import os
import re
import sys
from miscMethods import au2A

def xyzWrite(atoms, positions):
    output=[str(len(atoms))]
    output.append("Cu16 H2")
    fmtstr = "{{}} {{:.{0}f}} {{:.{0}f}} {{:.{0}f}}".format(6)
    for i in range(len(atoms)):
        output.append(fmtstr.format(atoms[i], positions[i][0], positions[i][1], positions[i][2]))
    return "\n".join(output)

def dimer2dict(atom1, atom2, r, units):
    """
    Creates a list of dicts in angstrom ready to create an xyz file 
    via dict2xyz for a dimer.
    
    Arguments: 
    atom1(str): abbreviation of first atom (e.g. H or Cu)
    atom2(str): abbreviation of secon atom
    r(real): distance between the first and second atom in units defined in units
    units(str): "angstrom" or "bohr" (Hartree atomic units)
    
    Returns:
    dict of molecule
    """
    
    #Convert to Angstrom
    if units=="angstrom":
        r = r
    elif units=="bohr":
        r = au2A(r)
    else:
        sys.exit("illegal unit")
        
    molDict=[]
    molDict.append({"atom":atom1, "position":[0.0, 0.0, 0.0]})
    molDict.append({"atom":atom2, "position":[0.0, 0.0, r]})
    
    return molDict
    



def atom2dict(atom1):
    """
    Creates a dict in angstrom ready to create an xyz file  via dict2xyz for an atom.
    
    Arguments: 
    atom1(str): abbreviation of first atom (e.g. H or Cu)
    """
    
    molDict=[]
    molDict.append({"atom":atom1, "position":[0.0, 0.0, 0.0]})
    
    return molDict


# In[33]:

def dict2xyz(molDict):
    """
    returns xyz string
    
    Arguments:
    molDict: list of dictionaries with entries atom(str) and position(list of reals, dimension 3)
    positions have to be in angstrom!
    filename: name of xyz file (hast to end on .xyz)
    """
       
    #prepare xyz file
    atoms=[]
    positions=[]
    for entry in molDict:
        atoms.append(entry["atom"])
        positions.append(entry["position"])
    
    return xyzWrite(atoms, positions)