dict) – dictionary with the default values.

  • kwargs (all the arguments you want to change.)

Returns:

  • (dict, dict) modified dictionary withe the default values and set of

  • kwargs without the used keys.

create_figure(dofs, respect_to_total_energy: bool = False, **kwargs)[source]

Creates the Color bar to be displayed at a side.

Parameters:

  • dofs – DOFs to be displayed in the distribution.

  • respect_to_total_energy (bool. Default=False) – if true, the maximum of energies will be calculated with respect to the total energy of all the DOFs, not only the selected ones.

  • change_def (kwargs for)

Return type:

(list, kwargs) normalized energies, not used kwargs.

energies_all_dof(**kwargs) → tuple[source]

Add all DOF with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

EnergiesVMol.energies_some_dof (kwargs for)

Return type:

(tuple) DOFs and their computed energies.

energies_angles(**kwargs) → tuple[source]

Add the angles with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

EnergiesVMol.energies_some_dof (kwargs for)

Return type:

(tuple) DOFs and their computed energies.

energies_bonds(**kwargs) → tuple[source]

Add the bonds with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

EnergiesVMol.energies_some_dof (**kwargs for)

Return type:

(tuple) DOFs and their computed energies.

energies_dihedrals(**kwargs) → tuple[source]

Add the dihedral angles with a color scale that represents the distribution of energy according to the JEDI method.

Parameters:

EnergiesVMol.energies_some_dof (kwargs for)

Return type:

(tuple) DOFs and their computed energies.

energies_some_dof(dofs, **kwargs) → tuple[source]

Add the dofs with a color scale that represents the distribution of energy according to the SITH method.

Parameters:

  • dofs (list of tuples.) – list of degrees of freedom defined according with 1-based indexing.

  • normalize – normalization of colors acording to the range of energies and the colormap.

  • VMolecule.add_dof (kwargs of)

Return type:

(list) VPython objects of the visual representation of DOFs.

show_bonds(**kwargs) → None[source]

Show the bonds in the molecule.

Parameters:

add_dof (kwargs for)

Return type:

(None)

Notes

The color is not related with the JEDI method. It could be changed with the kwarg color=rgb list.

show_bonds_of_DOF(dof: list, unique: bool = False, color: list = None) → dict[source]

Show bonds of a specific dof.

Parameters:

  • dof (int.) – index in sith object that corresponds to the dof you want to show.

  • unique (Bool. default False.. Default=False) – True if you want to remove all the other bonds and only keeping these ones.

  • color (list[3(int)]. default R G B for angles, distances, dihedrals.) – color that you want to use in this dof.

Returns:

  • (dict) all the DOFs in the system. keys -> dof names,

  • values -> vpython.objects

show_dof(dofs: list, **kwargs) → dict[source]

Show specific degrees of freedom.

Parameters:

  • dofs (list of tuples.) – list of degrees of freedom defined according with 1-based indexing.

  • add_dof. (kwargs for)

Returns:

  • (dict) all the DOFs in the system. keys -> dof names,

  • values -> vpython.objects

Notes

The color is not related with the JEDI method. It could be changed with the kwarg color=rgb list.

sith_inDOFs(dofs, **kwargs)[source]
traj_buttons() → button[source]

Create the buttons to move between stretching configurations.

Returns:

  • (vpython.button) Button that shows the index of the stretched

  • configuration displayed.

update_stretching(idef) → None[source]

Function that is called when the frame is changed. Set the internal atribute self.kwargs_edofs to keep fixed the parameters to update the visualization of dofs.

Parameters:

idef (int) – index of the stretching to be updated to.

Return type:

(None)

Module contents