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LOOS 4.1.0
The Lightweight Object Oriented Structural analysis library/toolkit
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This is the complete list of members for loos::Amber, including all inherited members.
| alignOnto(const AtomicGroup &) | loos::AtomicGroup | |
| allHaveProperty(const Atom::bits &property) const | loos::AtomicGroup | |
| Amber() (defined in loos::Amber) | loos::Amber | inline |
| Amber(const std::string &fname) | loos::Amber | inlineexplicit |
| Amber(std::istream &ifs) (defined in loos::Amber) | loos::Amber | inlineexplicit |
| anyHaveProperty(const Atom::bits &property) const | loos::AtomicGroup | |
| append(pAtom pa) | loos::AtomicGroup | inline |
| append(std::vector< pAtom > pas) | loos::AtomicGroup | |
| append(const AtomicGroup &grp) | loos::AtomicGroup | |
| apply(T func) | loos::AtomicGroup | inline |
| applyTransform(const XForm &) | loos::AtomicGroup | |
| asString() const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| AtomicGroup() (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| AtomicGroup(const int n) | loos::AtomicGroup | inline |
| AtomicGroup(const AtomicGroup &g) | loos::AtomicGroup | inline |
| atomOrderMapFrom(const AtomicGroup &g) | loos::AtomicGroup | |
| atoms (defined in loos::AtomicGroup) | loos::AtomicGroup | protected |
| begin(void) (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| begin(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| boundingBox(void) const | loos::AtomicGroup | |
| box (defined in loos::AtomicGroup) | loos::AtomicGroup | protected |
| centerAtOrigin(void) | loos::AtomicGroup | |
| centerOfElectrons(void) const | loos::AtomicGroup | |
| centerOfMass(void) const | loos::AtomicGroup | |
| centrifyByMolecule() const | loos::AtomicGroup | |
| centrifyByResidue() const | loos::AtomicGroup | |
| centroid(void) const | loos::AtomicGroup | |
| clearBonds(void) | loos::AtomicGroup | |
| clone(void) const | loos::Amber | inlinevirtual |
| const_iterator typedef (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| contactWith(const double dist, const AtomicGroup &grp, const uint min=1) const | loos::AtomicGroup | inline |
| contactWith(const double dist, const AtomicGroup &grp, const GCoord &box, const uint min=1) const | loos::AtomicGroup | inline |
| contains(const pAtom &p, const EqualsOp &op) const | loos::AtomicGroup | inline |
| contains(const pAtom &p) const | loos::AtomicGroup | inline |
| contains(const AtomicGroup &g, const EqualsOp &op) const | loos::AtomicGroup | inline |
| contains(const AtomicGroup &g) const | loos::AtomicGroup | inline |
| containsAny(const AtomicGroup &g, const EqualsOp &op) const | loos::AtomicGroup | inline |
| containsAny(const AtomicGroup &g) const | loos::AtomicGroup | inline |
| coordsAsVector() const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| copy(void) const | loos::Amber | inline |
| copyCoordinatesFrom(const AtomicGroup &g, const uint offset=0, const uint length=0) | loos::AtomicGroup | |
| copyCoordinatesWithIndex(const std::vector< GCoord > &coords) | loos::AtomicGroup | |
| copyMappedCoordinatesFrom(const AtomicGroup &g, const std::vector< uint > &order) | loos::AtomicGroup | |
| copyMappedCoordinatesFrom(const AtomicGroup &g) | loos::AtomicGroup | |
| copyVelocitiesWithIndex(const std::vector< GCoord > &velocities) | loos::AtomicGroup | |
| create(const std::string &fname) (defined in loos::Amber) | loos::Amber | inlinestatic |
| deduceAtomicNumberFromMass(const double tol=0.1) | loos::AtomicGroup | |
| deduceMassFromAtomicNumber() | loos::AtomicGroup | |
| differenceVectors(const AtomicGroup &other) | loos::AtomicGroup | |
| dipoleMoment(void) const | loos::AtomicGroup | |
| empty(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| end(void) (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| end(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| excise(const int offset, const int len=0) | loos::AtomicGroup | |
| findBonds(const double dist, const GCoord &box) | loos::AtomicGroup | inline |
| findBonds(const double dist) (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| findBonds(const GCoord &box) (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| findBonds() (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| findById(const int id) const | loos::AtomicGroup | |
| getAtom(const int i) const | loos::AtomicGroup | |
| getBondsAGs() const | loos::AtomicGroup | |
| getBondsIDs() const | loos::AtomicGroup | |
| getCoords(double **outseq, int *m, int *n) | loos::AtomicGroup | |
| getResidue(pAtom res) | loos::AtomicGroup | |
| getTransformedCoords(const XForm &) const | loos::AtomicGroup | |
| groupFromID(const std::vector< int > &id_list) const | loos::AtomicGroup | |
| groupFromID(const std::pair< int, int > &id_pair) const | loos::AtomicGroup | |
| hardContact(const AtomicGroup &group, double radius, const GCoord &box) const | loos::AtomicGroup | |
| hardContact2D(const AtomicGroup &group, double radius, const GCoord &box) const | loos::AtomicGroup | |
| hasBonds(void) const | loos::AtomicGroup | |
| hasCoords(void) const | loos::AtomicGroup | |
| intersect(const AtomicGroup &g, const EqualsOp &op) | loos::AtomicGroup | inline |
| intersect(const AtomicGroup &g) | loos::AtomicGroup | inline |
| isPeriodic(void) const | loos::AtomicGroup | inline |
| iterator typedef (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| kineticEnergy() | loos::AtomicGroup | |
| length(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| logisticContact(const AtomicGroup &group, double radius, int sigma, const GCoord &box) const | loos::AtomicGroup | |
| logisticContact2D(const AtomicGroup &group, double radius, int sigma, const GCoord &box) const | loos::AtomicGroup | |
| maxId(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| maxResid(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| merge(const AtomicGroup &g, const EqualsOp &op) | loos::AtomicGroup | inline |
| merge(const AtomicGroup &g) | loos::AtomicGroup | inline |
| mergeImage(pAtom &p) | loos::AtomicGroup | |
| mergeImage() | loos::AtomicGroup | |
| minId(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| minResid(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| momentsOfInertia(void) const | loos::AtomicGroup | |
| numberOfResidues(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| numberOfSegids(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| ocf(uint offset) | loos::AtomicGroup | |
| operator!=(AtomicGroup &rhs) | loos::AtomicGroup | inline |
| operator!=(const AtomicGroup &rhs) const | loos::AtomicGroup | inline |
| operator+(const AtomicGroup &rhs) (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| operator+(const pAtom &rhs) (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| operator+=(const AtomicGroup &rhs) (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| operator+=(const pAtom &rhs) (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| operator==(AtomicGroup &rhs) | loos::AtomicGroup | |
| operator==(const AtomicGroup &rhs) const | loos::AtomicGroup | |
| operator[](const int i) | loos::AtomicGroup | |
| operator[](const int i) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| orientAlong(const GCoord &) | loos::AtomicGroup | |
| packingScore(const AtomicGroup &other, const GCoord &box, bool norm) const | loos::AtomicGroup | |
| periodicBox(void) const | loos::AtomicGroup | inline |
| periodicBox(const GCoord &c) | loos::AtomicGroup | inline |
| periodicBox(const greal x, const greal y, const greal z) | loos::AtomicGroup | inline |
| perturbCoords(const greal) | loos::AtomicGroup | |
| principalAxes(void) const | loos::AtomicGroup | |
| principalAxesOrder(void) const | loos::AtomicGroup | |
| pruneBonds() | loos::AtomicGroup | |
| radius(const bool use_atom_as_reference=false) const | loos::AtomicGroup | |
| radiusOfGyration(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| read(std::istream &ifs) | loos::Amber | |
| reimage() | loos::AtomicGroup | |
| reimageByAtom() | loos::AtomicGroup | |
| remove(pAtom pa) | loos::AtomicGroup | inline |
| remove(std::vector< pAtom > pas) | loos::AtomicGroup | |
| remove(const AtomicGroup &grp) | loos::AtomicGroup | |
| removePeriodicBox() | loos::AtomicGroup | inline |
| renumber(const int start=1, const int stride=1) | loos::AtomicGroup | |
| resetAtomIndices() | loos::AtomicGroup | |
| rmsd(const AtomicGroup &) | loos::AtomicGroup | |
| rotate(const GCoord &axis, const greal angle_in_degrees) | loos::AtomicGroup | |
| scattering(const double qmin, const double max, const uint numValues, loos::FormFactorSet &formFactors) | loos::AtomicGroup | |
| select(const AtomSelector &sel) const | loos::AtomicGroup | |
| setCoords(double *seq, int m, int n) | loos::AtomicGroup | |
| setGroupConnectivity() (defined in loos::AtomicGroup) | loos::AtomicGroup | protected |
| sharedPeriodicBox() const | loos::AtomicGroup | inline |
| size(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | inline |
| sort(void) | loos::AtomicGroup | |
| sorted(void) const | loos::AtomicGroup | inline |
| sphericalVariance(const pAtom) const | loos::AtomicGroup | |
| sphericalVariance(const GCoord) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| splitByMolecule(void) const | loos::AtomicGroup | inline |
| splitByMolecule(const std::string &selection) const | loos::AtomicGroup | inline |
| splitByName(void) const | loos::AtomicGroup | |
| splitByResidue(void) const | loos::AtomicGroup | |
| splitByUniqueSegid(void) const | loos::AtomicGroup | |
| stacking(const AtomicGroup &, const GCoord &box, const double threshold) const | loos::AtomicGroup | |
| subset(const int offset, const int len=0) | loos::AtomicGroup | |
| superposition(const AtomicGroup &) | loos::AtomicGroup | |
| superposition_zero_singular_value (defined in loos::AtomicGroup) | loos::AtomicGroup | static |
| title() const | loos::Amber | inline |
| totalCharge(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| totalMass(void) const (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| translate(const GCoord &v) | loos::AtomicGroup | |
| value_type typedef (defined in loos::AtomicGroup) | loos::AtomicGroup | |
| within(const double dist, AtomicGroup &grp) const | loos::AtomicGroup | inline |
| within(const double dist, AtomicGroup &grp, const GCoord &box) const | loos::AtomicGroup | inline |
| ~Amber() (defined in loos::Amber) | loos::Amber | inlinevirtual |
| ~AtomicGroup() (defined in loos::AtomicGroup) | loos::AtomicGroup | inlinevirtual |
1.10.0