# fmt: off
import re
from collections import OrderedDict

import numpy as np

from ase import Atoms
from ase.io import write


def test_xsd_bond():
    # This writes xsd example with bond connectivity information, and checks
    # bond formats.

    # Example molecule
    atoms = Atoms('CH4', [[1.08288111e-09, 1.74602682e-09, -1.54703448e-09],
                          [-6.78446715e-01, 8.73516584e-01, -8.63073811e-02],
                          [-4.09602527e-01, -8.46016530e-01, -5.89280858e-01],
                          [8.52016070e-02, -2.98243876e-01, 1.06515792e+00],
                          [1.00284763e+00, 2.70743821e-01, -3.89569679e-01]])
    # Carbon(index 0), is connected to other hydrogen atoms (index 1-4)
    connectivitymatrix = np.array([[0, 1, 1, 1, 1],
                                   [1, 0, 0, 0, 0],
                                   [1, 0, 0, 0, 0],
                                   [1, 0, 0, 0, 0],
                                   [1, 0, 0, 0, 0]])
    write('xsd_test_CH4.xsd', atoms, connectivity=connectivitymatrix)

    # Read and see if the atom information and bond information matches.
    AtomIdsToBondIds = OrderedDict()
    BondIdsToConnectedAtomIds = OrderedDict()
    with open('xsd_test_CH4.xsd') as fd:
        for i, line in enumerate(fd):
            if '<Atom3d ' in line:
                AtomId = int(re.search(r'ID="(.*?)"', line).group(1))
                ConnectedBondIds = [
                    int(a) for a in re.search(
                        r'Connections="(.*?)"',
                        line).group(1).split(',')]
                AtomIdsToBondIds[AtomId] = ConnectedBondIds
            elif '<Bond ' in line:
                BondId = int(re.search(r'ID="(.*?)"', line).group(1))
                ConnectedAtomIds = [
                    int(a) for a in re.search(
                        r'Connects="(.*?)"',
                        line).group(1).split(',')]
                BondIdsToConnectedAtomIds[BondId] = ConnectedAtomIds
    # check if atom ids have been correctly assigned for each bond
    for AtomId in AtomIdsToBondIds:
        for BondId in AtomIdsToBondIds[AtomId]:
            assert AtomId in BondIdsToConnectedAtomIds[BondId]

    # make connectivity graph and see if it matches with input.
    AtomIds = list(AtomIdsToBondIds.keys())
    Newconnectivitymatrix = np.zeros((5, 5))
    for AtomId in AtomIdsToBondIds:
        for BondId in AtomIdsToBondIds[AtomId]:
            OtherAtomId = [
                a for a in BondIdsToConnectedAtomIds[BondId] if a != AtomId]
            i = AtomIds.index(AtomId)
            j = AtomIds.index(OtherAtomId[0])
            Newconnectivitymatrix[i, j] = 1
    for i in range(4):
        for j in range(4):
            assert connectivitymatrix[i, j] == Newconnectivitymatrix[i, j]
