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Studer Gabriel authored
Simon found issues when reading and writing CONECT statements in PDB io and provided code to fix it. yay Reading: OpenStructure did not read CONECT statements at all. By default, it still doesnt. Many PDB files out there don't provide these statements and we really don't want to rely on them. We rather want to assign connectivity based on the chemical component dictionary from the PDB. However, a valid use case are novel compounds that are not in the component dictionary. Reading connect statements can now be enabled in the pdb reader through the IOProfile. This may give issues in processing after reading. OpenStructure implements processors that are responsible for connectivity. Now that we build some of the connectivity already at the reading stage, this might cause trouble. To remedy most of the nightmares that can come out of that, the processors can now optionally skip connectivities between Hetatoms. Writing: That was a plain bug when writing CONECT statements for bond orders > 1.
Studer Gabriel authoredSimon found issues when reading and writing CONECT statements in PDB io and provided code to fix it. yay Reading: OpenStructure did not read CONECT statements at all. By default, it still doesnt. Many PDB files out there don't provide these statements and we really don't want to rely on them. We rather want to assign connectivity based on the chemical component dictionary from the PDB. However, a valid use case are novel compounds that are not in the component dictionary. Reading connect statements can now be enabled in the pdb reader through the IOProfile. This may give issues in processing after reading. OpenStructure implements processors that are responsible for connectivity. Now that we build some of the connectivity already at the reading stage, this might cause trouble. To remedy most of the nightmares that can come out of that, the processors can now optionally skip connectivities between Hetatoms. Writing: That was a plain bug when writing CONECT statements for bond orders > 1.
test_heuristic_conop.cc 8.19 KiB
// ------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
// Copyright (C) 2008-2020 by the OpenStructure authors
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
// ------------------------------------------------------------------------------
#include <ost/log.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/builder.hh>
#include <ost/conop/heuristic.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include "helper.hh"
using boost::unit_test_framework::test_suite;
using namespace ost;
using namespace ost::conop;
using namespace ost::mol;
void verify_connectivity_x(const ResidueHandle& res)
{
BOOST_CHECK(BondExists(res.FindAtom("XN"),
res.FindAtom("XCA")));
BOOST_CHECK(BondExists(res.FindAtom("XCA"),
res.FindAtom("XC")));
BOOST_CHECK(BondExists(res.FindAtom("XC"),
res.FindAtom("XO")));
BOOST_CHECK(BondExists(res.FindAtom("XCA"),
res.FindAtom("XCB")));
BOOST_CHECK(BondExists(res.FindAtom("XCB"),
res.FindAtom("XCG")));
if (res.GetKey()=="ARG") {
BOOST_CHECK(BondExists(res.FindAtom("XCB"),
res.FindAtom("XCG")));
BOOST_CHECK(BondExists(res.FindAtom("XCG"),
res.FindAtom("XCD")));
BOOST_CHECK(BondExists(res.FindAtom("XCD"),
res.FindAtom("XNE")));
BOOST_CHECK(BondExists(res.FindAtom("XNE"),
res.FindAtom("XCZ")));
BOOST_CHECK(BondExists(res.FindAtom("XCZ"),
res.FindAtom("XNH1")));
BOOST_CHECK(BondExists(res.FindAtom("XCZ"),
res.FindAtom("XNH2")));
// TODO: Check that no other atoms are connected!
}
if (res.GetKey()=="ILE") {
BOOST_CHECK(BondExists(res.FindAtom("XCG"),
res.FindAtom("XCD1")));
BOOST_CHECK(BondExists(res.FindAtom("XCG"),
res.FindAtom("XCD2")));
// TODO: Check that no other atoms are connected!
}
}
void verify_connectivity(const ResidueHandle& res)
{
BOOST_CHECK(BondExists(res.FindAtom("N"),
res.FindAtom("CA")));
BOOST_CHECK(BondExists(res.FindAtom("CA"),
res.FindAtom("C")));
BOOST_CHECK(BondExists(res.FindAtom("C"),
res.FindAtom("O")));
BOOST_CHECK(BondExists(res.FindAtom("CA"),
res.FindAtom("CB")));
BOOST_CHECK(BondExists(res.FindAtom("CB"),
res.FindAtom("CG")));
if (res.GetKey()=="ARG") {
BOOST_CHECK(BondExists(res.FindAtom("CB"),
res.FindAtom("CG")));
BOOST_CHECK(BondExists(res.FindAtom("CG"),
res.FindAtom("CD")));
BOOST_CHECK(BondExists(res.FindAtom("CD"),
res.FindAtom("NE")));
BOOST_CHECK(BondExists(res.FindAtom("NE"),
res.FindAtom("CZ")));
BOOST_CHECK(BondExists(res.FindAtom("CZ"),
res.FindAtom("NH1")));
BOOST_CHECK(BondExists(res.FindAtom("CZ"),
res.FindAtom("NH2")));
// TODO: Check that no other atoms are connected!
}
if (res.GetKey()=="ILE") {
BOOST_CHECK(BondExists(res.FindAtom("CG"),
res.FindAtom("CD1")));
BOOST_CHECK(BondExists(res.FindAtom("CG"),
res.FindAtom("CD2")));
// TODO: Check that no other atoms are connected!
}
}
BOOST_AUTO_TEST_SUITE( conop );
BOOST_AUTO_TEST_CASE(does_name_based_connect)
{
EntityHandle e=CreateEntity();
ChainHandle c=e.EditXCS().InsertChain("A");
ResidueHandle ile=make_leu(c);
ResidueHandle arg=make_arg(c);
HeuristicProcessor proc;
proc.Process(e);
verify_connectivity(arg);
verify_connectivity(ile);
}
BOOST_AUTO_TEST_CASE(does_assign_torsions) {
EntityHandle e=CreateEntity();
ChainHandle c=e.EditXCS().InsertChain("A");
ResidueHandle l1=make_leu(c);
ResidueHandle a2=make_arg(c);
ResidueHandle l3=make_leu(c);
e.EditXCS().Connect(l1.FindAtom("C"), a2.FindAtom("N"));
e.EditXCS().Connect(a2.FindAtom("C"), l3.FindAtom("N"));
HeuristicProcessor proc;
proc.SetAssignTorsions(true);
proc.Process(e);
BOOST_CHECK(a2.GetPhiTorsion().IsValid());
BOOST_CHECK(l3.GetPhiTorsion().IsValid());
BOOST_CHECK(l1.GetPsiTorsion().IsValid());
BOOST_CHECK(a2.GetPsiTorsion().IsValid());}
BOOST_AUTO_TEST_CASE(quack_types_unknown_residues) {
mol::EntityHandle e = Builder()
.Chain("A")
.Residue("GLY")
.Atom("N", geom::Vec3(-8.22, 35.20, 22.39))
.Atom("CA", geom::Vec3(-8.28, 36.36, 21.49))
.Atom("C", geom::Vec3(-8.59, 35.93, 20.06))
.Atom("O", geom::Vec3(-7.88, 36.30, 19.12))
.Atom("CB", geom::Vec3(-6.96, 37.11, 21.53))
.Residue("SEP")
.Atom("N", geom::Vec3(-9.66, 35.16, 19.91))
.Atom("CA", geom::Vec3(-10.08, 34.66, 18.61))
.Atom("CB", geom::Vec3(-10.90, 33.38, 18.79))
.Atom("OG", geom::Vec3(-12.22, 33.66, 19.22))
.Atom("C", geom::Vec3(-10.84, 35.69, 17.77))
.Atom("O", geom::Vec3(-10.99, 35.54, 16.56))
.Atom("P", geom::Vec3(-12.43, 33.20, 20.70))
.Atom("O1P", geom::Vec3(-11.55, 34.04, 21.65))
.Atom("O2P", geom::Vec3(-12.05, 31.71, 20.86))
.Atom("O3P", geom::Vec3(-13.92, 33.41, 21.07))
.Residue("GLY")
.Atom("N", geom::Vec3(-11.31, 36.75, 18.43))
.Atom("CA", geom::Vec3(-12.04, 37.81, 17.75))
.Atom("C", geom::Vec3(-12.34, 38.94, 18.73))
.Atom("O", geom::Vec3(-13.45, 39.03, 19.26))
;
HeuristicProcessor proc;
proc.Process(e);
BOOST_CHECK(e.FindResidue("A", 1).IsPeptideLinking());
BOOST_CHECK(e.FindResidue("A", 2).IsPeptideLinking());
BOOST_CHECK(e.FindResidue("A", 3).IsPeptideLinking());
BOOST_CHECK(mol::BondExists(e.FindAtom("A", 1, "C"), e.FindAtom("A", 2, "N")));
BOOST_CHECK(mol::BondExists(e.FindAtom("A", 2, "C"), e.FindAtom("A", 3, "N")));
}
BOOST_AUTO_TEST_CASE(hetatom_connect_heuristic) {
// STEP 1: Specify two atoms as hetatoms - they should be connected
// by the processor
mol::EntityHandle e = Builder()
.Chain("A")
.Residue("GLY")
.Atom("N", geom::Vec3(-8.22, 35.20, 22.39))
.Atom("CA", geom::Vec3(-8.28, 36.36, 21.49))
.Atom("C", geom::Vec3(-8.59, 35.93, 20.06))
.Atom("O", geom::Vec3(-7.88, 36.30, 19.12))
.Atom("CB", geom::Vec3(-6.96, 37.11, 21.53))
;
ost::mol::AtomHandleList atoms = e.GetAtomList();
atoms[0].SetHetAtom(true); // N
atoms[1].SetHetAtom(true); // CA
HeuristicProcessor proc;
proc.Process(e);
BOOST_CHECK(mol::BondExists(e.FindAtom("A", 1, "N"), e.FindAtom("A", 1, "CA")));
BOOST_CHECK(mol::BondExists(e.FindAtom("A", 1, "CA"), e.FindAtom("A", 1, "C")));
// STEP 2: Same thing again but we tell the processor NOT to connect
// hetatoms
e = Builder()
.Chain("A")
.Residue("GLY")
.Atom("N", geom::Vec3(-8.22, 35.20, 22.39)) .Atom("CA", geom::Vec3(-8.28, 36.36, 21.49))
.Atom("C", geom::Vec3(-8.59, 35.93, 20.06))
.Atom("O", geom::Vec3(-7.88, 36.30, 19.12))
.Atom("CB", geom::Vec3(-6.96, 37.11, 21.53))
;
atoms = e.GetAtomList();
atoms[0].SetHetAtom(true); // N
atoms[1].SetHetAtom(true); // CA
proc.SetConnectHetatm(false);
proc.Process(e);
BOOST_CHECK(!mol::BondExists(e.FindAtom("A", 1, "N"), e.FindAtom("A", 1, "CA")));
BOOST_CHECK(mol::BondExists(e.FindAtom("A", 1, "CA"), e.FindAtom("A", 1, "C")));
}
BOOST_AUTO_TEST_SUITE_END();