How to use the pybel.dsl.ProteinModification function in pybel

]),
    il6,
    BiologicalProcess('GO', 'cell cycle arrest'),
    hydrogen_peroxide,
    Protein('HGNC', 'CAT'),
    Gene('HGNC', 'CAT'),
    Protein('HGNC', 'HMGCR'),
    BiologicalProcess('GO', 'cholesterol biosynthetic process'),
    Gene('HGNC', 'APP', variants=Hgvs('c.275341G>C')),
    Gene('HGNC', 'APP'),
    Pathology('MESHD', 'Alzheimer Disease'),
    ComplexAbundance([Protein('HGNC', 'F3'), Protein('HGNC', 'F7')]),
    Protein('HGNC', 'F3'),
    Protein('HGNC', 'F7'),
    Protein('HGNC', 'F9'),
    Protein('HGNC', 'GSK3B', variants=ProteinModification('Ph', 'Ser', 9)),
    Protein('HGNC', 'GSK3B'),
    Pathology('MESHD', 'Psoriasis'),
    Pathology('MESHD', 'Skin Diseases'),
    Reaction(
        reactants=[
            Abundance('CHEBI', '(3S)-3-hydroxy-3-methylglutaryl-CoA'),
            Abundance('CHEBI', 'NADPH'),
            Abundance('CHEBI', 'hydron')
        ],
        products=[
            Abundance('CHEBI', 'NADP(+)'),
            Abundance('CHEBI', 'mevalonate')
        ]
    ),
    Abundance('CHEBI', '(3S)-3-hydroxy-3-methylglutaryl-CoA'),
    Abundance('CHEBI', 'NADPH'),

def test_canonicalize_variant_dsl(self):
        """Use the __str__ functions in the DSL to create BEL instead of external pybel.canonicalize."""
        self.assertEqual('var("p.Val600Glu")', str(Hgvs('p.Val600Glu')))
        self.assertEqual('var("p.Val600Glu")', str(ProteinSubstitution('Val', 600, 'Glu')))

        self.assertEqual('pmod(go:0006468 ! "protein phosphorylation")', str(ProteinModification('Ph')))
        self.assertEqual('pmod(TEST:Ph)', str(ProteinModification('Ph', namespace='TEST')))
        self.assertEqual('pmod(TEST:Ph, Ser)', str(ProteinModification('Ph', namespace='TEST', code='Ser')))
        self.assertEqual('pmod(TEST:Ph, Ser, 5)',
                         str(ProteinModification('Ph', namespace='TEST', code='Ser', position=5)))
        self.assertEqual('pmod(GO:"protein phosphorylation", Thr, 308)',
                         str(ProteinModification(name='protein phosphorylation', namespace='GO', code='Thr',
                                                 position=308)))

        self.assertEqual('frag("?")', str(Fragment()))
        self.assertEqual('frag("672_713")', str(Fragment(start=672, stop=713)))
        self.assertEqual('frag("?", "descr")', str(Fragment(description='descr')))
        self.assertEqual('frag("672_713", "descr")', str(Fragment(start=672, stop=713, description='descr')))

        self.assertEqual('gmod(go:0006306 ! "DNA methylation")', str(GeneModification('Me')))
        self.assertEqual('gmod(TEST:Me)', str(GeneModification('Me', namespace='TEST')))
        self.assertEqual('gmod(GO:"DNA Methylation")', str(GeneModification('DNA Methylation', namespace='GO')))

import unittest

from pybel.constants import FUNCTION, NAME, NAMESPACE, PROTEIN, VARIANTS, KIND, MEMBERS, FUSION, PARTNER_3P, PARTNER_5P, RANGE_3P, RANGE_5P
from pybel.dsl import (
    Abundance, BiologicalProcess, ComplexAbundance, Gene, MicroRna, NamedComplexAbundance, Pathology, Protein,
    ProteinModification, Reaction, Rna, ProteinFusion
)
from pybel.schema import validate_node
from pybel.testing.utils import n

HGNC = 'HGNC'
GO = 'GO'
YFG = 'YFG'

phosphorylation = ProteinModification('Ph')
protein_1 = Protein(HGNC, YFG)
protein_2 = Protein(HGNC, YFG, variants=phosphorylation)
rna_1 = Rna(HGNC, YFG)
micro_rna_1 = MicroRna(HGNC, 'YFMR')
gene_1 = Gene(HGNC, YFG)
biological_process_1 = BiologicalProcess(GO, 'YFBP')
pathology_1 = Pathology(GO, 'YFP')
abundance_1 = Abundance(n(), n())
abundance_2 = Abundance(n(), n())
reaction_1 = Reaction(reactants=[abundance_1], products=[abundance_2])
complex_1 = NamedComplexAbundance(n(), n())
enumerated_complex_1 = ComplexAbundance([
    protein_1,
    Protein(HGNC, n()),
])
protein_fusion = ProteinFusion(protein_1, protein_2)

Abundance('CHEBI', 'NADP(+)'),
    Abundance('CHEBI', 'nitric oxide'),
    ComplexAbundance([
        Protein('HGNC', 'ITGAV'),
        Protein('HGNC', 'ITGB3')
    ]),
    Protein('HGNC', 'ITGAV'),
    Protein('HGNC', 'ITGB3'),
    Protein('HGNC', 'FADD'),
    Abundance('TESTNS2', 'Abeta_42'),
    Protein('TESTNS2', 'GSK3 Family'),
    Protein('HGNC', 'PRKCA'),
    Protein('HGNC', 'CDK5'),
    Protein('HGNC', 'CASP8'),
    Protein('HGNC', 'AKT1',
            variants=ProteinModification(namespace='TESTNS2', name='PhosRes', code='Ser', position=473)),
    Protein('HGNC', 'HRAS', variants=ProteinModification('Palm')),
    BiologicalProcess('GO', 'apoptotic process'),
    CompositeAbundance([
        Abundance('TESTNS2', 'Abeta_42'),
        Protein('HGNC', 'CASP8'),
        Protein('HGNC', 'FADD')
    ]),
    Reaction(
        reactants=[Protein('HGNC', 'CDK5R1')],
        products=[Protein('HGNC', 'CDK5')],
    ),
    Protein('HGNC', 'PRKCB'),
    NamedComplexAbundance('TESTNS2', 'AP-1 Complex'),
    Protein('HGNC', 'PRKCE'),
    Protein('HGNC', 'PRKCD'),
    Protein('TESTNS2', 'CAPN Family'),

]),
    Reaction(
        reactants=[Protein('HGNC', 'CDK5R1')],
        products=[Protein('HGNC', 'CDK5')],
    ),
    Protein('HGNC', 'PRKCB'),
    NamedComplexAbundance('TESTNS2', 'AP-1 Complex'),
    Protein('HGNC', 'PRKCE'),
    Protein('HGNC', 'PRKCD'),
    Protein('TESTNS2', 'CAPN Family'),
    Gene('TESTNS2', 'AKT1 ortholog'),
    Protein('HGNC', 'HRAS'),
    Protein('HGNC', 'CDK5R1'),
    Protein('TESTNS2', 'PRKC'),
    BiologicalProcess('GO', 'neuron apoptotic process'),
    Protein('HGNC', 'MAPT', variants=ProteinModification('Ph')),
    Protein('HGNC', 'MAPT'),
    Gene('HGNC', 'ARRDC2'),
    Gene('HGNC', 'ARRDC3'),
    Gene('dbSNP', 'rs123456')
}

BEL_THOROUGH_EDGES = [
    (Gene('HGNC', 'AKT1', variants=Hgvs('p.Phe508del')), akt1, {
        EVIDENCE: dummy_evidence,
        CITATION: citation_1,
        RELATION: DIRECTLY_DECREASES,
    }),
    (akt1, Protein('HGNC', 'AKT1', variants=ProteinModification('Ph', 'Ser', 473)), {
        RELATION: HAS_VARIANT,
    }),
    (akt1, Protein('HGNC', 'AKT1', variants=Hgvs('p.C40*')), {

def test_protein_pmod(self):
        node = Protein(name='PLCG1', namespace='HGNC', variants=[ProteinModification(name='Ph', code='Tyr')])
        self.assertEqual('p(HGNC:PLCG1, pmod(go:0006468 ! "protein phosphorylation", Tyr))', str(node))

def _help_test_pmod_full(self, statement):
        result = self.parser.parseString(statement)

        expected = {
            KIND: PMOD,
            CONCEPT: {
                NAMESPACE: 'go',
                NAME: 'protein phosphorylation',
                IDENTIFIER: '0006468',
            },
            PMOD_CODE: 'Ser',
            PMOD_POSITION: 473,
        }

        self.assertEqual(expected, ProteinModification('Ph', code='Ser', position=473))
        self.assertEqual(expected, result.asDict())

for var in variants:
        if isinstance(var, dsl.Hgvs):
            if isinstance(node_data, dsl.Gene):
                logger.debug('Unhandled genetic variant: %s', node_data)
                continue

            hgvs_str = var.variant
            position, res_from, res_to = _parse_mutation(hgvs_str)
            if position is None and res_from is None and res_to is None:
                logger.info("Could not parse HGVS string %s", hgvs_str)
            else:
                mut_cond = MutCondition(position, res_from, res_to)
                muts.append(mut_cond)

        elif isinstance(var, dsl.ProteinModification):
            var_ns = var.entity.namespace
            if var_ns == pc.BEL_DEFAULT_NAMESPACE:
                var_id = var.entity.name
                mod_type = _pybel_indra_pmod_map.get(var_id)
                if mod_type is None:
                    logger.info("Unhandled modification type %s (%s)",
                                var_id, node_data)
                    continue
                mc = ModCondition(mod_type, var.get(pc.PMOD_CODE),
                                  var.get(pc.PMOD_POSITION))
                mods.append(mc)
        # FIXME These unhandled mod types should result in throwing out
        # the node (raise, or return None)
        elif isinstance(var, dsl.GeneModification):
            logger.debug('Unhandled node variant GMOD: %s', node_data)
        elif isinstance(var, dsl.Fragment):

if edge_type in {'inhibition'}:
        return graph.add_inhibits(
            source_bel, target_bel,
            citation='', evidence='', annotations={'sbgnml_edge': edge_type},
        )
    if edge_type in {'stimulation', 'necessary stimulation'}:
        return graph.add_activates(
            source_bel, target_bel,
            citation='', evidence='', annotations={'sbgnml_edge': edge_type},
        )

    print('##', source_bel, edge_type, target_bel)


STATE_TO_PMOD = {
    'P': dsl.ProteinModification('Ph'),
    'Ub': dsl.ProteinModification('Ub'),
}

SKIP_STATES = {
    'activated',
}


def _states_to_bel(states):
    if not states:
        return
    for state in states:
        if state in STATE_TO_PMOD:
            return STATE_TO_PMOD[state]
        if state in SKIP_STATES:
            return

return graph.add_inhibits(
            source_bel, target_bel,
            citation='', evidence='', annotations={'sbgnml_edge': edge_type},
        )
    if edge_type in {'stimulation', 'necessary stimulation'}:
        return graph.add_activates(
            source_bel, target_bel,
            citation='', evidence='', annotations={'sbgnml_edge': edge_type},
        )

    print('##', source_bel, edge_type, target_bel)


STATE_TO_PMOD = {
    'P': dsl.ProteinModification('Ph'),
    'Ub': dsl.ProteinModification('Ub'),
}

SKIP_STATES = {
    'activated',
}


def _states_to_bel(states):
    if not states:
        return
    for state in states:
        if state in STATE_TO_PMOD:
            return STATE_TO_PMOD[state]
        if state in SKIP_STATES:
            return
        logger.debug('unhandled state: %s', state)