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Commit 519c1cb7 authored by Bienchen's avatar Bienchen
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mmCIF Writer test, di-nucleotide

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modules/io/tests/test_mmcif_writer.cc
+ 107
− 31
View file @ 519c1cb7
......@@ -92,37 +92,25 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_poly_vs_non_poly)
mol::ChainHandle ch=edi.InsertChain("A");
edi.SetChainType(ch, mol::CHAINTYPE_POLY_PEPTIDE_L);
// ALA
mol::ResidueHandle r1=edi.AppendResidue(ch, "ALA"); // is_hetatm=false
edi.InsertAtom(r1, "N", geom::Vec3(44.987, 17.389, 12.362), "N", 0.81,
25.57);
edi.InsertAtom(r1, "CA", geom::Vec3(45.936, 16.434, 12.890), "C", 0.81,
28.21);
edi.InsertAtom(r1, "C", geom::Vec3(47.196, 17.227, 13.152), "C", 0.81,
33.78);
edi.InsertAtom(r1, "O", geom::Vec3(47.506, 18.153, 12.401), "O", 0.81,
23.02);
edi.InsertAtom(r1, "CB", geom::Vec3(46.244, 15.293, 11.961), "C", 0.81,
29.85);
mol::ResidueHandle r1=edi.AppendResidue(ch, "ALA");
edi.InsertAtom(r1, "N", geom::Vec3(44.987, 17.389, 12.362), "N");
edi.InsertAtom(r1, "CA", geom::Vec3(45.936, 16.434, 12.890), "C");
edi.InsertAtom(r1, "C", geom::Vec3(47.196, 17.227, 13.152), "C");
edi.InsertAtom(r1, "O", geom::Vec3(47.506, 18.153, 12.401), "O");
edi.InsertAtom(r1, "CB", geom::Vec3(46.244, 15.293, 11.961), "C");
// PRO
mol::ResidueHandle r2=edi.AppendResidue(ch, "PRO"); // is_hetatm=false
edi.InsertAtom(r2, "N", geom::Vec3(47.953, 16.910, 14.229), "N", 0.81,
32.19 );
edi.InsertAtom(r2, "CA", geom::Vec3(47.673, 15.829, 15.187), "C", 0.81,
33.89 );
edi.InsertAtom(r2, "C", geom::Vec3(46.564, 16.052, 16.233), "C", 0.81,
37.97 );
edi.InsertAtom(r2, "O", geom::Vec3(46.059, 17.169, 16.417), "O", 0.81,
34.43 );
edi.InsertAtom(r2, "CB", geom::Vec3(49.054, 15.755, 15.880), "C", 0.81,
36.60 );
edi.InsertAtom(r2, "CG", geom::Vec3(49.357, 17.213, 16.030), "C", 0.81,
34.77 );
edi.InsertAtom(r2, "CD", geom::Vec3(49.098, 17.714, 14.637), "C", 0.81,
34.62 );
edi.InsertAtom(r2, "OXT", geom::Vec3(46.144, 15.129, 16.950), "O", 0.81,
34.03 );
conop::HeuristicProcessor heu_proc;
mol::ResidueHandle r2=edi.AppendResidue(ch, "PRO");
edi.InsertAtom(r2, "N", geom::Vec3(47.953, 16.910, 14.229), "N");
edi.InsertAtom(r2, "CA", geom::Vec3(47.673, 15.829, 15.187), "C");
edi.InsertAtom(r2, "C", geom::Vec3(46.564, 16.052, 16.233), "C");
edi.InsertAtom(r2, "O", geom::Vec3(46.059, 17.169, 16.417), "O");
edi.InsertAtom(r2, "CB", geom::Vec3(49.054, 15.755, 15.880), "C");
edi.InsertAtom(r2, "CG", geom::Vec3(49.357, 17.213, 16.030), "C");
edi.InsertAtom(r2, "CD", geom::Vec3(49.098, 17.714, 14.637), "C");
edi.InsertAtom(r2, "OXT", geom::Vec3(46.144, 15.129, 16.950), "O");
// Make sure that the two residues r1, r2 are actually connected
conop::HeuristicProcessor heu_proc;
heu_proc.Process(ent);
BOOST_CHECK_EQUAL(mol::InSequence(r1, r2), true);
......@@ -132,14 +120,15 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_poly_vs_non_poly)
std::stringstream out;
writer.Write("test", out);
// Check that the mmCIF output contains 2 non-polymer entities
String s=out.str();
// Check that the mmCIF output contains 2 non-polymer entities
BOOST_CHECK_NE(
s.find("loop_\n_entity.id\n_entity.type\n1 non-polymer\n2 non-polymer"),
String::npos);
BOOST_CHECK_NE(
s.find("loop_\n_struct_asym.id\n_struct_asym.entity_id\nA 1\nB 2"),
String::npos);
// Check that atoms are HETATMs since non-poly
BOOST_CHECK_NE(s.find("HETATM N N ALA"), String::npos);
BOOST_CHECK_NE(s.find("HETATM C CA ALA"), String::npos);
BOOST_CHECK_NE(s.find("HETATM C C ALA"), String::npos);
......@@ -154,7 +143,94 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_poly_vs_non_poly)
BOOST_CHECK_NE(s.find("HETATM C CD PRO"), String::npos);
BOOST_CHECK_NE(s.find("HETATM O OXT PRO"), String::npos);
// write mmCIF, check atoms are marked HETATM
// Nucleic acid: 2 bases in a chain are 2 entities for RCSB (check 4K9A)
ent=mol::CreateEntity();
edi=ent.EditXCS();
ch=edi.InsertChain("A");
edi.SetChainType(ch, mol::CHAINTYPE_POLY_RN);
// G
r1=edi.AppendResidue(ch, "G");
r1.SetChemClass(mol::ChemClass('R'));
edi.InsertAtom(r1, "OP3", geom::Vec3(-19.992, -12.612, -22.535), "O");
edi.InsertAtom(r1, "P", geom::Vec3(-20.743, -13.990, -22.451), "P");
edi.InsertAtom(r1, "OP1", geom::Vec3(-20.093, -14.853, -23.494), "O");
edi.InsertAtom(r1, "OP2", geom::Vec3(-20.592, -14.510, -21.074), "O");
edi.InsertAtom(r1, "O5'", geom::Vec3(-22.258, -13.779, -22.864), "O");
edi.InsertAtom(r1, "C5'", geom::Vec3(-22.956, -12.621, -22.414), "C");
edi.InsertAtom(r1, "C4'", geom::Vec3(-24.433, -12.831, -22.071), "C");
edi.InsertAtom(r1, "O4'", geom::Vec3(-24.958, -11.618, -21.688), "O");
edi.InsertAtom(r1, "C3'", geom::Vec3(-25.196, -13.187, -23.283), "C");
edi.InsertAtom(r1, "O3'", geom::Vec3(-26.335, -13.801, -22.833), "O");
edi.InsertAtom(r1, "C2'", geom::Vec3(-25.568, -11.908, -23.910), "C");
edi.InsertAtom(r1, "O2'", geom::Vec3(-26.792, -12.071, -24.602), "O");
edi.InsertAtom(r1, "C1'", geom::Vec3(-25.819, -11.112, -22.709), "C");
edi.InsertAtom(r1, "N9", geom::Vec3(-25.646, -9.689, -22.974), "N");
edi.InsertAtom(r1, "C8", geom::Vec3(-26.518, -8.728, -22.814), "C");
edi.InsertAtom(r1, "N7", geom::Vec3(-25.994, -7.595, -23.153), "N");
edi.InsertAtom(r1, "C5", geom::Vec3(-24.781, -7.838, -23.527), "C");
edi.InsertAtom(r1, "C6", geom::Vec3(-23.815, -7.062, -23.942), "C");
edi.InsertAtom(r1, "O6", geom::Vec3(-23.953, -5.880, -24.055), "O");
edi.InsertAtom(r1, "N1", geom::Vec3(-22.652, -7.575, -24.269), "N");
edi.InsertAtom(r1, "C2", geom::Vec3(-22.453, -8.886, -24.153), "C");
edi.InsertAtom(r1, "N2", geom::Vec3(-21.312, -9.419, -24.474), "N");
edi.InsertAtom(r1, "N3", geom::Vec3(-23.422, -9.638, -23.738), "N");
edi.InsertAtom(r1, "C4", geom::Vec3(-24.577, -9.122, -23.422), "C");
// A
r2=edi.AppendResidue(ch, "A");
r2.SetChemClass(mol::ChemClass('R'));
edi.InsertAtom(r2, "P", geom::Vec3(-27.082, -11.572, -26.017), "P");
edi.InsertAtom(r2, "OP1", geom::Vec3(-28.487, -11.993, -26.469), "O");
edi.InsertAtom(r2, "OP2", geom::Vec3(-27.228, -10.079, -25.961), "O");
edi.InsertAtom(r2, "O5'", geom::Vec3(-26.066, -11.826, -27.005), "O");
edi.InsertAtom(r2, "C5'", geom::Vec3(-25.894, -13.010, -27.689), "C");
edi.InsertAtom(r2, "C4'", geom::Vec3(-24.500, -13.055, -28.234), "C");
edi.InsertAtom(r2, "O4'", geom::Vec3(-24.168, -11.802, -28.703), "O");
edi.InsertAtom(r2, "C3'", geom::Vec3(-23.540, -13.333, -27.140), "C");
edi.InsertAtom(r2, "O3'", geom::Vec3(-22.424, -13.995, -27.663), "O");
edi.InsertAtom(r2, "C2'", geom::Vec3(-23.101, -11.988, -26.770), "C");
edi.InsertAtom(r2, "O2'", geom::Vec3(-21.831, -12.081, -26.257), "O");
edi.InsertAtom(r2, "C1'", geom::Vec3(-23.037, -11.318, -28.071), "C");
edi.InsertAtom(r2, "N9", geom::Vec3(-23.277, -9.902, -27.855), "N");
edi.InsertAtom(r2, "C8", geom::Vec3(-24.331, -9.311, -27.370), "C");
edi.InsertAtom(r2, "N7", geom::Vec3(-24.073, -8.040, -27.362), "N");
edi.InsertAtom(r2, "C5", geom::Vec3(-22.856, -7.821, -27.812), "C");
edi.InsertAtom(r2, "C6", geom::Vec3(-22.091, -6.735, -27.998), "C");
edi.InsertAtom(r2, "N6", geom::Vec3(-22.544, -5.535, -27.711), "N");
edi.InsertAtom(r2, "N1", geom::Vec3(-20.885, -6.823, -28.480), "N");
edi.InsertAtom(r2, "C2", geom::Vec3(-20.381, -8.034, -28.799), "C");
edi.InsertAtom(r2, "N3", geom::Vec3(-21.167, -9.113, -28.595), "N");
edi.InsertAtom(r2, "C4", geom::Vec3(-22.379, -8.993, -28.116), "C");
// Make sure that the two residues r1, r2 are actually connected
/* In the RCSB entry 4K9A, G O2' and A P are linked, but we force a regular
nucleotide link for the test
*/
edi.Connect(r1.FindAtom("O3'"), r2.FindAtom("P"));
BOOST_CHECK_EQUAL(mol::InSequence(r1, r2), true);
// Create mmCIF stream
writer = MMCifWriter();
writer.SetStructure(ent, SetDefaultCompoundLib(), false);
writer.Write("test", out);
s=out.str();
// Check that the mmCIF output contains 2 non-polymer entities
BOOST_CHECK_NE(
s.find("loop_\n_entity.id\n_entity.type\n1 non-polymer\n2 non-polymer"),
String::npos);
BOOST_CHECK_NE(
s.find("loop_\n_struct_asym.id\n_struct_asym.entity_id\nA 1\nB 2"),
String::npos);
// Check that atoms are HETATMs since non-poly
for(auto i: ch.GetAtomList()){
BOOST_CHECK_NE(s.find("HETATM "+
i.GetElement()+" "+
i.GetName()+" "+
i.GetResidue().GetName()),
String::npos);
}
// 3AXH, 1A4G
BOOST_TEST_MESSAGE(" done.");
}
......
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