# Path: mordred/surface_area/_mesh.py
# class SphereMesh(object):
#     def __init__(self, level=4):
#         t = (1.0 + np.sqrt(5.0)) / 2.0
#         self.vertices = np.array(
#             [
#                 (-1, t, 0),
#                 (1, t, 0),
#                 (-1, -t, 0),
#                 (1, -t, 0),
#                 (0, -1, t),
#                 (0, 1, t),
#                 (0, -1, -t),
#                 (0, 1, -t),
#                 (t, 0, -1),
#                 (t, 0, 1),
#                 (-t, 0, -1),
#                 (-t, 0, 1),
#             ],
#             dtype="float",
#         )
# 
#         self.faces = np.array(
#             [
#                 (0, 11, 5),
#                 (0, 5, 1),
#                 (0, 1, 7),
#                 (0, 7, 10),
#                 (0, 10, 11),
#                 (1, 5, 9),
#                 (5, 11, 4),
#                 (11, 10, 2),
#                 (10, 7, 6),
#                 (7, 1, 8),
#                 (3, 9, 4),
#                 (3, 4, 2),
#                 (3, 2, 6),
#                 (3, 6, 8),
#                 (3, 8, 9),
#                 (4, 9, 5),
#                 (2, 4, 11),
#                 (6, 2, 10),
#                 (8, 6, 7),
#                 (9, 8, 1),
#             ],
#             dtype="int",
#         )
# 
#         self.normalize(0)
# 
#         self.level = 1
#         self.subdivide(level)
# 
#     def normalize(self, begin):
#         self.vertices[begin:] /= np.sqrt((self.vertices[begin:] ** 2).sum(axis=1))[
#             :, np.newaxis
#         ]
# 
#     def _subdivide(self):
#         self.level += 1
# 
#         Nv = len(self.vertices)
#         Nf = len(self.faces)
# 
#         A = self.faces[:, 0]
#         B = self.faces[:, 1]
#         C = self.faces[:, 2]
# 
#         Av = self.vertices[A]
#         Bv = self.vertices[B]
#         Cv = self.vertices[C]
# 
#         self.vertices = np.r_[self.vertices, Av + Bv, Bv + Cv, Av + Cv]
#         self.normalize(Nv)
# 
#         AB = np.arange(len(self.faces)) + Nv
#         BC = AB + Nf
#         AC = AB + 2 * Nf
# 
#         self.faces = (
#             np.concatenate([A, B, C, AB, AB, AB, AC, AC, AC, BC, BC, BC])
#             .reshape(3, -1)
#             .T
#         )
# 
#     def subdivide(self, level):
#         for _ in range(level - self.level):
#             self._subdivide()
# 
#     def __len__(self):
#         return len(self.vertices)
# 
# Path: mordred/_util.py
# def atoms_to_numpy(f, mol, dtype="float"):
#     return np.fromiter((f(a) for a in mol.GetAtoms()), dtype, mol.GetNumAtoms())
# 
# Path: mordred/_atomic_property.py
# def getter(short, **attrs):
#     def proc(f):
# def get_gasteiger_charge(atom):
#     def __init__(self, data=None):
#     def load(cls, name, conv=float):
#         def read(v):
#     def __getitem__(self, i):
#     def map(self, f):
# def GetElementSymbol(i):
#     def GetAtomicNumber(symbol):
#     def GetAtomicNumber(symbol):
# def get_valence_electrons(atom):
# def get_sigma_electrons(atom):
# def get_intrinsic_state(atom):
# def get_core_count(atom):
# def get_eta_epsilon(atom):
# def get_eta_beta_sigma(atom):
# def get_eta_nonsigma_contribute(bond):
# def get_eta_beta_delta(atom):
# def get_other_atom(bond, atom):
# def get_eta_beta_non_sigma(atom):
# def get_eta_gamma(atom):
# def get_atomic_number(a):
# def get_mass(a):
# def get_vdw_volume(a):
# def get_sanderson_en(a):
# def get_pauling_en(a):
# def get_allred_rocow_en(a):
# def get_polarizability(a):
# def get_ionization_potential(a):
# def get_mc_gowan_volume(a):
# def get_properties(charge=False, valence=False):
#     def __str__(self):
#     def get_long(self):
#     def as_argument(self):
#     def parameters(self):
#     def __new__(cls, explicit_hydrogens, prop):
#     def __init__(self, explicit_hydrogens, prop):
#     def calculate(self):
#     def carbon(self):
# class PeriodicTable(object):
# class AtomicProperty(Descriptor):
#     N = atom.GetAtomicNum()
#     Z = atom.GetAtomicNum() - atom.GetFormalCharge()
#     Z = atom.GetAtomicNum()
#     PN = period[Z]


from collections import defaultdict
from ._mesh import SphereMesh
from .._util import atoms_to_numpy
from .._atomic_property import GetAtomicNumber, vdw_radii
            from Bio.PDB import PDBParser
import numpy as np

        :type conformer: int
        :param conformer: conformer id

        :type solvent_radius: float
        :param solvent_radius: solvent radius

        :type level: int
        :param level: mesh level

        :rtype: SurfaceArea
        """
        rs = atoms_to_numpy(lambda a: vdw_radii[a.GetAtomicNum()] + solvent_radius, mol)

        conf = mol.GetConformer(conformer)

        ps = np.array([list(conf.GetAtomPosition(i)) for i in range(mol.GetNumAtoms())])

        return cls(rs, ps, level)

    @classmethod
    def from_pdb(cls, pdb, solvent_radius=1.4, level=3):
        try:
        except ImportError:
            raise ImportError("There isn't biopython package.")

        rs = []
        coords = []

        for atom in PDBParser().get_structure("", pdb).get_atoms():

# Path: mordred/surface_area/_mesh.py
# class SphereMesh(object):
#     def __init__(self, level=4):
#         t = (1.0 + np.sqrt(5.0)) / 2.0
#         self.vertices = np.array(
#             [
#                 (-1, t, 0),
#                 (1, t, 0),
#                 (-1, -t, 0),
#                 (1, -t, 0),
#                 (0, -1, t),
#                 (0, 1, t),
#                 (0, -1, -t),
#                 (0, 1, -t),
#                 (t, 0, -1),
#                 (t, 0, 1),
#                 (-t, 0, -1),
#                 (-t, 0, 1),
#             ],
#             dtype="float",
#         )
# 
#         self.faces = np.array(
#             [
#                 (0, 11, 5),
#                 (0, 5, 1),
#                 (0, 1, 7),
#                 (0, 7, 10),
#                 (0, 10, 11),
#                 (1, 5, 9),
#                 (5, 11, 4),
#                 (11, 10, 2),
#                 (10, 7, 6),
#                 (7, 1, 8),
#                 (3, 9, 4),
#                 (3, 4, 2),
#                 (3, 2, 6),
#                 (3, 6, 8),
#                 (3, 8, 9),
#                 (4, 9, 5),
#                 (2, 4, 11),
#                 (6, 2, 10),
#                 (8, 6, 7),
#                 (9, 8, 1),
#             ],
#             dtype="int",
#         )
# 
#         self.normalize(0)
# 
#         self.level = 1
#         self.subdivide(level)
# 
#     def normalize(self, begin):
#         self.vertices[begin:] /= np.sqrt((self.vertices[begin:] ** 2).sum(axis=1))[
#             :, np.newaxis
#         ]
# 
#     def _subdivide(self):
#         self.level += 1
# 
#         Nv = len(self.vertices)
#         Nf = len(self.faces)
# 
#         A = self.faces[:, 0]
#         B = self.faces[:, 1]
#         C = self.faces[:, 2]
# 
#         Av = self.vertices[A]
#         Bv = self.vertices[B]
#         Cv = self.vertices[C]
# 
#         self.vertices = np.r_[self.vertices, Av + Bv, Bv + Cv, Av + Cv]
#         self.normalize(Nv)
# 
#         AB = np.arange(len(self.faces)) + Nv
#         BC = AB + Nf
#         AC = AB + 2 * Nf
# 
#         self.faces = (
#             np.concatenate([A, B, C, AB, AB, AB, AC, AC, AC, BC, BC, BC])
#             .reshape(3, -1)
#             .T
#         )
# 
#     def subdivide(self, level):
#         for _ in range(level - self.level):
#             self._subdivide()
# 
#     def __len__(self):
#         return len(self.vertices)
# 
# Path: mordred/_util.py
# def atoms_to_numpy(f, mol, dtype="float"):
#     return np.fromiter((f(a) for a in mol.GetAtoms()), dtype, mol.GetNumAtoms())
# 
# Path: mordred/_atomic_property.py
# def getter(short, **attrs):
#     def proc(f):
# def get_gasteiger_charge(atom):
#     def __init__(self, data=None):
#     def load(cls, name, conv=float):
#         def read(v):
#     def __getitem__(self, i):
#     def map(self, f):
# def GetElementSymbol(i):
#     def GetAtomicNumber(symbol):
#     def GetAtomicNumber(symbol):
# def get_valence_electrons(atom):
# def get_sigma_electrons(atom):
# def get_intrinsic_state(atom):
# def get_core_count(atom):
# def get_eta_epsilon(atom):
# def get_eta_beta_sigma(atom):
# def get_eta_nonsigma_contribute(bond):
# def get_eta_beta_delta(atom):
# def get_other_atom(bond, atom):
# def get_eta_beta_non_sigma(atom):
# def get_eta_gamma(atom):
# def get_atomic_number(a):
# def get_mass(a):
# def get_vdw_volume(a):
# def get_sanderson_en(a):
# def get_pauling_en(a):
# def get_allred_rocow_en(a):
# def get_polarizability(a):
# def get_ionization_potential(a):
# def get_mc_gowan_volume(a):
# def get_properties(charge=False, valence=False):
#     def __str__(self):
#     def get_long(self):
#     def as_argument(self):
#     def parameters(self):
#     def __new__(cls, explicit_hydrogens, prop):
#     def __init__(self, explicit_hydrogens, prop):
#     def calculate(self):
#     def carbon(self):
# class PeriodicTable(object):
# class AtomicProperty(Descriptor):
#     N = atom.GetAtomicNum()
#     Z = atom.GetAtomicNum() - atom.GetFormalCharge()
#     Z = atom.GetAtomicNum()
#     PN = period[Z]


# Path: mordred/surface_area/_sasa.py
from collections import defaultdict
from ._mesh import SphereMesh
from .._util import atoms_to_numpy
from .._atomic_property import GetAtomicNumber, vdw_radii
            from Bio.PDB import PDBParser
import numpy as np


        :type conformer: int
        :param conformer: conformer id

        :type solvent_radius: float
        :param solvent_radius: solvent radius

        :type level: int
        :param level: mesh level

        :rtype: SurfaceArea
        """
        rs = atoms_to_numpy(lambda a: vdw_radii[a.GetAtomicNum()] + solvent_radius, mol)

        conf = mol.GetConformer(conformer)

        ps = np.array([list(conf.GetAtomPosition(i)) for i in range(mol.GetNumAtoms())])

        return cls(rs, ps, level)

    @classmethod
    def from_pdb(cls, pdb, solvent_radius=1.4, level=3):
        try:
        except ImportError:
            raise ImportError("There isn't biopython package.")

        rs = []
        coords = []

        for atom in PDBParser().get_structure("", pdb).get_atoms():

            rs.append(vdw_radii[GetAtomicNumber(atom.element)] + solvent_radius)