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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/STRUCTURE/rotamerLibrary.h>
#include <BALL/FORMAT/HINFile.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/STRUCTURE/geometricProperties.h>
#include <BALL/STRUCTURE/defaultProcessors.h>
#include <BALL/KERNEL/system.h>
///////////////////////////
START_TEST(RotamerLibrary)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace BALL;
FragmentDB frag_db("fragments/Fragments.db");
RotamerLibrary* rl_ptr = 0;
CHECK(RotamerLibrary::RotamerLibrary())
rl_ptr = new RotamerLibrary;
TEST_NOT_EQUAL(rl_ptr, 0)
ABORT_IF(rl_ptr == 0)
TEST_EQUAL(rl_ptr->getNumberOfRotamers(), 466829)
RESULT
CHECK(RotamerLibrary::RotamerLibrary(const String& filename, const FragmentDB& fragment_db))
RotamerLibrary rl("rotamers/bbind99.Aug.lib", frag_db);
TEST_EQUAL(rl.getNumberOfRotamers(), 320)
RESULT
CHECK(RotamerLibrary::RotamerLibrary(const FragmentDB& fragment_db))
RotamerLibrary rl(frag_db);
TEST_EQUAL(rl.getNumberOfRotamers(), 0)
RESULT
RotamerLibrary rl_ind("rotamers/bbind99.Aug.lib", frag_db);
CHECK(RotamerLibrary::RotamerLibrary(const RotamerLibrary& rotamer_library))
RotamerLibrary rl2(rl_ind);
TEST_EQUAL(rl2.getNumberOfRotamers(), 320)
// Make sure the old stuff hasn't changed
TEST_EQUAL(rl_ind.getNumberOfRotamers(), 320)
RESULT
CHECK(RotamerLibrary& RotamerLibrary::operator = (const RotamerLibrary& rotamer_library))
RotamerLibrary rl2;
rl2 = rl_ind;
TEST_EQUAL(rl2.getNumberOfRotamers(), 320)
// Make sure the old stuff hasn't changed
TEST_EQUAL(rl_ind.getNumberOfRotamers(), 320)
RESULT
CHECK(ResidueRotamerSet* getRotamerSet(const String& name))
ResidueRotamerSet* rrs = rl_ind.getRotamerSet("LYS");
TEST_NOT_EQUAL(rrs, 0)
ABORT_IF(rrs == 0)
TEST_EQUAL(rrs->getNumberOfRotamers(), 81)
RESULT
CHECK(ResidueRotamerSet* getRotamerSet(const String& name, float phi, float psi))
ResidueRotamerSet* rrs = rl_ptr->getRotamerSet("LYS", 180, 60);
TEST_NOT_EQUAL(rrs, 0)
ABORT_IF(rrs == 0)
TEST_EQUAL(rrs->getNumberOfRotamers(), 81)
RESULT
CHECK(ResidueRotamerSet* getRotamerSet(const Residue& residue))
System S;
HINFile ags_file(BALL_TEST_DATA_PATH(AlaGlySer.hin));
ags_file >> S;
ABORT_IF(S.countResidues() != 3)
Residue& ser(*++(++S.beginResidue()));
ResidueRotamerSet* rrs = rl_ptr->getRotamerSet(ser);
TEST_NOT_EQUAL(rrs, 0)
ABORT_IF(rrs == 0)
TEST_EQUAL(rrs->getNumberOfRotamers(), 3)
RESULT
CHECK(Size RotamerLibrary::getNumberOfRotamers() const)
TEST_EQUAL(rl_ind.getNumberOfRotamers(), 320)
RESULT
CHECK(Size RotamerLibrary::getNumberOfRotamers(const String& name) const)
TEST_EQUAL(rl_ind.getNumberOfRotamers("LYS"), 81)
RESULT
CHECK(Size RotamerLibrary::getNumberOfRotamerSets() const)
TEST_EQUAL(rl_ind.getNumberOfRotamerSets(), 18)
RESULT
CHECK(void RotamerLibrary::addRotamer(const String& name, const Rotamer& rotamer, Size number_of_torsions, Index phi, Index psi))
TEST_EQUAL(rl_ptr->getNumberOfRotamers(), 466829)
Rotamer rotamer;
rl_ptr->addRotamer("SER", rotamer, 1, -60, 80);
TEST_EQUAL(rl_ptr->getNumberOfRotamers(), 466830)
RESULT
CHECK(void RotamerLibrary::addRotamer(const String& name, const Rotamer& rotamer, Size number_of_torsions))
TEST_EQUAL(rl_ind.getNumberOfRotamers(), 320)
Rotamer rot;
rl_ind.addRotamer("LYS", rot, 4);
TEST_EQUAL(rl_ind.getNumberOfRotamers(), 321)
RESULT
CHECK(bool RotamerLibrary::isBackboneDependent() const)
TEST_EQUAL(rl_ind.isBackboneDependent(), false)
TEST_EQUAL(rl_ptr->isBackboneDependent(), true)
RESULT
CHECK(void RotamerLibrary::setBackboneDependent(bool dependent))
TEST_EQUAL(rl_ind.isBackboneDependent(), false)
rl_ind.setBackboneDependent(true);
TEST_EQUAL(rl_ind.isBackboneDependent(), true)
rl_ind.setBackboneDependent(false);
TEST_EQUAL(rl_ind.isBackboneDependent(), false)
RESULT
CHECK(bool RotamerLibrary::hasRotamers(const String& name) const)
TEST_EQUAL(rl_ind.hasRotamers("GLY"), false)
TEST_EQUAL(rl_ind.hasRotamers("TRP"), true)
RESULT
CHECK(bool RotamerLibrary::validate())
TEST_EQUAL(rl_ind.validate(), true)
TEST_EQUAL(rl_ptr->validate(), true)
RESULT
CHECK(void RotamerLibrary::sort())
RotamerLibrary rl("rotamers/bbdep02.May.lib", frag_db);
ResidueRotamerSet* rrs = rl.getRotamerSet("SER", -180, -140);
TEST_NOT_EQUAL(rrs, 0)
ABORT_IF(rrs == 0)
Rotamer rotamer = rrs->getRotamer(0);
TEST_REAL_EQUAL(rotamer.P, 0.292117)
rl.sort();
rrs = rl.getRotamerSet("SER", -180, -140);
TEST_NOT_EQUAL(rrs, 0)
ABORT_IF(rrs == 0)
rotamer = rrs->getRotamer(0);
TEST_REAL_EQUAL(rotamer.P, 0.700818)
RESULT
CHECK(void RotamerLibrary::clear())
RotamerLibrary rl(rl_ind);
TEST_EQUAL(rl.getNumberOfRotamers(), 321)
rl.clear();
TEST_EQUAL(rl.getNumberOfRotamers(), 0)
RESULT
CHECK(RotamerLibrary::~RotamerLibrary())
delete rl_ptr;
RESULT
ResidueChecker rc(frag_db);
rc.disable(ResidueChecker::OVERLAPPING_ATOMS);
CHECK(Side chain positions for Ser)
System S;
HINFile ags_file(BALL_TEST_DATA_PATH(AlaGlySer.hin));
ags_file >> S;
ABORT_IF(S.countResidues() != 3)
Residue& ala(*S.beginResidue());
Residue& gly(*++S.beginResidue());
Residue& ser(*++(++S.beginResidue()));
TEST_EQUAL(ala.countAtoms(), 12)
TEST_EQUAL(gly.countAtoms(), 7)
TEST_EQUAL(ser.countAtoms(), 12)
ResidueRotamerSet rrs(ala, 1);
TEST_EQUAL(rrs.getNumberOfTorsions(), 0)
TEST_EQUAL(rrs.getNumberOfRotamers(), 0)
ResidueRotamerSet rrs_gly(gly, 1);
TEST_EQUAL(rrs_gly.getNumberOfTorsions(), 0)
TEST_EQUAL(rrs_gly.getNumberOfRotamers(), 0)
ResidueRotamerSet rrs_ser(ser, 1);
TEST_EQUAL(rrs_ser.getNumberOfTorsions(), 1)
TEST_EQUAL(rrs_ser.getNumberOfRotamers(), 0)
Rotamer r = rrs_ser.getRotamer(ser);
PRECISION(1E-1)
TEST_REAL_EQUAL(r.P, 1.0)
TEST_REAL_EQUAL(r.chi1, 179.941)
TEST_REAL_EQUAL(r.chi2, 0.0)
TEST_REAL_EQUAL(r.chi3, 0.0)
TEST_REAL_EQUAL(r.chi4, 0.0)
S.apply(rc);
TEST_EQUAL(rc.getStatus(), true)
Rotamer r1;
r1.chi1 = Angle(0.0);
rrs_ser.setRotamer(ser, r1);
Rotamer r2 = rrs_ser.getRotamer(ser);
TEST_REAL_EQUAL(r2.chi1, 0.0)
Angle a = calculateTorsionAngle(*ser.getAtom("N"), *ser.getAtom("CA"), *ser.getAtom("CB"), *ser.getAtom("OG"));
TEST_REAL_EQUAL(a, 0.0)
S.apply(rc);
TEST_EQUAL(rc.getStatus(), true)
RESULT
CHECK(Side chain positions for Pro)
System S;
HINFile ags_file(BALL_TEST_DATA_PATH(GPG.hin));
ags_file >> S;
ABORT_IF(S.countResidues() != 3)
Residue& gly1(*S.beginResidue());
Residue& pro(*++S.beginResidue());
Residue& gly2(*++(++S.beginResidue()));
TEST_EQUAL(gly1.countAtoms(), 9)
TEST_EQUAL(pro.countAtoms(), 14)
TEST_EQUAL(gly2.countAtoms(), 8)
ResidueRotamerSet rrs_gly1(gly1, 1);
TEST_EQUAL(rrs_gly1.getNumberOfTorsions(), 0)
TEST_EQUAL(rrs_gly1.getNumberOfRotamers(), 0)
ResidueRotamerSet rrs_gly2(gly2, 1);
TEST_EQUAL(rrs_gly2.getNumberOfTorsions(), 0)
TEST_EQUAL(rrs_gly2.getNumberOfRotamers(), 0)
ResidueRotamerSet rrs_pro(pro, 2);
TEST_EQUAL(rrs_pro.getNumberOfTorsions(), 2)
TEST_EQUAL(rrs_pro.getNumberOfRotamers(), 0)
Rotamer r = rrs_pro.getRotamer(pro);
PRECISION(1E-3)
TEST_REAL_EQUAL(r.P, 1.0)
TEST_REAL_EQUAL(r.chi1, Angle(0.557364).toDegree())
TEST_REAL_EQUAL(r.chi2, Angle(-0.637879).toDegree())
TEST_REAL_EQUAL(r.chi3, 0.0)
TEST_REAL_EQUAL(r.chi4, 0.0)
S.apply(rc);
TEST_EQUAL(rc.getStatus(), true)
Rotamer r1;
r1.chi1 = 25.9;
r1.chi2 = -44.0;
rrs_pro.setRotamer(pro, r1);
Rotamer r1_r = rrs_pro.getRotamer(pro);
TEST_REAL_EQUAL(r1_r.chi1, r1.chi1)
TEST_REAL_EQUAL(r1_r.chi2, r1.chi2)
Angle c1 = calculateTorsionAngle(*pro.getAtom("N"), *pro.getAtom("CA"), *pro.getAtom("CB"), *pro.getAtom("CG"));
Angle c2 = calculateTorsionAngle(*pro.getAtom("CA"), *pro.getAtom("CB"), *pro.getAtom("CG"), *pro.getAtom("CD"));
TEST_REAL_EQUAL(c1.toDegree(), r1.chi1)
TEST_REAL_EQUAL(c2.toDegree(), r1.chi2)
S.apply(rc);
TEST_EQUAL(rc.getStatus(), true)
String outfile_name;
NEW_TMP_FILE(outfile_name)
HINFile outfile(outfile_name, std::ios::out);
outfile << S;
outfile.close();
Rotamer r2;
r2.chi1 = -23.7;
r2.chi2 = 39.0;
rrs_pro.setRotamer(pro, r2);
Rotamer r2_r = rrs_pro.getRotamer(pro);
TEST_REAL_EQUAL(r2_r.chi1, r2.chi1)
TEST_REAL_EQUAL(r2_r.chi2, r2.chi2)
c1 = calculateTorsionAngle(*pro.getAtom("N"), *pro.getAtom("CA"), *pro.getAtom("CB"), *pro.getAtom("CG"));
c2 = calculateTorsionAngle(*pro.getAtom("CA"), *pro.getAtom("CB"), *pro.getAtom("CG"), *pro.getAtom("CD"));
TEST_REAL_EQUAL(c1.toDegree(), r2.chi1)
TEST_REAL_EQUAL(c2.toDegree(), r2.chi2)
S.apply(rc);
TEST_EQUAL(rc.getStatus(), true)
NEW_TMP_FILE(outfile_name)
outfile.open(outfile_name, std::ios::out);
outfile << S;
RESULT
CHECK(Side chain conformations for Dunbrack library)
System S;
HINFile infile(BALL_TEST_DATA_PATH(all_amino.hin));
infile >> S;
infile.close();
TEST_EQUAL(S.countResidues(), 20)
ClearChargeProcessor cc;
// Remove all charges -- they are somewhat bogus and would upset the residue checker.
S.apply(cc);
RotamerLibrary rl("rotamers/bbind99.Aug.lib", frag_db);
TEST_EQUAL(rl.getNumberOfRotamers(), 320)
ABORT_IF((rl.getNumberOfRotamers() != 320) || (S.countResidues() != 20))
ResidueIterator res_it(S.beginResidue());
for (; +res_it; ++res_it)
{
STATUS("checking rotamers for " << res_it->getName())
ResidueRotamerSet* rss = rl.getRotamerSet(*res_it);
if (rss != 0)
{
// needed if the Residue is different from standard from fragment DB
rss->setTemplateResidue(*res_it, rss->getNumberOfTorsions());
STATUS(" - " << rss->getNumberOfRotamers() << " rotamers")
for (Position i = 0; i < rss->getNumberOfRotamers(); i++)
{
rss->setRotamer(*res_it, rss->getRotamer(i));
res_it->apply(rc);
TEST_EQUAL(rc.getStatus(), true)
// Store suspicious conformations for subsequent debugging.
if (!rc.getStatus())
{
String outfile_name;
NEW_TMP_FILE(outfile_name)
HINFile outfile(outfile_name, std::ios::out);
outfile << S;
}
}
}
}
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
