Simple function for reading external molecule files

1

There was an excellent post on : How to read multiple external geometry files? Improve documentation

Currently, I use a function like the one below, to read geometry external files. I was searching for a more simple method in the psi4.core classes that might implement something similar and more generalized to read many other common formats.

def read_mol_file(fname, format_str):
    """
    Reads an external xyz file from working directory
    into a string and returns a molecule_string that 
    can used with psi4.gemometry()
    --------
    fname : Must be of the form 'filename.format' or 'fname.txt'
    format_str: supports formats: ['xyz+', , ] 
    """
    file_str = open(fname, 'r').read() 
    mol_str = qcdb.Molecule.from_string(file_str, 
                                dtype=format_str)
    mol_psi4_str = mol_str.create_psi4_string_from_molecule()
    return mol_psi4_str
2

Have you tried passing the string into geometry directly?

Also, you forgot to close the file object.

3

Oh! yes, just the string works for sure, but are the other external file formats supported by psi4.geometry(mol_str) too? From what I saw in psi4numpy tutorials and psi4 docs, I think xyz and zmatrix are supported. Will it work for .pdb , .sdf etc too?

4

I don’t expect it to, but try it yourself and find out.