OEBio Functions

OECopyCrystalSymmetry

bool OECopyCrystalSymmetry(const OEChem::OEMolBase &, OEChem::OEMolBase &)

OEExpandCrystalSymmetry

bool OEExpandCrystalSymmetry(OEChem::OEMolBase &, float radius, float *center=0)

OEGetAlignment

OESequenceAlignment OEGetAlignment(OEChem::OEMolBase &m1, OEChem::OEMolBase &m2,
                                   unsigned int assume=OEAssumption::Default,
                                   unsigned int method=OESeqAlignmentMethod::PAM250,
                                   int gap=-10, int extend=-2)

OEGetAlignmentMethodName

const char *OEGetAlignmentMethodName(unsigned int methodIdx)

OEGetChis

OESystem::OEIterBase<unsigned> *OEGetChis(OEHierResidue &res)
OESystem::OEIterBase<unsigned> *OEGetChis(OEChem::OEAtomBase *atom,
                                          unsigned assume=OEAssumption::Default)

OEGetCrystalSymmetry

bool OEGetCrystalSymmetry(const OEChem::OEMolBase &, float &a, float &b, float &c,
                          float &alpha, float &beta, float &gamma,
                          unsigned int &sgnumber)

OEGetPhi

double OEGetPhi(OEHierResidue &res)
double OEGetPhi(OEChem::OEAtomBase *atom,
                unsigned assume=OEAssumption::Default)

OEGetProteinTorsionName

const char *OEGetProteinTorsionName(unsigned torType)

OEGetPsi

double OEGetPsi(OEHierResidue &res)
double OEGetPsi(OEChem::OEAtomBase *atom,
                unsigned assume=OEAssumption::Default)

OEGetResidueAtoms

OESystem::OEIterBase<OEChem::OEAtomBase> *
  OEGetResidueAtoms(OEChem::OEAtomBase *atom,
                    unsigned assume=OEAssumption::Default)
OESystem::OEIterBase<const OEChem::OEAtomBase> *
  OEGetResidueAtoms(const OEChem::OEAtomBase *atom,
                    unsigned assume=OEAssumption::Default)
OESystem::OEIterBase<OEChem::OEAtomBase> *
  OEGetResidueAtoms(OEChem::OEMolBase &mol, const OEChem::OEResidue &residue,
                    unsigned assume=OEAssumption::Default)
OESystem::OEIterBase<const OEChem::OEAtomBase> *
  OEGetResidueAtoms(const OEChem::OEMolBase &mol,
                    const OEChem::OEResidue &residue,
                    unsigned assume=OEAssumption::Default)

OEGetRotamers

OESystem::OEIterBase<OERotamer> *
  OEGetRotamers(const OEBio::OEHierResidue &residue,
                unsigned int library=OERotamerLibrary::Default)
OESystem::OEIterBase<OERotamer> *OEGetRotamers(unsigned int &residueIndex,
                                               unsigned int library=OERotamerLibrary::Default)

OEGetSpaceGroup

bool OEGetSpaceGroup(std::string &, unsigned int, bool shortname=false)

OEGetSpaceGroupNumber

int OEGetSpaceGroupNumber(const std::string &)

OEGetTorsion

double OEGetTorsion(OEHierResidue &res, unsigned torType)
double OEGetTorsion(OEChem::OEAtomBase *atom, unsigned torType,
                    unsigned assume=OEAssumption::Default)

OEHasBondedResidues

bool OEHasBondedResidues(OEChem::OEMolBase &mol,
                         unsigned assume=OEAssumption::Default)

OEHasCrystalSymmetry

bool OEHasCrystalSymmetry(const OEChem::OEMolBase &)

OEIsStandardProteinResidue

bool OEIsStandardProteinResidue(OEHierResidue &res)

OERMSD

double OERMSD(const OEChem::OEMolBase &ref, const OEChem::OEMolBase &fit,
              OESequenceAlignment &align, bool onlyCAlpha=true,
              bool overlay=false, double *rot=0, double *trans=0)

OESetCrystalSymmetry

bool OESetCrystalSymmetry(OEChem::OEMolBase &, float a, float b, float c,
                          float alpha, float beta, float gamma,
                          unsigned int sgnumber)

OESetRotamer

bool OESetRotamer(OEBio::OEHierResidue &residue, const OERotamer &rotamer)

OESetTorsion

bool OESetTorsion(OEHierResidue &res, unsigned torType, double radians)
bool OESetTorsion(OEChem::OEAtomBase *atom, unsigned torType, double radians,
                  unsigned assume=OEAssumption::Default)

OESwapAIEResidueAtoms

bool OESwapAIEResidueAtoms(OEChem::OEMolBase &mol, OEHierResidue &res)
bool OESwapAIEResidueAtoms(OEChem::OEMCMolBase &mol, OEHierResidue &res)
bool OESwapAIEResidueAtoms(OEChem::OEMolBase &mol, OEChem::OEAtomBase *atom,
                           unsigned assume=OEAssumption::Default)
bool OESwapAIEResidueAtoms(OEChem::OEMCMolBase &mol, OEChem::OEAtomBase *atom,
                           unsigned assume=OEAssumption::Default)

OEWriteAlignment

bool OEWriteAlignment(OEPlatform::oeostream &ofs,
                      const OESequenceAlignment &align)