"""
This type stub file was generated by pyright.
"""

"""Wrappers for PSEA, a program for secondary structure assignment.

See this citation for P-SEA, PMID: 9183534

Labesse G, Colloc'h N, Pothier J, Mornon J-P:  P-SEA: a new efficient
assignment of secondary structure from C_alpha.
Comput Appl Biosci 1997 , 13:291-295

ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/
"""
def run_psea(fname):
    """Run PSEA and return output filename.

    Note that this assumes the P-SEA binary is called "psea" and that it is
    on the path.

    Note that P-SEA will write an output file in the current directory using
    the input filename with extension ".sea".

    Note that P-SEA will write output to the terminal while run.
    """
    ...

def psea(pname): # -> str:
    """Parse PSEA output file."""
    ...

def psea2HEC(pseq): # -> list[Unknown]:
    """Translate PSEA secondary structure string into HEC."""
    ...

def annotate(m, ss_seq): # -> None:
    """Apply secondary structure information to residues in model."""
    ...

class PSEA:
    """Define PSEA class.

    PSEA object is a wrapper to PSEA program for secondary structure assignment.
    """
    def __init__(self, model, filename) -> None:
        """Initialize the class."""
        ...
    
    def get_seq(self): # -> list[Unknown]:
        """Return secondary structure string."""
        ...
    


if __name__ == "__main__":
    p = ...
    s = ...
