chemtools.toolbox.interactions.NCI¶

class
chemtools.toolbox.interactions.
NCI
(density, rdgradient, grid, hessian=None)[source]¶ NonCovalent Interactions (NCI) Class.
Initialize class using density, reduced density gradient and UniformGrid instance.
Parameters:  density (np.array) – Density evaluated on grid points of cube.
 rdgradient (np.array) – Reduced density gradient evaluated on grid points of cube
 grid (instance of UniformGrid, optional) – Cubic grid used for calculating and visualizing the NCI. If None, it is constructed from molecule with spacing=0.1 and extension=2.0.
 hessian (np.array, optional) – Hessian of density evaluated on grid points of cube. This is a array with shape (n, 6) where n is the number of grid points of cube.

classmethod
from_molecule
(molecule, spin='ab', index=None, grid=None)[source]¶ Initialize class from
Molecule
object.Parameters:  molecule (instance of Molecule class.) – Instance of Molecular class.
 spin (str, optional) – The type of occupied spin orbitals; options are ‘a’, ‘b’ & ‘ab’.
 index (int or Sequence of int, optional) – Sequence of integers representing the index of spin orbitals. If None, all occupied spin orbitals are included.
 grid (instance of Grid, optional) – Grid used for calculating and visualizing the property values. If None, a cubic grid is constructed from molecule with spacing=0.1 & extension=2.0.

signed_density
¶ Signed electron density.
Electron density \(\rho\left(\mathbf{r}\right)\) evaluated on a grid, signed by the second eigenvalue of the Hessian at that point, i.e. \(\text{sgn}\left(\lambda_2\right) \times \rho\left(\mathbf{r}\right)\).

eigvalues
¶ Eigenvalues of Hessian.

generate_plot
(fname, color='b', denslim=(0.2, 0.2), rdglim=(0.0, 2.0))[source]¶ Plot reduced density gradient.
Reduced density gradient vs. \(\text{sgn}\left(\lambda_2\right) \times \rho\left(\mathbf{r}\right)\).
Parameters:  fname (str) – A string representing the path to a fname for storing the plot. If the given fname does not have a proper extension, the ‘png’ format is used by default, i.e. plot is saved as fname.png.
 color (str, optional) – Color of plot. To customize color, see http://matplotlib.org/users/colors.html
 denslim (tuple, optional) – The minimum and maximum of the (signed) density in the plot.
 rdglim (tuple, optional) – The minimum and maximum of the reduced density gradient in the plot.

generate_scripts
(fname, isosurf=0.5, denscut=0.05)[source]¶ Generate cube files and VMD script to visualize noncovalent interactions (NCI).
Generate density and reduced density gradient cube files, as well as a VMD (Visual Molecular Dynamics) script to visualize noncovalent interactions (NCI).
Parameters:  fname (str) – Name of generated cube files and vmd script.
 isosurf (float, optional) – Value of reduced density gradient (RDG) isosurface used in VMD script.
 denscut (float, optional) – Density cutoff used in creating reduced density gradient cube file. Similar to NCIPlot program, reduced density gradient of points with density > denscut will be set to 100.0 to display reduced density gradient isosurface subject to the constraint of low density. To visualize all reduced density gradient isosurfaces, disregarding of the corresponding density value, set this argument equal to infinity using float(‘inf’).
Note
The generated cube files and script imitate the NCIPlot software version 1.0.

classmethod
from_file
(fname, spin='ab', index=None, grid=None)¶ Initialize class using wavefunction file.
Parameters:  fname (str) – A string representing the path to a molecule’s fname.
 spin (str, optional) – The type of occupied spin orbitals; options are ‘a’, ‘b’ & ‘ab’.
 index (int or Sequence of int, optional) – Sequence of integers representing the index of spin orbitals. If None, all occupied spin orbitals are included.
 grid (instance of Grid, optional) – Grid used for calculating and visualizing the property values. If None, a cubic grid is constructed from molecule with spacing=0.1 & extension=2.0.