4075885785

Build Type

push

github

Committed by Shyue Ping Ong

Commit Message

Merge branch 'master' of github.com:materialsproject/pymatgen

Run Details

96 of 96 new or added lines in 27 files covered. (100.0%)

81013 of 102710 relevant lines covered (78.88%)

0.79 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

91.27

/pymatgen/analysis/tests/test_graphs.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.


from __future__ import annotations

import copy
import os
import unittest
import warnings
from shutil import which

import networkx as nx
import networkx.algorithms.isomorphism as iso
import pytest
from monty.serialization import loadfn
from pytest import approx

from pymatgen.analysis.graphs import (
    MoleculeGraph,
    MolGraphSplitError,
    PeriodicSite,
    StructureGraph,
)
from pymatgen.analysis.local_env import (
    CovalentBondNN,
    CutOffDictNN,
    MinimumDistanceNN,
    MinimumOKeeffeNN,
    OpenBabelNN,
    VoronoiNN,
)
from pymatgen.command_line.critic2_caller import Critic2Analysis
from pymatgen.core import Lattice, Molecule, Site, Structure
from pymatgen.core.structure import FunctionalGroups
from pymatgen.util.testing import PymatgenTest

try:
    from openbabel import openbabel
except ImportError:
    openbabel = None
try:
    import pygraphviz
except ImportError:
    pygraphviz = None

__author__ = "Matthew Horton, Evan Spotte-Smith"
__version__ = "0.1"
__maintainer__ = "Matthew Horton"
__email__ = "mkhorton@lbl.gov"
__status__ = "Beta"
__date__ = "August 2017"

module_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
molecule_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules")


class StructureGraphTest(PymatgenTest):
    def setUp(self):
        self.maxDiff = None

        # trivial example, simple square lattice for testing
        structure = Structure(Lattice.tetragonal(5.0, 50.0), ["H"], [[0, 0, 0]])
        self.square_sg = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
        self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
        self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
        self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
        self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
        # TODO: decorating still fails because the structure graph gives a CN of 8 for this square lattice
        # self.square_sg.decorate_structure_with_ce_info()

        # body-centered square lattice for testing
        structure = Structure(Lattice.tetragonal(5.0, 50.0), ["H", "He"], [[0, 0, 0], [0.5, 0.5, 0.5]])
        self.bc_square_sg = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
        self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
        self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
        self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
        self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
        self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, 0, 0))
        self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
        self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(-1, -1, 0))
        self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))

        # body-centered square lattice for testing
        # directions reversed, should be equivalent to bc_square
        structure = Structure(Lattice.tetragonal(5.0, 50.0), ["H", "He"], [[0, 0, 0], [0.5, 0.5, 0.5]])
        self.bc_square_sg_r = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
        self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
        self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
        self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
        self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
        self.bc_square_sg_r.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, 0, 0))
        self.bc_square_sg_r.add_edge(1, 0, from_jimage=(-1, 0, 0), to_jimage=(0, 0, 0))
        self.bc_square_sg_r.add_edge(1, 0, from_jimage=(-1, -1, 0), to_jimage=(0, 0, 0))
        self.bc_square_sg_r.add_edge(1, 0, from_jimage=(0, -1, 0), to_jimage=(0, 0, 0))

        # MoS2 example, structure graph obtained from critic2
        # (not ground state, from mp-1023924, single layer)
        stdout_file = os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2_critic2_stdout.txt")
        with open(stdout_file) as f:
            reference_stdout = f.read()
        self.structure = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2.cif"))
        c2o = Critic2Analysis(self.structure, reference_stdout)
        self.mos2_sg = c2o.structure_graph(include_critical_points=False)

        latt = Lattice.cubic(4.17)
        species = ["Ni", "O"]
        coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
        self.NiO = Structure.from_spacegroup(225, latt, species, coords).get_primitive_structure()

        # BCC example.
        self.bcc = Structure(Lattice.cubic(5.0), ["He", "He"], [[0, 0, 0], [0.5, 0.5, 0.5]])

        warnings.simplefilter("ignore")

    def tearDown(self):
        warnings.simplefilter("default")

    def test_inappropriate_construction(self):
        # Check inappropriate strategy
        with pytest.raises(ValueError):
            StructureGraph.with_local_env_strategy(self.NiO, CovalentBondNN())

    def test_properties(self):
        assert self.mos2_sg.name == "bonds"
        assert self.mos2_sg.edge_weight_name == "bond_length"
        assert self.mos2_sg.edge_weight_unit == "Å"
        assert self.mos2_sg.get_coordination_of_site(0) == 6
        assert len(self.mos2_sg.get_connected_sites(0)) == 6
        assert isinstance(self.mos2_sg.get_connected_sites(0)[0].site, PeriodicSite)
        assert str(self.mos2_sg.get_connected_sites(0)[0].site.specie) == "S"
        assert self.mos2_sg.get_connected_sites(0, jimage=(0, 0, 100))[0].site.frac_coords[2] == approx(100.303027)

        # these two graphs should be equivalent
        for n in range(len(self.bc_square_sg)):
            assert self.bc_square_sg.get_coordination_of_site(n) == self.bc_square_sg_r.get_coordination_of_site(n)

        # test we're not getting duplicate connected sites
        # thanks to Jack D. Sundberg for reporting this bug

        # known example where this bug occurred due to edge weights not being
        # bit-for-bit identical in otherwise identical edges
        nacl_lattice = Lattice(
            [
                [3.48543625, 0.0, 2.01231756],
                [1.16181208, 3.28610081, 2.01231756],
                [0.0, 0.0, 4.02463512],
            ]
        )
        nacl = Structure(nacl_lattice, ["Na", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])

        nacl_graph = StructureGraph.with_local_env_strategy(nacl, CutOffDictNN({("Cl", "Cl"): 5.0}))

        assert len(nacl_graph.get_connected_sites(1)) == 12
        assert len(nacl_graph.graph.get_edge_data(1, 1)) == 6

    def test_set_node_attributes(self):
        self.square_sg.set_node_attributes()

        specie = nx.get_node_attributes(self.square_sg.graph, "specie")
        coords = nx.get_node_attributes(self.square_sg.graph, "coords")
        properties = nx.get_node_attributes(self.square_sg.graph, "properties")

        for idx, site in enumerate(self.square_sg.structure):
            assert str(specie[idx]) == str(site.specie)
            assert coords[idx][0] == site.coords[0]
            assert coords[idx][1] == site.coords[1]
            assert coords[idx][2] == site.coords[2]
            assert properties[idx] == site.properties

    def test_edge_editing(self):
        square = copy.deepcopy(self.square_sg)

        square.alter_edge(
            0,
            0,
            to_jimage=(1, 0, 0),
            new_weight=0.0,
            new_edge_properties={"foo": "bar"},
        )
        new_edge = square.graph.get_edge_data(0, 0)[0]
        assert new_edge["weight"] == 0.0
        assert new_edge["foo"] == "bar"

        square.break_edge(0, 0, to_jimage=(1, 0, 0))

        assert len(square.graph.get_edge_data(0, 0)) == 1

    def test_insert_remove(self):
        struct_copy = copy.deepcopy(self.square_sg.structure)
        square_copy = copy.deepcopy(self.square_sg)

        # Ensure that insert_node appropriately wraps Structure.insert()
        struct_copy.insert(1, "O", [0.5, 0.5, 0.5])
        square_copy.insert_node(1, "O", [0.5, 0.5, 0.5])
        assert struct_copy == square_copy.structure

        # Test that removal is also equivalent between Structure and StructureGraph.structure
        struct_copy.remove_sites([1])
        square_copy.remove_nodes([1])
        assert struct_copy == square_copy.structure

        square_copy.insert_node(
            1, "O", [0.5, 0.5, 0.5], edges=[{"from_index": 1, "to_index": 0, "to_jimage": (0, 0, 0)}]
        )
        assert square_copy.get_coordination_of_site(1) == 1

        # Test that StructureGraph.graph is correctly updated
        square_copy.insert_node(
            1, "H", [0.5, 0.5, 0.75], edges=[{"from_index": 1, "to_index": 2, "to_jimage": (0, 0, 0)}]
        )
        square_copy.remove_nodes([1])

        assert square_copy.graph.number_of_nodes() == 2
        assert square_copy.graph.number_of_edges() == 3

    def test_substitute(self):
        structure = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "Li2O.cif"))
        molecule = FunctionalGroups["methyl"]

        structure_copy = copy.deepcopy(structure)
        structure_copy_graph = copy.deepcopy(structure)

        sg = StructureGraph.with_local_env_strategy(structure, MinimumDistanceNN())
        sg_copy = copy.deepcopy(sg)

        # Ensure that strings and molecules lead to equivalent substitutions
        sg.substitute_group(1, molecule, MinimumDistanceNN)
        sg_copy.substitute_group(1, "methyl", MinimumDistanceNN)
        assert sg == sg_copy

        # Ensure that the underlying structure has been modified as expected
        structure_copy.substitute(1, "methyl")
        assert structure_copy == sg.structure

        # Test inclusion of graph dictionary
        graph_dict = {
            (0, 1): {"weight": 0.5},
            (0, 2): {"weight": 0.5},
            (0, 3): {"weight": 0.5},
        }

        sg_with_graph = StructureGraph.with_local_env_strategy(structure_copy_graph, MinimumDistanceNN())
        sg_with_graph.substitute_group(1, "methyl", MinimumDistanceNN, graph_dict=graph_dict)
        edge = sg_with_graph.graph.get_edge_data(11, 13)[0]
        assert edge["weight"] == 0.5

    def test_auto_image_detection(self):
        sg = StructureGraph.with_empty_graph(self.structure)
        sg.add_edge(0, 0)

        assert len(list(sg.graph.edges(data=True))) == 3

    def test_str(self):
        square_sg_str_ref = """Structure Graph
Structure:
Full Formula (H1)
Reduced Formula: H2
abc   :   5.000000   5.000000  50.000000
angles:  90.000000  90.000000  90.000000
Sites (1)
  #  SP      a    b    c
---  ----  ---  ---  ---
  0  H       0    0    0
Graph: bonds
from    to  to_image
----  ----  ------------
   0     0  (1, 0, 0)
   0     0  (-1, 0, 0)
   0     0  (0, 1, 0)
   0     0  (0, -1, 0)
"""

        mos2_sg_str_ref = """Structure Graph
Structure:
Full Formula (Mo1 S2)
Reduced Formula: MoS2
abc   :   3.190316   3.190315  17.439502
angles:  90.000000  90.000000 120.000006
Sites (3)
  #  SP           a         b         c
---  ----  --------  --------  --------
  0  Mo    0.333333  0.666667  0.213295
  1  S     0.666667  0.333333  0.303027
  2  S     0.666667  0.333333  0.123562
Graph: bonds
from    to  to_image      bond_length (A)
----  ----  ------------  ------------------
   0     1  (-1, 0, 0)    2.417e+00
   0     1  (0, 0, 0)     2.417e+00
   0     1  (0, 1, 0)     2.417e+00
   0     2  (0, 1, 0)     2.417e+00
   0     2  (-1, 0, 0)    2.417e+00
   0     2  (0, 0, 0)     2.417e+00
"""

        # don't care about testing Py 2.7 unicode support,
        # change Å to A
        self.mos2_sg.graph.graph["edge_weight_units"] = "A"
        self.assertStrContentEqual(str(self.square_sg), square_sg_str_ref)
        self.assertStrContentEqual(str(self.mos2_sg), mos2_sg_str_ref)

    def test_mul(self):
        square_sg_mul = self.square_sg * (2, 1, 1)

        square_sg_mul_ref_str = """Structure Graph
Structure:
Full Formula (H2)
Reduced Formula: H2
abc   :  10.000000   5.000000  50.000000
angles:  90.000000  90.000000  90.000000
Sites (2)
  #  SP      a    b    c
---  ----  ---  ---  ---
  0  H     0      0    0
  1  H     0.5    0   -0
Graph: bonds
from    to  to_image
----  ----  ------------
   0     0  (0, 1, 0)
   0     0  (0, -1, 0)
   0     1  (0, 0, 0)
   0     1  (-1, 0, 0)
   1     1  (0, 1, 0)
   1     1  (0, -1, 0)
"""
        square_sg_mul_actual_str = str(square_sg_mul)

        # only testing bonds portion,
        # the c frac_coord of the second H can vary from
        # 0 to -0 depending on machine precision
        square_sg_mul_ref_str = "\n".join(square_sg_mul_ref_str.splitlines()[11:])
        square_sg_mul_actual_str = "\n".join(square_sg_mul_actual_str.splitlines()[11:])

        self.assertStrContentEqual(square_sg_mul_actual_str, square_sg_mul_ref_str)

        # test sequential multiplication
        sq_sg_1 = self.square_sg * (2, 2, 1)
        sq_sg_1 = sq_sg_1 * (2, 2, 1)
        sq_sg_2 = self.square_sg * (4, 4, 1)
        assert sq_sg_1.graph.number_of_edges() == sq_sg_2.graph.number_of_edges()
        # TODO: the below test still gives 8 != 4
        # self.assertEqual(self.square_sg.get_coordination_of_site(0), 4)

        mos2_sg_mul = self.mos2_sg * (3, 3, 1)
        for idx in mos2_sg_mul.structure.indices_from_symbol("Mo"):
            assert mos2_sg_mul.get_coordination_of_site(idx) == 6

        mos2_sg_premul = StructureGraph.with_local_env_strategy(self.structure * (3, 3, 1), MinimumDistanceNN())
        assert mos2_sg_mul == mos2_sg_premul

        # test 3D Structure

        nio_sg = StructureGraph.with_local_env_strategy(self.NiO, MinimumDistanceNN())
        nio_sg = nio_sg * 3

        for n in range(len(nio_sg)):
            assert nio_sg.get_coordination_of_site(n) == 6

    @unittest.skipIf(pygraphviz is None or not (which("neato") and which("fdp")), "graphviz executables not present")
    def test_draw(self):
        # draw MoS2 graph
        self.mos2_sg.draw_graph_to_file("MoS2_single.pdf", image_labels=True, hide_image_edges=False)
        mos2_sg = self.mos2_sg * (9, 9, 1)
        mos2_sg.draw_graph_to_file("MoS2.pdf", algo="neato")

        # draw MoS2 graph that's been successively multiplied
        mos2_sg_2 = self.mos2_sg * (3, 3, 1)
        mos2_sg_2 = mos2_sg_2 * (3, 3, 1)
        mos2_sg_2.draw_graph_to_file("MoS2_twice_mul.pdf", algo="neato", hide_image_edges=True)

        # draw MoS2 graph that's generated from a pre-multiplied Structure
        mos2_sg_premul = StructureGraph.with_local_env_strategy(self.structure * (3, 3, 1), MinimumDistanceNN())
        mos2_sg_premul.draw_graph_to_file("MoS2_premul.pdf", algo="neato", hide_image_edges=True)

        # draw graph for a square lattice
        self.square_sg.draw_graph_to_file("square_single.pdf", hide_image_edges=False)
        square_sg = self.square_sg * (5, 5, 1)
        square_sg.draw_graph_to_file("square.pdf", algo="neato", image_labels=True, node_labels=False)

        # draw graph for a body-centered square lattice
        self.bc_square_sg.draw_graph_to_file("bc_square_single.pdf", hide_image_edges=False)
        bc_square_sg = self.bc_square_sg * (9, 9, 1)
        bc_square_sg.draw_graph_to_file("bc_square.pdf", algo="neato", image_labels=False)

        # draw graph for a body-centered square lattice defined in an alternative way
        self.bc_square_sg_r.draw_graph_to_file("bc_square_r_single.pdf", hide_image_edges=False)
        bc_square_sg_r = self.bc_square_sg_r * (9, 9, 1)
        bc_square_sg_r.draw_graph_to_file("bc_square_r.pdf", algo="neato", image_labels=False)

        # delete generated test files
        test_files = (
            "bc_square_r_single.pdf",
            "bc_square_r.pdf",
            "bc_square_single.pdf",
            "bc_square.pdf",
            "MoS2_premul.pdf",
            "MoS2_single.pdf",
            "MoS2_twice_mul.pdf",
            "MoS2.pdf",
            "square_single.pdf",
            "square.pdf",
        )
        for test_file in test_files:
            os.remove(test_file)

    def test_to_from_dict(self):
        d = self.mos2_sg.as_dict()
        sg = StructureGraph.from_dict(d)
        d2 = sg.as_dict()
        assert d == d2

    def test_from_local_env_and_equality_and_diff(self):
        nn = MinimumDistanceNN()
        sg = StructureGraph.with_local_env_strategy(self.structure, nn)

        assert sg.graph.number_of_edges() == 6

        nn2 = MinimumOKeeffeNN()
        sg2 = StructureGraph.with_local_env_strategy(self.structure, nn2)

        assert sg == sg2
        assert sg == self.mos2_sg

        # TODO: find better test case where graphs are different
        diff = sg.diff(sg2)
        assert diff["dist"] == 0

        assert self.square_sg.get_coordination_of_site(0) == 2

    def test_from_edges(self):
        edges = {
            (0, 0, (0, 0, 0), (1, 0, 0)): None,
            (0, 0, (0, 0, 0), (-1, 0, 0)): None,
            (0, 0, (0, 0, 0), (0, 1, 0)): None,
            (0, 0, (0, 0, 0), (0, -1, 0)): None,
        }

        structure = Structure(Lattice.tetragonal(5.0, 50.0), ["H"], [[0, 0, 0]])

        sg = StructureGraph.with_edges(structure, edges)

        assert sg == self.square_sg

    def test_extract_molecules(self):
        structure_file = os.path.join(
            PymatgenTest.TEST_FILES_DIR,
            "H6PbCI3N_mp-977013_symmetrized.cif",
        )

        s = Structure.from_file(structure_file)

        nn = MinimumDistanceNN()
        sg = StructureGraph.with_local_env_strategy(s, nn)

        molecules = sg.get_subgraphs_as_molecules()
        assert molecules[0].composition.formula == "H3 C1"
        assert len(molecules) == 1

        molecules = self.mos2_sg.get_subgraphs_as_molecules()
        assert len(molecules) == 0

    def test_types_and_weights_of_connections(self):
        types = self.mos2_sg.types_and_weights_of_connections

        assert len(types["Mo-S"]) == 6
        assert types["Mo-S"][0] == approx(2.416931678417331)

    def test_weight_statistics(self):
        weight_statistics = self.mos2_sg.weight_statistics

        assert len(weight_statistics["all_weights"]) == 6
        assert weight_statistics["min"] == approx(2.4169314100201875)
        assert weight_statistics["variance"] == approx(0, abs=1e-10)

    def test_types_of_coordination_environments(self):
        types = self.mos2_sg.types_of_coordination_environments()
        assert types == ["Mo-S(6)", "S-Mo(3)"]

        types_anonymous = self.mos2_sg.types_of_coordination_environments(anonymous=True)
        assert types_anonymous == ["A-B(3)", "A-B(6)"]

    def test_no_duplicate_hops(self):
        test_structure = Structure(
            lattice=[[2.990355, -5.149042, 0.0], [2.990355, 5.149042, 0.0], [0.0, 0.0, 24.51998]],
            species=["Ba"],
            coords=[[0.005572, 0.994428, 0.151095]],
        )

        nn = MinimumDistanceNN(cutoff=6, get_all_sites=True)

        sg = StructureGraph.with_local_env_strategy(test_structure, nn)

        assert sg.graph.number_of_edges() == 3

    def test_sort(self):
        sg = copy.deepcopy(self.bc_square_sg_r)
        # insert an unsorted edge, don't use sg.add_edge as it auto-sorts
        sg.graph.add_edge(3, 1, to_jimage=(0, 0, 0))
        sg.graph.add_edge(2, 1, to_jimage=(0, 0, 0))

        assert list(sg.graph.edges)[-2:] == [(3, 1, 0), (2, 1, 0)]
        sg.sort()
        assert list(sg.graph.edges)[-2:] == [(1, 3, 0), (1, 2, 0)]


class MoleculeGraphTest(unittest.TestCase):
    def setUp(self):
        cyclohexene = Molecule.from_file(
            os.path.join(
                PymatgenTest.TEST_FILES_DIR,
                "graphs/cyclohexene.xyz",
            )
        )
        self.cyclohexene = MoleculeGraph.with_empty_graph(
            cyclohexene, edge_weight_name="strength", edge_weight_units=""
        )
        self.cyclohexene.add_edge(0, 1, weight=1.0)
        self.cyclohexene.add_edge(1, 2, weight=1.0)
        self.cyclohexene.add_edge(2, 3, weight=2.0)
        self.cyclohexene.add_edge(3, 4, weight=1.0)
        self.cyclohexene.add_edge(4, 5, weight=1.0)
        self.cyclohexene.add_edge(5, 0, weight=1.0)
        self.cyclohexene.add_edge(0, 6, weight=1.0)
        self.cyclohexene.add_edge(0, 7, weight=1.0)
        self.cyclohexene.add_edge(1, 8, weight=1.0)
        self.cyclohexene.add_edge(1, 9, weight=1.0)
        self.cyclohexene.add_edge(2, 10, weight=1.0)
        self.cyclohexene.add_edge(3, 11, weight=1.0)
        self.cyclohexene.add_edge(4, 12, weight=1.0)
        self.cyclohexene.add_edge(4, 13, weight=1.0)
        self.cyclohexene.add_edge(5, 14, weight=1.0)
        self.cyclohexene.add_edge(5, 15, weight=1.0)

        butadiene = Molecule.from_file(
            os.path.join(
                PymatgenTest.TEST_FILES_DIR,
                "graphs/butadiene.xyz",
            )
        )
        self.butadiene = MoleculeGraph.with_empty_graph(butadiene, edge_weight_name="strength", edge_weight_units="")
        self.butadiene.add_edge(0, 1, weight=2.0)
        self.butadiene.add_edge(1, 2, weight=1.0)
        self.butadiene.add_edge(2, 3, weight=2.0)
        self.butadiene.add_edge(0, 4, weight=1.0)
        self.butadiene.add_edge(0, 5, weight=1.0)
        self.butadiene.add_edge(1, 6, weight=1.0)
        self.butadiene.add_edge(2, 7, weight=1.0)
        self.butadiene.add_edge(3, 8, weight=1.0)
        self.butadiene.add_edge(3, 9, weight=1.0)

        ethylene = Molecule.from_file(
            os.path.join(
                PymatgenTest.TEST_FILES_DIR,
                "graphs/ethylene.xyz",
            )
        )
        self.ethylene = MoleculeGraph.with_empty_graph(ethylene, edge_weight_name="strength", edge_weight_units="")
        self.ethylene.add_edge(0, 1, weight=2.0)
        self.ethylene.add_edge(0, 2, weight=1.0)
        self.ethylene.add_edge(0, 3, weight=1.0)
        self.ethylene.add_edge(1, 4, weight=1.0)
        self.ethylene.add_edge(1, 5, weight=1.0)

        self.pc = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "graphs", "PC.xyz"))
        self.pc_edges = [
            [5, 10],
            [5, 12],
            [5, 11],
            [5, 3],
            [3, 7],
            [3, 4],
            [3, 0],
            [4, 8],
            [4, 9],
            [4, 1],
            [6, 1],
            [6, 0],
            [6, 2],
        ]
        self.pc_frag1 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "graphs", "PC_frag1.xyz"))
        self.pc_frag1_edges = [[0, 2], [4, 2], [2, 1], [1, 3]]
        self.tfsi = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "graphs", "TFSI.xyz"))
        self.tfsi_edges = (
            [14, 1],
            [1, 4],
            [1, 5],
            [1, 7],
            [7, 11],
            [7, 12],
            [7, 13],
            [14, 0],
            [0, 2],
            [0, 3],
            [0, 6],
            [6, 8],
            [6, 9],
            [6, 10],
        )

        warnings.simplefilter("ignore")

    def tearDown(self):
        warnings.simplefilter("default")
        del self.ethylene
        del self.butadiene
        del self.cyclohexene

    @unittest.skipIf(not openbabel, "OpenBabel not present. Skipping...")
    def test_construction(self):
        edges_frag = {(e[0], e[1]): {"weight": 1.0} for e in self.pc_frag1_edges}
        mol_graph = MoleculeGraph.with_edges(self.pc_frag1, edges_frag)
        # dumpfn(mol_graph.as_dict(), os.path.join(module_dir,"pc_frag1_mg.json"))
        ref_mol_graph = loadfn(os.path.join(module_dir, "pc_frag1_mg.json"))
        assert mol_graph == ref_mol_graph
        assert mol_graph.graph.adj == ref_mol_graph.graph.adj
        for node in mol_graph.graph.nodes:
            assert mol_graph.graph.nodes[node]["specie"] == ref_mol_graph.graph.nodes[node]["specie"]
            for ii in range(3):
                assert mol_graph.graph.nodes[node]["coords"][ii] == ref_mol_graph.graph.nodes[node]["coords"][ii]

        edges_pc = {(e[0], e[1]): {"weight": 1.0} for e in self.pc_edges}
        mol_graph = MoleculeGraph.with_edges(self.pc, edges_pc)
        # dumpfn(mol_graph.as_dict(), os.path.join(module_dir,"pc_mg.json"))
        ref_mol_graph = loadfn(os.path.join(module_dir, "pc_mg.json"))
        assert mol_graph == ref_mol_graph
        assert mol_graph.graph.adj == ref_mol_graph.graph.adj
        for node in mol_graph.graph:
            assert mol_graph.graph.nodes[node]["specie"] == ref_mol_graph.graph.nodes[node]["specie"]
            for ii in range(3):
                assert mol_graph.graph.nodes[node]["coords"][ii] == ref_mol_graph.graph.nodes[node]["coords"][ii]

        mol_graph_edges = MoleculeGraph.with_edges(self.pc, edges=edges_pc)
        mol_graph_strat = MoleculeGraph.with_local_env_strategy(self.pc, OpenBabelNN())

        assert mol_graph_edges.isomorphic_to(mol_graph_strat)

        # Check inappropriate strategy
        with pytest.raises(ValueError):
            MoleculeGraph.with_local_env_strategy(self.pc, VoronoiNN())

    def test_properties(self):
        assert self.cyclohexene.name == "bonds"
        assert self.cyclohexene.edge_weight_name == "strength"
        assert self.cyclohexene.edge_weight_unit == ""
        assert self.cyclohexene.get_coordination_of_site(0) == 4
        assert self.cyclohexene.get_coordination_of_site(2) == 3
        assert self.cyclohexene.get_coordination_of_site(15) == 1
        assert len(self.cyclohexene.get_connected_sites(0)) == 4
        assert isinstance(self.cyclohexene.get_connected_sites(0)[0].site, Site)
        assert str(self.cyclohexene.get_connected_sites(0)[0].site.specie) == "H"

    def test_set_node_attributes(self):
        self.ethylene.set_node_attributes()

        specie = nx.get_node_attributes(self.ethylene.graph, "specie")
        coords = nx.get_node_attributes(self.ethylene.graph, "coords")
        properties = nx.get_node_attributes(self.ethylene.graph, "properties")

        for idx, site in enumerate(self.ethylene.molecule):
            assert str(specie[idx]) == str(site.specie)
            assert coords[idx][0] == site.coords[0]
            assert coords[idx][1] == site.coords[1]
            assert coords[idx][2] == site.coords[2]
            assert properties[idx] == site.properties

    def test_coordination(self):
        molecule = Molecule(["C", "C"], [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]])

        mg = MoleculeGraph.with_empty_graph(molecule)
        assert mg.get_coordination_of_site(0) == 0

        assert self.cyclohexene.get_coordination_of_site(0) == 4

    def test_edge_editing(self):
        self.cyclohexene.alter_edge(0, 1, new_weight=0.0, new_edge_properties={"foo": "bar"})
        new_edge = self.cyclohexene.graph.get_edge_data(0, 1)[0]
        assert new_edge["weight"] == 0.0
        assert new_edge["foo"] == "bar"

        self.cyclohexene.break_edge(0, 1)
        assert self.cyclohexene.graph.get_edge_data(0, 1) is None

        # Replace the now-broken edge
        self.cyclohexene.add_edge(0, 1, weight=1.0)

    def test_insert_remove(self):
        mol_copy = copy.deepcopy(self.ethylene.molecule)
        eth_copy = copy.deepcopy(self.ethylene)

        # Ensure that insert_node appropriately wraps Molecule.insert()
        mol_copy.insert(1, "O", [0.5, 0.5, 0.5])
        eth_copy.insert_node(1, "O", [0.5, 0.5, 0.5])
        assert mol_copy == eth_copy.molecule

        # Test that removal is also equivalent between Molecule and MoleculeGraph.molecule
        mol_copy.remove_sites([1])
        eth_copy.remove_nodes([1])
        assert mol_copy == eth_copy.molecule

        eth_copy.insert_node(
            1,
            "O",
            [0.5, 0.5, 0.5],
            edges=[{"from_index": 1, "to_index": 2}, {"from_index": 1, "to_index": 3}],
        )
        assert eth_copy.get_coordination_of_site(1) == 2

        # Test that MoleculeGraph.graph is correctly updated
        eth_copy.remove_nodes([1, 2])
        assert eth_copy.graph.number_of_nodes() == 5
        assert eth_copy.graph.number_of_edges() == 2

    def test_get_disconnected(self):
        disconnected = Molecule(
            ["C", "H", "H", "H", "H", "He"],
            [
                [0.0000, 0.0000, 0.0000],
                [-0.3633, -0.5138, -0.8900],
                [1.0900, 0.0000, 0.0000],
                [-0.3633, 1.0277, 0.0000],
                [-0.3633, -0.5138, -0.8900],
                [5.0000, 5.0000, 5.0000],
            ],
        )

        no_he = Molecule(
            ["C", "H", "H", "H", "H"],
            [
                [0.0000, 0.0000, 0.0000],
                [-0.3633, -0.5138, -0.8900],
                [1.0900, 0.0000, 0.0000],
                [-0.3633, 1.0277, 0.0000],
                [-0.3633, -0.5138, -0.8900],
            ],
        )

        just_he = Molecule(["He"], [[5.0000, 5.0000, 5.0000]])

        dis_mg = MoleculeGraph.with_empty_graph(disconnected)
        dis_mg.add_edge(0, 1)
        dis_mg.add_edge(0, 2)
        dis_mg.add_edge(0, 3)
        dis_mg.add_edge(0, 4)

        fragments = dis_mg.get_disconnected_fragments()
        assert len(fragments) == 2
        assert fragments[0].molecule == no_he
        assert fragments[1].molecule == just_he

        con_mg = MoleculeGraph.with_empty_graph(no_he)
        con_mg.add_edge(0, 1)
        con_mg.add_edge(0, 2)
        con_mg.add_edge(0, 3)
        con_mg.add_edge(0, 4)
        fragments = con_mg.get_disconnected_fragments()
        assert len(fragments) == 1

    def test_split(self):
        bonds = [(0, 1), (4, 5)]
        alterations = {
            (2, 3): {"weight": 1.0},
            (0, 5): {"weight": 2.0},
            (1, 2): {"weight": 2.0},
            (3, 4): {"weight": 2.0},
        }
        # Perform retro-Diels-Alder reaction - turn product into reactants
        reactants = self.cyclohexene.split_molecule_subgraphs(bonds, allow_reverse=True, alterations=alterations)
        assert isinstance(reactants, list)

        reactants = sorted(reactants, key=len)
        # After alterations, reactants should be ethylene and butadiene
        assert reactants[0] == self.ethylene
        assert reactants[1] == self.butadiene

        with pytest.raises(MolGraphSplitError):
            self.cyclohexene.split_molecule_subgraphs([(0, 1)])

        # Test naive charge redistribution
        hydroxide = Molecule(["O", "H"], [[0, 0, 0], [0.5, 0.5, 0.5]], charge=-1)
        oh_mg = MoleculeGraph.with_empty_graph(hydroxide)

        oh_mg.add_edge(0, 1)

        new_mgs = oh_mg.split_molecule_subgraphs([(0, 1)])
        for mg in new_mgs:
            if str(mg.molecule[0].specie) == "O":
                assert mg.molecule.charge == -1
            else:
                assert mg.molecule.charge == 0

        # Trying to test to ensure that remapping of nodes to atoms works
        diff_species = Molecule(
            ["C", "I", "Cl", "Br", "F"],
            [
                [0.8314, -0.2682, -0.9102],
                [1.3076, 1.3425, -2.2038],
                [-0.8429, -0.7410, -1.1554],
                [1.9841, -1.7636, -1.2953],
                [1.0098, 0.1231, 0.3916],
            ],
        )

        diff_spec_mg = MoleculeGraph.with_empty_graph(diff_species)
        diff_spec_mg.add_edge(0, 1)
        diff_spec_mg.add_edge(0, 2)
        diff_spec_mg.add_edge(0, 3)
        diff_spec_mg.add_edge(0, 4)

        for i in range(1, 5):
            bond = (0, i)

            split_mgs = diff_spec_mg.split_molecule_subgraphs([bond])
            for split_mg in split_mgs:
                species = nx.get_node_attributes(split_mg.graph, "specie")

                for j in range(len(split_mg.graph.nodes)):
                    atom = split_mg.molecule[j]
                    assert species[j] == str(atom.specie)

    def test_build_unique_fragments(self):
        edges = {(e[0], e[1]): None for e in self.pc_edges}
        mol_graph = MoleculeGraph.with_edges(self.pc, edges)
        unique_fragment_dict = mol_graph.build_unique_fragments()
        unique_fragments = []
        for key in unique_fragment_dict:
            for fragment in unique_fragment_dict[key]:
                unique_fragments.append(fragment)
        assert len(unique_fragments) == 295
        nm = iso.categorical_node_match("specie", "ERROR")
        for ii in range(295):
            # Test that each fragment is unique
            for jj in range(ii + 1, 295):
                assert not nx.is_isomorphic(
                    unique_fragments[ii].graph,
                    unique_fragments[jj].graph,
                    node_match=nm,
                )

            # Test that each fragment correctly maps between Molecule and graph
            assert len(unique_fragments[ii].molecule) == len(unique_fragments[ii].graph.nodes)
            species = nx.get_node_attributes(unique_fragments[ii].graph, "specie")
            coords = nx.get_node_attributes(unique_fragments[ii].graph, "coords")

            mol = unique_fragments[ii].molecule
            for ss, site in enumerate(mol):
                assert str(species[ss]) == str(site.specie)
                assert coords[ss][0] == site.coords[0]
                assert coords[ss][1] == site.coords[1]
                assert coords[ss][2] == site.coords[2]

            # Test that each fragment is connected
            assert nx.is_connected(unique_fragments[ii].graph.to_undirected())

    def test_find_rings(self):
        rings = self.cyclohexene.find_rings(including=[0])
        assert sorted(rings[0]) == [(0, 5), (1, 0), (2, 1), (3, 2), (4, 3), (5, 4)]
        no_rings = self.butadiene.find_rings()
        assert no_rings == []

    def test_isomorphic(self):
        ethylene = Molecule.from_file(
            os.path.join(
                PymatgenTest.TEST_FILES_DIR,
                "graphs/ethylene.xyz",
            )
        )
        # switch carbons
        ethylene[0], ethylene[1] = ethylene[1], ethylene[0]

        eth_copy = MoleculeGraph.with_edges(
            ethylene,
            {
                (0, 1): {"weight": 2},
                (1, 2): {"weight": 1},
                (1, 3): {"weight": 1},
                (0, 4): {"weight": 1},
                (0, 5): {"weight": 1},
            },
        )
        # If they are equal, they must also be isomorphic
        eth_copy = copy.deepcopy(self.ethylene)
        assert self.ethylene.isomorphic_to(eth_copy)
        assert not self.butadiene.isomorphic_to(self.ethylene)

    def test_substitute(self):
        molecule = FunctionalGroups["methyl"]
        molgraph = MoleculeGraph.with_edges(
            molecule,
            {(0, 1): {"weight": 1}, (0, 2): {"weight": 1}, (0, 3): {"weight": 1}},
        )

        eth_mol = copy.deepcopy(self.ethylene)
        eth_str = copy.deepcopy(self.ethylene)
        # Ensure that strings and molecules lead to equivalent substitutions
        eth_mol.substitute_group(5, molecule, MinimumDistanceNN)
        eth_str.substitute_group(5, "methyl", MinimumDistanceNN)
        assert eth_mol == eth_str

        graph_dict = {
            (0, 1): {"weight": 1.0},
            (0, 2): {"weight": 1.0},
            (0, 3): {"weight": 1.0},
        }
        eth_mg = copy.deepcopy(self.ethylene)
        eth_graph = copy.deepcopy(self.ethylene)

        # Check that MoleculeGraph input is handled properly
        eth_graph.substitute_group(5, molecule, MinimumDistanceNN, graph_dict=graph_dict)
        eth_mg.substitute_group(5, molgraph, MinimumDistanceNN)
        assert eth_graph.graph.get_edge_data(5, 6)[0]["weight"] == 1.0
        assert eth_mg == eth_graph

    def test_replace(self):
        eth_copy_sub = copy.deepcopy(self.ethylene)
        eth_copy_repl = copy.deepcopy(self.ethylene)
        # First, perform a substitution as above
        eth_copy_sub.substitute_group(5, "methyl", MinimumDistanceNN)
        eth_copy_repl.replace_group(5, "methyl", MinimumDistanceNN)
        # Test that replacement on a terminal atom is equivalent to substitution
        assert eth_copy_repl.molecule == eth_copy_sub.molecule
        assert eth_copy_repl == eth_copy_sub

        # Methyl carbon should have coordination 4
        assert eth_copy_repl.get_coordination_of_site(5) == 4
        # Now swap one functional group for another
        eth_copy_repl.replace_group(5, "amine", MinimumDistanceNN)
        assert ["C", "C", "H", "H", "H", "N", "H", "H"] == [str(s) for s in eth_copy_repl.molecule.species]
        assert len(eth_copy_repl.graph.nodes) == 8
        # Amine nitrogen should have coordination 3
        assert eth_copy_repl.get_coordination_of_site(5) == 3

    def test_as_from_dict(self):
        d = self.cyclohexene.as_dict()
        mg = MoleculeGraph.from_dict(d)
        d2 = mg.as_dict()
        assert str(d) == str(d2)

    def test_sort(self):
        sg = copy.deepcopy(self.ethylene)
        # insert an unsorted edge, don't use sg.add_edge as it auto-sorts

        assert list(sg.graph.edges) == [(0, 1, 0), (0, 2, 0), (0, 3, 0), (1, 4, 0), (1, 5, 0)]
        sg.sort()
        assert list(sg.graph.edges) == [(4, 5, 0), (0, 4, 0), (1, 4, 0), (2, 5, 0), (3, 5, 0)]


if __name__ == "__main__":
    unittest.main()

materialsproject / pymatgen / 4075885785

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous