import utils import datetime import os import unittest import warnings import sys from io import StringIO TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..')) utils.set_search_paths(TOPDIR) import ihm.dumper import ihm.format import ihm.location import ihm.representation import ihm.startmodel import ihm.dataset import ihm.protocol import ihm.analysis import ihm.model import ihm.reference import ihm.restraint import ihm.geometry import ihm.source import ihm.flr import ihm.multi_state_scheme from test_format_bcif import MockFh, MockMsgPack def _get_dumper_output(dumper, system, check=True): dumper._check = check fh = StringIO() writer = ihm.format.CifWriter(fh) dumper.dump(system, writer) return fh.getvalue() def _get_dumper_bcif_output(dumper, system): fh = MockFh() writer = ihm.format_bcif.BinaryCifWriter(fh) sys.modules['msgpack'] = MockMsgPack dumper.dump(system, writer) writer.flush() return fh.data class Tests(unittest.TestCase): def test_write(self): """Test write() function""" sys1 = ihm.System(id='system1') sys2 = ihm.System(id='system 2+3') fh = StringIO() ihm.dumper.write(fh, [sys1, sys2]) lines = fh.getvalue().split('\n') self.assertEqual(lines[:2], ["data_system1", "_entry.id system1"]) self.assertEqual(lines[16:18], ["data_system23", "_entry.id 'system 2+3'"]) def test_write_checks(self): """Test write() function with checks enabled or disabled""" s = ihm.System(id='system1') s.entities.append(ihm.Entity('AHC')) # Duplicate entity s.entities.append(ihm.Entity('AHC')) fh = StringIO() # Duplicate entity should cause a check failure by default self.assertRaises(ValueError, ihm.dumper.write, fh, [s]) # But OK if checks are disabled fh = StringIO() ihm.dumper.write(fh, [s], check=False) self.assertEqual(s.entities[0]._id, 1) self.assertEqual(s.entities[1]._id, 2) def test_write_custom_dumper(self): """Test write() function with custom dumper""" class MyDumper(ihm.dumper.Dumper): def dump(self, system, writer): with writer.category("_custom_category") as loc: loc.write(myfield="foo", field2="bar") sys1 = ihm.System(id='system1') fh = StringIO() ihm.dumper.write(fh, [sys1], dumpers=[MyDumper]) lines = fh.getvalue().split('\n') self.assertEqual(sorted(lines[-3:-1]), ['_custom_category.field2 bar', '_custom_category.myfield foo']) def test_dumper(self): """Test Dumper base class""" dumper = ihm.dumper.Dumper() dumper.finalize(None) dumper.dump(None, None) def test_prettyprint_seq(self): """Test _prettyprint_seq() function""" seq = ['x' * 30, 'y' * 20, 'z' * 10] # No line breaks self.assertEqual(list(ihm.dumper._prettyprint_seq(seq, 100)), ['x' * 30 + 'y' * 20 + 'z' * 10]) # Break inserted between sequence items self.assertEqual(list(ihm.dumper._prettyprint_seq(seq, 55)), ['x' * 30 + 'y' * 20, 'z' * 10]) # Items longer than width will exceed line length self.assertEqual(list(ihm.dumper._prettyprint_seq(seq, 25)), ['x' * 30, 'y' * 20, 'z' * 10]) # Empty sequence self.assertEqual(list(ihm.dumper._prettyprint_seq([], 25)), []) def test_entry_dumper(self): """Test EntryDumper""" system = ihm.System(id='test_model') dumper = ihm.dumper._EntryDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, "data_test_model\n_entry.id test_model\n") def test_entry_dumper_data_chars(self): """Test allowed characters in data_ block with EntryDumper""" system = ihm.System(id='foo99-bar94_ABC $#^% x') dumper = ihm.dumper._EntryDumper() out = _get_dumper_output(dumper, system).split('\n')[0] # Whitespace and special characters (except - _) should be removed self.assertEqual(out, "data_foo99-bar94_ABCx") def test_audit_conform_dumper(self): """Test AuditConformDumper""" system = ihm.System() dumper = ihm.dumper._AuditConformDumper() out = _get_dumper_output(dumper, system) lines = sorted(out.split('\n')) self.assertEqual(lines[1].split()[0], "_audit_conform.dict_location") self.assertEqual(lines[2].rstrip('\r\n'), "_audit_conform.dict_name mmcif_ihm.dic") self.assertEqual(lines[3].split()[0], "_audit_conform.dict_version") def test_struct_dumper(self): """Test StructDumper""" system = ihm.System(title='test model', model_details="test details") dumper = ihm.dumper._StructDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """_struct.entry_id model _struct.pdbx_model_details 'test details' _struct.pdbx_structure_determination_methodology integrative _struct.title 'test model' """) def test_comment_dumper(self): """Test CommentDumper""" system = ihm.System() system.comments.extend(("Comment 1", "Comment 2")) dumper = ihm.dumper._CommentDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# Comment 1 # Comment 2 """) # Comments should be ignored in BinaryCIF output out = _get_dumper_bcif_output(dumper, system) self.assertEqual(out['dataBlocks'], []) def test_software(self): """Test SoftwareDumper""" system = ihm.System() c1 = ihm.Citation( pmid='25161197', title='foo', journal="Mol Cell Proteomics", volume=13, page_range=(2927, 2943), year=2014, authors=['auth1', 'auth2', 'auth3'], doi='doi1') system.software.append(ihm.Software( name='test', classification='test code', description='Some test program', version=1, location='http://test.org')) system.software.append(ihm.Software( name='foo', classification='test code', description='Other test program', location='http://test2.org', citation=c1)) # Duplicate should be removed system.software.append(ihm.Software( name='foo', classification='x', description='y', location='z')) dumper = ihm.dumper._CitationDumper() dumper.finalize(system) dumper = ihm.dumper._SoftwareDumper() dumper.finalize(system) self.assertEqual(len(dumper._software_by_id), 2) # Repeated calls to finalize() should yield identical results dumper.finalize(system) self.assertEqual(len(dumper._software_by_id), 2) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _software.pdbx_ordinal _software.name _software.classification _software.description _software.version _software.type _software.location _software.citation_id 1 test 'test code' 'Some test program' 1 program http://test.org . 2 foo 'test code' 'Other test program' . program http://test2.org 1 # """) def test_citation(self): """Test CitationDumper""" system = ihm.System() c1 = ihm.Citation( pmid='25161197', title="Structural characterization by cross-linking reveals the\n" "detailed architecture of a coatomer-related heptameric\n" "module from the nuclear pore complex.", journal="Mol Cell Proteomics", volume=13, page_range=(2927, 2943), year=2014, authors=['Shi Y', 'Fernandez-Martinez J', 'Tjioe E', 'Pellarin R', 'Kim SJ', 'Williams R', 'Schneidman-Duhovny D', 'Sali A', 'Rout MP', 'Chait BT'], doi='10.1074/mcp.M114.041673') system.citations.extend((c1, c1)) # duplicates should be removed dumper = ihm.dumper._CitationDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI 1 ;Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. ; 'Mol Cell Proteomics' 13 2927 2943 2014 25161197 10.1074/mcp.M114.041673 # # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 'Shi Y' 1 1 'Fernandez-Martinez J' 2 1 'Tjioe E' 3 1 'Pellarin R' 4 1 'Kim SJ' 5 1 'Williams R' 6 1 'Schneidman-Duhovny D' 7 1 'Sali A' 8 1 'Rout MP' 9 1 'Chait BT' 10 # """) # Handle no last page c1.page_range = 'e1637' dumper = ihm.dumper._CitationDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) self.assertIn("'Mol Cell Proteomics' 13 e1637 . 2014 ", out) def test_citation_primary(self): """Test CitationDumper with a primary citation""" system = ihm.System() c1 = ihm.Citation(pmid='x', title='y', journal='z', year=2014, authors=[], volume=1, page_range=1, doi='d') c2 = ihm.Citation(pmid='x2', title='y2', journal='z2', year=2015, authors=[], volume=1, page_range=1, doi='e', is_primary=True) system.citations.extend((c1, c2)) dumper = ihm.dumper._CitationDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary y2 z2 1 1 . 2015 x2 e 2 y z 1 1 . 2014 x d # """) def test_citation_multiple_primary(self): """Test CitationDumper with multiple primary citations""" system = ihm.System() c1 = ihm.Citation(pmid='x', title='y', journal='z', year=2014, authors=[], volume=1, page_range=1, doi='d', is_primary=True) c2 = ihm.Citation(pmid='x2', title='y2', journal='z2', year=2015, authors=[], volume=1, page_range=1, doi='e', is_primary=True) system.citations.extend((c1, c2)) dumper = ihm.dumper._CitationDumper() self.assertRaises(ValueError, dumper.finalize, system) def test_audit_author_empty(self): """Test AuditAuthorDumper with empty list""" system = ihm.System() c1 = ihm.Citation( pmid='25161197', title='foo', journal="Mol Cell Proteomics", volume=13, page_range=(2927, 2943), year=2014, authors=['auth1', 'auth2', 'auth3'], doi='doi1') c2 = ihm.Citation( pmid='45161197', title='bar', journal="Mol Cell Proteomics", volume=13, page_range=(2927, 2943), year=2014, authors=['auth2', 'auth4'], doi='doi2') system.citations.extend((c1, c2)) # Citations indirectly referenced by software should *not* be used c3 = ihm.Citation( pmid='455', title='baz', journal="Mol Cell Proteomics", volume=13, page_range=(2927, 2943), year=2014, authors=['auth5', 'auth6', 'auth7'], doi='doi3') software = ihm.Software(name='test', classification='test code', description='Some test program', version=1, location='http://test.org', citation=c3) system.software.append(software) dumper = ihm.dumper._AuditAuthorDumper() out = _get_dumper_output(dumper, system) # auth2 is repeated in the input; we should see it only once in the # output self.assertEqual(out, """# loop_ _audit_author.name _audit_author.pdbx_ordinal auth1 1 auth2 2 auth3 3 auth4 4 # """) def test_omitted_unknown(self): """Test that Dumpers handle omitted/unknown values correctly""" system = ihm.System() system.authors.extend((None, ihm.unknown, '.', '?')) dumper = ihm.dumper._AuditAuthorDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _audit_author.name _audit_author.pdbx_ordinal . 1 ? 2 '.' 3 '?' 4 # """) def test_audit_author(self): """Test AuditAuthorDumper""" system = ihm.System() system.authors.extend(('auth1', 'auth2', 'auth3')) dumper = ihm.dumper._AuditAuthorDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _audit_author.name _audit_author.pdbx_ordinal auth1 1 auth2 2 auth3 3 # """) def test_audit_revision_dumper(self): """Test AuditRevisionDumper""" system = ihm.System() rev = ihm.Revision(data_content_type='Structure model', minor=2, major=0, date=datetime.date(year=1979, month=5, day=3)) rev.groups.extend(('group1', 'group2')) rev.categories.extend(('cat1', 'cat2')) rev.items.append('item1') d = ihm.RevisionDetails(provider="repository", type="Initial release", description="Test desc") rev.details.append(d) system.revisions.append(rev) rev = ihm.Revision(data_content_type=None, major=None, minor=None, date=None) system.revisions.append(rev) rev = ihm.Revision(data_content_type=None, major=None, minor=None, date=ihm.unknown) system.revisions.append(rev) dumper = ihm.dumper._AuditRevisionDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 0 2 1979-05-03 2 . . . . 3 . . . ? # # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' 'Test desc' # # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 1 'Structure model' group1 2 1 'Structure model' group2 # # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 1 'Structure model' cat1 2 1 'Structure model' cat2 # # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 1 'Structure model' item1 # """) def test_data_usage_dumper(self): """Test DataUsageDumper""" system = ihm.System() system.data_usage.append( ihm.License("some license", url="someurl", name="somename")) system.data_usage.append(ihm.Disclaimer("some disclaimer")) system.data_usage.append(ihm.DataUsage("misc usage")) dumper = ihm.dumper._DataUsageDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_data_usage.id _pdbx_data_usage.type _pdbx_data_usage.details _pdbx_data_usage.url _pdbx_data_usage.name 1 license 'some license' someurl somename 2 disclaimer 'some disclaimer' . . 3 other 'misc usage' . . # """) def test_grant(self): """Test GrantDumper""" system = ihm.System() g1 = ihm.Grant(funding_organization="NIH", country="United States", grant_number="foo") g2 = ihm.Grant(funding_organization="NSF", country="United States", grant_number="bar") system.grants.extend((g1, g2)) dumper = ihm.dumper._GrantDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal NIH 'United States' foo 1 NSF 'United States' bar 2 # """) def test_entity_dumper(self): """Test EntityDumper""" system = ihm.System() e1 = ihm.Entity('AHC', description='foo', source=ihm.source.Manipulated()) e2 = ihm.Entity('AHCD', description='baz', source=ihm.source.Natural()) e3 = ihm.Entity('AHD', description='bar', source=ihm.source.Synthetic()) water = ihm.Entity([ihm.WaterChemComp()]) system.entities.extend((e1, e2, e3, water)) system.asym_units.append(ihm.AsymUnit(e1, 'foo')) system.asym_units.append(ihm.AsymUnit(e2, 'bar')) system.asym_units.append(ihm.AsymUnit(e3, 'baz1')) system.asym_units.append(ihm.AsymUnit(e3, 'baz2')) system.asym_units.append(ihm.WaterAsymUnit(water, number=10)) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.details 1 polymer man foo 366.413 1 . 2 polymer nat baz 499.516 1 . 3 polymer syn bar 378.362 2 . 4 water nat . 18.015 10 . # """) def test_entity_duplicates(self): """Test EntityDumper with duplicate non-branched entities""" system = ihm.System() system.entities.append(ihm.Entity('AHC')) system.entities.append(ihm.Entity('AHC')) dumper = ihm.dumper._EntityDumper() self.assertRaises(ValueError, dumper.finalize, system) # Also test with checks skipped dumper._check = False dumper.finalize(system) self.assertEqual(system.entities[0]._id, 1) self.assertEqual(system.entities[1]._id, 2) def test_entity_duplicate_branched(self): """Test EntityDumper with duplicate branched entities""" system = ihm.System() sacc1 = ihm.SaccharideChemComp('NAG') sacc2 = ihm.SaccharideChemComp('FUC') system.entities.append(ihm.Entity([sacc1, sacc2])) system.entities.append(ihm.Entity([sacc1, sacc2])) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) # Duplicate "sequences" are OK for branched entities self.assertEqual(out, """# loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.details 1 branched man . . 0 . 2 branched man . . 0 . # """) def test_entity_empty(self): """Test EntityDumper with empty entity""" system = ihm.System() system.entities.append(ihm.Entity('')) dumper = ihm.dumper._EntityDumper() with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") dumper.finalize(system) # Assign IDs _ = _get_dumper_output(dumper, system) self.assertEqual(len(w), 1) self.assertIn('At least one empty Entity', str(w[0].message)) def test_entity_duplicate_empty(self): """Test EntityDumper with duplicate empty entities""" system = ihm.System() system.entities.append(ihm.Entity('')) system.entities.append(ihm.Entity('')) dumper = ihm.dumper._EntityDumper() with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") dumper.finalize(system) # Assign IDs _ = _get_dumper_output(dumper, system) self.assertIn('At least one empty Entity', str(w[0].message)) def test_entity_src_nat_dumper(self): """Test EntitySrcNatDumper""" system = ihm.System() system.entities.append(ihm.Entity('AHC', description='foo', source=ihm.source.Manipulated())) s = ihm.source.Natural(ncbi_taxonomy_id='1234', scientific_name='Test latin name', common_name='Test common name', strain='test strain') system.entities.append(ihm.Entity('AHCD', description='baz', source=s)) ihm.dumper._EntityDumper().finalize(system) dumper = ihm.dumper._EntitySrcNatDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _entity_src_nat.entity_id _entity_src_nat.pdbx_src_id _entity_src_nat.pdbx_ncbi_taxonomy_id _entity_src_nat.pdbx_organism_scientific _entity_src_nat.common_name _entity_src_nat.strain 2 1 1234 'Test latin name' 'Test common name' 'test strain' # """) def test_entity_src_syn_dumper(self): """Test EntitySrcSynDumper""" system = ihm.System() system.entities.append(ihm.Entity('AHC', description='foo', source=ihm.source.Manipulated())) s = ihm.source.Synthetic(ncbi_taxonomy_id='1234', scientific_name='Test latin name', common_name='Test common name', strain='test strain') system.entities.append(ihm.Entity('AHCD', description='baz', source=s)) ihm.dumper._EntityDumper().finalize(system) dumper = ihm.dumper._EntitySrcSynDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) # _pdbx_entity_src_syn.strain is not used in current PDB entries self.assertEqual(out, """# loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name 2 1 1234 'Test latin name' 'Test common name' # """) def test_entity_src_gen_dumper(self): """Test EntitySrcGenDumper""" system = ihm.System() system.entities.append(ihm.Entity('AHC', description='foo', source=ihm.source.Natural())) system.entities.append( ihm.Entity('AHCG', description='bar', source=ihm.source.Manipulated(gene=None, host=None))) gene = ihm.source.Details(ncbi_taxonomy_id='1234', scientific_name='Test latin name', common_name='Test common name', strain='test strain') host = ihm.source.Details(ncbi_taxonomy_id='5678', scientific_name='Other latin name', common_name='Other common name', strain='other strain') s = ihm.source.Manipulated(gene=gene, host=host) system.entities.append(ihm.Entity('AHCD', description='baz', source=s)) ihm.dumper._EntityDumper().finalize(system) dumper = ihm.dumper._EntitySrcGenDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_strain _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_strain 3 2 1234 'Test latin name' 'Test common name' 'test strain' 5678 'Other latin name' 'Other common name' 'other strain' # """) def test_struct_ref(self): """Test StructRefDumper""" system = ihm.System() lpep = ihm.LPeptideAlphabet() sd = ihm.reference.SeqDif(seq_id=2, db_monomer=lpep['W'], monomer=lpep['S'], details='Test mutation') # Test non-mandatory db_monomer and monomer sd2 = ihm.reference.SeqDif(seq_id=3, db_monomer=None, monomer=None, details='Test mutation') r1 = ihm.reference.UniProtSequence( db_code='NUP84_YEAST', accession='P52891', sequence='MELWPTYQT', details='test sequence') r1.alignments.append(ihm.reference.Alignment(db_begin=3, seq_dif=[sd, sd2])) r2 = ihm.reference.UniProtSequence( db_code='testcode', accession='testacc', sequence='MELSPTYQT', details='test2') r2.alignments.append(ihm.reference.Alignment( db_begin=4, db_end=5, entity_begin=2, entity_end=3)) r2.alignments.append(ihm.reference.Alignment( db_begin=9, db_end=9, entity_begin=4, entity_end=4)) r3 = ihm.reference.UniProtSequence( db_code='testcode2', accession='testacc2', sequence=None) r3.alignments.append(ihm.reference.Alignment( db_begin=4, db_end=5, entity_begin=2, entity_end=3)) r4 = ihm.reference.UniProtSequence( db_code='testcode3', accession='testacc3', sequence=ihm.unknown) r4.alignments.append(ihm.reference.Alignment( db_begin=4, db_end=5, entity_begin=2, entity_end=3)) # Duplicate reference; should be omitted even though details differ r5 = ihm.reference.UniProtSequence( db_code='NUP84_YEAST', accession='P52891', sequence='MELWPTYQT', details='other test sequence') r5.alignments.append(ihm.reference.Alignment(db_begin=3, seq_dif=[sd, sd2])) system.entities.append(ihm.Entity('LSPT', references=[r1, r2, r3, r4, r5])) # Duplicate reference, but should be included as it pertains to a # different Entity r3a = ihm.reference.UniProtSequence( db_code='testcode2', accession='testacc2', sequence=None) r3a.alignments.append(ihm.reference.Alignment( db_begin=4, db_end=5, entity_begin=2, entity_end=3)) system.entities.append(ihm.Entity('LSPTW', references=[r3a])) # Reference containing non-standard residues r6 = ihm.reference.UniProtSequence( db_code='testcode4', accession='testacc4', sequence='AA(FOO)ALS(BAR)TW') system.entities.append(ihm.Entity('LSATW', references=[r6])) r6.alignments.append(ihm.reference.Alignment(db_begin=5, db_end=9)) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign entity IDs dumper = ihm.dumper._StructRefDumper() dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.details 1 1 UNP NUP84_YEAST P52891 3 LWPTYQT 'test sequence' 2 1 UNP testcode testacc 4 SPTYQT test2 3 1 UNP testcode2 testacc2 4 . . 4 1 UNP testcode3 testacc3 4 ? . 5 2 UNP testcode2 testacc2 4 . . 6 3 UNP testcode4 testacc4 5 LS(BAR)TW . # # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end 1 1 1 4 3 6 2 2 2 3 4 5 3 2 4 4 9 9 4 3 2 3 4 5 5 4 2 3 4 5 7 5 2 3 4 5 8 6 1 5 5 9 # # loop_ _struct_ref_seq_dif.pdbx_ordinal _struct_ref_seq_dif.align_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.details 1 1 2 TRP SER 'Test mutation' 2 1 3 ? ? 'Test mutation' # """) def test_struct_ref_bad_align(self): """Test StructRefDumper with bad entity align""" system = ihm.System() r = ihm.reference.UniProtSequence( db_code='NUP84_YEAST', accession='P52891', sequence='MELSPTYQT', details='test sequence') r.alignments.append(ihm.reference.Alignment(entity_begin=90)) system.entities.append(ihm.Entity('LSPT', references=[r])) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign entity IDs dumper = ihm.dumper._StructRefDumper() dumper.finalize(system) # Assign IDs with self.assertRaises(IndexError) as cm: _get_dumper_output(dumper, system) self.assertIn('is (90-4), out of range 1-4', str(cm.exception)) # Should work with checks disabled _ = _get_dumper_output(dumper, system, check=False) def test_struct_ref_bad_db_align(self): """Test StructRefDumper with bad db align""" system = ihm.System() r = ihm.reference.UniProtSequence( db_code='NUP84_YEAST', accession='P52891', sequence='M(FOO)LSPTYQT', details='test sequence') r.alignments.append(ihm.reference.Alignment(db_begin=90)) system.entities.append(ihm.Entity('LSPT', references=[r])) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign entity IDs dumper = ihm.dumper._StructRefDumper() dumper.finalize(system) # Assign IDs with self.assertRaises(IndexError) as cm: _get_dumper_output(dumper, system) self.assertIn('is (90-9), out of range 1-9', str(cm.exception)) # Should work with checks disabled _ = _get_dumper_output(dumper, system, check=False) def test_struct_ref_seq_mismatch(self): """Test StructRefDumper with sequence mismatch""" system = ihm.System() r = ihm.reference.UniProtSequence( db_code='NUP84_YEAST', accession='P52891', sequence='MELSPTYQT', details='test sequence') system.entities.append(ihm.Entity('LSPT', references=[r])) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign entity IDs dumper = ihm.dumper._StructRefDumper() dumper.finalize(system) # Assign IDs with self.assertRaises(ValueError) as cm: _get_dumper_output(dumper, system) self.assertIn('does not match entity canonical sequence', str(cm.exception)) # Should work with checks disabled _ = _get_dumper_output(dumper, system, check=False) def test_struct_ref_seq_dif_outrange(self): """Test StructRefDumper with SeqDif out of range""" system = ihm.System() lpep = ihm.LPeptideAlphabet() sd = ihm.reference.SeqDif(seq_id=40, db_monomer=lpep['W'], monomer=lpep['S'], details='Test mutation') r = ihm.reference.UniProtSequence( db_code='NUP84_YEAST', accession='P52891', sequence='MELSPTYQT', details='test sequence') r.alignments.append(ihm.reference.Alignment(seq_dif=[sd])) system.entities.append(ihm.Entity('LSPT', references=[r])) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign entity IDs dumper = ihm.dumper._StructRefDumper() dumper.finalize(system) # Assign IDs with self.assertRaises(IndexError) as cm: _get_dumper_output(dumper, system) self.assertIn('is 40, out of range 1-4', str(cm.exception)) # Should work with checks disabled _ = _get_dumper_output(dumper, system, check=False) def test_struct_ref_seq_dif_mismatch(self): """Test StructRefDumper with SeqDif code mismatch""" system = ihm.System() lpep = ihm.LPeptideAlphabet() sd = ihm.reference.SeqDif(seq_id=2, db_monomer=lpep['W'], monomer=lpep['Y'], details='Test mutation') r = ihm.reference.UniProtSequence( db_code='NUP84_YEAST', accession='P52891', sequence='MELWPTYQT', details='test sequence') r.alignments.append(ihm.reference.Alignment(seq_dif=[sd])) system.entities.append(ihm.Entity('LSPT', references=[r])) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign entity IDs dumper = ihm.dumper._StructRefDumper() dumper.finalize(system) # Assign IDs with self.assertRaises(ValueError) as cm: _get_dumper_output(dumper, system) self.assertIn('one-letter code (Y) does not match', str(cm.exception)) self.assertIn('(S at position 2)', str(cm.exception)) # Should work with checks disabled _ = _get_dumper_output(dumper, system, check=False) def test_struct_ref_seq_dif_ins_del(self): """Test StructRefDumper with SeqDif insertions and deletions""" system = ihm.System() lpep = ihm.LPeptideAlphabet() sd1 = ihm.reference.SeqDif(seq_id=2, db_monomer=lpep['G'], monomer=None, details='deletion') sd2 = ihm.reference.SeqDif(seq_id=3, db_monomer=lpep['C'], monomer=None, details='insertion') r = ihm.reference.UniProtSequence( db_code='NUP84_YEAST', accession='P52891', sequence='MEWPTYQT', details='test sequence') r.alignments.append(ihm.reference.Alignment(seq_dif=[sd1, sd2])) system.entities.append(ihm.Entity('MEWPTYQT', references=[r])) dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # Assign entity IDs dumper = ihm.dumper._StructRefDumper() dumper.finalize(system) # Assign IDs # Insertions and deletions are not currently checked, so # this should pass _ = _get_dumper_output(dumper, system) def test_chem_comp_dumper(self): """Test ChemCompDumper""" system = ihm.System() system.entities.append(ihm.Entity('ACGTTA')) system.entities.append(ihm.Entity('ACGA', alphabet=ihm.RNAAlphabet)) system.entities.append(ihm.Entity(('DA', 'DC'), alphabet=ihm.DNAAlphabet)) dumper = ihm.dumper._ChemCompDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _chem_comp.id _chem_comp.type _chem_comp.name _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' "ADENOSINE-5'-MONOPHOSPHATE" 'C10 H14 N5 O7 P' 347.224 ALA 'L-peptide linking' ALANINE 'C3 H7 N O2' 89.094 C 'RNA linking' "CYTIDINE-5'-MONOPHOSPHATE" 'C9 H14 N3 O8 P' 323.198 CYS 'L-peptide linking' CYSTEINE 'C3 H7 N O2 S' 121.154 DA 'DNA linking' "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" 'C10 H14 N5 O6 P' 331.225 DC 'DNA linking' "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" 'C9 H14 N3 O7 P' 307.199 G 'RNA linking' "GUANOSINE-5'-MONOPHOSPHATE" 'C10 H14 N5 O8 P' 363.223 GLY 'peptide linking' GLYCINE 'C2 H5 N O2' 75.067 THR 'L-peptide linking' THREONINE 'C4 H9 N O3' 119.120 # """) def test_chem_comp_ccd_descriptors(self): """Test ChemCompDumper with ccd or descriptors""" system = ihm.System() comp1 = ihm.NonPolymerChemComp("C1", name='C1', ccd='MA') comp2 = ihm.NonPolymerChemComp("C2", name='C2', descriptors=['foo', 'bar']) system.entities.append(ihm.Entity([comp1, comp2])) dumper = ihm.dumper._ChemCompDumper() # Cannot output ChemComp with ccd or descriptors to IHM files self.assertRaises(ValueError, _get_dumper_output, dumper, system) def test_chem_descriptor_dumper(self): """Test ChemDescriptorDumper""" system = ihm.System() d1 = ihm.ChemDescriptor('EDC', smiles='CCN=C=NCCCN(C)C', inchi_key='LMDZBCPBFSXMTL-UHFFFAOYSA-N') system.orphan_chem_descriptors.append(d1) dumper = ihm.dumper._ChemDescriptorDumper() dumper.finalize(system) # Assign descriptor IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_chemical_component_descriptor.id _ihm_chemical_component_descriptor.auth_name _ihm_chemical_component_descriptor.chemical_name _ihm_chemical_component_descriptor.common_name _ihm_chemical_component_descriptor.smiles _ihm_chemical_component_descriptor.smiles_canonical _ihm_chemical_component_descriptor.inchi _ihm_chemical_component_descriptor.inchi_key 1 EDC . . CCN=C=NCCCN(C)C . . LMDZBCPBFSXMTL-UHFFFAOYSA-N # """) def test_entity_poly_dumper(self): """Test EntityPolyDumper""" system = ihm.System() e1 = ihm.Entity('ACGT') # sequence containing glycine e2 = ihm.Entity(('A', 'C', 'C', 'UNK', 'MSE')) # no glycine # All D-peptides (with glycine) e3 = ihm.Entity(('DAL', 'DCY', 'G'), alphabet=ihm.DPeptideAlphabet) # All D-peptides (without glycine) e4 = ihm.Entity(('DAL', 'DCY'), alphabet=ihm.DPeptideAlphabet) # Mix of L- and D-peptides dpep_al = ihm.DPeptideAlphabet() e5 = ihm.Entity(('A', dpep_al['DCY'], 'G')) # Non-polymeric entity e6 = ihm.Entity([ihm.NonPolymerChemComp('HEM')]) # Sequence containing a non-standard residue e7 = ihm.Entity((ihm.NonPolymerChemComp('ACE'), 'C', 'C')) system.entities.extend((e1, e2, e3, e4, e5, e6, e7)) # One protein entity is modeled (with an asym unit) the other not; # this should be reflected in pdbx_strand_id system.asym_units.append(ihm.AsymUnit(e1, 'foo', strand_id='a')) system.asym_units.append(ihm.AsymUnit(e1, 'bar', strand_id='b')) rna = ihm.Entity('AC', alphabet=ihm.RNAAlphabet) dna = ihm.Entity(('DA', 'DC'), alphabet=ihm.DNAAlphabet) hybrid = ihm.Entity(rna.sequence + dna.sequence) system.entities.extend((rna, dna, hybrid)) ed = ihm.dumper._EntityDumper() ed.finalize(system) # Assign entity IDs sd = ihm.dumper._StructAsymDumper() sd.finalize(system) # Assign asym IDs dumper = ihm.dumper._EntityPolyDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_strand_id _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can 1 polypeptide(L) no no a,b ACGT ACGT 2 polypeptide(L) no no . ACC(UNK)(MSE) ACCXM 3 polypeptide(D) no no . (DAL)(DCY)G ACG 4 polypeptide(D) no no . (DAL)(DCY) AC 5 polypeptide(L) no no . A(DCY)G ACG 7 polypeptide(L) no yes . (ACE)CC XCC 8 polyribonucleotide no no . AC AC 9 polydeoxyribonucleotide no no . (DA)(DC) AC 10 'polydeoxyribonucleotide/polyribonucleotide hybrid' no no . AC(DA)(DC) ACAC # """) def test_entity_nonpoly_dumper(self): """Test EntityNonPolyDumper""" system = ihm.System() # Polymeric entity e1 = ihm.Entity('ACGT') # Non-polymeric entity e2 = ihm.Entity([ihm.NonPolymerChemComp('HEM')], description='heme') e3 = ihm.Entity([ihm.WaterChemComp()]) # Branched entity e4 = ihm.Entity([ihm.SaccharideChemComp('NAG'), ihm.SaccharideChemComp('FUC')]) system.entities.extend((e1, e2, e3, e4)) ed = ihm.dumper._EntityDumper() ed.finalize(system) # Assign entity IDs dumper = ihm.dumper._EntityNonPolyDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 heme HEM 3 . HOH # """) def test_entity_poly_seq_dumper(self): """Test EntityPolySeqDumper""" system = ihm.System() system.entities.append(ihm.Entity('ACGT')) system.entities.append(ihm.Entity('ACC')) system.entities.append(ihm.Entity('AC', alphabet=ihm.RNAAlphabet)) system.entities.append(ihm.Entity(('DA', 'DC'), alphabet=ihm.DNAAlphabet)) # Non-polymeric entity system.entities.append(ihm.Entity([ihm.NonPolymerChemComp('HEM')])) ed = ihm.dumper._EntityDumper() ed.finalize(system) # Assign IDs dumper = ihm.dumper._EntityPolySeqDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ALA . 1 2 CYS . 1 3 GLY . 1 4 THR . 2 1 ALA . 2 2 CYS . 2 3 CYS . 3 1 A . 3 2 C . 4 1 DA . 4 2 DC . # """) def test_poly_seq_scheme_dumper(self): """Test PolySeqSchemeDumper""" system = ihm.System() e1 = ihm.Entity('ACGT') e2 = ihm.Entity('ACC') e3 = ihm.Entity('AC', alphabet=ihm.RNAAlphabet) e4 = ihm.Entity(('DA', 'DC'), alphabet=ihm.DNAAlphabet) # Non-polymeric entity e5 = ihm.Entity([ihm.NonPolymerChemComp('HEM')]) system.entities.extend((e1, e2, e3, e4, e5)) system.asym_units.append(ihm.AsymUnit(e1, 'foo')) system.asym_units.append(ihm.AsymUnit(e2, 'bar', auth_seq_id_map=5)) system.asym_units.append(ihm.AsymUnit(e3, 'baz')) system.asym_units.append(ihm.AsymUnit(e4, 'test', strand_id='X', auth_seq_id_map={1: (1, 'A'), 2: (1, 'B')})) system.asym_units.append(ihm.AsymUnit(e5, 'heme')) ihm.dumper._EntityDumper().finalize(system) ihm.dumper._StructAsymDumper().finalize(system) dumper = ihm.dumper._PolySeqSchemeDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 ALA 1 1 ALA ALA A . A 1 2 CYS 2 2 CYS CYS A . A 1 3 GLY 3 3 GLY GLY A . A 1 4 THR 4 4 THR THR A . B 2 1 ALA 6 6 ALA ALA B . B 2 2 CYS 7 7 CYS CYS B . B 2 3 CYS 8 8 CYS CYS B . C 3 1 A 1 1 A A C . C 3 2 C 2 2 C C C . D 4 1 DA 1 1 DA DA X A D 4 2 DC 1 1 DC DC X B # """) def test_poly_seq_scheme_unknown_auth_seq(self): """Test PolySeqSchemeDumper with explicit unknown auth_seq_num""" system = ihm.System() e1 = ihm.Entity('ACGT') system.entities.append(e1) a1 = ihm.AsymUnit(e1, 'foo', orig_auth_seq_id_map={1: 3, 2: 4, 3: ihm.unknown, 4: 6}) system.asym_units.append(a1) ihm.dumper._EntityDumper().finalize(system) ihm.dumper._StructAsymDumper().finalize(system) dumper = ihm.dumper._PolySeqSchemeDumper() out = _get_dumper_output(dumper, system) # If auth_seq_num is ?, so should pdb_mon_id and auth_mon_id; # see, e.g. PDB ID 8qb4 self.assertEqual(out, """# loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 ALA 1 3 ALA ALA A . A 1 2 CYS 2 4 CYS CYS A . A 1 3 GLY 3 ? ? ? A . A 1 4 THR 4 6 THR THR A . # """) def test_poly_seq_scheme_dumper_not_modeled(self): """Test PolySeqSchemeDumper with not-modeled residues""" system, m1, asym = self._make_test_model() rr = ihm.model.NotModeledResidueRange(asym, 1, 2) m1.not_modeled_residue_ranges.append(rr) m2 = ihm.model.Model(assembly=m1.assembly, protocol=m1.protocol, representation=m1.representation, name='2nd test model') rr = ihm.model.NotModeledResidueRange(asym, 2, 4) m2.not_modeled_residue_ranges.append(rr) m3 = ihm.model.Model(assembly=m1.assembly, protocol=m1.protocol, representation=m1.representation, name='3rd test model') rr = ihm.model.NotModeledResidueRange(asym, 2, 3) m3.not_modeled_residue_ranges.append(rr) mg = system.state_groups[0][0][0] mg.extend((m1, m2, m3)) ihm.dumper._EntityDumper().finalize(system) ihm.dumper._StructAsymDumper().finalize(system) dumper = ihm.dumper._PolySeqSchemeDumper() out = _get_dumper_output(dumper, system) # Only residue 2 is not-modeled in all three Models self.assertEqual(out, """# loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 ALA 1 1 ALA ALA A . A 1 2 CYS 2 ? ? ? A . A 1 3 GLY 3 3 GLY GLY A . A 1 4 THR 4 4 THR THR A . # """) def test_poly_seq_scheme_dumper_no_not_modeled(self): """Test PolySeqSchemeDumper with no not-modeled residue list""" # Older model with no not_modeled_residue_ranges member (e.g. # older versions of python-modelcif) system, m1, asym = self._make_test_model() del m1.not_modeled_residue_ranges mg = system.state_groups[0][0][0] mg.append(m1) ihm.dumper._EntityDumper().finalize(system) ihm.dumper._StructAsymDumper().finalize(system) dumper = ihm.dumper._PolySeqSchemeDumper() out = _get_dumper_output(dumper, system) # all residues are modeled self.assertEqual(out, """# loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 ALA 1 1 ALA ALA A . A 1 2 CYS 2 2 CYS CYS A . A 1 3 GLY 3 3 GLY GLY A . A 1 4 THR 4 4 THR THR A . # """) def test_nonpoly_scheme_dumper(self): """Test NonPolySchemeDumper""" system = ihm.System() e1 = ihm.Entity('ACGT') e2 = ihm.Entity([ihm.NonPolymerChemComp('HEM')]) e3 = ihm.Entity([ihm.NonPolymerChemComp('ZN')]) system.entities.extend((e1, e2, e3)) system.asym_units.append(ihm.AsymUnit(e1, 'foo')) system.asym_units.append(ihm.AsymUnit(e2, 'baz', strand_id='Q')) system.asym_units.append(ihm.AsymUnit(e3, 'bar', auth_seq_id_map=5)) ihm.dumper._EntityDumper().finalize(system) ihm.dumper._StructAsymDumper().finalize(system) dumper = ihm.dumper._NonPolySchemeDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HEM 1 1 1 HEM Q . C 3 ZN 1 6 6 ZN C . # """) def test_collection_dumper(self): """Test CollectionDumper""" system = ihm.System() c = ihm.Collection('foo', name='bar', details='more text') system.collections.append(c) dumper = ihm.dumper._CollectionDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_entry_collection.id _ihm_entry_collection.name _ihm_entry_collection.details foo bar 'more text' # """) def test_struct_asym_dumper(self): """Test StructAsymDumper""" system = ihm.System() e1 = ihm.Entity('ACGT') e2 = ihm.Entity('ACC') e1._id = 1 e2._id = 2 system.entities.extend((e1, e2)) system.asym_units.append(ihm.AsymUnit(e1, 'foo', id='Z')) system.asym_units.append(ihm.AsymUnit(e1, 'bar')) system.asym_units.append(ihm.AsymUnit(e2, 'baz', id='A')) system.asym_units.append(ihm.AsymUnit(e2, 'tmp')) dumper = ihm.dumper._StructAsymDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _struct_asym.id _struct_asym.entity_id _struct_asym.details Z 1 foo B 1 bar A 2 baz C 2 tmp # """) def test_struct_asym_dumper_duplicate_ids(self): """Test StructAsymDumper detection of duplicate user IDs""" system = ihm.System() e1 = ihm.Entity('ACGT') system.entities.append(e1) a1 = ihm.AsymUnit(e1, 'foo', id='Z') a2 = ihm.AsymUnit(e1, 'baz', id='Z') system.asym_units.extend((a1, a2)) dumper = ihm.dumper._StructAsymDumper() self.assertRaises(ValueError, dumper.finalize, system) def test_assembly_all_modeled(self): """Test AssemblyDumper, all components modeled""" system = ihm.System() e1 = ihm.Entity('ACG', description='foo') e2 = ihm.Entity('AW', description='baz') a1 = ihm.AsymUnit(e1) a2 = ihm.AsymUnit(e1) a3 = ihm.AsymUnit(e2) system.entities.extend((e1, e2)) system.asym_units.extend((a1, a2, a3)) system.orphan_assemblies.append( ihm.Assembly((a1, a2(2, 3)), name='foo')) # Out of order assembly (should be ordered on output) system.orphan_assemblies.append(ihm.Assembly((a3, a2), name='bar', description='desc1')) # Duplicate (equal) assembly (should be ignored, but description # merged in) a = ihm.Assembly((a2, a3), description='desc2') system.orphan_assemblies.append(a) # Another duplicate with duplicate description (should be ignored) a = ihm.Assembly((a2, a3), description='desc2') system.orphan_assemblies.append(a) # Duplicate (identical) assembly (should be ignored, including # description) system.orphan_assemblies.append(a) # Assign entity, asym and range IDs ihm.dumper._EntityDumper().finalize(system) ihm.dumper._StructAsymDumper().finalize(system) system._make_complete_assembly() # Assign and check segment IDs dumper = ihm.dumper._EntityPolySegmentDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_entity_poly_segment.id _ihm_entity_poly_segment.entity_id _ihm_entity_poly_segment.seq_id_begin _ihm_entity_poly_segment.seq_id_end _ihm_entity_poly_segment.comp_id_begin _ihm_entity_poly_segment.comp_id_end 1 1 1 3 ALA GLY 2 2 1 2 ALA TRP 3 1 2 3 CYS GLY # """) d = ihm.dumper._AssemblyDumper() d.finalize(system) self.assertEqual(system.complete_assembly._id, 1) self.assertEqual([asmb._id for asmb in system.orphan_assemblies], [2, 3, 3, 3, 3]) out = _get_dumper_output(d, system) self.assertEqual(out, """# loop_ _ihm_struct_assembly.id _ihm_struct_assembly.name _ihm_struct_assembly.description 1 'Complete assembly' 'All known components' 2 foo . 3 bar 'desc1 & desc2' # # loop_ _ihm_struct_assembly_details.id _ihm_struct_assembly_details.assembly_id _ihm_struct_assembly_details.parent_assembly_id _ihm_struct_assembly_details.entity_description _ihm_struct_assembly_details.entity_id _ihm_struct_assembly_details.asym_id _ihm_struct_assembly_details.entity_poly_segment_id 1 1 1 foo 1 A 1 2 1 1 foo 1 B 1 3 1 1 baz 2 C 2 4 2 2 foo 1 A 1 5 2 2 foo 1 B 3 6 3 3 foo 1 B 1 7 3 3 baz 2 C 2 # """) def test_assembly_subset_modeled(self): """Test AssemblyDumper, subset of components modeled""" system = ihm.System() e1 = ihm.Entity('ACG', description='foo') e2 = ihm.Entity('EW', description='bar') a1 = ihm.AsymUnit(e1) system.entities.extend((e1, e2)) system.asym_units.append(a1) # Note that no asym unit uses entity e2, so it won't be included # in the assembly # Assign entity and asym IDs ihm.dumper._EntityDumper().finalize(system) ihm.dumper._StructAsymDumper().finalize(system) system._make_complete_assembly() # Assign and check segment IDs dumper = ihm.dumper._EntityPolySegmentDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_entity_poly_segment.id _ihm_entity_poly_segment.entity_id _ihm_entity_poly_segment.seq_id_begin _ihm_entity_poly_segment.seq_id_end _ihm_entity_poly_segment.comp_id_begin _ihm_entity_poly_segment.comp_id_end 1 1 1 3 ALA GLY # """) d = ihm.dumper._AssemblyDumper() d.finalize(system) out = _get_dumper_output(d, system) self.assertEqual(out, """# loop_ _ihm_struct_assembly.id _ihm_struct_assembly.name _ihm_struct_assembly.description 1 'Complete assembly' 'All known components' # # loop_ _ihm_struct_assembly_details.id _ihm_struct_assembly_details.assembly_id _ihm_struct_assembly_details.parent_assembly_id _ihm_struct_assembly_details.entity_description _ihm_struct_assembly_details.entity_id _ihm_struct_assembly_details.asym_id _ihm_struct_assembly_details.entity_poly_segment_id 1 1 1 foo 1 A 1 # """) def test_external_reference_dumper(self): """Test ExternalReferenceDumper""" system = ihm.System() repo1 = ihm.location.Repository(doi="foo", details='test repo') repo2 = ihm.location.Repository(doi="10.5281/zenodo.46266", url='nup84-v1.0.zip', top_directory=os.path.join('foo', 'bar')) repo3 = ihm.location.Repository(doi="10.5281/zenodo.58025", url='foo.spd') loc = ihm.location.InputFileLocation(repo=repo1, path='bar', file_format='TXT') system.locations.append(loc) # Duplicates should be ignored loc = ihm.location.InputFileLocation(repo=repo1, path='bar') system.locations.append(loc) # Different file, same repository loc = ihm.location.InputFileLocation(repo=repo1, path='baz') system.locations.append(loc) # Different repository loc = ihm.location.OutputFileLocation(repo=repo2, path='baz') system.locations.append(loc) # Repository containing a single file (not an archive) loc = ihm.location.InputFileLocation(repo=repo3, path='foo.spd', details='EM micrographs') system.locations.append(loc) # Path can also be None for Repository containing a single file loc = ihm.location.InputFileLocation(repo=repo3, path=None, details='EM micrographs') system.locations.append(loc) with utils.temporary_directory('') as tmpdir: # Force tmpdir to be a relative path (in Python 3.12 or later # it will be an absolute path) rel_tmpdir = os.path.relpath(tmpdir) bar = os.path.join(rel_tmpdir, 'test_mmcif_extref.tmp') with open(bar, 'w') as f: f.write("abcd") # Local file system.locations.append(ihm.location.WorkflowFileLocation(bar)) # DatabaseLocations should be ignored system.locations.append(ihm.location.PDBLocation( '1abc', '1.0', 'test details')) d = ihm.dumper._ExternalReferenceDumper() d.finalize(system) self.assertEqual(len(d._ref_by_id), 6) self.assertEqual(len(d._repo_by_id), 4) # Repeated calls to finalize() should yield identical results d.finalize(system) self.assertEqual(len(d._ref_by_id), 6) self.assertEqual(len(d._repo_by_id), 4) out = _get_dumper_output(d, system) self.assertEqual(out, """# loop_ _ihm_external_reference_info.reference_id _ihm_external_reference_info.reference_provider _ihm_external_reference_info.reference_type _ihm_external_reference_info.reference _ihm_external_reference_info.refers_to _ihm_external_reference_info.associated_url _ihm_external_reference_info.details 1 . DOI foo Other . 'test repo' 2 Zenodo DOI 10.5281/zenodo.46266 Archive nup84-v1.0.zip . 3 Zenodo DOI 10.5281/zenodo.58025 File foo.spd . 4 . 'Supplementary Files' . Other . . # # loop_ _ihm_external_files.id _ihm_external_files.reference_id _ihm_external_files.file_path _ihm_external_files.content_type _ihm_external_files.file_format _ihm_external_files.file_size_bytes _ihm_external_files.details 1 1 bar 'Input data or restraints' TXT . . 2 1 baz 'Input data or restraints' . . . 3 2 foo/bar/baz 'Modeling or post-processing output' . . . 4 3 foo.spd 'Input data or restraints' . . 'EM micrographs' 5 3 . 'Input data or restraints' . . 'EM micrographs' 6 4 %s 'Modeling workflow or script' . 4 . # """ % bar.replace(os.sep, '/')) def test_dataset_dumper_duplicates_details(self): """DatasetDumper ignores duplicate datasets with differing details""" system = ihm.System() dump = ihm.dumper._DatasetDumper() loc = ihm.location.PDBLocation('1abc', '1.0', 'test details') ds1 = ihm.dataset.PDBDataset(loc) system.orphan_datasets.append(ds1) # A duplicate dataset should be ignored even if details differ loc = ihm.location.PDBLocation('1abc', '1.0', 'other details') ds2 = ihm.dataset.PDBDataset(loc) system.orphan_datasets.append(ds2) ds3 = ihm.dataset.PDBDataset(loc, details='other dataset details') system.orphan_datasets.append(ds3) dump.finalize(system) # Assign IDs self.assertEqual(ds1._id, 1) self.assertEqual(ds2._id, 1) self.assertEqual(ds3._id, 1) self.assertEqual(len(dump._dataset_by_id), 1) def test_dataset_dumper_duplicates_samedata_sameloc(self): """DatasetDumper doesn't duplicate same datasets in same location""" system = ihm.System() loc1 = ihm.location.DatabaseLocation("abc", "1.0", "") # Identical datasets in the same location aren't duplicated cx1 = ihm.dataset.CXMSDataset(loc1) cx2 = ihm.dataset.CXMSDataset(loc1) dump = ihm.dumper._DatasetDumper() system.orphan_datasets.extend((cx1, cx2)) dump.finalize(system) # Assign IDs self.assertEqual(cx1._id, 1) self.assertEqual(cx2._id, 1) self.assertEqual(len(dump._dataset_by_id), 1) def test_dataset_dumper_duplicates_samedata_diffloc(self): """DatasetDumper is OK with same datasets in different locations""" system = ihm.System() loc1 = ihm.location.DatabaseLocation("abc", "1.0", "") loc2 = ihm.location.DatabaseLocation("xyz", "1.0", "") cx1 = ihm.dataset.CXMSDataset(loc1) cx2 = ihm.dataset.CXMSDataset(loc2) dump = ihm.dumper._DatasetDumper() system.orphan_datasets.extend((cx1, cx2)) dump.finalize(system) # Assign IDs self.assertEqual(cx1._id, 1) self.assertEqual(cx2._id, 2) self.assertEqual(len(dump._dataset_by_id), 2) def test_dataset_dumper_duplicates_diffdata_sameloc(self): """DatasetDumper is OK with different datasets in same location""" system = ihm.System() # Different datasets in same location are OK (but odd) loc2 = ihm.location.DatabaseLocation("xyz", "1.0", "") cx2 = ihm.dataset.CXMSDataset(loc2) em3d = ihm.dataset.EMDensityDataset(loc2) dump = ihm.dumper._DatasetDumper() system.orphan_datasets.extend((cx2, em3d)) dump.finalize(system) # Assign IDs self.assertEqual(cx2._id, 1) self.assertEqual(em3d._id, 2) self.assertEqual(len(dump._dataset_by_id), 2) def test_dataset_dumper_allow_duplicates(self): """DatasetDumper is OK with duplicates if allow_duplicates=True""" system = ihm.System() emloc1 = ihm.location.EMDBLocation("abc") emloc2 = ihm.location.EMDBLocation("abc") emloc1._allow_duplicates = True em3d_1 = ihm.dataset.EMDensityDataset(emloc1) em3d_2 = ihm.dataset.EMDensityDataset(emloc2) dump = ihm.dumper._DatasetDumper() system.orphan_datasets.extend((em3d_1, em3d_2)) dump.finalize(system) # Assign IDs self.assertEqual(em3d_1._id, 1) self.assertEqual(em3d_2._id, 2) self.assertEqual(len(dump._dataset_by_id), 2) def test_dataset_dumper_group_finalize(self): """Test DatasetDumper finalize of dataset groups""" system = ihm.System() loc = ihm.location.InputFileLocation(repo='foo', path='baz') ds1 = ihm.dataset.CXMSDataset(loc) group1 = ihm.dataset.DatasetGroup([ds1]) # Duplicate group group2 = ihm.dataset.DatasetGroup([ds1]) system.orphan_datasets.append(ds1) system.orphan_dataset_groups.extend((group1, group2)) d = ihm.dumper._DatasetDumper() d.finalize(system) # Assign IDs self.assertEqual(len(d._dataset_by_id), 1) self.assertEqual(len(d._dataset_group_by_id), 1) # Repeated calls to finalize should yield identical results d.finalize(system) self.assertEqual(len(d._dataset_by_id), 1) self.assertEqual(len(d._dataset_group_by_id), 1) def test_dataset_dumper_dump(self): """Test DatasetDumper.dump()""" system = ihm.System() loc = ihm.location.InputFileLocation(repo='foo', path='bar') loc._id = 97 ds1 = ihm.dataset.CXMSDataset(loc) system.orphan_datasets.append(ds1) # group1 contains just the first dataset (but duplicated) group1 = ihm.dataset.DatasetGroup([ds1, ds1], name="first") system.orphan_dataset_groups.append(group1) loc = ihm.location.InputFileLocation(repo='foo2', path='bar2') loc._id = 98 ds2 = ihm.dataset.CXMSDataset(loc) # group2 contains all datasets so far (ds1 & ds2) group2 = ihm.dataset.DatasetGroup([ds1, ds2], name="all so far") system.orphan_dataset_groups.append(group2) loc = ihm.location.PDBLocation('1abc', '1.0', 'test details') ds3 = ihm.dataset.PDBDataset(loc, details='test dataset details') system.orphan_datasets.append(ds3) ds3.parents.append(ds2) # Ignore duplicates ds3.parents.append(ds2) # Derived dataset with (shared) transformation loc = ihm.location.PDBLocation('1cde', version='foo', details='bar') dst = ihm.dataset.Dataset(loc, details='bar') t = ihm.geometry.Transformation( rot_matrix=[[-0.64, 0.09, 0.77], [0.76, -0.12, 0.64], [0.15, 0.99, 0.01]], tr_vector=[1., 2., 3.]) td = ihm.dataset.TransformedDataset(dst, transform=t) ds3.parents.append(td) loc = ihm.location.PDBLocation('1cdf', version='foo', details='bar') dst = ihm.dataset.Dataset(loc, details='baz') # Same transformation as before td = ihm.dataset.TransformedDataset(dst, transform=t) ds3.parents.append(td) # Dataset with no location ds4 = ihm.dataset.PDBDataset(None) system.orphan_datasets.append(ds4) # Dataset with multiple locations ds5 = ihm.dataset.PDBDataset(None) loc = ihm.location.PDBLocation('2xyz', '1.0', 'other details') ds5._add_location(loc) loc = ihm.location.InputFileLocation(repo='foo', path='bar') loc._id = 102 ds5._add_location(loc) system.orphan_datasets.append(ds5) # Transformation not referenced by any object trans2 = ihm.geometry.Transformation([[1, 0, 0], [0, 1, 0], [0, 0, 1]], [4., 5., 6.]) system._orphan_dataset_transforms.append(trans2) d = ihm.dumper._DatasetDumper() d.finalize(system) # Assign IDs out = _get_dumper_output(d, system) self.assertEqual(out, """# loop_ _ihm_dataset_list.id _ihm_dataset_list.data_type _ihm_dataset_list.database_hosted _ihm_dataset_list.details 1 'Crosslinking-MS data' NO . 2 'Crosslinking-MS data' NO . 3 Other YES bar 4 Other YES baz 5 'Experimental model' YES 'test dataset details' 6 'Experimental model' NO . 7 'Experimental model' YES . # # loop_ _ihm_dataset_group.id _ihm_dataset_group.name _ihm_dataset_group.application _ihm_dataset_group.details 1 first . . 2 'all so far' . . # # loop_ _ihm_dataset_group_link.group_id _ihm_dataset_group_link.dataset_list_id 1 1 2 1 2 2 # # loop_ _ihm_dataset_external_reference.id _ihm_dataset_external_reference.dataset_list_id _ihm_dataset_external_reference.file_id 1 1 97 2 2 98 3 7 102 # # loop_ _ihm_dataset_related_db_reference.id _ihm_dataset_related_db_reference.dataset_list_id _ihm_dataset_related_db_reference.db_name _ihm_dataset_related_db_reference.accession_code _ihm_dataset_related_db_reference.version _ihm_dataset_related_db_reference.details 1 3 PDB 1cde foo bar 2 4 PDB 1cdf foo bar 3 5 PDB 1abc 1.0 'test details' 4 7 PDB 2xyz 1.0 'other details' # # loop_ _ihm_related_datasets.dataset_list_id_derived _ihm_related_datasets.dataset_list_id_primary _ihm_related_datasets.transformation_id 5 2 . 5 3 1 5 4 1 # # loop_ _ihm_data_transformation.id _ihm_data_transformation.rot_matrix[1][1] _ihm_data_transformation.rot_matrix[2][1] _ihm_data_transformation.rot_matrix[3][1] _ihm_data_transformation.rot_matrix[1][2] _ihm_data_transformation.rot_matrix[2][2] _ihm_data_transformation.rot_matrix[3][2] _ihm_data_transformation.rot_matrix[1][3] _ihm_data_transformation.rot_matrix[2][3] _ihm_data_transformation.rot_matrix[3][3] _ihm_data_transformation.tr_vector[1] _ihm_data_transformation.tr_vector[2] _ihm_data_transformation.tr_vector[3] 1 -0.640000 0.760000 0.150000 0.090000 -0.120000 0.990000 0.770000 0.640000 0.010000 1.000 2.000 3.000 2 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 4.000 5.000 6.000 # """) def test_dataset_dumper_dump_invalid_transform(self): """Test DatasetDumper.dump() with invalid transformed dataset""" system = ihm.System() loc = ihm.location.PDBLocation('1cdf', version='foo', details='bar') loc._id = 1 dst = ihm.dataset.Dataset(loc, details='baz') t = ihm.geometry.Transformation( rot_matrix=None, tr_vector=[1., 2., 3.]) td = ihm.dataset.TransformedDataset(dst, transform=t) loc = ihm.location.InputFileLocation(repo='foo', path='bar') loc._id = 2 ds2 = ihm.dataset.CXMSDataset(loc) ds2.parents.append(td) system.orphan_datasets.append(ds2) d = ihm.dumper._DatasetDumper() d.finalize(system) # Assign IDs self.assertRaises(ValueError, _get_dumper_output, d, system) # OK if checks are disabled _ = _get_dumper_output(d, system, check=False) def test_model_representation_dump(self): """Test ModelRepresentationDumper""" system = ihm.System() e1 = ihm.Entity('AAAAAAAA', description='bar') system.entities.append(e1) asym = ihm.AsymUnit(e1, 'foo') system.asym_units.append(asym) s1 = ihm.representation.AtomicSegment( asym(1, 2), starting_model=None, rigid=True) s2 = ihm.representation.ResidueSegment( asym(3, 4), starting_model=None, rigid=False, primitive='sphere') s3 = ihm.representation.MultiResidueSegment( asym(1, 2), starting_model=None, rigid=False, primitive='gaussian') s4 = ihm.representation.FeatureSegment( asym(3, 4), starting_model=None, rigid=True, primitive='other', count=3, description='test segment') r1 = ihm.representation.Representation((s1, s2), name='foo', details='foo details') r2 = ihm.representation.Representation((s3, s4), name='bar') system.orphan_representations.extend((r1, r2)) e1._id = 42 asym._id = 'X' # Assign segment IDs ihm.dumper._EntityPolySegmentDumper().finalize(system) dumper = ihm.dumper._ModelRepresentationDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_model_representation.id _ihm_model_representation.name _ihm_model_representation.details 1 foo 'foo details' 2 bar . # # loop_ _ihm_model_representation_details.id _ihm_model_representation_details.representation_id _ihm_model_representation_details.entity_id _ihm_model_representation_details.entity_description _ihm_model_representation_details.entity_asym_id _ihm_model_representation_details.entity_poly_segment_id _ihm_model_representation_details.model_object_primitive _ihm_model_representation_details.starting_model_id _ihm_model_representation_details.model_mode _ihm_model_representation_details.model_granularity _ihm_model_representation_details.model_object_count _ihm_model_representation_details.description 1 1 42 bar X 1 atomistic . rigid by-atom . . 2 1 42 bar X 2 sphere . flexible by-residue . . 3 2 42 bar X 1 gaussian . flexible multi-residue . . 4 2 42 bar X 2 other . rigid by-feature 3 'test segment' # """) def test_starting_model_dumper(self): """Test StartingModelDumper""" class TestStartingModel(ihm.startmodel.StartingModel): def get_atoms(self): asym = self.asym_unit return [ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', type_symbol='C', x=-8.0, y=-5.0, z=91.0, biso=42.)] def get_seq_dif(self): return [ihm.startmodel.MSESeqDif(db_seq_id=5, seq_id=7), ihm.startmodel.SeqDif(db_seq_id=6, seq_id=8, db_comp_id='LEU', details='LEU -> GLY')] system = ihm.System() e1 = ihm.Entity('A' * 6 + 'MG' + 'A' * 12, description='foo') system.entities.append(e1) asym = ihm.AsymUnit(e1, 'bar') system.asym_units.append(asym) loc = ihm.location.PDBLocation('1abc', '1.0', 'test details') dstemplate = ihm.dataset.PDBDataset(loc) loc = ihm.location.PDBLocation('2xyz', '1.0', 'test details') dstarget = ihm.dataset.PDBDataset(loc) ali = ihm.location.InputFileLocation(repo='foo', path='test.ali') script = ihm.location.WorkflowFileLocation(repo='foo', path='test.py') software = ihm.Software(name='test', classification='test code', description='Some test program', version=1, location='http://test.org') s1 = ihm.startmodel.Template( dataset=dstemplate, asym_id='C', seq_id_range=(-9, 0), # 1,10 in IHM numbering template_seq_id_range=(101, 110), sequence_identity=30.) s2 = ihm.startmodel.Template( dataset=dstemplate, asym_id='D', seq_id_range=(-5, 2), # 5,12 in IHM numbering template_seq_id_range=(201, 210), sequence_identity=ihm.startmodel.SequenceIdentity(40., None), alignment_file=ali) s3 = ihm.startmodel.Template( dataset=dstemplate, asym_id='D', seq_id_range=(-5, 2), # 5,12 in IHM numbering template_seq_id_range=(201, 210), sequence_identity=ihm.startmodel.SequenceIdentity(ihm.unknown, ihm.unknown), alignment_file=ali) s4 = ihm.startmodel.Template( dataset=dstemplate, asym_id='D', seq_id_range=(None, None), template_seq_id_range=(None, None), sequence_identity=ihm.startmodel.SequenceIdentity(None, None), alignment_file=ali) sm = TestStartingModel(asym(1, 12), dstarget, 'A', [s1, s2, s3, s4], offset=10, script_file=script, software=software) system.orphan_starting_models.append(sm) sm = TestStartingModel(asym(1, 15), dstarget, 'A', [], description="test desc") system.orphan_starting_models.append(sm) e1._id = 42 asym._id = 99 dstemplate._id = 101 dstarget._id = 102 ali._id = 5 script._id = 8 software._id = 99 # Assign and check segment IDs dumper = ihm.dumper._EntityPolySegmentDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_entity_poly_segment.id _ihm_entity_poly_segment.entity_id _ihm_entity_poly_segment.seq_id_begin _ihm_entity_poly_segment.seq_id_end _ihm_entity_poly_segment.comp_id_begin _ihm_entity_poly_segment.comp_id_end 1 42 1 12 ALA ALA 2 42 1 15 ALA ALA # """) dumper = ihm.dumper._StartingModelDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_starting_model_details.starting_model_id _ihm_starting_model_details.entity_id _ihm_starting_model_details.entity_description _ihm_starting_model_details.asym_id _ihm_starting_model_details.entity_poly_segment_id _ihm_starting_model_details.starting_model_source _ihm_starting_model_details.starting_model_auth_asym_id _ihm_starting_model_details.starting_model_sequence_offset _ihm_starting_model_details.dataset_list_id _ihm_starting_model_details.description 1 42 foo 99 1 'experimental model' A 10 102 . 2 42 foo 99 2 'experimental model' A 0 102 'test desc' # # loop_ _ihm_starting_computational_models.starting_model_id _ihm_starting_computational_models.software_id _ihm_starting_computational_models.script_file_id 1 99 8 # # loop_ _ihm_starting_comparative_models.id _ihm_starting_comparative_models.starting_model_id _ihm_starting_comparative_models.starting_model_auth_asym_id _ihm_starting_comparative_models.starting_model_seq_id_begin _ihm_starting_comparative_models.starting_model_seq_id_end _ihm_starting_comparative_models.template_auth_asym_id _ihm_starting_comparative_models.template_seq_id_begin _ihm_starting_comparative_models.template_seq_id_end _ihm_starting_comparative_models.template_sequence_identity _ihm_starting_comparative_models.template_sequence_identity_denominator _ihm_starting_comparative_models.template_dataset_list_id _ihm_starting_comparative_models.alignment_file_id 1 1 A 1 10 C 101 110 30.000 1 101 . 2 1 A 5 12 D 201 210 40.000 . 101 5 3 1 A 5 12 D 201 210 ? ? 101 5 4 1 A . . D . . . . 101 5 # # loop_ _ihm_starting_model_coord.starting_model_id _ihm_starting_model_coord.group_PDB _ihm_starting_model_coord.id _ihm_starting_model_coord.type_symbol _ihm_starting_model_coord.atom_id _ihm_starting_model_coord.comp_id _ihm_starting_model_coord.entity_id _ihm_starting_model_coord.asym_id _ihm_starting_model_coord.seq_id _ihm_starting_model_coord.Cartn_x _ihm_starting_model_coord.Cartn_y _ihm_starting_model_coord.Cartn_z _ihm_starting_model_coord.B_iso_or_equiv _ihm_starting_model_coord.ordinal_id 1 ATOM 1 C CA ALA 42 99 1 -8.000 -5.000 91.000 42.000 1 2 ATOM 1 C CA ALA 42 99 1 -8.000 -5.000 91.000 42.000 2 # # loop_ _ihm_starting_model_seq_dif.id _ihm_starting_model_seq_dif.entity_id _ihm_starting_model_seq_dif.asym_id _ihm_starting_model_seq_dif.seq_id _ihm_starting_model_seq_dif.comp_id _ihm_starting_model_seq_dif.starting_model_id _ihm_starting_model_seq_dif.db_asym_id _ihm_starting_model_seq_dif.db_seq_id _ihm_starting_model_seq_dif.db_comp_id _ihm_starting_model_seq_dif.details 1 42 99 7 MET 1 A 5 MSE 'Conversion of modified residue MSE to MET' 2 42 99 8 GLY 1 A 6 LEU 'LEU -> GLY' 3 42 99 7 MET 2 A 5 MSE 'Conversion of modified residue MSE to MET' 4 42 99 8 GLY 2 A 6 LEU 'LEU -> GLY' # """) def test_starting_model_dumper_atom_range(self): """Test StartingModelDumper with invalid atom seq_id""" class TestStartingModel(ihm.startmodel.StartingModel): def get_atoms(self): asym = self.asym_unit return [ihm.model.Atom(asym_unit=asym, seq_id=99, atom_id='CA', type_symbol='C', x=-8.0, y=-5.0, z=91.0, biso=42.)] system = ihm.System() e1 = ihm.Entity('ACG', description='foo') system.entities.append(e1) asym = ihm.AsymUnit(e1, 'bar') system.asym_units.append(asym) loc = ihm.location.PDBLocation('2xyz', '1.0', 'test details') dstarget = ihm.dataset.PDBDataset(loc) sm = TestStartingModel(asym(1, 3), dstarget, 'A', []) system.orphan_starting_models.append(sm) e1._id = 42 asym._id = 99 dstarget._id = 8 sm._id = 5 # Assign and check segment IDs dumper = ihm.dumper._EntityPolySegmentDumper() dumper.finalize(system) dumper = ihm.dumper._StartingModelDumper() with self.assertRaises(IndexError) as cm: _get_dumper_output(dumper, system) self.assertIn('Starting model 5 atom seq_id (99) out of range (1-3)', str(cm.exception)) # Should work with checks disabled _ = _get_dumper_output(dumper, system, check=False) def test_modeling_protocol(self): """Test ProtocolDumper""" class MockObject: pass system = ihm.System() p1 = ihm.protocol.Protocol('equilibration') assembly = ihm.Assembly(description='foo') assembly._id = 42 dsg = MockObject() dsg._id = 99 dsg2 = MockObject() dsg2._id = 101 software = MockObject() software._id = 80 script = MockObject() script._id = 90 p1.steps.append(ihm.protocol.Step( assembly=assembly, dataset_group=dsg, method='Monte Carlo', num_models_begin=0, num_models_end=500, multi_scale=True, ensemble=True, name='s1')) p1.steps.append(ihm.protocol.Step( assembly=assembly, dataset_group=dsg, method='Replica exchange', num_models_begin=500, num_models_end=2000, multi_scale=True, ensemble=False)) system.orphan_protocols.append(p1) p2 = ihm.protocol.Protocol('sampling', details='extra details') p2.steps.append(ihm.protocol.Step( assembly=assembly, dataset_group=dsg2, method='Replica exchange', num_models_begin=2000, num_models_end=1000, multi_scale=True, software=software, script_file=script, description='test step')) system.orphan_protocols.append(p2) dumper = ihm.dumper._ProtocolDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_modeling_protocol.id _ihm_modeling_protocol.protocol_name _ihm_modeling_protocol.num_steps _ihm_modeling_protocol.details 1 equilibration 2 . 2 sampling 1 'extra details' # # loop_ _ihm_modeling_protocol_details.id _ihm_modeling_protocol_details.protocol_id _ihm_modeling_protocol_details.step_id _ihm_modeling_protocol_details.struct_assembly_id _ihm_modeling_protocol_details.dataset_group_id _ihm_modeling_protocol_details.step_name _ihm_modeling_protocol_details.step_method _ihm_modeling_protocol_details.num_models_begin _ihm_modeling_protocol_details.num_models_end _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.ordered_flag _ihm_modeling_protocol_details.ensemble_flag _ihm_modeling_protocol_details.software_id _ihm_modeling_protocol_details.script_file_id _ihm_modeling_protocol_details.description 1 1 1 42 99 s1 'Monte Carlo' 0 500 YES NO NO YES . . . 2 1 2 42 99 . 'Replica exchange' 500 2000 YES NO NO NO . . . 3 2 1 42 101 . 'Replica exchange' 2000 1000 YES NO NO NO 80 90 'test step' # """) def test_post_process(self): """Test PostProcessDumper""" class MockObject: pass system = ihm.System() p1 = ihm.protocol.Protocol('refinement') system.orphan_protocols.append(p1) a1 = ihm.analysis.Analysis() a1.steps.append(ihm.analysis.EmptyStep()) a2 = ihm.analysis.Analysis() a2.steps.append(ihm.analysis.FilterStep( feature='energy/score', num_models_begin=1000, num_models_end=200)) a2.steps.append(ihm.analysis.ClusterStep( feature='RMSD', num_models_begin=200, num_models_end=42)) asmb1 = MockObject() asmb1._id = 101 dg1 = MockObject() dg1._id = 301 software = MockObject() software._id = 401 script = MockObject() script._id = 501 a2.steps.append(ihm.analysis.ValidationStep( feature='energy/score', num_models_begin=42, num_models_end=42, assembly=asmb1, dataset_group=dg1, software=software, script_file=script, details='test step')) p1.analyses.extend((a1, a2)) dumper = ihm.dumper._ProtocolDumper() dumper.finalize(system) # assign protocol IDs dumper = ihm.dumper._PostProcessDumper() dumper.finalize(system) # assign analysis IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_modeling_post_process.id _ihm_modeling_post_process.protocol_id _ihm_modeling_post_process.analysis_id _ihm_modeling_post_process.step_id _ihm_modeling_post_process.type _ihm_modeling_post_process.feature _ihm_modeling_post_process.num_models_begin _ihm_modeling_post_process.num_models_end _ihm_modeling_post_process.struct_assembly_id _ihm_modeling_post_process.dataset_group_id _ihm_modeling_post_process.software_id _ihm_modeling_post_process.script_file_id _ihm_modeling_post_process.details 1 1 1 1 none none . . . . . . . 2 1 2 1 filter energy/score 1000 200 . . . . . 3 1 2 2 cluster RMSD 200 42 . . . . . 4 1 2 3 validation energy/score 42 42 101 301 401 501 'test step' # """) def test_model_dumper(self): """Test ModelDumper""" class MockObject: pass system = ihm.System() state = ihm.model.State() system.state_groups.append(ihm.model.StateGroup([state])) protocol = MockObject() protocol._id = 42 assembly = ihm.Assembly() assembly._id = 99 representation = ihm.representation.Representation() representation._id = 32 model = ihm.model.Model(assembly=assembly, protocol=protocol, representation=representation, name='test model') model2 = ihm.model.Model(assembly=assembly, protocol=protocol, representation=representation, name='test model2') model3 = ihm.model.Model(assembly=assembly, protocol=protocol, representation=representation, name='test model3') # Existing IDs should be overwritten model3._id = 999 # Group contains multiple copies of model - should be pruned on output group = ihm.model.ModelGroup([model, model, model2], name='Group1') state.append(group) group2 = ihm.model.ModelGroup([model3], name='Group 2', details='group 2 details') state.append(group2) dumper = ihm.dumper._ModelDumper() dumper.finalize(system) # assign model/group IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.assembly_id _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 'test model' 99 42 32 2 'test model2' 99 42 32 3 'test model3' 99 42 32 # # loop_ _ihm_model_group.id _ihm_model_group.name _ihm_model_group.details 1 Group1 . 2 'Group 2' 'group 2 details' # # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 1 2 2 3 # """) def test_model_representative_dumper(self): """Test ModelRepresentativeDumper""" class MockObject: pass system = ihm.System() m1 = ihm.model.Model(assembly=None, protocol=None, representation=None) m1._id = 5 m2 = ihm.model.Model(assembly=None, protocol=None, representation=None) m2._id = 8 group = ihm.model.ModelGroup([m1, m2]) group._id = 42 self.assertRaises(ValueError, ihm.model.ModelRepresentative, m1, "bad criteria") group.representatives.extend([ ihm.model.ModelRepresentative(m1, "medoid"), ihm.model.ModelRepresentative(m2, "lowest energy")]) state = ihm.model.State() state.append(group) system.state_groups.append(ihm.model.StateGroup([state])) dumper = ihm.dumper._ModelRepresentativeDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_model_representative.id _ihm_model_representative.model_group_id _ihm_model_representative.model_id _ihm_model_representative.selection_criteria 1 42 5 medoid 2 42 8 'lowest energy' # """) def _make_test_model(self, water=False, seq='ACGT'): class MockObject: pass system = ihm.System() state = ihm.model.State() system.state_groups.append(ihm.model.StateGroup([state])) if water: e1 = ihm.Entity([ihm.WaterChemComp()]) else: e1 = ihm.Entity(seq, description="Nup84") e1._id = 9 system.entities.append(e1) if water: asym = ihm.WaterAsymUnit(e1, number=3, details='foo') else: asym = ihm.AsymUnit(e1, 'foo') asym._id = 'X' system.asym_units.append(asym) protocol = MockObject() protocol._id = 42 assembly = ihm.Assembly([asym]) assembly._id = 99 s = ihm.representation.ResidueSegment(asym, True, 'sphere') representation = ihm.representation.Representation([s]) representation._id = 32 model = ihm.model.Model(assembly=assembly, protocol=protocol, representation=representation, name='test model') group = ihm.model.ModelGroup([model]) state.append(group) return system, model, asym def test_range_checker_asmb_asym(self): """Test RangeChecker class checking assembly asym ID match""" system, model, asym = self._make_test_model() asym2 = ihm.AsymUnit(asym.entity, 'bar') asym2._id = 'Y' system.asym_units.append(asym2) # Handle multiple ranges for a given asym model.assembly.append(asym(1, 2)) # RangeChecker should ignore entities in the assembly model.assembly.append(asym.entity) # Everything is represented for a in asym, asym2: s = ihm.representation.AtomicSegment(a, rigid=True) model.representation.append(s) s = ihm.representation.FeatureSegment(a, rigid=False, primitive='sphere', count=2) model.representation.append(s) rngcheck = ihm.dumper._RangeChecker(model) rngcheck_nocheck = ihm.dumper._RangeChecker(model, check=False) # Atom is OK (good asym) atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Sphere is OK (good asym) sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) rngcheck(sphere) # Atom is not OK (bad asym) atom = ihm.model.Atom(asym_unit=asym2, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) rngcheck_nocheck(atom) # Sphere is not OK (bad asym) sphere = ihm.model.Sphere(asym_unit=asym2, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) rngcheck_nocheck(sphere) def test_range_checker_asmb_seq_id(self): """Test RangeChecker class checking assembly seq_id range""" system, model, asym = self._make_test_model() # Only part of asym is in the assembly asmb = ihm.Assembly([asym(1, 2)]) model.assembly = asmb # Everything is represented s = ihm.representation.AtomicSegment(asym, rigid=True) model.representation.append(s) s = ihm.representation.FeatureSegment(asym, rigid=False, primitive='sphere', count=2) model.representation.append(s) rngcheck = ihm.dumper._RangeChecker(model) self.assertIsNone(rngcheck._last_asmb_range_matched) self.assertIsNone(rngcheck._last_asmb_asym_matched) # Atom is OK (good range) atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Cache should now be set self.assertEqual(rngcheck._last_asmb_range_matched, (1, 2)) self.assertEqual(rngcheck._last_asmb_asym_matched, 'X') # 2nd check with same seq_id should use the cache atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Sphere is OK (good range) sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) rngcheck(sphere) # Atom is not OK (bad range) atom = ihm.model.Atom(asym_unit=asym, seq_id=10, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) # Sphere is not OK (bad range) sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 10), x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) def test_range_checker_duplicate_atoms(self): """Test RangeChecker class checking duplicate atoms""" system, model, asym = self._make_test_model() asmb = ihm.Assembly([asym]) model.assembly = asmb # Everything is represented s = ihm.representation.AtomicSegment(asym, rigid=True) model.representation.append(s) rngcheck = ihm.dumper._RangeChecker(model) atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Error to write another atom with same atom_id to same seq_id atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) # It's fine though if alt_id is different atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', type_symbol='C', x=1.0, y=2.0, z=3.0, alt_id='A') rngcheck(atom) atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', type_symbol='C', x=1.0, y=2.0, z=3.0, alt_id='B') rngcheck(atom) atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', type_symbol='C', x=1.0, y=2.0, z=3.0, alt_id='A') self.assertRaises(ValueError, rngcheck, atom) def test_range_checker_duplicate_atoms_water(self): """Test RangeChecker class checking duplicate water atoms""" system, model, asym = self._make_test_model(water=True) asmb = ihm.Assembly([asym]) model.assembly = asmb # Everything is represented s = ihm.representation.AtomicSegment(asym, rigid=True) model.representation.append(s) rngcheck = ihm.dumper._RangeChecker(model) atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='O', type_symbol='O', x=1.0, y=2.0, z=3.0, het=True) rngcheck(atom) atom = ihm.model.Atom(asym_unit=asym, seq_id=2, atom_id='O', type_symbol='O', x=1.0, y=2.0, z=3.0, het=True) rngcheck(atom) atom = ihm.model.Atom(asym_unit=asym, seq_id=2, atom_id='O', type_symbol='O', x=1.0, y=2.0, z=3.0, het=True) self.assertRaises(ValueError, rngcheck, atom) def test_range_checker_repr_asym(self): """Test RangeChecker class checking representation asym ID match""" system, model, asym = self._make_test_model() asym2 = ihm.AsymUnit(asym.entity, 'bar') asym2._id = 'Y' system.asym_units.append(asym2) model.assembly.append(asym2) # Add multiple representation segments for asym s = ihm.representation.AtomicSegment(asym(1, 2), rigid=True) model.representation.append(s) s = ihm.representation.FeatureSegment(asym, rigid=False, primitive='sphere', count=2) model.representation.append(s) rngcheck = ihm.dumper._RangeChecker(model) # Atom is OK (good asym) atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Sphere is OK (good asym) sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) rngcheck(sphere) # Atom is not OK (bad asym) atom = ihm.model.Atom(asym_unit=asym2, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) # Sphere is not OK (bad asym) sphere = ihm.model.Sphere(asym_unit=asym2, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) def test_range_checker_repr_seq_id(self): """Test RangeChecker class checking representation seq_id range""" system, model, asym = self._make_test_model() asym2 = ihm.AsymUnit(asym.entity, 'bar') asym2._id = 'Y' system.asym_units.append(asym2) model.assembly.append(asym2) heme = ihm.NonPolymerChemComp("HEM", name='heme', formula='C34 H32 Fe N4 O4') entity_heme = ihm.Entity([heme], description='Heme') entity_heme._id = 99 system.entities.append(entity_heme) asym_nonpol = ihm.AsymUnit(entity_heme, 'baz') asym_nonpol._id = 'Z' system.asym_units.append(asym_nonpol) model.assembly.append(asym_nonpol) # Add multiple representation segments for asym2 s = ihm.representation.AtomicSegment(asym2(1, 2), rigid=True) model.representation.append(s) s = ihm.representation.FeatureSegment(asym2(1, 2), rigid=False, primitive='sphere', count=2) model.representation.append(s) s = ihm.representation.AtomicSegment(asym_nonpol, rigid=True) model.representation.append(s) rngcheck = ihm.dumper._RangeChecker(model) self.assertIsNone(rngcheck._last_repr_segment_matched) # Atom is OK (good range) atom = ihm.model.Atom(asym_unit=asym2, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Cache should now be set self.assertEqual( rngcheck._last_repr_segment_matched.asym_unit.seq_id_range, (1, 2)) # 2nd check with same seq_id should use the cache atom = ihm.model.Atom(asym_unit=asym2, seq_id=1, atom_id='CA', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Sphere is OK (good range) sphere = ihm.model.Sphere(asym_unit=asym2, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) rngcheck(sphere) # Atom is not OK (bad range) atom = ihm.model.Atom(asym_unit=asym2, seq_id=4, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) # Sphere is not OK (bad range) sphere = ihm.model.Sphere(asym_unit=asym2, seq_id_range=(1, 4), x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) # Atom in a nonpolymer must have no seq_id (or seq_id==1) atom = ihm.model.Atom(asym_unit=asym_nonpol, seq_id=None, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) atom = ihm.model.Atom(asym_unit=asym_nonpol, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) atom = ihm.model.Atom(asym_unit=asym2, seq_id=None, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) atom = ihm.model.Atom(asym_unit=asym_nonpol, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) def test_range_checker_repr_type_atomic(self): """Test RangeChecker class type checking against AtomicSegments""" system, model, asym = self._make_test_model() # Replace test model's residue representation with atomic s = ihm.representation.AtomicSegment(asym, rigid=False) model.representation = ihm.representation.Representation([s]) rngcheck = ihm.dumper._RangeChecker(model) # Atom is OK atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Sphere is not OK sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 1), x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) def test_range_checker_repr_type_residue(self): """Test RangeChecker class type checking against ResidueSegments""" system, model, asym = self._make_test_model() # Test model already has ResidueSegment representation rngcheck = ihm.dumper._RangeChecker(model) # Atom is not OK atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) # Multi-residue Sphere is not OK sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) # Single-residue Sphere is OK sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 1), x=1.0, y=2.0, z=3.0, radius=4.0) rngcheck(sphere) def test_range_checker_repr_type_multi_residue(self): """Test RangeChecker class type checking against MultiResidueSegments""" system, model, asym = self._make_test_model() # Replace test model's residue representation with multi-residue s = ihm.representation.MultiResidueSegment(asym, rigid=False, primitive='sphere') model.representation = ihm.representation.Representation([s]) rngcheck = ihm.dumper._RangeChecker(model) # Atom is not OK atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) # Sphere is OK if it matches the asym range exactly sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 4), x=1.0, y=2.0, z=3.0, radius=4.0) rngcheck(sphere) sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) def test_range_checker_repr_type_feature(self): """Test RangeChecker class type checking against FeatureSegments""" system, model, asym = self._make_test_model() # Replace test model's residue representation with feature s = ihm.representation.FeatureSegment(asym, rigid=False, primitive='sphere', count=2) model.representation = ihm.representation.Representation([s]) rngcheck = ihm.dumper._RangeChecker(model) # Atom is not OK atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0) self.assertRaises(ValueError, rngcheck, atom) # Sphere is OK if it falls entirely within the segment range sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 2), x=1.0, y=2.0, z=3.0, radius=4.0) rngcheck(sphere) sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 20), x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) def test_model_dumper_spheres(self): """Test ModelDumper with spheres""" system, model, asym = self._make_test_model() # Replace test model's residue representation with feature s = ihm.representation.FeatureSegment(asym, rigid=False, primitive='sphere', count=2) r = ihm.representation.Representation([s]) r._id = 32 model.representation = r model._spheres = [ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 3), x=1.0, y=2.0, z=3.0, radius=4.0), ihm.model.Sphere(asym_unit=asym, seq_id_range=(4, 4), x=4.0, y=5.0, z=6.0, radius=1.0, rmsf=8.0)] dumper = ihm.dumper._ModelDumper() dumper.finalize(system) # assign model/group IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.assembly_id _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 'test model' 99 42 32 # # loop_ _ihm_model_group.id _ihm_model_group.name _ihm_model_group.details 1 . . # # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 # # loop_ _ihm_sphere_obj_site.id _ihm_sphere_obj_site.entity_id _ihm_sphere_obj_site.seq_id_begin _ihm_sphere_obj_site.seq_id_end _ihm_sphere_obj_site.asym_id _ihm_sphere_obj_site.Cartn_x _ihm_sphere_obj_site.Cartn_y _ihm_sphere_obj_site.Cartn_z _ihm_sphere_obj_site.object_radius _ihm_sphere_obj_site.rmsf _ihm_sphere_obj_site.model_id 1 9 1 3 X 1.000 2.000 3.000 4.000 . 1 2 9 4 4 X 4.000 5.000 6.000 1.000 8.000 1 # """) def test_model_dumper_atoms(self): """Test ModelDumper with atoms""" system, model, asym = self._make_test_model() # Replace test model's residue representation with atomic s = ihm.representation.AtomicSegment(asym, rigid=False) r = ihm.representation.Representation([s]) r._id = 32 model.representation = r model._atoms = [ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='C', type_symbol='C', x=1.0, y=2.0, z=3.0), ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', type_symbol='C', x=10.0, y=20.0, z=30.0, het=True), ihm.model.Atom(asym_unit=asym, seq_id=2, atom_id='N', type_symbol='N', x=4.0, y=5.0, z=6.0, biso=42.0, occupancy=0.2, alt_id='A')] dumper = ihm.dumper._ModelDumper() dumper.finalize(system) # assign model/group IDs # With auth_seq_id == seq_id out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.assembly_id _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 'test model' 99 42 32 # # loop_ _ihm_model_group.id _ihm_model_group.name _ihm_model_group.details 1 . . # # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 # # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.auth_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.label_entity_id _atom_site.auth_asym_id _atom_site.auth_comp_id _atom_site.B_iso_or_equiv _atom_site.pdbx_PDB_model_num _atom_site.ihm_model_id ATOM 1 C C . ALA 1 1 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1 HETATM 2 C CA . ALA 1 1 ? X 10.000 20.000 30.000 . 9 X ALA . 1 1 ATOM 3 N N A CYS 2 2 ? X 4.000 5.000 6.000 0.200 9 X CYS 42.000 1 1 # # loop_ _atom_type.symbol C N # """) # Test dump_atoms with add_ihm=False fh = StringIO() writer = ihm.format.CifWriter(fh) dumper.dump_atoms(system, writer, add_ihm=False) self.assertNotIn('ihm_model_id', fh.getvalue()) # With auth_seq_id == seq_id-1 asym.auth_seq_id_map = -1 out = _get_dumper_output(dumper, system) self.assertEqual( out.split('\n')[44:47:2], ["ATOM 1 C C . ALA 1 0 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1", "ATOM 3 N N A CYS 2 1 ? X 4.000 5.000 6.000 " "0.200 9 X CYS 42.000 1 1"]) # With auth_seq_id map asym.auth_seq_id_map = {1: 42, 2: 99} out = _get_dumper_output(dumper, system) self.assertEqual( out.split('\n')[44:47:2], ["ATOM 1 C C . ALA 1 42 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1", "ATOM 3 N N A CYS 2 99 ? X 4.000 5.000 6.000 " "0.200 9 X CYS 42.000 1 1"]) # With duplicate atom IDs (atoms[0] is already 'C') model._atoms[1].atom_id = 'C' self.assertRaises(ValueError, _get_dumper_output, dumper, system) # Should work though if checks are disabled _ = _get_dumper_output(dumper, system, check=False) def test_model_dumper_assembly_asym_check(self): """Test ModelDumper Assembly asym check""" system, model, asym = self._make_test_model() dumper = ihm.dumper._ModelDumper() dumper.finalize(system) # assign model/group IDs # No atoms for assembly's asym with self.assertRaises(ValueError) as cm: _get_dumper_output(dumper, system) self.assertIn("reference asym IDs that don't have coordinates", str(cm.exception)) self.assertIn("ID 99, asym IDs X", str(cm.exception)) # Should work though if checks are disabled _ = _get_dumper_output(dumper, system, check=False) def test_model_dumper_water_atoms(self): """Test ModelDumper with water atoms""" system, model, asym = self._make_test_model(water=True) # Replace test model's residue representation with atomic s = ihm.representation.AtomicSegment(asym, rigid=False) r = ihm.representation.Representation([s]) r._id = 32 model.representation = r # No mapping for third water, so will get auth_seq_id=3 asym.auth_seq_id_map = {1: 42, 2: 99} model._atoms = [ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='O', type_symbol='O', het=True, x=1.0, y=2.0, z=3.0), ihm.model.Atom(asym_unit=asym, seq_id=2, atom_id='O', type_symbol='O', het=True, x=4.0, y=5.0, z=6.0), ihm.model.Atom(asym_unit=asym, seq_id=3, atom_id='O', type_symbol='O', het=True, x=7.0, y=8.0, z=9.0)] dumper = ihm.dumper._ModelDumper() dumper.finalize(system) # assign model/group IDs out = _get_dumper_output(dumper, system) self.assertEqual( out.split('\n')[44:47], ['HETATM 1 O O . HOH . 42 ? X 1.000 2.000 3.000 . 9 X HOH . 1 1', 'HETATM 2 O O . HOH . 99 ? X 4.000 5.000 6.000 . 9 X HOH . 1 1', 'HETATM 3 O O . HOH . 3 ? X 7.000 8.000 9.000 . 9 X HOH . 1 1']) def test_not_modeled_residue_range_dumper(self): """Test NotModeledResidueRangeDumper""" system, model, asym = self._make_test_model() rr1 = ihm.model.NotModeledResidueRange(asym, 1, 2) rr2 = ihm.model.NotModeledResidueRange( asym, 3, 4, reason="Highly variable models with poor precision") model.not_modeled_residue_ranges.extend((rr1, rr2)) dumper = ihm.dumper._ModelDumper() dumper.finalize(system) # assign model/group IDs dumper = ihm.dumper._NotModeledResidueRangeDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_residues_not_modeled.id _ihm_residues_not_modeled.model_id _ihm_residues_not_modeled.entity_description _ihm_residues_not_modeled.entity_id _ihm_residues_not_modeled.asym_id _ihm_residues_not_modeled.seq_id_begin _ihm_residues_not_modeled.seq_id_end _ihm_residues_not_modeled.comp_id_begin _ihm_residues_not_modeled.comp_id_end _ihm_residues_not_modeled.reason 1 1 Nup84 9 X 1 2 ALA CYS . 2 1 Nup84 9 X 3 4 GLY THR 'Highly variable models with poor precision' # """) def test_not_modeled_residue_range_bad_range(self): """Test NotModeledResidueRangeDumper with bad residue ranges""" for badrng, exc in [((10, 14), IndexError), ((-4, 1), IndexError), ((3, 1), ValueError)]: system, model, asym = self._make_test_model() # Disable construction-time check so that we # can see dump time check asym.entity._range_check = False rr1 = ihm.model.NotModeledResidueRange(asym, *badrng) asym.entity._range_check = True model.not_modeled_residue_ranges.append(rr1) dumper = ihm.dumper._ModelDumper() dumper.finalize(system) # assign model/group IDs dumper = ihm.dumper._NotModeledResidueRangeDumper() self.assertRaises(exc, _get_dumper_output, dumper, system) # Should be OK if checks are disabled _ = _get_dumper_output(dumper, system, check=False) def test_ensemble_dumper(self): """Test EnsembleDumper""" class MockObject: pass pp = MockObject() pp._id = 99 system = ihm.System() m1 = ihm.model.Model(assembly='a1', protocol='p1', representation='r1') m2 = ihm.model.Model(assembly='a2', protocol='p2', representation='r2') group = ihm.model.ModelGroup([m1, m2]) group._id = 42 e1 = ihm.model.Ensemble(model_group=group, num_models=10, post_process=pp, name='cluster1', clustering_method='Hierarchical', clustering_feature='RMSD', precision=4.2, superimposed=True) loc = ihm.location.OutputFileLocation(repo='foo', path='bar') loc._id = 3 e2 = ihm.model.Ensemble(model_group=group, num_models=10, file=loc, details='test details') ss1 = ihm.model.IndependentSubsample(name='ss1', num_models=5) ss2 = ihm.model.IndependentSubsample(name='ss2', num_models=5, model_group=group, file=loc) ss3 = ihm.model.RandomSubsample(name='ss3', num_models=5) e2.subsamples.extend((ss1, ss2, ss3)) # Ensemble without a model group e3 = ihm.model.Ensemble(model_group=None, num_models=10, details='no-group details') system.ensembles.extend((e1, e2, e3)) dumper = ihm.dumper._EnsembleDumper() dumper.finalize(system) # assign IDs # Should raise an error since ss3 is not the same type as ss1/ss2 self.assertRaises(TypeError, _get_dumper_output, dumper, system) del e2.subsamples[2] out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_ensemble_info.ensemble_id _ihm_ensemble_info.ensemble_name _ihm_ensemble_info.post_process_id _ihm_ensemble_info.model_group_id _ihm_ensemble_info.ensemble_clustering_method _ihm_ensemble_info.ensemble_clustering_feature _ihm_ensemble_info.num_ensemble_models _ihm_ensemble_info.num_ensemble_models_deposited _ihm_ensemble_info.ensemble_precision_value _ihm_ensemble_info.ensemble_file_id _ihm_ensemble_info.details _ihm_ensemble_info.model_group_superimposed_flag _ihm_ensemble_info.sub_sample_flag _ihm_ensemble_info.sub_sampling_type 1 cluster1 99 42 Hierarchical RMSD 10 2 4.200 . . YES NO . 2 . . 42 . . 10 2 . 3 'test details' . YES independent 3 . . . . . 10 . . . 'no-group details' . NO . # # loop_ _ihm_ensemble_sub_sample.id _ihm_ensemble_sub_sample.name _ihm_ensemble_sub_sample.ensemble_id _ihm_ensemble_sub_sample.num_models _ihm_ensemble_sub_sample.num_models_deposited _ihm_ensemble_sub_sample.model_group_id _ihm_ensemble_sub_sample.file_id 1 ss1 2 5 0 . . 2 ss2 2 5 2 42 3 # """) def test_density_dumper(self): """Test DensityDumper""" class MockObject: pass system = ihm.System() e1 = ihm.Entity('AHCD') e1._id = 9 asym = ihm.AsymUnit(e1) asym._id = 'X' group = MockObject() group._id = 42 ens = ihm.model.Ensemble(model_group=group, num_models=10) loc = ihm.location.OutputFileLocation(repo='foo', path='bar') loc._id = 3 ens.densities.append(ihm.model.LocalizationDensity(loc, asym(1, 2))) ens.densities.append(ihm.model.LocalizationDensity(loc, asym)) ens._id = 5 system.ensembles.append(ens) # Assign segment IDs ihm.dumper._EntityPolySegmentDumper().finalize(system) dumper = ihm.dumper._DensityDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_localization_density_files.id _ihm_localization_density_files.file_id _ihm_localization_density_files.ensemble_id _ihm_localization_density_files.entity_id _ihm_localization_density_files.asym_id _ihm_localization_density_files.entity_poly_segment_id 1 3 5 9 X 1 2 3 5 9 X 2 # """) def test_entity_poly_segment_dumper(self): """Test EntityPolySegmentDumper""" system = ihm.System() e1 = ihm.Entity('AHCD') e2 = ihm.Entity('ACG') e3 = ihm.Entity([ihm.NonPolymerChemComp('HEM')]) a1 = ihm.AsymUnit(e1) a1._id = 'X' system.entities.extend((e1, e2, e3)) system.asym_units.append(a1) res1 = e2.residue(1) res2 = e2.residue(2) system.orphan_features.append(ihm.restraint.ResidueFeature([e2])) system.orphan_features.append(ihm.restraint.ResidueFeature([res2])) system.orphan_features.append(ihm.restraint.NonPolyFeature([e3])) system._make_complete_assembly() ihm.dumper._EntityDumper().finalize(system) # assign entity IDs dumper = ihm.dumper._EntityPolySegmentDumper() dumper.finalize(system) # assign IDs # e1 isn't directly used in anything (a1 is used instead, in the # assembly) so should have no range ID self.assertFalse(hasattr(e1, '_range_id')) self.assertEqual(a1._range_id, 1) # e2 is use, in a ResidueFeature, so should have a range ID self.assertEqual(e2._range_id, 2) # non-polymers don't have ranges self.assertEqual(e3._range_id, None) # res2 should have been assigned a range, but not res1 self.assertFalse(hasattr(res1, '_range_id')) self.assertEqual(res2._range_id, 3) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_entity_poly_segment.id _ihm_entity_poly_segment.entity_id _ihm_entity_poly_segment.seq_id_begin _ihm_entity_poly_segment.seq_id_end _ihm_entity_poly_segment.comp_id_begin _ihm_entity_poly_segment.comp_id_end 1 1 1 4 ALA ASP 2 2 1 3 ALA GLY 3 2 2 2 CYS CYS # """) def test_entity_poly_segment_dumper_bad_range(self): """Test EntityPolySegmentDumper with bad residue ranges""" for badrng, exc in [((10, 14), IndexError), ((-4, 1), IndexError), ((3, 1), ValueError)]: system = ihm.System() e1 = ihm.Entity('AHCD') system.entities.append(e1) # Disable construction-time check so that we # can see dump time check e1._range_check = False system.orphan_features.append( ihm.restraint.ResidueFeature([e1(*badrng)])) e1._range_check = True dumper = ihm.dumper._EntityDumper() dumper.finalize(system) # assign IDs dumper = ihm.dumper._EntityPolySegmentDumper() dumper.finalize(system) # assign IDs self.assertRaises(exc, _get_dumper_output, dumper, system) # Should be OK though if checks are disabled _ = _get_dumper_output(dumper, system, check=False) def test_single_state(self): """Test MultiStateDumper with a single state""" system = ihm.System() state = ihm.model.State() system.state_groups.append(ihm.model.StateGroup([state])) dumper = ihm.dumper._MultiStateDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, "") def test_multi_state(self): """Test MultiStateDumper with multiple states""" system = ihm.System() sg1 = ihm.model.StateGroup() sg2 = ihm.model.StateGroup() system.state_groups.extend((sg1, sg2)) state1 = ihm.model.State(type='complex formation', name='unbound', experiment_type="Fraction of bulk", details="Unbound molecule 1") state1.append(ihm.model.ModelGroup(name="group1")) state1.append(ihm.model.ModelGroup(name="group2")) state2 = ihm.model.State(type='complex formation', name='bound', experiment_type="Fraction of bulk", details="Unbound molecule 2") state2.append(ihm.model.ModelGroup(name="group3")) sg1.extend((state1, state2)) state3 = ihm.model.State(population_fraction=0.4) state3.append(ihm.model.ModelGroup(name="group4")) sg2.append(state3) dumper = ihm.dumper._ModelDumper() dumper.finalize(system) # assign model group IDs dumper = ihm.dumper._MultiStateDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_multi_state_modeling.state_id _ihm_multi_state_modeling.state_group_id _ihm_multi_state_modeling.population_fraction _ihm_multi_state_modeling.state_type _ihm_multi_state_modeling.state_name _ihm_multi_state_modeling.experiment_type _ihm_multi_state_modeling.details 1 1 . 'complex formation' unbound 'Fraction of bulk' 'Unbound molecule 1' 2 1 . 'complex formation' bound 'Fraction of bulk' 'Unbound molecule 2' 3 2 0.400 . . . . # # loop_ _ihm_multi_state_model_group_link.state_id _ihm_multi_state_model_group_link.model_group_id 1 1 1 2 2 3 3 4 # """) def test_orphan_model_groups(self): """Test detection of ModelGroups not in States""" system = ihm.System() m1 = ihm.model.Model(assembly='a1', protocol='p1', representation='r1') group = ihm.model.ModelGroup([m1]) group._id = 42 e1 = ihm.model.Ensemble(model_group=group, num_models=10, post_process=None, name='cluster1', clustering_method='Hierarchical', clustering_feature='RMSD', precision=4.2) system.ensembles.append(e1) dumper = ihm.dumper._ModelDumper() self.assertRaises(ValueError, dumper.finalize, system) def test_ordered(self): """Test OrderedDumper""" system = ihm.System() mg1 = ihm.model.ModelGroup(name="group1") mg1._id = 42 mg2 = ihm.model.ModelGroup(name="group2") mg2._id = 82 mg3 = ihm.model.ModelGroup(name="group3") mg3._id = 92 proc = ihm.model.OrderedProcess("time steps") edge = ihm.model.ProcessEdge(mg1, mg2) step = ihm.model.ProcessStep([edge], "Linear reaction") proc.steps.append(step) system.ordered_processes.append(proc) proc = ihm.model.OrderedProcess("time steps", "Proc 2") edge1 = ihm.model.ProcessEdge(mg1, mg2) edge2 = ihm.model.ProcessEdge(mg1, mg3) step = ihm.model.ProcessStep([edge1, edge2], "Branched reaction") proc.steps.append(step) system.ordered_processes.append(proc) dumper = ihm.dumper._OrderedDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_ordered_model.process_id _ihm_ordered_model.process_description _ihm_ordered_model.ordered_by _ihm_ordered_model.step_id _ihm_ordered_model.step_description _ihm_ordered_model.edge_id _ihm_ordered_model.edge_description _ihm_ordered_model.model_group_id_begin _ihm_ordered_model.model_group_id_end 1 . 'time steps' 1 'Linear reaction' 1 . 42 82 2 'Proc 2' 'time steps' 1 'Branched reaction' 1 . 42 82 2 'Proc 2' 'time steps' 1 'Branched reaction' 2 . 42 92 # """) def test_em3d_restraint_dumper(self): """Test EM3DRestraintDumper""" class MockObject: pass system = ihm.System() dataset = MockObject() dataset._id = 97 dataset2 = MockObject() dataset2._id = 87 assembly = MockObject() assembly._id = 99 citation = MockObject() citation._id = 8 r = ihm.restraint.EM3DRestraint( dataset=dataset, assembly=assembly, segment=False, fitting_method='Gaussian mixture model', number_of_gaussians=40, details='GMM fitting') r2 = ihm.restraint.EM3DRestraint( dataset=dataset2, assembly=assembly, segment=True, fitting_method='Gaussian mixture model', fitting_method_citation=citation, number_of_gaussians=30, details='Other details') m = ihm.model.Model(assembly='foo', protocol='bar', representation='baz') m._id = 42 m2 = ihm.model.Model(assembly='foo', protocol='bar', representation='baz') m2._id = 44 system.restraints.extend((r, r2, MockObject())) r.fits[m] = ihm.restraint.EM3DRestraintFit(0.4) r.fits[m2] = ihm.restraint.EM3DRestraintFit() r2.fits[m2] = ihm.restraint.EM3DRestraintFit() dumper = ihm.dumper._EM3DDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_3dem_restraint.id _ihm_3dem_restraint.dataset_list_id _ihm_3dem_restraint.fitting_method _ihm_3dem_restraint.fitting_method_citation_id _ihm_3dem_restraint.struct_assembly_id _ihm_3dem_restraint.map_segment_flag _ihm_3dem_restraint.number_of_gaussians _ihm_3dem_restraint.model_id _ihm_3dem_restraint.cross_correlation_coefficient _ihm_3dem_restraint.details 1 97 'Gaussian mixture model' . 99 NO 40 42 0.400 'GMM fitting' 2 97 'Gaussian mixture model' . 99 NO 40 44 . 'GMM fitting' 3 87 'Gaussian mixture model' 8 99 YES 30 44 . 'Other details' # """) def test_sas_restraint_dumper(self): """Test SASRestraintDumper""" class MockObject: pass system = ihm.System() dataset = MockObject() dataset._id = 97 assembly = MockObject() assembly._id = 99 r = ihm.restraint.SASRestraint( dataset=dataset, assembly=assembly, segment=False, fitting_method='FoXS', fitting_atom_type='Heavy atoms', multi_state=False, radius_of_gyration=21.07, details='FoXS fitting') m = ihm.model.Model(assembly='foo', protocol='bar', representation='baz') m._id = 42 m2 = ihm.model.Model(assembly='foo', protocol='bar', representation='baz') m2._id = 44 system.restraints.extend((r, MockObject())) r.fits[m] = ihm.restraint.SASRestraintFit(4.69) r.fits[m2] = ihm.restraint.SASRestraintFit() dumper = ihm.dumper._SASDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_sas_restraint.id _ihm_sas_restraint.dataset_list_id _ihm_sas_restraint.model_id _ihm_sas_restraint.struct_assembly_id _ihm_sas_restraint.profile_segment_flag _ihm_sas_restraint.fitting_atom_type _ihm_sas_restraint.fitting_method _ihm_sas_restraint.fitting_state _ihm_sas_restraint.radius_of_gyration _ihm_sas_restraint.chi_value _ihm_sas_restraint.details 1 97 42 99 NO 'Heavy atoms' FoXS Single 21.070 4.690 'FoXS fitting' 2 97 44 99 NO 'Heavy atoms' FoXS Single 21.070 . 'FoXS fitting' # """) def test_em2d_restraint_dumper(self): """Test EM2DRestraintDumper""" class MockObject: pass system = ihm.System() dataset = MockObject() dataset._id = 97 assembly = MockObject() assembly._id = 99 r = ihm.restraint.EM2DRestraint( dataset=dataset, assembly=assembly, segment=False, number_raw_micrographs=400, pixel_size_width=0.6, pixel_size_height=0.5, image_resolution=30.0, number_of_projections=100, details='Test fit') m = ihm.model.Model(assembly='foo', protocol='bar', representation='baz') m._id = 42 m2 = ihm.model.Model(assembly='foo', protocol='bar', representation='baz') m2._id = 44 system.restraints.extend((r, MockObject())) r.fits[m] = ihm.restraint.EM2DRestraintFit( cross_correlation_coefficient=0.4, rot_matrix=[[-0.64, 0.09, 0.77], [0.76, -0.12, 0.64], [0.15, 0.99, 0.01]], tr_vector=[1., 2., 3.]) r.fits[m2] = ihm.restraint.EM2DRestraintFit() dumper = ihm.dumper._EM2DDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_2dem_class_average_restraint.id _ihm_2dem_class_average_restraint.dataset_list_id _ihm_2dem_class_average_restraint.number_raw_micrographs _ihm_2dem_class_average_restraint.pixel_size_width _ihm_2dem_class_average_restraint.pixel_size_height _ihm_2dem_class_average_restraint.image_resolution _ihm_2dem_class_average_restraint.image_segment_flag _ihm_2dem_class_average_restraint.number_of_projections _ihm_2dem_class_average_restraint.struct_assembly_id _ihm_2dem_class_average_restraint.details 1 97 400 0.600 0.500 30.000 NO 100 99 'Test fit' # # loop_ _ihm_2dem_class_average_fitting.id _ihm_2dem_class_average_fitting.restraint_id _ihm_2dem_class_average_fitting.model_id _ihm_2dem_class_average_fitting.cross_correlation_coefficient _ihm_2dem_class_average_fitting.rot_matrix[1][1] _ihm_2dem_class_average_fitting.rot_matrix[2][1] _ihm_2dem_class_average_fitting.rot_matrix[3][1] _ihm_2dem_class_average_fitting.rot_matrix[1][2] _ihm_2dem_class_average_fitting.rot_matrix[2][2] _ihm_2dem_class_average_fitting.rot_matrix[3][2] _ihm_2dem_class_average_fitting.rot_matrix[1][3] _ihm_2dem_class_average_fitting.rot_matrix[2][3] _ihm_2dem_class_average_fitting.rot_matrix[3][3] _ihm_2dem_class_average_fitting.tr_vector[1] _ihm_2dem_class_average_fitting.tr_vector[2] _ihm_2dem_class_average_fitting.tr_vector[3] 1 1 42 0.400 -0.640000 0.760000 0.150000 0.090000 -0.120000 0.990000 0.770000 0.640000 0.010000 1.000 2.000 3.000 2 1 44 . . . . . . . . . . . . . # """) def test_cross_link_restraint_dumper(self): """Test CrossLinkRestraintDumper""" class MockObject: pass system = ihm.System() e1 = ihm.Entity('ATC', description='foo') e2 = ihm.Entity('DEF', description='bar') system.entities.extend((e1, e2)) asym1 = ihm.AsymUnit(e1) asym2 = ihm.AsymUnit(e2) system.asym_units.extend((asym1, asym2)) dataset = MockObject() dataset._id = 97 dss = ihm.ChemDescriptor('DSS') r = ihm.restraint.CrossLinkRestraint(dataset=dataset, linker=dss) # intra, unambiguous xxl1 = ihm.restraint.ExperimentalCrossLink( e1.residue(2), e1.residue(3)) # inter, ambiguous xxl2 = ihm.restraint.ExperimentalCrossLink( e1.residue(2), e2.residue(3)) xxl3 = ihm.restraint.ExperimentalCrossLink( e1.residue(2), e2.residue(2)) # duplicate crosslink, should be combined with the original (xxl2) xxl4 = ihm.restraint.ExperimentalCrossLink( e1.residue(2), e2.residue(3)) # should end up in own group, not with xxl4 (since xxl4==xxl2) xxl5 = ihm.restraint.ExperimentalCrossLink( e1.residue(1), e2.residue(1), details='test xl') r.experimental_cross_links.extend(([xxl1], [xxl2, xxl3], [xxl4, xxl5])) system.restraints.extend((r, MockObject())) d = ihm.restraint.UpperBoundDistanceRestraint(25.0) xl1 = ihm.restraint.ResidueCrossLink( xxl1, asym1, asym1, d, psi=0.5, sigma1=1.0, sigma2=2.0, restrain_all=True) d = ihm.restraint.LowerBoundDistanceRestraint(34.0) xl2 = ihm.restraint.AtomCrossLink( xxl3, asym1, asym2, 'C', 'N', d, restrain_all=False) # Duplicates should be ignored xl3 = ihm.restraint.AtomCrossLink( xxl3, asym1, asym2, 'C', 'N', d, restrain_all=False) # Restraints on pseudo sites ps = ihm.restraint.PseudoSite(x=10., y=20., z=30.) ps._id = 89 psxl = ihm.restraint.CrossLinkPseudoSite(site=ps) xl4 = ihm.restraint.ResidueCrossLink( xxl5, asym1, asym2, d, psi=0.5, sigma1=1.0, sigma2=2.0, restrain_all=True, pseudo2=[psxl]) m = MockObject() m._id = 99 psxl = ihm.restraint.CrossLinkPseudoSite(site=ps, model=m) m = MockObject() m._id = 990 psxl2 = ihm.restraint.CrossLinkPseudoSite(site=ps, model=m) xl5 = ihm.restraint.ResidueCrossLink( xxl2, asym1, asym2, d, psi=0.5, sigma1=1.0, sigma2=2.0, restrain_all=True, pseudo2=[psxl, psxl2]) r.cross_links.extend((xl1, xl2, xl3, xl4, xl5)) model = ihm.model.Model(assembly=None, protocol=None, representation=None) model._id = 201 xl1.fits[model] = ihm.restraint.CrossLinkFit(psi=0.1, sigma1=4.2, sigma2=2.1) # Fit of a ModelGroup model_group = ihm.model.ModelGroup([model]) model_group._id = 301 xl1.fits[model_group] = ihm.restraint.CrossLinkGroupFit( num_models=40, median_distance=4.0, details='test fit') # Fit of an Ensemble both with and without a ModelGroup ens1 = ihm.model.Ensemble(model_group=model_group, num_models=10) ens1._id = 401 xl1.fits[ens1] = ihm.restraint.CrossLinkGroupFit( num_models=30, median_distance=3.0) ens2 = ihm.model.Ensemble(model_group=None, num_models=20) ens2._id = 501 xl1.fits[ens2] = ihm.restraint.CrossLinkGroupFit( num_models=50, median_distance=9.0) ihm.dumper._EntityDumper().finalize(system) # assign entity IDs ihm.dumper._StructAsymDumper().finalize(system) # assign asym IDs ihm.dumper._ChemDescriptorDumper().finalize(system) # descriptor IDs dumper = ihm.dumper._CrossLinkDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_cross_link_list.id _ihm_cross_link_list.group_id _ihm_cross_link_list.entity_description_1 _ihm_cross_link_list.entity_id_1 _ihm_cross_link_list.seq_id_1 _ihm_cross_link_list.comp_id_1 _ihm_cross_link_list.entity_description_2 _ihm_cross_link_list.entity_id_2 _ihm_cross_link_list.seq_id_2 _ihm_cross_link_list.comp_id_2 _ihm_cross_link_list.linker_chem_comp_descriptor_id _ihm_cross_link_list.linker_type _ihm_cross_link_list.dataset_list_id _ihm_cross_link_list.details 1 1 foo 1 2 THR foo 1 3 CYS 1 DSS 97 . 2 2 foo 1 2 THR bar 2 3 PHE 1 DSS 97 . 3 2 foo 1 2 THR bar 2 2 GLU 1 DSS 97 . 4 3 foo 1 1 ALA bar 2 1 ASP 1 DSS 97 'test xl' # # loop_ _ihm_cross_link_restraint.id _ihm_cross_link_restraint.group_id _ihm_cross_link_restraint.entity_id_1 _ihm_cross_link_restraint.asym_id_1 _ihm_cross_link_restraint.seq_id_1 _ihm_cross_link_restraint.comp_id_1 _ihm_cross_link_restraint.entity_id_2 _ihm_cross_link_restraint.asym_id_2 _ihm_cross_link_restraint.seq_id_2 _ihm_cross_link_restraint.comp_id_2 _ihm_cross_link_restraint.atom_id_1 _ihm_cross_link_restraint.atom_id_2 _ihm_cross_link_restraint.restraint_type _ihm_cross_link_restraint.conditional_crosslink_flag _ihm_cross_link_restraint.model_granularity _ihm_cross_link_restraint.distance_threshold _ihm_cross_link_restraint.psi _ihm_cross_link_restraint.sigma_1 _ihm_cross_link_restraint.sigma_2 _ihm_cross_link_restraint.pseudo_site_flag 1 1 1 A 2 THR 1 A 3 CYS . . 'upper bound' ALL by-residue 25.000 0.500 1.000 2.000 NO 2 3 1 A 2 THR 2 B 2 GLU C N 'lower bound' ANY by-atom 34.000 . . . NO 3 4 1 A 1 ALA 2 B 1 ASP . . 'lower bound' ALL by-residue 34.000 0.500 1.000 2.000 YES 4 2 1 A 2 THR 2 B 3 PHE . . 'lower bound' ALL by-residue 34.000 0.500 1.000 2.000 YES # # loop_ _ihm_cross_link_pseudo_site.id _ihm_cross_link_pseudo_site.restraint_id _ihm_cross_link_pseudo_site.cross_link_partner _ihm_cross_link_pseudo_site.pseudo_site_id _ihm_cross_link_pseudo_site.model_id 1 3 2 89 . 2 4 2 89 99 3 4 2 89 990 # # loop_ _ihm_cross_link_result.id _ihm_cross_link_result.restraint_id _ihm_cross_link_result.ensemble_id _ihm_cross_link_result.model_group_id _ihm_cross_link_result.num_models _ihm_cross_link_result.distance_threshold _ihm_cross_link_result.median_distance _ihm_cross_link_result.details 1 1 . 301 40 25.000 4.000 'test fit' 2 1 401 301 30 25.000 3.000 . 3 1 501 . 50 25.000 9.000 . # # loop_ _ihm_cross_link_result_parameters.id _ihm_cross_link_result_parameters.restraint_id _ihm_cross_link_result_parameters.model_id _ihm_cross_link_result_parameters.psi _ihm_cross_link_result_parameters.sigma_1 _ihm_cross_link_result_parameters.sigma_2 1 1 201 0.100 4.200 2.100 # """) def test_cross_link_restraint_dumper_range_check(self): """Test CrossLinkRestraintDumper with out-of-range residue""" class MockObject: pass system = ihm.System() e1 = ihm.Entity('ATC', description='foo') system.entities.append(e1) asym1 = ihm.AsymUnit(e1) system.asym_units.append(asym1) dataset = MockObject() dataset._id = 97 dss = ihm.ChemDescriptor('DSS') r = ihm.restraint.CrossLinkRestraint(dataset=dataset, linker=dss) # Disable construction-time check so that we # can see dump time check e1._range_check = False xxl1 = ihm.restraint.ExperimentalCrossLink( e1.residue(2), e1.residue(300)) e1._range_check = True r.experimental_cross_links.append([xxl1]) system.restraints.append(r) d = ihm.restraint.UpperBoundDistanceRestraint(25.0) xl1 = ihm.restraint.ResidueCrossLink( xxl1, asym1, asym1, d, psi=0.5, sigma1=1.0, sigma2=2.0, restrain_all=True) r.cross_links.append(xl1) ihm.dumper._EntityDumper().finalize(system) # assign entity IDs ihm.dumper._StructAsymDumper().finalize(system) # assign asym IDs ihm.dumper._ChemDescriptorDumper().finalize(system) # descriptor IDs dumper = ihm.dumper._CrossLinkDumper() dumper.finalize(system) # assign IDs self.assertRaises(IndexError, _get_dumper_output, dumper, system) # Should work though if checks are disabled _ = _get_dumper_output(dumper, system, check=False) def test_geometric_object_dumper(self): """Test GeometricObjectDumper""" system = ihm.System() center = ihm.geometry.Center(1., 2., 3.) trans = ihm.geometry.Transformation([[1, 0, 0], [0, 1, 0], [0, 0, 1]], [1., 2., 3.]) sphere = ihm.geometry.Sphere(center=center, transformation=trans, radius=2.2, name='my sphere', description='a test sphere') torus = ihm.geometry.Torus(center=center, transformation=trans, major_radius=5.6, minor_radius=1.2) half_torus = ihm.geometry.HalfTorus( center=center, transformation=trans, major_radius=5.6, minor_radius=1.2, thickness=0.1, inner=True) axis = ihm.geometry.XAxis() plane = ihm.geometry.XYPlane() system.orphan_geometric_objects.extend((sphere, torus, half_torus, axis, plane)) # Transformation not referenced by any object trans2 = ihm.geometry.Transformation([[1, 0, 0], [0, 1, 0], [0, 0, 1]], [4., 5., 6.]) system._orphan_geometric_transforms.append(trans2) # Center not referenced by any object center2 = ihm.geometry.Center(8., 9., 10.) system._orphan_centers.append(center2) dumper = ihm.dumper._GeometricObjectDumper() dumper.finalize(system) # assign IDs self.assertEqual(len(dumper._objects_by_id), 5) self.assertEqual(len(dumper._centers_by_id), 2) self.assertEqual(len(dumper._transformations_by_id), 2) # Repeated calls to finalize should yield identical results dumper.finalize(system) self.assertEqual(len(dumper._objects_by_id), 5) self.assertEqual(len(dumper._centers_by_id), 2) self.assertEqual(len(dumper._transformations_by_id), 2) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_geometric_object_center.id _ihm_geometric_object_center.xcoord _ihm_geometric_object_center.ycoord _ihm_geometric_object_center.zcoord 1 1.000 2.000 3.000 2 8.000 9.000 10.000 # # loop_ _ihm_geometric_object_transformation.id _ihm_geometric_object_transformation.rot_matrix[1][1] _ihm_geometric_object_transformation.rot_matrix[2][1] _ihm_geometric_object_transformation.rot_matrix[3][1] _ihm_geometric_object_transformation.rot_matrix[1][2] _ihm_geometric_object_transformation.rot_matrix[2][2] _ihm_geometric_object_transformation.rot_matrix[3][2] _ihm_geometric_object_transformation.rot_matrix[1][3] _ihm_geometric_object_transformation.rot_matrix[2][3] _ihm_geometric_object_transformation.rot_matrix[3][3] _ihm_geometric_object_transformation.tr_vector[1] _ihm_geometric_object_transformation.tr_vector[2] _ihm_geometric_object_transformation.tr_vector[3] 1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000 2.000 3.000 2 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 4.000 5.000 6.000 # # loop_ _ihm_geometric_object_list.object_id _ihm_geometric_object_list.object_type _ihm_geometric_object_list.object_name _ihm_geometric_object_list.object_description 1 sphere 'my sphere' 'a test sphere' 2 torus . . 3 half-torus . . 4 axis . . 5 plane . . # # loop_ _ihm_geometric_object_sphere.object_id _ihm_geometric_object_sphere.center_id _ihm_geometric_object_sphere.transformation_id _ihm_geometric_object_sphere.radius_r 1 1 1 2.200 # # loop_ _ihm_geometric_object_torus.object_id _ihm_geometric_object_torus.center_id _ihm_geometric_object_torus.transformation_id _ihm_geometric_object_torus.major_radius_R _ihm_geometric_object_torus.minor_radius_r 2 1 1 5.600 1.200 3 1 1 5.600 1.200 # # loop_ _ihm_geometric_object_half_torus.object_id _ihm_geometric_object_half_torus.thickness_th _ihm_geometric_object_half_torus.section 3 0.100 'inner half' # # loop_ _ihm_geometric_object_axis.object_id _ihm_geometric_object_axis.axis_type _ihm_geometric_object_axis.transformation_id 4 x-axis . # # loop_ _ihm_geometric_object_plane.object_id _ihm_geometric_object_plane.plane_type _ihm_geometric_object_plane.transformation_id 5 xy-plane . # """) def test_geometric_object_dumper_invalid_rotation(self): """Test GeometricObjectDumper with invalid rotation""" system = ihm.System() center = ihm.geometry.Center(1., 2., 3.) trans = ihm.geometry.Transformation(None, [1., 2., 3.]) sphere = ihm.geometry.Sphere(center=center, transformation=trans, radius=2.2, name='my sphere', description='a test sphere') system.orphan_geometric_objects.append(sphere) dumper = ihm.dumper._GeometricObjectDumper() dumper.finalize(system) self.assertRaises(ValueError, _get_dumper_output, dumper, system) # OK if checks are disabled _ = _get_dumper_output(dumper, system, check=False) def test_geometric_object_dumper_invalid_translation(self): """Test GeometricObjectDumper with invalid translation""" system = ihm.System() center = ihm.geometry.Center(1., 2., 3.) trans = ihm.geometry.Transformation([[1, 0, 0], [0, 1, 0], [0, 0, 1]], ihm.unknown) sphere = ihm.geometry.Sphere(center=center, transformation=trans, radius=2.2, name='my sphere', description='a test sphere') system.orphan_geometric_objects.append(sphere) dumper = ihm.dumper._GeometricObjectDumper() dumper.finalize(system) self.assertRaises(ValueError, _get_dumper_output, dumper, system) # OK if checks are disabled _ = _get_dumper_output(dumper, system, check=False) def test_feature_dumper(self): """Test FeatureDumper""" system = ihm.System() e1 = ihm.Entity('ACGT') e2 = ihm.Entity([ihm.NonPolymerChemComp('HEM')]) system.entities.extend((e1, e2)) a1 = ihm.AsymUnit(e1, 'foo') a2 = ihm.AsymUnit(e1, 'baz') a3 = ihm.AsymUnit(e2, 'heme') system.asym_units.extend((a1, a2, a3)) f = ihm.restraint.ResidueFeature([a1, a2(2, 3), e1, e1(2, 3)], details='test feature') system.orphan_features.append(f) # Duplicate feature, should be pruned from output f = ihm.restraint.ResidueFeature([a1, a2(2, 3), e1, e1(2, 3)], details='other details') system.orphan_features.append(f) # Cannot make a ResidueFeature that includes a non-polymer 'residue' self.assertRaises(ValueError, ihm.restraint.ResidueFeature, [a1, a3]) # Polymeric atom feature f = ihm.restraint.AtomFeature([a1.residue(1).atom('CA'), a2.residue(2).atom('N'), e1.residue(1).atom('CB')]) system.orphan_features.append(f) # Nonpolymeric atom feature f = ihm.restraint.AtomFeature([a3.residue(1).atom('FE'), e2.residue(1).atom('FE')]) system.orphan_features.append(f) # Cannot make one feature that selects both polymer and nonpolymer self.assertRaises(ValueError, ihm.restraint.AtomFeature, [a1.residue(1).atom('CA'), a2.residue(2).atom('N'), a3.residue(1).atom('FE')]) # Nonpolymeric feature f = ihm.restraint.NonPolyFeature([a3, e2]) system.orphan_features.append(f) # Cannot make a NonPolyFeature that includes a polymer 'residue' self.assertRaises(ValueError, ihm.restraint.NonPolyFeature, [a1, a3]) # Pseudo site feature ps = ihm.restraint.PseudoSite(x=10., y=20., z=30.) ps._id = 89 f = ihm.restraint.PseudoSiteFeature(site=ps) system.orphan_features.append(f) # Duplicate Pseudo site feature ps = ihm.restraint.PseudoSite(x=10., y=20., z=30.) f = ihm.restraint.PseudoSiteFeature(site=ps) system.orphan_features.append(f) ihm.dumper._EntityDumper().finalize(system) # assign entity IDs ihm.dumper._StructAsymDumper().finalize(system) # assign asym IDs dumper = ihm.dumper._FeatureDumper() dumper.finalize(system) # assign IDs self.assertEqual(len(dumper._features_by_id), 5) # Repeated calls to finalize should yield identical results dumper.finalize(system) self.assertEqual(len(dumper._features_by_id), 5) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_feature_list.feature_id _ihm_feature_list.feature_type _ihm_feature_list.entity_type _ihm_feature_list.details 1 'residue range' polymer 'test feature' 2 atom polymer . 3 atom non-polymer . 4 ligand non-polymer . 5 'pseudo site' other . # # loop_ _ihm_poly_residue_feature.ordinal_id _ihm_poly_residue_feature.feature_id _ihm_poly_residue_feature.entity_id _ihm_poly_residue_feature.asym_id _ihm_poly_residue_feature.seq_id_begin _ihm_poly_residue_feature.comp_id_begin _ihm_poly_residue_feature.seq_id_end _ihm_poly_residue_feature.comp_id_end 1 1 1 A 1 ALA 4 THR 2 1 1 B 2 CYS 3 GLY 3 1 1 . 1 ALA 4 THR 4 1 1 . 2 CYS 3 GLY # # loop_ _ihm_poly_atom_feature.ordinal_id _ihm_poly_atom_feature.feature_id _ihm_poly_atom_feature.entity_id _ihm_poly_atom_feature.asym_id _ihm_poly_atom_feature.seq_id _ihm_poly_atom_feature.comp_id _ihm_poly_atom_feature.atom_id 1 2 1 A 1 ALA CA 2 2 1 B 2 CYS N 3 2 1 . 1 ALA CB # # loop_ _ihm_non_poly_feature.ordinal_id _ihm_non_poly_feature.feature_id _ihm_non_poly_feature.entity_id _ihm_non_poly_feature.asym_id _ihm_non_poly_feature.comp_id _ihm_non_poly_feature.atom_id 1 3 2 C HEM FE 2 3 2 . HEM FE 3 4 2 C HEM . 4 4 2 . HEM . # # loop_ _ihm_pseudo_site_feature.feature_id _ihm_pseudo_site_feature.pseudo_site_id 5 89 # """) def test_feature_dumper_no_residues(self): """Test FeatureDumper with an empty ResidueFeature""" system = ihm.System() f = ihm.restraint.ResidueFeature([]) system.orphan_features.append(f) dumper = ihm.dumper._FeatureDumper() dumper.finalize(system) # assign IDs self.assertEqual(len(dumper._features_by_id), 1) self.assertRaises(ValueError, _get_dumper_output, dumper, system) def test_feature_dumper_base_class(self): """Test FeatureDumper with a Feature base class""" system = ihm.System() f = ihm.restraint.Feature() system.orphan_features.append(f) dumper = ihm.dumper._FeatureDumper() dumper.finalize(system) # assign IDs self.assertEqual(len(dumper._features_by_id), 1) self.assertRaises(ValueError, _get_dumper_output, dumper, system) # Should be OK if checks are disabled out = _get_dumper_output(dumper, system, check=False) self.assertEqual(out, """# loop_ _ihm_feature_list.feature_id _ihm_feature_list.feature_type _ihm_feature_list.entity_type _ihm_feature_list.details 1 ? ? . # """) def test_pseudo_site_dumper(self): """Test PseudoSiteDumper""" system = ihm.System() ps1 = ihm.restraint.PseudoSite(x=10., y=20., z=30.) ps2 = ihm.restraint.PseudoSite(x=10., y=20., z=30., radius=40., description="test pseudo") # Duplicate pseudo site, should be pruned ps3 = ihm.restraint.PseudoSite(x=10., y=20., z=30., radius=40., description="other pseudo") system.orphan_pseudo_sites.extend((ps1, ps2, ps3)) dumper = ihm.dumper._PseudoSiteDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_pseudo_site.id _ihm_pseudo_site.Cartn_x _ihm_pseudo_site.Cartn_y _ihm_pseudo_site.Cartn_z _ihm_pseudo_site.radius _ihm_pseudo_site.description 1 10.000 20.000 30.000 . . 2 10.000 20.000 30.000 40.000 'test pseudo' # """) def test_geometric_restraint_dumper(self): """Test GeometricRestraintDumper""" class MockObject: pass system = ihm.System() feat = MockObject() feat._id = 44 geom = MockObject() geom._id = 23 dataset = MockObject() dataset._id = 97 dist = ihm.restraint.UpperBoundDistanceRestraint(25.0) r = ihm.restraint.CenterGeometricRestraint( dataset=dataset, geometric_object=geom, feature=feat, distance=dist, harmonic_force_constant=2.0, restrain_all=False) system.restraints.append(r) dumper = ihm.dumper._GeometricRestraintDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_geometric_object_distance_restraint.id _ihm_geometric_object_distance_restraint.object_id _ihm_geometric_object_distance_restraint.feature_id _ihm_geometric_object_distance_restraint.object_characteristic _ihm_geometric_object_distance_restraint.restraint_type _ihm_geometric_object_distance_restraint.harmonic_force_constant _ihm_geometric_object_distance_restraint.distance_lower_limit _ihm_geometric_object_distance_restraint.distance_upper_limit _ihm_geometric_object_distance_restraint.group_conditionality _ihm_geometric_object_distance_restraint.dataset_list_id 1 23 44 center 'upper bound' 2.000 . 25.000 ANY 97 # """) def test_derived_distance_restraint_dumper(self): """Test DerivedDistanceRestraintDumper""" class MockObject: pass system = ihm.System() feat1 = MockObject() feat1._id = 44 feat2 = MockObject() feat2._id = 84 dataset = MockObject() dataset._id = 97 dist = ihm.restraint.LowerBoundDistanceRestraint(25.0) unkdist = ihm.restraint.DistanceRestraint() r1 = ihm.restraint.DerivedDistanceRestraint( dataset=dataset, feature1=feat1, feature2=feat2, distance=dist, probability=0.8) r2 = ihm.restraint.DerivedDistanceRestraint( dataset=dataset, feature1=feat1, feature2=feat2, distance=dist, probability=0.4) r3 = ihm.restraint.DerivedDistanceRestraint( dataset=dataset, feature1=feat1, feature2=feat2, distance=unkdist, probability=0.6, mic_value=0.4) rg = ihm.restraint.RestraintGroup((r2, r3)) system.restraints.extend((r1, r2)) # r2 is in restraints and groups system.restraint_groups.append(rg) dumper = ihm.dumper._DerivedDistanceRestraintDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_derived_distance_restraint.id _ihm_derived_distance_restraint.group_id _ihm_derived_distance_restraint.feature_id_1 _ihm_derived_distance_restraint.feature_id_2 _ihm_derived_distance_restraint.restraint_type _ihm_derived_distance_restraint.distance_lower_limit _ihm_derived_distance_restraint.distance_upper_limit _ihm_derived_distance_restraint.probability _ihm_derived_distance_restraint.mic_value _ihm_derived_distance_restraint.group_conditionality _ihm_derived_distance_restraint.dataset_list_id 1 . 44 84 'lower bound' 25.000 . 0.800 . . 97 2 1 44 84 'lower bound' 25.000 . 0.400 . . 97 3 1 44 84 . . . 0.600 0.400 . 97 # """) def test_derived_distance_restraint_dumper_fail(self): """Test DerivedDistanceRestraintDumper multi-group failure""" class MockObject: pass system = ihm.System() feat1 = MockObject() feat2 = MockObject() dataset = MockObject() dist = ihm.restraint.LowerBoundDistanceRestraint(25.0) r1 = ihm.restraint.DerivedDistanceRestraint( dataset=dataset, feature1=feat1, feature2=feat2, distance=dist, probability=0.8) rg1 = ihm.restraint.RestraintGroup([r1]) rg2 = ihm.restraint.RestraintGroup([r1]) system.restraint_groups.extend((rg1, rg2)) dumper = ihm.dumper._DerivedDistanceRestraintDumper() # r1 cannot be in multiple groups (rg1 and rg2) self.assertRaises(ValueError, dumper.finalize, system) def test_hdx_restraint_dumper(self): """Test HDXRestraintDumper""" class MockObject: pass system = ihm.System() feat = MockObject() feat._id = 44 dataset = MockObject() dataset._id = 97 r1 = ihm.restraint.HDXRestraint( dataset=dataset, feature=feat, protection_factor=1.0, details="foo") r2 = ihm.restraint.HDXRestraint(dataset=None, feature=feat) system.restraints.extend((r1, r2)) dumper = ihm.dumper._HDXRestraintDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_hdx_restraint.id _ihm_hdx_restraint.feature_id _ihm_hdx_restraint.protection_factor _ihm_hdx_restraint.dataset_list_id _ihm_hdx_restraint.details 1 44 1.000 97 foo 2 44 . . . # """) def test_bad_restraint_groups(self): """Test RestraintGroups containing unsupported restraints""" class MockObject: pass s = ihm.System() dataset = MockObject() dataset.parents = [] assembly = ihm.Assembly() # Empty restraint groups are OK (even though they don't get IDs) rg = ihm.restraint.RestraintGroup([]) s.restraint_groups.append(rg) fh = StringIO() ihm.dumper.write(fh, [s]) r = ihm.restraint.SASRestraint( dataset=dataset, assembly=assembly, segment=False, fitting_method='FoXS', fitting_atom_type='Heavy atoms', multi_state=False, radius_of_gyration=21.07, details='FoXS fitting') rg = ihm.restraint.RestraintGroup([r]) s.restraint_groups.append(rg) fh = StringIO() # SASRestraint is an unsupported type in RestraintGroup self.assertRaises(TypeError, ihm.dumper.write, fh, [s]) def test_predicted_contact_restraint_dumper(self): """Test PredictedContactRestraintDumper""" class MockObject: pass system = ihm.System() e1 = ihm.Entity('AHC') a1 = ihm.AsymUnit(e1) e2 = ihm.Entity('GWT') a2 = ihm.AsymUnit(e2) system.entities.extend((e1, e2)) system.asym_units.extend((a1, a2)) dataset = MockObject() dataset._id = 97 software = MockObject() software._id = 34 dist = ihm.restraint.LowerBoundDistanceRestraint(25.0) dist2 = ihm.restraint.UpperBoundDistanceRestraint(14.0) r1 = ihm.restraint.PredictedContactRestraint( dataset=dataset, resatom1=a1.residue(1), resatom2=a2.residue(2), distance=dist, probability=0.8, by_residue=True, software=software) r2 = ihm.restraint.PredictedContactRestraint( dataset=dataset, resatom1=a1.residue(1).atom('CA'), resatom2=a2.residue(2).atom('CB'), by_residue=True, distance=dist, probability=0.4) r3 = ihm.restraint.PredictedContactRestraint( dataset=dataset, resatom1=a1.residue(1), resatom2=a2.residue(2), distance=dist2, probability=0.6, by_residue=False) rg = ihm.restraint.RestraintGroup((r2, r3)) system.restraints.extend((r1, r2)) # r2 is in restraints and groups system.restraint_groups.append(rg) ihm.dumper._EntityDumper().finalize(system) # assign entity IDs ihm.dumper._StructAsymDumper().finalize(system) # assign asym IDs dumper = ihm.dumper._PredictedContactRestraintDumper() dumper.finalize(system) # assign IDs out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_predicted_contact_restraint.id _ihm_predicted_contact_restraint.group_id _ihm_predicted_contact_restraint.entity_id_1 _ihm_predicted_contact_restraint.asym_id_1 _ihm_predicted_contact_restraint.comp_id_1 _ihm_predicted_contact_restraint.seq_id_1 _ihm_predicted_contact_restraint.rep_atom_1 _ihm_predicted_contact_restraint.entity_id_2 _ihm_predicted_contact_restraint.asym_id_2 _ihm_predicted_contact_restraint.comp_id_2 _ihm_predicted_contact_restraint.seq_id_2 _ihm_predicted_contact_restraint.rep_atom_2 _ihm_predicted_contact_restraint.restraint_type _ihm_predicted_contact_restraint.distance_lower_limit _ihm_predicted_contact_restraint.distance_upper_limit _ihm_predicted_contact_restraint.probability _ihm_predicted_contact_restraint.model_granularity _ihm_predicted_contact_restraint.dataset_list_id _ihm_predicted_contact_restraint.software_id 1 . 1 A ALA 1 . 2 B TRP 2 . 'lower bound' 25.000 . 0.800 by-residue 97 34 2 1 1 A ALA 1 CA 2 B TRP 2 CB 'lower bound' 25.000 . 0.400 by-residue 97 . 3 1 1 A ALA 1 . 2 B TRP 2 . 'upper bound' . 14.000 0.600 by-feature 97 . # """) def test_multi_state_scheme_dumper(self): """ Test MultiStateScheme dumper""" class MockObject: pass cur_connectivity_1 = \ ihm.multi_state_scheme.Connectivity( begin_state='s1') r1 = MockObject() r2 = MockObject() system = ihm.System() mss1 = ihm.multi_state_scheme.MultiStateScheme( name="mss1", details="details1", connectivities=[cur_connectivity_1], relaxation_times=[r1, r2]) mss2 = ihm.multi_state_scheme.MultiStateScheme( name="mss2") system.multi_state_schemes.append(mss1) system.multi_state_schemes.append(mss2) # Check whether a scheme that was added twice is written twice system.multi_state_schemes.append(mss1) dumper = ihm.dumper._MultiStateSchemeDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_multi_state_scheme.id _ihm_multi_state_scheme.name _ihm_multi_state_scheme.details 1 mss1 details1 2 mss2 . # """) def test_multi_state_scheme_connectivity_dumper(self): """ Test MultiStateSchemeConnectivity dumper""" class MockObject: pass cur_state_1 = MockObject() cur_state_1._id = 1 cur_state_2 = MockObject() cur_state_2._id = 2 cur_datasetgroup_1 = MockObject() cur_datasetgroup_1._id = 10 cur_kinetic_rate_1 = MockObject() cur_kinetic_rate_1._id = 1 cur_kinetic_rate_2 = MockObject() cur_kinetic_rate_2._id = 2 cur_relaxation_time_1 = MockObject() cur_relaxation_time_1._id = 4 cur_relaxation_time_2 = MockObject() cur_relaxation_time_2._id = 5 # Prepare the system system = ihm.System() # Create the connectivities mssc1 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1) mssc2 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2) mssc3 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, details="details3", dataset_group=cur_datasetgroup_1, kinetic_rate=cur_kinetic_rate_1) mssc4 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, details="details4", kinetic_rate=cur_kinetic_rate_1, relaxation_time=cur_relaxation_time_1) mssc5 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, details="details5", dataset_group=cur_datasetgroup_1, relaxation_time=cur_relaxation_time_2) # Check whether a duplicate entry with the same information is # written twice mssc6 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, details="details5", dataset_group=cur_datasetgroup_1, relaxation_time=cur_relaxation_time_2) mssc7 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, details="details7", dataset_group=cur_datasetgroup_1, relaxation_time=cur_relaxation_time_2) # Create the multi-state schemes mss1 = ihm.multi_state_scheme.MultiStateScheme( name="mss1") mss1.add_connectivity(mssc1) mss2 = ihm.multi_state_scheme.MultiStateScheme( name="mss2", connectivities=[mssc1, mssc2]) mss2.add_connectivity(mssc3) mss2.add_connectivity(mssc4) mss2.add_connectivity(mssc5) mss2.add_connectivity(mssc6) mss2.add_connectivity(mssc6) # Check whether a given _id is kept mssc7._id = '107' mss2.add_connectivity(mssc7) system.multi_state_schemes.append(mss1) system.multi_state_schemes.append(mss2) ihm.dumper._MultiStateSchemeDumper().finalize(system) dumper = ihm.dumper._MultiStateSchemeConnectivityDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_multi_state_scheme_connectivity.id _ihm_multi_state_scheme_connectivity.scheme_id _ihm_multi_state_scheme_connectivity.begin_state_id _ihm_multi_state_scheme_connectivity.end_state_id _ihm_multi_state_scheme_connectivity.dataset_group_id _ihm_multi_state_scheme_connectivity.details 1 1 1 . . . 2 2 1 . . . 3 2 1 2 . . 4 2 1 2 10 details3 5 2 1 2 . details4 6 2 1 2 10 details5 7 2 1 2 10 details5 107 2 1 2 10 details7 # """) def test_relaxation_time_dumper(self): """Test RelaxationTime dumpers. Tests both, _ihm_relaxation_time and _ihm_relaxation_time_multi_state_scheme""" class MockObject: pass cur_dataset_group_1 = MockObject() cur_dataset_group_1._id = 1 cur_external_file_1 = MockObject() cur_external_file_1._id = 2 cur_state_1 = MockObject() cur_state_1._id = 101 cur_state_2 = MockObject() cur_state_2._id = 102 cur_state_3 = MockObject() cur_state_3._id = 103 system = ihm.System() r1 = ihm.multi_state_scheme.RelaxationTime( value=3.0, unit='seconds', amplitude="0.5", details="details1") r2 = ihm.multi_state_scheme.RelaxationTime( value=4.0, unit='milliseconds', details="details2", dataset_group=cur_dataset_group_1, file=cur_external_file_1) r3 = ihm.multi_state_scheme.RelaxationTime( value=6.0, unit='seconds', details="details3", dataset_group=cur_dataset_group_1, file=cur_external_file_1) mss1 = ihm.multi_state_scheme.MultiStateScheme( name="mss1", relaxation_times=[r1] ) mss1.add_relaxation_time(r2) mss1.add_relaxation_time(r1) mssc1 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, relaxation_time=r3 ) mssc2 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_3, relaxation_time=r3 ) # a multi-state scheme connectivity without a relaxation time mssc3 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_2, end_state=cur_state_3, kinetic_rate='rate' ) # a multi-state scheme that has None as relaxation time mssc4 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_3, end_state=cur_state_2, relaxation_time=None, kinetic_rate='rate' ) mss2 = ihm.multi_state_scheme.MultiStateScheme( name="mss2", connectivities=[mssc1, mssc2, mssc3, mssc4] ) system.multi_state_schemes.append(mss1) system.multi_state_schemes.append(mss2) ihm.dumper._MultiStateSchemeConnectivityDumper().finalize(system) ihm.dumper._MultiStateSchemeDumper().finalize(system) f = ihm.flr.FLRData() r4 = ihm.multi_state_scheme.RelaxationTime(value=5.0, unit='seconds', amplitude="0.6", details="details4") cur_fret_analysis = MockObject() c = ihm.flr.RelaxationTimeFretAnalysisConnection( fret_analysis=cur_fret_analysis, relaxation_time=r4, details='.') f.relaxation_time_fret_analysis_connections.append(c) f.relaxation_time_fret_analysis_connections.append(c) system.flr_data.append(f) # Explicitly setting an _id r5 = ihm.multi_state_scheme.RelaxationTime(value=10.0, unit='seconds', amplitude="0.1", details="details5") r5._id = '105' mss1.add_relaxation_time(r5) mss2.add_relaxation_time(None) ihm.dumper._FLRRelaxationTimeFretAnalysisConnectionDumper().finalize( system) dumper = ihm.dumper._RelaxationTimeDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_relaxation_time.id _ihm_relaxation_time.value _ihm_relaxation_time.unit _ihm_relaxation_time.amplitude _ihm_relaxation_time.dataset_group_id _ihm_relaxation_time.external_file_id _ihm_relaxation_time.details 1 3.000 seconds 0.5 . . details1 2 4.000 milliseconds . 1 2 details2 105 10.000 seconds 0.1 . . details5 3 6.000 seconds . 1 2 details3 4 5.000 seconds 0.6 . . details4 # # loop_ _ihm_relaxation_time_multi_state_scheme.id _ihm_relaxation_time_multi_state_scheme.relaxation_time_id _ihm_relaxation_time_multi_state_scheme.scheme_id _ihm_relaxation_time_multi_state_scheme.scheme_connectivity_id _ihm_relaxation_time_multi_state_scheme.details 1 1 1 . . 2 2 1 . . 3 1 1 . . 4 105 1 . . 5 3 2 1 . 6 3 2 2 . 7 4 . . . # """) def test_kinetic_rate_dumper(self): """"Test KineticRate dumper""" class MockObject: pass cur_dataset_group_1 = MockObject() cur_dataset_group_1._id = 1 cur_external_file_1 = MockObject() cur_external_file_1._id = 2 cur_state_1 = MockObject() cur_state_1._id = 101 cur_state_2 = MockObject() cur_state_2._id = 102 cur_state_3 = MockObject() cur_state_3._id = 103 e_k2 = ihm.multi_state_scheme.PopulationEquilibriumConstant( value=4.0, unit='unit_placeholder') e_k3 = ihm.multi_state_scheme.PopulationEquilibriumConstant( value=5.0) e_k4 = ihm.multi_state_scheme.KineticRateEquilibriumConstant( value=6.0 ) e_k5 = ihm.multi_state_scheme.EquilibriumConstant(value=7.0, unit='unit7') # k1 => id 1 k1 = ihm.multi_state_scheme.KineticRate( transition_rate_constant=3.0, details="transition rate constant 1" ) # k2 => id 2 k2 = ihm.multi_state_scheme.KineticRate( equilibrium_constant=e_k2, details='equilibrium constant 2', dataset_group=cur_dataset_group_1, file=cur_external_file_1 ) # k3 => id 3 k3 = ihm.multi_state_scheme.KineticRate( transition_rate_constant=6.0, equilibrium_constant=e_k3, details='equilibrium constant 3', dataset_group=cur_dataset_group_1 ) # k4 => id 4 k4 = ihm.multi_state_scheme.KineticRate( equilibrium_constant=e_k4, details='equilibrium constant 4' ) # k5 => id 5 k5 = ihm.multi_state_scheme.KineticRate( equilibrium_constant=e_k5, details='equilibrium constant 5' ) # mssc1 => id 1 mssc1 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, kinetic_rate=k1 ) # mssc2 => id 2 mssc2 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, kinetic_rate=k2 ) # mssc3 => id 3 mssc3 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, kinetic_rate=k3 ) # mssc4 => id 4 mssc4 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_1, end_state=cur_state_2, kinetic_rate=k4 ) # mssc5 => id 5 mssc5 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_2, end_state=cur_state_1, kinetic_rate=k5 ) mss1 = ihm.multi_state_scheme.MultiStateScheme( name="mss1", connectivities=[mssc1, mssc2, mssc3, mssc4] ) mss1.add_connectivity(mssc5) # A multi-state scheme connectivity without a kinetic rate mssc6 = ihm.multi_state_scheme.Connectivity( begin_state=cur_state_2, end_state=cur_state_3, relaxation_time='rt' ) mss1.add_connectivity(mssc6) system = ihm.System() system.multi_state_schemes.append(mss1) ihm.dumper._MultiStateSchemeConnectivityDumper().finalize(system) ihm.dumper._MultiStateSchemeDumper().finalize(system) dumper = ihm.dumper._KineticRateDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_kinetic_rate.id _ihm_kinetic_rate.transition_rate_constant _ihm_kinetic_rate.equilibrium_constant _ihm_kinetic_rate.equilibrium_constant_determination_method _ihm_kinetic_rate.equilibrium_constant_unit _ihm_kinetic_rate.details _ihm_kinetic_rate.scheme_connectivity_id _ihm_kinetic_rate.dataset_group_id _ihm_kinetic_rate.external_file_id 1 3.000 . . . 'transition rate constant 1' 1 . . 2 . 4.000 'equilibrium constant is determined from population' unit_placeholder 'equilibrium constant 2' 2 1 2 3 6.000 5.000 'equilibrium constant is determined from population' . 'equilibrium constant 3' 3 1 . 4 . 6.000 'equilibrium constant is determined from kinetic rates, kAB/kBA' . 'equilibrium constant 4' 4 . . 5 . 7.000 'equilibrium constant is determined from another method not listed' unit7 'equilibrium constant 5' 5 . . # """) f = ihm.flr.FLRData() k4 = ihm.multi_state_scheme.KineticRate( transition_rate_constant=4.0, details="transition rate constant 4") cur_fret_analysis = MockObject() c = ihm.flr.KineticRateFretAnalysisConnection( fret_analysis=cur_fret_analysis, kinetic_rate=k4, details='.') f.kinetic_rate_fret_analysis_connections.append(c) f.kinetic_rate_fret_analysis_connections.append(c) system.flr_data.append(f) ihm.dumper._FLRKineticRateFretAnalysisConnectionDumper().finalize( system) dumper = ihm.dumper._KineticRateDumper() dumper.finalize(system) out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _ihm_kinetic_rate.id _ihm_kinetic_rate.transition_rate_constant _ihm_kinetic_rate.equilibrium_constant _ihm_kinetic_rate.equilibrium_constant_determination_method _ihm_kinetic_rate.equilibrium_constant_unit _ihm_kinetic_rate.details _ihm_kinetic_rate.scheme_connectivity_id _ihm_kinetic_rate.dataset_group_id _ihm_kinetic_rate.external_file_id 1 3.000 . . . 'transition rate constant 1' 1 . . 2 . 4.000 'equilibrium constant is determined from population' unit_placeholder 'equilibrium constant 2' 2 1 2 3 6.000 5.000 'equilibrium constant is determined from population' . 'equilibrium constant 3' 3 1 . 4 . 6.000 'equilibrium constant is determined from kinetic rates, kAB/kBA' . 'equilibrium constant 4' 4 . . 5 . 7.000 'equilibrium constant is determined from another method not listed' unit7 'equilibrium constant 5' 5 . . 6 4.000 . . . 'transition rate constant 4' . . . # """) def test_flr_dumper(self): """Test FLR dumpers""" class MockObject: pass cur_state = MockObject() cur_state._id = 1 cur_model_1 = MockObject() cur_model_1._id = 1 cur_model_2 = MockObject() cur_model_2._id = 2 dataset_1 = MockObject() dataset_1._id = 1 dataset_group_1 = MockObject() dataset_group_1._id = 1 cur_ihm_modeling_protocol = MockObject() cur_ihm_modeling_protocol._id = 1 system = ihm.System() # Fill the system cur_flr_data = ihm.flr.FLRData() cur_entity_1 = ihm.Entity("AG", description='Entity_1') cur_entity_2 = ihm.Entity("CCCCCCCCCC", description='Entity_2') system.entities.extend([cur_entity_1, cur_entity_2]) asym1 = ihm.AsymUnit(cur_entity_1, id='C') system.asym_units.append(asym1) # FLR cur_entity_assembly = ihm.flr.EntityAssembly() cur_entity_assembly.add_entity(entity=cur_entity_1, num_copies=1) cur_entity_assembly.add_entity(entity=cur_entity_2, num_copies=2) cur_instrument = ihm.flr.Instrument(details='My_Instrument') cur_inst_setting_1 = ihm.flr.InstSetting(details='My_Inst_setting_1') cur_inst_setting_2 = ihm.flr.InstSetting(details='My_Inst_setting_2') cur_exp_condition_1 = ihm.flr.ExpCondition( details='My_Exp_condition_1') cur_exp_condition_2 = ihm.flr.ExpCondition( details='My_Exp_condition_2') cur_sample_condition_1 = ihm.flr.SampleCondition( details='My_Sample_condition_1') cur_sample_condition_2 = ihm.flr.SampleCondition( details='My_Sample_condition_2') cur_sample_1 = ihm.flr.Sample(entity_assembly=cur_entity_assembly, num_of_probes=2, condition=cur_sample_condition_1, description='Sample_1', details='Details sample 1', solvent_phase='liquid') cur_sample_2 = ihm.flr.Sample(entity_assembly=cur_entity_assembly, num_of_probes=2, condition=cur_sample_condition_2, description='Sample_2', details='Details sample 2', solvent_phase='liquid') # Reference sample cur_sample_3 = ihm.flr.Sample(entity_assembly=cur_entity_assembly, num_of_probes=1, condition=cur_sample_condition_1, description='Reference Sample', details='Details Reference Sample', solvent_phase='liquid') cur_experiment = ihm.flr.Experiment() cur_experiment.add_entry(instrument=cur_instrument, inst_setting=cur_inst_setting_1, exp_condition=cur_exp_condition_1, sample=cur_sample_1) cur_experiment.add_entry(instrument=cur_instrument, inst_setting=cur_inst_setting_2, exp_condition=cur_exp_condition_2, sample=cur_sample_2) cur_experiment.add_entry(instrument=cur_instrument, inst_setting=cur_inst_setting_1, exp_condition=cur_exp_condition_1, sample=cur_sample_3) # Probes cur_probe_1 = ihm.flr.Probe() cur_probe_2 = ihm.flr.Probe() cur_probe_list_1 = ihm.flr.ProbeList(chromophore_name='Donor1', reactive_probe_flag=False, probe_origin='extrinsic', probe_link_type='covalent') cur_probe_list_2 = ihm.flr.ProbeList( chromophore_name='Acceptor2', reactive_probe_flag=True, reactive_probe_name='Acceptor1 reactive', probe_origin='extrinsic', probe_link_type='covalent') # Chem descriptor ID 1 cur_chem_desc_probe_1_chromophore = ihm.ChemDescriptor( auth_name='Donor1_chromophore_chem_desc', chem_comp_id=None, common_name=None, smiles='C1') cur_chem_desc_probe_1_chromophore._id = 1 # Chem descriptor ID 2 cur_chem_desc_probe_2_chromophore = ihm.ChemDescriptor( auth_name='Donor2_chromophore_chem_desc', chem_comp_id=None, common_name=None, smiles='C2') cur_chem_desc_probe_2_chromophore._id = 2 # Chem descriptor ID 3 cur_chem_desc_probe_2_reactive = ihm.ChemDescriptor( auth_name='Donor1_reactive_chem_desc', chem_comp_id=None, common_name=None, smiles='R1') cur_chem_desc_probe_2_reactive._id = 3 cur_probe_descriptor_1 = ihm.flr.ProbeDescriptor( reactive_probe_chem_descriptor=None, chromophore_chem_descriptor=cur_chem_desc_probe_1_chromophore, chromophore_center_atom='CB') cur_probe_descriptor_2 = ihm.flr.ProbeDescriptor( reactive_probe_chem_descriptor=cur_chem_desc_probe_2_reactive, chromophore_chem_descriptor=cur_chem_desc_probe_2_chromophore, chromophore_center_atom='CB') cur_probe_1.probe_descriptor = cur_probe_descriptor_1 cur_probe_1.probe_list_entry = cur_probe_list_1 cur_probe_2.probe_descriptor = cur_probe_descriptor_2 cur_probe_2.probe_list_entry = cur_probe_list_2 # Modified residue # Chem descriptor ID 4 cur_chem_descriptor_modified_residue = ihm.ChemDescriptor( auth_name='Modified_residue', smiles='Modified') cur_chem_comp_mutated_residue = ihm.ChemComp( id='Cys', code='C', code_canonical='C') cur_chem_descriptor_modified_residue._id = 4 # cur_chem_comp_mutated_residue._id = 5 # Poly_probe_position cur_poly_probe_position_1 = ihm.flr.PolyProbePosition( resatom=cur_entity_1.residue(1), # no atom ID given mutation_flag=True, modification_flag=True, auth_name='Position_1', mutated_chem_comp_id=cur_chem_comp_mutated_residue, modified_chem_descriptor=cur_chem_descriptor_modified_residue) cur_poly_probe_position_2 = ihm.flr.PolyProbePosition( # using asym instead of only entity resatom=asym1.residue(2).atom('CB'), mutation_flag=False, modification_flag=False, auth_name='Position_2') cur_poly_probe_position_3 = ihm.flr.PolyProbePosition( resatom=cur_entity_2.residue(10).atom('CB'), mutation_flag=True, modification_flag=True, auth_name='Position_3', mutated_chem_comp_id=cur_chem_comp_mutated_residue, modified_chem_descriptor=cur_chem_descriptor_modified_residue) # Sample_probe_details cur_sample_probe_details_1 = ihm.flr.SampleProbeDetails( sample=cur_sample_1, probe=cur_probe_1, fluorophore_type='donor', poly_probe_position=cur_poly_probe_position_1, description='Donor in position1-position3') cur_sample_probe_details_2 = ihm.flr.SampleProbeDetails( sample=cur_sample_1, probe=cur_probe_2, fluorophore_type='acceptor', poly_probe_position=cur_poly_probe_position_3, description='Acceptor in position1-position3') cur_sample_probe_details_3 = ihm.flr.SampleProbeDetails( sample=cur_sample_2, probe=cur_probe_1, fluorophore_type='donor', poly_probe_position=cur_poly_probe_position_2, description='Donor in position2-position3') cur_sample_probe_details_4 = ihm.flr.SampleProbeDetails( sample=cur_sample_2, probe=cur_probe_2, fluorophore_type='acceptor', poly_probe_position=cur_poly_probe_position_3, description='Acceptor in position2-position3') cur_sample_probe_details_5 = ihm.flr.SampleProbeDetails( sample=cur_sample_3, probe=cur_probe_1, fluorophore_type='donor', poly_probe_position=cur_poly_probe_position_1, description='Donor-only on reference sample') # Poly_probe_conjugate # Chem Descriptor ID 5 cur_poly_probe_conjugate_chem_descriptor = ihm.ChemDescriptor( auth_name='Conjugate', smiles='Conj1') cur_poly_probe_conjugate_chem_descriptor._id = 5 cur_poly_probe_conjugate_1 = ihm.flr.PolyProbeConjugate( sample_probe=cur_sample_probe_details_1, chem_descriptor=cur_poly_probe_conjugate_chem_descriptor, ambiguous_stoichiometry=False) cur_poly_probe_conjugate_2 = ihm.flr.PolyProbeConjugate( sample_probe=cur_sample_probe_details_2, chem_descriptor=cur_poly_probe_conjugate_chem_descriptor, ambiguous_stoichiometry=False) cur_poly_probe_conjugate_3 = ihm.flr.PolyProbeConjugate( sample_probe=cur_sample_probe_details_3, chem_descriptor=cur_poly_probe_conjugate_chem_descriptor, ambiguous_stoichiometry=False) cur_poly_probe_conjugate_4 = ihm.flr.PolyProbeConjugate( sample_probe=cur_sample_probe_details_4, chem_descriptor=cur_poly_probe_conjugate_chem_descriptor, ambiguous_stoichiometry=False) cur_poly_probe_conjugate_5 = ihm.flr.PolyProbeConjugate( sample_probe=cur_sample_probe_details_5, chem_descriptor=cur_poly_probe_conjugate_chem_descriptor, ambiguous_stoichiometry=False) cur_flr_data.poly_probe_conjugates.extend( (cur_poly_probe_conjugate_1, cur_poly_probe_conjugate_2, cur_poly_probe_conjugate_3, cur_poly_probe_conjugate_4, cur_poly_probe_conjugate_5)) # Forster_radius cur_forster_radius = ihm.flr.FRETForsterRadius( donor_probe=cur_probe_1, acceptor_probe=cur_probe_2, forster_radius=52.0, reduced_forster_radius=53.2) # Fret_calibration_parameters cur_fret_calibration_parameters_1 = ihm.flr.FRETCalibrationParameters( phi_acceptor=0.35, alpha=2.4, gg_gr_ratio=0.4, a_b=0.8) cur_fret_calibration_parameters_2 = ihm.flr.FRETCalibrationParameters( phi_acceptor=0.35, alpha=2.4, gg_gr_ratio=0.38, a_b=0.8) # LifetimeFitModel cur_lifetime_fit_model = ihm.flr.LifetimeFitModel( name='Lifetime fit model 1', description='Description of model') # RefMeasurementLifetime cur_lifetime_1 = ihm.flr.RefMeasurementLifetime(species_fraction=0.6, lifetime=3.2) cur_lifetime_2 = ihm.flr.RefMeasurementLifetime(species_fraction=0.4, lifetime=1.4) # RefMeasurement cur_ref_measurement_1 = ihm.flr.RefMeasurement( ref_sample_probe=cur_sample_probe_details_5, details='Reference Measurement 1') cur_ref_measurement_1.add_lifetime(cur_lifetime_1) cur_ref_measurement_1.add_lifetime(cur_lifetime_2) # RefMeasurementGroup cur_lifetime_ref_measurement_group = ihm.flr.RefMeasurementGroup( details='Reference measurement group 1') cur_lifetime_ref_measurement_group.add_ref_measurement( cur_ref_measurement_1) # FretAnalysis cur_fret_analysis_1 = ihm.flr.FRETAnalysis( experiment=cur_experiment, sample_probe_1=cur_sample_probe_details_1, sample_probe_2=cur_sample_probe_details_2, forster_radius=cur_forster_radius, type='intensity-based', calibration_parameters=cur_fret_calibration_parameters_1, method_name='PDA', chi_square_reduced=1.5, dataset=dataset_1) cur_fret_analysis_2 = ihm.flr.FRETAnalysis( experiment=cur_experiment, sample_probe_1=cur_sample_probe_details_3, sample_probe_2=cur_sample_probe_details_4, forster_radius=cur_forster_radius, type='intensity-based', calibration_parameters=cur_fret_calibration_parameters_2, method_name='PDA', chi_square_reduced=1.8, dataset=dataset_1) # lifetime-based FRETAnalysis cur_fret_analysis_3 = ihm.flr.FRETAnalysis( experiment=cur_experiment, sample_probe_1=cur_sample_probe_details_1, sample_probe_2=cur_sample_probe_details_2, forster_radius=cur_forster_radius, type='lifetime-based', lifetime_fit_model=cur_lifetime_fit_model, ref_measurement_group=cur_lifetime_ref_measurement_group, method_name='Lifetime fit', chi_square_reduced=1.6, dataset=dataset_1) # Peak_assignment cur_peak_assignment = ihm.flr.PeakAssignment( method_name='Population', details='Peaks were assigned by population fractions.') # Fret_distance_restraints cur_fret_distance_restraint_1 = ihm.flr.FRETDistanceRestraint( sample_probe_1=cur_sample_probe_details_1, sample_probe_2=cur_sample_probe_details_2, analysis=cur_fret_analysis_1, distance=53.5, distance_error_plus=2.5, distance_error_minus=2.3, distance_type='_E', state=cur_state, population_fraction=0.80, peak_assignment=cur_peak_assignment) cur_fret_distance_restraint_2 = ihm.flr.FRETDistanceRestraint( sample_probe_1=cur_sample_probe_details_3, sample_probe_2=cur_sample_probe_details_4, analysis=cur_fret_analysis_2, distance=49.0, distance_error_plus=2.0, distance_error_minus=2.1, distance_type='_E', state=cur_state, population_fraction=0.80, peak_assignment=cur_peak_assignment) cur_fret_distance_restraint_3 = ihm.flr.FRETDistanceRestraint( sample_probe_1=cur_sample_probe_details_1, sample_probe_2=cur_sample_probe_details_2, analysis=cur_fret_analysis_3, distance=53.5, distance_error_plus=2.5, distance_error_minus=2.3, distance_type='_E', state=cur_state, population_fraction=0.80, peak_assignment=cur_peak_assignment) cur_fret_dist_restraint_group = ihm.flr.FRETDistanceRestraintGroup() cur_fret_dist_restraint_group.add_distance_restraint( cur_fret_distance_restraint_1) cur_fret_dist_restraint_group.add_distance_restraint( cur_fret_distance_restraint_2) cur_fret_dist_restraint_group.add_distance_restraint( cur_fret_distance_restraint_3) cur_flr_data.distance_restraint_groups.append( cur_fret_dist_restraint_group) # fret_model_quality cur_fret_model_quality_1 = ihm.flr.FRETModelQuality( model=cur_model_1, chi_square_reduced=1.3, dataset_group=dataset_group_1, method=None) cur_fret_model_quality_2 = ihm.flr.FRETModelQuality( model=cur_model_2, chi_square_reduced=1.9, dataset_group=dataset_group_1, method=None) cur_flr_data.fret_model_qualities.extend( (cur_fret_model_quality_1, cur_fret_model_quality_2)) # fret_model_distance cur_fret_model_distance_1_1 = ihm.flr.FRETModelDistance( restraint=cur_fret_distance_restraint_1, model=cur_model_1, distance=52.0) cur_fret_model_distance_1_2 = ihm.flr.FRETModelDistance( restraint=cur_fret_distance_restraint_2, model=cur_model_1, distance=50.0) cur_fret_model_distance_2_1 = ihm.flr.FRETModelDistance( restraint=cur_fret_distance_restraint_1, model=cur_model_2, distance=53.8) cur_fret_model_distance_2_2 = ihm.flr.FRETModelDistance( restraint=cur_fret_distance_restraint_2, model=cur_model_2, distance=49.4) cur_flr_data.fret_model_distances.extend( (cur_fret_model_distance_1_1, cur_fret_model_distance_1_2, cur_fret_model_distance_2_1, cur_fret_model_distance_2_2)) # FPS modeling cur_fps_global_parameters = ihm.flr.FPSGlobalParameters( forster_radius=52, conversion_function_polynom_order=3, repetition=1000, av_grid_rel=0.2, av_min_grid_a=0.4, av_allowed_sphere=0.5, av_search_nodes=3, av_e_samples_k=200, sim_viscosity_adjustment=1, sim_dt_adjustment=1, sim_max_iter_k=200, sim_max_force=400, sim_clash_tolerance_a=1, sim_reciprocal_kt=10, sim_clash_potential='^2', convergence_e=100, convergence_k=0.001, convergence_f=0.001, convergence_t=0.002) cur_fps_modeling_1 = ihm.flr.FPSModeling( protocol=cur_ihm_modeling_protocol, restraint_group=cur_fret_dist_restraint_group, global_parameter=cur_fps_global_parameters, probe_modeling_method="AV3") cur_fps_modeling_2 = ihm.flr.FPSModeling( protocol=cur_ihm_modeling_protocol, restraint_group=cur_fret_dist_restraint_group, global_parameter=cur_fps_global_parameters, probe_modeling_method="MPP") # Modeling by AV cur_fps_av_parameters_1 = ihm.flr.FPSAVParameter( num_linker_atoms=15, linker_length=20.0, linker_width=3.5, probe_radius_1=10.0, probe_radius_2=5.0, probe_radius_3=3.5) cur_fps_av_modeling_1 = ihm.flr.FPSAVModeling( fps_modeling=cur_fps_modeling_1, sample_probe=cur_sample_probe_details_1, parameter=cur_fps_av_parameters_1) cur_fps_av_modeling_3 = ihm.flr.FPSAVModeling( fps_modeling=cur_fps_modeling_1, sample_probe=cur_sample_probe_details_3, parameter=cur_fps_av_parameters_1) cur_flr_data.fps_modeling.append(cur_fps_av_modeling_1) cur_flr_data.fps_modeling.append(cur_fps_av_modeling_3) # Modeling by mean probe position cur_mpp_atom_position_1 = ihm.flr.FPSMPPAtomPosition( atom=asym1.residue(1).atom('CA'), x=1.0, y=1.0, z=1.0) cur_mpp_atom_position_2 = ihm.flr.FPSMPPAtomPosition( atom=asym1.residue(2).atom('CA'), x=2.0, y=2.0, z=2.0) cur_mpp_atom_position_group = ihm.flr.FPSMPPAtomPositionGroup() cur_mpp_atom_position_group.add_atom_position(cur_mpp_atom_position_1) cur_mpp_atom_position_group.add_atom_position(cur_mpp_atom_position_2) cur_mean_probe_position_2 = ihm.flr.FPSMeanProbePosition( sample_probe=cur_sample_probe_details_2, x=1.0, y=2.0, z=3.0) cur_mean_probe_position_4 = ihm.flr.FPSMeanProbePosition( sample_probe=cur_sample_probe_details_4, x=1.0, y=2.0, z=3.0) cur_fps_mpp_modeling_2 = ihm.flr.FPSMPPModeling( fps_modeling=cur_fps_modeling_2, mpp=cur_mean_probe_position_2, mpp_atom_position_group=cur_mpp_atom_position_group) cur_fps_mpp_modeling_4 = ihm.flr.FPSMPPModeling( fps_modeling=cur_fps_modeling_2, mpp=cur_mean_probe_position_4, mpp_atom_position_group=cur_mpp_atom_position_group) cur_flr_data.fps_modeling.append(cur_fps_mpp_modeling_2) cur_flr_data.fps_modeling.append(cur_fps_mpp_modeling_4) # KineticRateFretAnalysisConnection cur_kinetic_rate1 = ihm.multi_state_scheme.KineticRate( transition_rate_constant=1.0) cur_kinetic_rate2 = ihm.multi_state_scheme.KineticRate( transition_rate_constant=2.0) cur_kinetic_rate_fret_analysis_connection1 = \ ihm.flr.KineticRateFretAnalysisConnection( fret_analysis=cur_fret_analysis_1, kinetic_rate=cur_kinetic_rate1, details='connection1') cur_kinetic_rate_fret_analysis_connection2 = \ ihm.flr.KineticRateFretAnalysisConnection( fret_analysis=cur_fret_analysis_2, kinetic_rate=cur_kinetic_rate2, details='connection2') cur_flr_data.kinetic_rate_fret_analysis_connections.append( cur_kinetic_rate_fret_analysis_connection1) cur_flr_data.kinetic_rate_fret_analysis_connections.append( cur_kinetic_rate_fret_analysis_connection2) # RelaxationTimeFretAnalysisConnection cur_relaxation_time1 = \ ihm.multi_state_scheme.RelaxationTime(value=3.0, unit='seconds') cur_relaxation_time2 = \ ihm.multi_state_scheme.RelaxationTime(value=4.0, unit='milliseconds') cur_relaxation_time_fret_analysis_connection1 = \ ihm.flr.RelaxationTimeFretAnalysisConnection( fret_analysis=cur_fret_analysis_1, relaxation_time=cur_relaxation_time1, details='connection3') cur_relaxation_time_fret_analysis_connection2 = \ ihm.flr.RelaxationTimeFretAnalysisConnection( fret_analysis=cur_fret_analysis_3, relaxation_time=cur_relaxation_time2, details='connection4') cur_flr_data.relaxation_time_fret_analysis_connections.append( cur_relaxation_time_fret_analysis_connection1) cur_flr_data.relaxation_time_fret_analysis_connections.append( cur_relaxation_time_fret_analysis_connection2) system.flr_data = [cur_flr_data] ihm.dumper._EntityDumper().finalize(system) # assign entity IDs ihm.dumper._StructAsymDumper().finalize(system) # assign asym IDs ihm.dumper._ChemCompDumper().finalize(system) experiment_dumper = ihm.dumper._FLRExperimentDumper() experiment_dumper.finalize(system) inst_setting_dumper = ihm.dumper._FLRInstSettingDumper() inst_setting_dumper.finalize(system) exp_condition_dumper = ihm.dumper._FLRExpConditionDumper() exp_condition_dumper.finalize(system) instrument_dumper = ihm.dumper._FLRInstrumentDumper() instrument_dumper.finalize(system) entity_assembly_dumper = ihm.dumper._FLREntityAssemblyDumper() entity_assembly_dumper.finalize(system) sample_condition_dumper = ihm.dumper._FLRSampleConditionDumper() sample_condition_dumper.finalize(system) sample_dumper = ihm.dumper._FLRSampleDumper() sample_dumper.finalize(system) probe_dumper = ihm.dumper._FLRProbeDumper() probe_dumper.finalize(system) sample_probe_details_dumper = ihm.dumper._FLRSampleProbeDetailsDumper() sample_probe_details_dumper.finalize(system) poly_probe_pos_dumper = ihm.dumper._FLRPolyProbePositionDumper() poly_probe_pos_dumper.finalize(system) conjugate_dumper = ihm.dumper._FLRConjugateDumper() conjugate_dumper.finalize(system) radii_dumper = ihm.dumper._FLRForsterRadiusDumper() radii_dumper.finalize(system) parameters_dumper = ihm.dumper._FLRCalibrationParametersDumper() parameters_dumper.finalize(system) lifetime_fit_model_dumper = ihm.dumper._FLRLifetimeFitModelDumper() lifetime_fit_model_dumper.finalize(system) ref_measurement_dumper = ihm.dumper._FLRRefMeasurementDumper() ref_measurement_dumper.finalize(system) analysis_dumper = ihm.dumper._FLRAnalysisDumper() analysis_dumper.finalize(system) peak_assignment_dumper = ihm.dumper._FLRPeakAssignmentDumper() peak_assignment_dumper.finalize(system) distance_restraint_dumper = ihm.dumper._FLRDistanceRestraintDumper() distance_restraint_dumper.finalize(system) model_quality_dumper = ihm.dumper._FLRModelQualityDumper() model_quality_dumper.finalize(system) model_distance_dumper = ihm.dumper._FLRModelDistanceDumper() model_distance_dumper.finalize(system) fps_modeling_dumper = ihm.dumper._FLRFPSModelingDumper() fps_modeling_dumper.finalize(system) av_dumper = ihm.dumper._FLRFPSAVModelingDumper() av_dumper.finalize(system) mpp_dumper = ihm.dumper._FLRFPSMPPModelingDumper() mpp_dumper.finalize(system) # assign IDs # Assign IDs to the kinetic rates ihm.dumper._KineticRateDumper().finalize(system) # Assign IDs to the relaxation times ihm.dumper._RelaxationTimeDumper().finalize(system) kinetic_rate_fret_analysis_connection_dumper = \ ihm.dumper._FLRKineticRateFretAnalysisConnectionDumper() kinetic_rate_fret_analysis_connection_dumper.finalize(system) relaxation_time_fret_analysis_connection_dumper = \ ihm.dumper._FLRRelaxationTimeFretAnalysisConnectionDumper() relaxation_time_fret_analysis_connection_dumper.finalize(system) out = _get_dumper_output(experiment_dumper, system) self.assertEqual(out, """# loop_ _flr_experiment.ordinal_id _flr_experiment.id _flr_experiment.instrument_id _flr_experiment.inst_setting_id _flr_experiment.exp_condition_id _flr_experiment.sample_id _flr_experiment.details 1 1 1 1 1 1 . 2 1 1 2 2 2 . 3 1 1 1 1 3 . # """) out = _get_dumper_output(inst_setting_dumper, system) self.assertEqual(out, """# loop_ _flr_inst_setting.id _flr_inst_setting.details 1 My_Inst_setting_1 2 My_Inst_setting_2 # """) out = _get_dumper_output(exp_condition_dumper, system) self.assertEqual(out, """# loop_ _flr_exp_condition.id _flr_exp_condition.details 1 My_Exp_condition_1 2 My_Exp_condition_2 # """) out = _get_dumper_output(instrument_dumper, system) self.assertEqual(out, """# loop_ _flr_instrument.id _flr_instrument.details 1 My_Instrument # """) out = _get_dumper_output(entity_assembly_dumper, system) self.assertEqual(out, """# loop_ _flr_entity_assembly.ordinal_id _flr_entity_assembly.assembly_id _flr_entity_assembly.entity_id _flr_entity_assembly.num_copies _flr_entity_assembly.entity_description 1 1 1 1 Entity_1 2 1 2 2 Entity_2 # """) out = _get_dumper_output(sample_condition_dumper, system) self.assertEqual(out, """# loop_ _flr_sample_condition.id _flr_sample_condition.details 1 My_Sample_condition_1 2 My_Sample_condition_2 # """) out = _get_dumper_output(sample_dumper, system) self.assertEqual(out, """# loop_ _flr_sample.id _flr_sample.entity_assembly_id _flr_sample.num_of_probes _flr_sample.sample_condition_id _flr_sample.sample_description _flr_sample.sample_details _flr_sample.solvent_phase 1 1 2 1 Sample_1 'Details sample 1' liquid 2 1 2 2 Sample_2 'Details sample 2' liquid 3 1 1 1 'Reference Sample' 'Details Reference Sample' liquid # """) out = _get_dumper_output(probe_dumper, system) self.assertEqual(out, """# loop_ _flr_probe_list.probe_id _flr_probe_list.chromophore_name _flr_probe_list.reactive_probe_flag _flr_probe_list.reactive_probe_name _flr_probe_list.probe_origin _flr_probe_list.probe_link_type 1 Donor1 NO . extrinsic covalent 2 Acceptor2 YES 'Acceptor1 reactive' extrinsic covalent # # loop_ _flr_probe_descriptor.probe_id _flr_probe_descriptor.reactive_probe_chem_descriptor_id _flr_probe_descriptor.chromophore_chem_descriptor_id _flr_probe_descriptor.chromophore_center_atom 1 . 1 CB 2 3 2 CB # """) out = _get_dumper_output(sample_probe_details_dumper, system) self.assertEqual(out, """# loop_ _flr_sample_probe_details.sample_probe_id _flr_sample_probe_details.sample_id _flr_sample_probe_details.probe_id _flr_sample_probe_details.fluorophore_type _flr_sample_probe_details.description _flr_sample_probe_details.poly_probe_position_id 1 1 1 donor 'Donor in position1-position3' 1 2 1 2 acceptor 'Acceptor in position1-position3' 2 3 2 1 donor 'Donor in position2-position3' 3 4 2 2 acceptor 'Acceptor in position2-position3' 2 5 3 1 donor 'Donor-only on reference sample' 1 # """) out = _get_dumper_output(poly_probe_pos_dumper, system) self.assertEqual(out, """# loop_ _flr_poly_probe_position.id _flr_poly_probe_position.entity_id _flr_poly_probe_position.entity_description _flr_poly_probe_position.asym_id _flr_poly_probe_position.seq_id _flr_poly_probe_position.comp_id _flr_poly_probe_position.atom_id _flr_poly_probe_position.mutation_flag _flr_poly_probe_position.modification_flag _flr_poly_probe_position.auth_name 1 1 Entity_1 . 1 ALA . YES YES Position_1 2 2 Entity_2 . 10 CYS CB YES YES Position_3 3 1 Entity_1 C 2 GLY CB NO NO Position_2 # # loop_ _flr_poly_probe_position_mutated.id _flr_poly_probe_position_mutated.chem_comp_id _flr_poly_probe_position_mutated.atom_id 1 Cys . 2 Cys CB # # loop_ _flr_poly_probe_position_modified.id _flr_poly_probe_position_modified.chem_descriptor_id _flr_poly_probe_position_modified.atom_id 1 4 . 2 4 CB # """) out = _get_dumper_output(conjugate_dumper, system) self.assertEqual(out, """# loop_ _flr_poly_probe_conjugate.id _flr_poly_probe_conjugate.sample_probe_id _flr_poly_probe_conjugate.chem_descriptor_id _flr_poly_probe_conjugate.ambiguous_stoichiometry_flag _flr_poly_probe_conjugate.probe_stoichiometry 1 1 5 NO . 2 2 5 NO . 3 3 5 NO . 4 4 5 NO . 5 5 5 NO . # """) out = _get_dumper_output(radii_dumper, system) self.assertEqual(out, """# loop_ _flr_fret_forster_radius.id _flr_fret_forster_radius.donor_probe_id _flr_fret_forster_radius.acceptor_probe_id _flr_fret_forster_radius.forster_radius _flr_fret_forster_radius.reduced_forster_radius 1 1 2 52.000 53.200 # """) out = _get_dumper_output(parameters_dumper, system) self.assertEqual(out, """# loop_ _flr_fret_calibration_parameters.id _flr_fret_calibration_parameters.phi_acceptor _flr_fret_calibration_parameters.alpha _flr_fret_calibration_parameters.alpha_sd _flr_fret_calibration_parameters.gG_gR_ratio _flr_fret_calibration_parameters.beta _flr_fret_calibration_parameters.gamma _flr_fret_calibration_parameters.delta _flr_fret_calibration_parameters.a_b 1 0.350 2.400 . 0.400 . . . 0.800 2 0.350 2.400 . 0.380 . . . 0.800 # """) out = _get_dumper_output(ref_measurement_dumper, system) self.assertEqual(out, """# loop_ _flr_reference_measurement_group.id _flr_reference_measurement_group.num_measurements _flr_reference_measurement_group.details 1 1 'Reference measurement group 1' # # loop_ _flr_reference_measurement_group_link.group_id _flr_reference_measurement_group_link.reference_measurement_id 1 1 # # loop_ _flr_reference_measurement.id _flr_reference_measurement.reference_sample_probe_id _flr_reference_measurement.num_species _flr_reference_measurement.details 1 5 2 'Reference Measurement 1' # # loop_ _flr_reference_measurement_lifetime.ordinal_id _flr_reference_measurement_lifetime.reference_measurement_id _flr_reference_measurement_lifetime.species_name _flr_reference_measurement_lifetime.species_fraction _flr_reference_measurement_lifetime.lifetime 1 1 . 0.600 3.200 2 1 . 0.400 1.400 # """) out = _get_dumper_output(lifetime_fit_model_dumper, system) self.assertEqual(out, """# loop_ _flr_lifetime_fit_model.id _flr_lifetime_fit_model.name _flr_lifetime_fit_model.description _flr_lifetime_fit_model.external_file_id _flr_lifetime_fit_model.citation_id 1 'Lifetime fit model 1' 'Description of model' . . # """) out = _get_dumper_output(analysis_dumper, system) self.assertEqual(out, """# loop_ _flr_fret_analysis.id _flr_fret_analysis.experiment_id _flr_fret_analysis.type _flr_fret_analysis.sample_probe_id_1 _flr_fret_analysis.sample_probe_id_2 _flr_fret_analysis.forster_radius_id _flr_fret_analysis.dataset_list_id _flr_fret_analysis.external_file_id _flr_fret_analysis.software_id 1 1 intensity-based 1 2 1 1 . . 2 1 intensity-based 3 4 1 1 . . 3 1 lifetime-based 1 2 1 1 . . # # loop_ _flr_fret_analysis_intensity.ordinal_id _flr_fret_analysis_intensity.analysis_id _flr_fret_analysis_intensity.calibration_parameters_id _flr_fret_analysis_intensity.donor_only_fraction _flr_fret_analysis_intensity.chi_square_reduced _flr_fret_analysis_intensity.method_name _flr_fret_analysis_intensity.details 1 1 1 . 1.500 PDA . 2 2 2 . 1.800 PDA . # # loop_ _flr_fret_analysis_lifetime.ordinal_id _flr_fret_analysis_lifetime.analysis_id _flr_fret_analysis_lifetime.reference_measurement_group_id _flr_fret_analysis_lifetime.lifetime_fit_model_id _flr_fret_analysis_lifetime.donor_only_fraction _flr_fret_analysis_lifetime.chi_square_reduced _flr_fret_analysis_lifetime.method_name _flr_fret_analysis_lifetime.details 1 3 1 1 . 1.600 'Lifetime fit' . # """) out = _get_dumper_output(peak_assignment_dumper, system) self.assertEqual(out, """# loop_ _flr_peak_assignment.id _flr_peak_assignment.method_name _flr_peak_assignment.details 1 Population 'Peaks were assigned by population fractions.' # """) out = _get_dumper_output(distance_restraint_dumper, system) self.assertEqual(out, """# loop_ _flr_fret_distance_restraint.ordinal_id _flr_fret_distance_restraint.id _flr_fret_distance_restraint.group_id _flr_fret_distance_restraint.sample_probe_id_1 _flr_fret_distance_restraint.sample_probe_id_2 _flr_fret_distance_restraint.state_id _flr_fret_distance_restraint.analysis_id _flr_fret_distance_restraint.distance _flr_fret_distance_restraint.distance_error_plus _flr_fret_distance_restraint.distance_error_minus _flr_fret_distance_restraint.distance_type _flr_fret_distance_restraint.population_fraction _flr_fret_distance_restraint.peak_assignment_id 1 1 1 1 2 1 1 53.500 2.500 2.300 _E 0.800 1 2 2 1 3 4 1 2 49.000 2.000 2.100 _E 0.800 1 3 3 1 1 2 1 3 53.500 2.500 2.300 _E 0.800 1 # """) out = _get_dumper_output(model_quality_dumper, system) self.assertEqual(out, """# loop_ _flr_fret_model_quality.model_id _flr_fret_model_quality.chi_square_reduced _flr_fret_model_quality.dataset_group_id _flr_fret_model_quality.method _flr_fret_model_quality.details 1 1.300 1 . . 2 1.900 1 . . # """) out = _get_dumper_output(model_distance_dumper, system) self.assertEqual(out, """# loop_ _flr_fret_model_distance.id _flr_fret_model_distance.restraint_id _flr_fret_model_distance.model_id _flr_fret_model_distance.distance _flr_fret_model_distance.distance_deviation 1 1 1 52.000 1.500 2 2 1 50.000 -1.000 3 1 2 53.800 -0.300 4 2 2 49.400 -0.400 # """) out = _get_dumper_output(fps_modeling_dumper, system) self.assertEqual(out, """# loop_ _flr_FPS_modeling.id _flr_FPS_modeling.ihm_modeling_protocol_ordinal_id _flr_FPS_modeling.restraint_group_id _flr_FPS_modeling.global_parameter_id _flr_FPS_modeling.probe_modeling_method _flr_FPS_modeling.details 1 1 1 1 AV3 . 2 1 1 1 MPP . # # loop_ _flr_FPS_global_parameter.id _flr_FPS_global_parameter.forster_radius_value _flr_FPS_global_parameter.conversion_function_polynom_order _flr_FPS_global_parameter.repetition _flr_FPS_global_parameter.AV_grid_rel _flr_FPS_global_parameter.AV_min_grid_A _flr_FPS_global_parameter.AV_allowed_sphere _flr_FPS_global_parameter.AV_search_nodes _flr_FPS_global_parameter.AV_E_samples_k _flr_FPS_global_parameter.sim_viscosity_adjustment _flr_FPS_global_parameter.sim_dt_adjustment _flr_FPS_global_parameter.sim_max_iter_k _flr_FPS_global_parameter.sim_max_force _flr_FPS_global_parameter.sim_clash_tolerance_A _flr_FPS_global_parameter.sim_reciprocal_kT _flr_FPS_global_parameter.sim_clash_potential _flr_FPS_global_parameter.convergence_E _flr_FPS_global_parameter.convergence_K _flr_FPS_global_parameter.convergence_F _flr_FPS_global_parameter.convergence_T 1 52 3 1000 0.200 0.400 0.500 3 200 1 1 200 400 1 10 ^2 100 0.001 0.001 0.002 # """) out = _get_dumper_output(av_dumper, system) self.assertEqual(out, """# loop_ _flr_FPS_AV_parameter.id _flr_FPS_AV_parameter.num_linker_atoms _flr_FPS_AV_parameter.linker_length _flr_FPS_AV_parameter.linker_width _flr_FPS_AV_parameter.probe_radius_1 _flr_FPS_AV_parameter.probe_radius_2 _flr_FPS_AV_parameter.probe_radius_3 1 15 20.000 3.500 10.000 5.000 3.500 # # loop_ _flr_FPS_AV_modeling.id _flr_FPS_AV_modeling.sample_probe_id _flr_FPS_AV_modeling.FPS_modeling_id _flr_FPS_AV_modeling.parameter_id 1 1 1 1 2 3 1 1 # """) out = _get_dumper_output(mpp_dumper, system) self.assertEqual(out, """# loop_ _flr_FPS_mean_probe_position.id _flr_FPS_mean_probe_position.sample_probe_id _flr_FPS_mean_probe_position.mpp_xcoord _flr_FPS_mean_probe_position.mpp_ycoord _flr_FPS_mean_probe_position.mpp_zcoord 1 2 1.000 2.000 3.000 2 4 1.000 2.000 3.000 # # loop_ _flr_FPS_MPP_atom_position.id _flr_FPS_MPP_atom_position.entity_id _flr_FPS_MPP_atom_position.seq_id _flr_FPS_MPP_atom_position.comp_id _flr_FPS_MPP_atom_position.atom_id _flr_FPS_MPP_atom_position.asym_id _flr_FPS_MPP_atom_position.xcoord _flr_FPS_MPP_atom_position.ycoord _flr_FPS_MPP_atom_position.zcoord _flr_FPS_MPP_atom_position.group_id 1 1 1 ALA CA C 1.000 1.000 1.000 1 2 1 2 GLY CA C 2.000 2.000 2.000 1 # # loop_ _flr_FPS_MPP_modeling.ordinal_id _flr_FPS_MPP_modeling.FPS_modeling_id _flr_FPS_MPP_modeling.mpp_id _flr_FPS_MPP_modeling.mpp_atom_position_group_id 1 2 1 1 2 2 2 1 # """) out = _get_dumper_output( kinetic_rate_fret_analysis_connection_dumper, system) self.assertEqual(out, """# loop_ _flr_kinetic_rate_analysis.id _flr_kinetic_rate_analysis.fret_analysis_id _flr_kinetic_rate_analysis.kinetic_rate_id _flr_kinetic_rate_analysis.details 1 1 1 connection1 2 2 2 connection2 # """) out = _get_dumper_output( relaxation_time_fret_analysis_connection_dumper, system) self.assertEqual(out, """# loop_ _flr_relaxation_time_analysis.id _flr_relaxation_time_analysis.fret_analysis_id _flr_relaxation_time_analysis.relaxation_time_id _flr_relaxation_time_analysis.details 1 1 1 connection3 2 3 2 connection4 # """) def test_variant_base(self): """Test Variant base class""" v = ihm.dumper.Variant() self.assertIsNone(v.get_dumpers()) self.assertEqual( v.get_system_writer('system', 'writer_class', 'writer'), 'writer') def test_write_variant(self): """Test write() function with Variant object""" sys1 = ihm.System(id='system1') fh = StringIO() ihm.dumper.write(fh, [sys1], variant=ihm.dumper.IHMVariant()) def test_ignore_writer(self): """Test _IgnoreWriter utility class""" class BaseWriter: def flush(self): return 'flush called' def write_comment(self, comment): return 'write comment ' + comment s = ihm.dumper._IgnoreWriter(BaseWriter(), []) # These methods are not usually called in ordinary operation, but # we should provide them for Writer compatibility self.assertEqual(s.flush(), 'flush called') self.assertEqual(s.write_comment('foo'), 'write comment foo') def test_write_ignore_variant(self): """Test write() function with IgnoreVariant object""" sys1 = ihm.System(id='system1') fh = StringIO() ihm.dumper.write(fh, [sys1]) self.assertIn('_ihm_struct_assembly', fh.getvalue()) # Test exclude of ihm_struct_assembly category fh = StringIO() ihm.dumper.write( fh, [sys1], variant=ihm.dumper.IgnoreVariant(['_ihm_struct_assembly'])) self.assertNotIn('_ihm_struct_assembly', fh.getvalue()) # Should be case-insensitive and tolerant of missing underscore fh = StringIO() ihm.dumper.write( fh, [sys1], variant=ihm.dumper.IgnoreVariant(['IHM_STRUCT_ASSEMBLY', 'AUDIT_CONFORM'])) self.assertNotIn('_ihm_struct_assembly', fh.getvalue()) def test_dumper_unwrapped(self): """Test dumper output with line wrapping disabled""" system = ihm.System() system.software.append(ihm.Software( name='long-software-name', classification='test code', description='Some test program', version=1, location='http://some-long-url.org')) dumper = ihm.dumper._SoftwareDumper() dumper.finalize(system) try: ihm.dumper.set_line_wrap(False) out = _get_dumper_output(dumper, system) finally: ihm.dumper.set_line_wrap(True) self.assertEqual(out, """# loop_ _software.pdbx_ordinal _software.name _software.classification _software.description _software.version _software.type _software.location _software.citation_id 1 long-software-name 'test code' 'Some test program' 1 program http://some-long-url.org . # """) # noqa: E501 def test_entity_branch_list_dumper(self): """Test EntityBranchListDumper""" system = ihm.System() system.entities.append(ihm.Entity( [ihm.SaccharideChemComp('NAG'), ihm.SaccharideChemComp('FUC')])) # Non-branched entity system.entities.append(ihm.Entity('ACGT')) ed = ihm.dumper._EntityDumper() ed.finalize(system) # Assign IDs dumper = ihm.dumper._EntityBranchListDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.hetero 1 1 NAG . 1 2 FUC . # """) def test_entity_branch_dumper(self): """Test EntityBranchDumper""" system = ihm.System() system.entities.append(ihm.Entity( [ihm.SaccharideChemComp('NAG'), ihm.SaccharideChemComp('FUC')])) # Non-branched entity system.entities.append(ihm.Entity('ACGT')) ed = ihm.dumper._EntityDumper() ed.finalize(system) # Assign IDs dumper = ihm.dumper._EntityBranchDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 1 oligosaccharide # """) def test_branch_scheme_dumper(self): """Test BranchSchemeDumper""" system = ihm.System() e1 = ihm.Entity([ihm.SaccharideChemComp('NAG'), ihm.SaccharideChemComp('FUC')]) e2 = ihm.Entity([ihm.SaccharideChemComp('FUC'), ihm.SaccharideChemComp('BGC')]) e3 = ihm.Entity([ihm.SaccharideChemComp('NAG'), ihm.SaccharideChemComp('BGC')]) # Non-branched entity e4 = ihm.Entity('ACT') system.entities.extend((e1, e2, e3, e4)) system.asym_units.append(ihm.AsymUnit(e1, 'foo')) system.asym_units.append(ihm.AsymUnit(e2, 'bar', auth_seq_id_map=5)) system.asym_units.append(ihm.AsymUnit( e3, 'bar', auth_seq_id_map={1: 6, 2: (7, 'A')}, orig_auth_seq_id_map={1: 100})) system.asym_units.append(ihm.AsymUnit(e4, 'baz')) ihm.dumper._EntityDumper().finalize(system) ihm.dumper._StructAsymDumper().finalize(system) dumper = ihm.dumper._BranchSchemeDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_ins_code _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_asym_id A 1 NAG 1 1 . 1 NAG NAG A A 1 FUC 2 2 . 2 FUC FUC A B 2 FUC 1 6 . 6 FUC FUC B B 2 BGC 2 7 . 7 BGC BGC B C 3 NAG 1 6 . 100 NAG NAG C C 3 BGC 2 7 A 7 BGC BGC C # """) def test_branch_descriptor_dumper(self): """Test BranchDescriptorDumper""" system = ihm.System() e1 = ihm.Entity([ihm.SaccharideChemComp('NAG')]) bd1 = ihm.BranchDescriptor('foo', type='typ1', program='prog', program_version='1.0') bd2 = ihm.BranchDescriptor('bar', type='typ2') e1.branch_descriptors.extend((bd1, bd2)) system.entities.append(e1) ihm.dumper._EntityDumper().finalize(system) dumper = ihm.dumper._BranchDescriptorDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 1 foo typ1 prog 1.0 2 1 bar typ2 . . # """) def test_branch_link_dumper(self): """Test BranchLinkDumper""" system = ihm.System() e1 = ihm.Entity([ihm.SaccharideChemComp('NAG'), ihm.SaccharideChemComp('BMC'), ihm.SaccharideChemComp('FUC')]) lnk1 = ihm.BranchLink(num1=1, atom_id1='CA', leaving_atom_id1='H1', num2=2, atom_id2='N', leaving_atom_id2='H2', order='sing', details='foo') lnk2 = ihm.BranchLink(num1=2, atom_id1='CA', leaving_atom_id1='H1', num2=3, atom_id2='N', leaving_atom_id2='H2') e1.branch_links.extend((lnk1, lnk2)) system.entities.append(e1) ihm.dumper._EntityDumper().finalize(system) dumper = ihm.dumper._BranchLinkDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.value_order _pdbx_entity_branch_link.details 1 1 1 NAG CA H1 2 BMC N H2 sing foo 2 1 2 BMC CA H1 3 FUC N H2 . . # """) def test_database_dumper(self): """Test DatabaseDumper""" system = ihm.System() dumper = ihm.dumper._DatabaseDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, '') system = ihm.System( databases=[ihm.Database(id='foo', code='bar'), ihm.Database(id='baz', code='1abc', accession='1abcxyz', doi='1.2.3.4')]) dumper = ihm.dumper._DatabaseDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """# loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI foo bar . . baz 1abc 1abcxyz 1.2.3.4 # """) def test_database_status_dumper(self): """Test DatabaseStatusDumper""" system = ihm.System() self.assertEqual(system.database_status._map, {}) system.database_status._map = { 'status_code': 'REL', 'entry_id': '5FD1', 'recvd_initial_deposition_date': '1993-06-29', 'deposit_site': ihm.unknown, 'process_site': 'BNL', 'sg_entry': None} dumper = ihm.dumper._DatabaseStatusDumper() out = _get_dumper_output(dumper, system) # sort to remove dict order self.assertEqual("\n".join(sorted(out.split('\n'))), """ _pdbx_database_status.deposit_site ? _pdbx_database_status.entry_id 5FD1 _pdbx_database_status.process_site BNL _pdbx_database_status.recvd_initial_deposition_date 1993-06-29 _pdbx_database_status.sg_entry . _pdbx_database_status.status_code REL""") if __name__ == '__main__': unittest.main()