ectoolkits.structures.tools module#

ectoolkits.structures.tools.count_heavy_atoms(smiles: str) → int[source]#

Count the number of heavy atoms (non-hydrogen) in a SMILES string.

Parameters:

smiles (str) – SMILES string.

Returns:

Number of heavy atoms.

Return type:

int

Raises:

ValueError – If the SMILES string is invalid.

Example

count_heavy_atoms(“CCO”) # returns 3

ectoolkits.structures.tools.get_exclude_water_count(ads_smiles: list, ads_counts: list, bulk_smiles: list, bulk_counts: list, water_heavy_atom_equiv: int = 1) → int[source]#

Estimate the number of equivalent water molecules to be excluded based on heavy atom count.

Parameters:

  • ads_smiles (list) – List of adsorbate SMILES strings.

  • ads_counts (list) – List of adsorbate molecule counts.

  • bulk_smiles (list) – List of bulk molecule SMILES strings.

  • bulk_counts (list) – List of bulk molecule counts.

  • water_heavy_atom_equiv (int) – Number of heavy atoms equivalent to one water molecule.

Returns:

Estimated number of water molecules to exclude.

Return type:

int

Example

get_exclude_water_count([“CCO”], [2], [“O=C=O”], [1], 3)

ectoolkits.structures.tools.get_packmol_inp(filename: str, count: int, n_vec_a: list, n_vec_b: list, d1_a: float, d2_a: float, d1_b: float, d2_b: float, low_z: float, up_z: float, radius: float) → str[source]#

Generate PACKMOL input structure block for a molecule.

Parameters:

  • filename (str) – Path to the XYZ file.

  • count (int) – Number of molecules to place.

  • n_vec_a (list) – Normal vector A [x, y, z].

  • n_vec_b (list) – Normal vector B [x, y, z].

  • d1_a (float) – Distance range for vector A.

  • d2_a (float) – Distance range for vector A.

  • d1_b (float) – Distance range for vector B.

  • d2_b (float) – Distance range for vector B.

  • low_z (float) – Z direction limits.

  • up_z (float) – Z direction limits.

  • radius (float) – Minimum distance between molecules.

Returns:

A string block to be written in a PACKMOL input file.

Return type:

str

ectoolkits.structures.tools.smiles2xyz(smiles: str, filename: str)[source]#

Convert a SMILES string to a 3D XYZ structure using RDKit and ASE.

Parameters:

  • smiles (str) – SMILES representation of the molecule.

  • filename (str) – Output filename in XYZ format.

Returns:

None

Example

smiles2xyz(“CCO”, “ethanol.xyz”)