pychemcurv.analysis¶
This module implements the CurvatureAnalyze class to perform curvature analyses on molecular or periodic structures.
CurvatureAnalyzer class¶
- class pychemcurv.analysis.CurvatureAnalyzer(structure, bond_tol=0.2, rcut=2.5, bond_order=None)[source]¶
This class provides helpful methods to analyze the local curvature on all atoms of a given structure. The structure is either a molecule or a periodic structure. Once the structure is read, the class determines the connectivity of the structure in order to define all vertices. The connectivity is defined on a distance criterion.
The class needs a pymatgen.Structure or pymatgen.Molecule object as first argument. The other arguments are used to defined if two atoms are bonded or not.
- Parameters
structure (Structure, Molecule) – A Structure or Molecule pymatgen objects
bond_tol (float) – Tolerance used to determine if two atoms are bonded. Look at pymatgen.core.CovalentBond.is_bonded.
rcut (float) – Cutoff distance in case the bond is not not known
bond_order (dict) – Not yet implemented
- property vertices¶
List of vertices associated to each atom of the molecule
- property bonds¶
Set of tuples of bonded atom index
- property vertices_idx¶
List of tuples of the indexes of atoms in each vetex. The first index is atom A, the following are atoms of \(\star(A)\).
- property data¶
Return a Data Frame that contains all the geometric and hybridization data.
- property distance_matrix¶
Returns the distance matrix between all atoms. For periodic structures, this returns the nearest image distances.
- static from_file(path, periodic=None)[source]¶
Returns a CurvatureAnalyze object from the structure at the given path. This method relies on the file format supported with pymatgen Molecule and Structure classes.
Supported formats for periodic structure include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT, vasprun.xml, CSSR, Netcdf and pymatgen’s JSON serialized structures.
Supported formats for molecule include include xyz, gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and pymatgen’s JSON serialized molecules.
- Parameters
path (str) – Path to the structure file
periodic (bool) – if True, assume that the file correspond to a periodic structure. Default is None. The method tries to read the file, first from the Molecule class and second from the Structure class of pymatgen.