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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::cryst::Spacegroup Class Reference

#include <spacegroup.hh>

Public Member Functions

 Spacegroup ()
 
 Spacegroup (std::string name_in)
 
void set_spacegroup (std::string name_in)
 
std::string name () const
 
numeric::xyzMatrix< core::Real >
const & 		f2c () const
 
numeric::xyzMatrix< core::Real >
const & 		c2f () const
 
core::Real A () const
 
core::Real B () const
 
core::Real C () const
 
core::Real alpha () const
 
core::Real beta () const
 
core::Real gamma () const
 
core::Real volume () const
 
SpacegroupSetting setting () const
 
utility::vector1
< core::kinematics::RT > const & 		symmops () const
 
core::kinematics::RT symmop (core::Size i) const
 
core::Size nsymmops () const
 
CheshireCell cheshire_cell () const
 
core::Size minmult () const
 
void set_parameters (core::Real a_in, core::Real b_in, core::Real c_in, core::Real alpha_in, core::Real beta_in, core::Real gamma_in)
 
std::string get_moveable_dofs () const
 
numeric::xyzVector< core::Size > get_nsubdivisions () const
 
numeric::xyzVector< core::Size > get_trans_dofs ()
 
core::Size get_nrot_dofs ()
 
std::string pdbname () const
 

Private Member Functions

void get_symmops (utility::vector1< core::kinematics::RT > &rt_out, CheshireCell &cc) const
 

Private Attributes

std::string name_
 
SpacegroupSetting setting_
 
numeric::xyzMatrix< core::Real > f2c_
 
numeric::xyzMatrix< core::Real > c2f_
 
core::Real a_
 
core::Real b_
 
core::Real c_
 
core::Real alpha_
 
core::Real beta_
 
core::Real gamma_
 
core::Real V_
 
core::Size ncopies_
 
utility::vector1
< core::kinematics::RT > 		symmops_
 
CheshireCell cc_
 

Constructor & Destructor Documentation

protocols::cryst::Spacegroup::Spacegroup ( )

References a_, alpha_, b_, beta_, c_, gamma_, name_, ncopies_, protocols::cryst::NOSETTING, setting_, and V_.

protocols::cryst::Spacegroup::Spacegroup ( std::string  name_in)

References a_, alpha_, b_, beta_, c_, gamma_, ncopies_, set_spacegroup(), and V_.

Member Function Documentation

core::Real protocols::cryst::Spacegroup::A ( ) const
inline

References a_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

core::Real protocols::cryst::Spacegroup::alpha ( ) const
inline

References alpha_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

core::Real protocols::cryst::Spacegroup::B ( ) const
inline

References b_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

core::Real protocols::cryst::Spacegroup::beta ( ) const
inline

References beta_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

core::Real protocols::cryst::Spacegroup::C ( ) const
inline

References c_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

numeric::xyzMatrix<core::Real> const& protocols::cryst::Spacegroup::c2f ( ) const
inline

References c2f_.

Referenced by protocols::cryst::crystRMSfast().

CheshireCell protocols::cryst::Spacegroup::cheshire_cell ( ) const
inline

References cc_.

numeric::xyzMatrix<core::Real> const& protocols::cryst::Spacegroup::f2c ( ) const
inline

References f2c_.

Referenced by protocols::cryst::crystRMSfast().

core::Real protocols::cryst::Spacegroup::gamma ( ) const
inline

References gamma_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

std::string protocols::cryst::Spacegroup::get_moveable_dofs ( ) const
inline

References get_symmops(), protocols::cryst::CheshireCell::high, and protocols::cryst::CheshireCell::low.

core::Size protocols::cryst::Spacegroup::get_nrot_dofs ( )
inline

References protocols::cryst::MONOCLINIC, setting_, and protocols::cryst::TRICLINIC.

numeric::xyzVector<core::Size> protocols::cryst::Spacegroup::get_nsubdivisions ( ) const
inline

References protocols::cryst::denom(), protocols::mean_field::max(), nsymmops(), and symmops_.

Referenced by protocols::cryst::UpdateCrystInfo::apply(), and protocols::cryst::DockLatticeMover::initialize().

void protocols::cryst::Spacegroup::get_symmops ( utility::vector1< core::kinematics::RT > &  rt_out,
CheshireCell &  cc 
) const
private

References protocols::cryst::get_symmops_Aba2(), protocols::cryst::get_symmops_Abm2(), protocols::cryst::get_symmops_Ama2(), protocols::cryst::get_symmops_Amm2(), protocols::cryst::get_symmops_B11m(), protocols::cryst::get_symmops_C121(), protocols::cryst::get_symmops_C12slashc1(), protocols::cryst::get_symmops_C12slashm1(), protocols::cryst::get_symmops_C1c1(), protocols::cryst::get_symmops_C1m1(), protocols::cryst::get_symmops_C222(), protocols::cryst::get_symmops_C2221(), protocols::cryst::get_symmops_Ccc2(), protocols::cryst::get_symmops_Ccca__2(), protocols::cryst::get_symmops_Cccm(), protocols::cryst::get_symmops_Cmc21(), protocols::cryst::get_symmops_Cmca(), protocols::cryst::get_symmops_Cmcm(), protocols::cryst::get_symmops_Cmm2(), protocols::cryst::get_symmops_Cmma(), protocols::cryst::get_symmops_Cmmm(), protocols::cryst::get_symmops_F222(), protocols::cryst::get_symmops_F23(), protocols::cryst::get_symmops_F4132(), protocols::cryst::get_symmops_F432(), protocols::cryst::get_symmops_Fdd2(), protocols::cryst::get_symmops_Fddd__2(), protocols::cryst::get_symmops_Fdminus3__2(), protocols::cryst::get_symmops_Fdminus3c__2(), protocols::cryst::get_symmops_Fdminus3m__2(), protocols::cryst::get_symmops_Fminus43c(), protocols::cryst::get_symmops_Fminus43m(), protocols::cryst::get_symmops_Fmm2(), protocols::cryst::get_symmops_Fmminus3(), protocols::cryst::get_symmops_Fmminus3c(), protocols::cryst::get_symmops_Fmminus3m(), protocols::cryst::get_symmops_Fmmm(), protocols::cryst::get_symmops_I212121(), protocols::cryst::get_symmops_I213(), protocols::cryst::get_symmops_I222(), protocols::cryst::get_symmops_I23(), protocols::cryst::get_symmops_I4(), protocols::cryst::get_symmops_I41(), protocols::cryst::get_symmops_I4122(), protocols::cryst::get_symmops_I4132(), protocols::cryst::get_symmops_I41cd(), protocols::cryst::get_symmops_I41md(), protocols::cryst::get_symmops_I41slasha__2(), protocols::cryst::get_symmops_I41slashacd__2(), protocols::cryst::get_symmops_I41slashamd__2(), protocols::cryst::get_symmops_I422(), protocols::cryst::get_symmops_I432(), protocols::cryst::get_symmops_I4cm(), protocols::cryst::get_symmops_I4mm(), protocols::cryst::get_symmops_I4slashm(), protocols::cryst::get_symmops_I4slashmcm(), protocols::cryst::get_symmops_I4slashmmm(), protocols::cryst::get_symmops_Iaminus3(), protocols::cryst::get_symmops_Iaminus3d(), protocols::cryst::get_symmops_Iba2(), protocols::cryst::get_symmops_Ibam(), protocols::cryst::get_symmops_Ibca(), protocols::cryst::get_symmops_Ima2(), protocols::cryst::get_symmops_Iminus4(), protocols::cryst::get_symmops_Iminus42d(), protocols::cryst::get_symmops_Iminus42m(), protocols::cryst::get_symmops_Iminus43d(), protocols::cryst::get_symmops_Iminus43m(), protocols::cryst::get_symmops_Iminus4c2(), protocols::cryst::get_symmops_Iminus4m2(), protocols::cryst::get_symmops_Imm2(), protocols::cryst::get_symmops_Imma(), protocols::cryst::get_symmops_Imminus3(), protocols::cryst::get_symmops_Imminus3m(), protocols::cryst::get_symmops_Immm(), protocols::cryst::get_symmops_P1(), protocols::cryst::get_symmops_P121(), protocols::cryst::get_symmops_P1211(), protocols::cryst::get_symmops_P121slashc1(), protocols::cryst::get_symmops_P121slashm1(), protocols::cryst::get_symmops_P121slashn1(), protocols::cryst::get_symmops_P12slashc1(), protocols::cryst::get_symmops_P12slashm1(), protocols::cryst::get_symmops_P1c1(), protocols::cryst::get_symmops_P1m1(), protocols::cryst::get_symmops_P21212(), protocols::cryst::get_symmops_P212121(), protocols::cryst::get_symmops_P213(), protocols::cryst::get_symmops_P222(), protocols::cryst::get_symmops_P2221(), protocols::cryst::get_symmops_P23(), protocols::cryst::get_symmops_P3(), protocols::cryst::get_symmops_P31(), protocols::cryst::get_symmops_P3112(), protocols::cryst::get_symmops_P312(), protocols::cryst::get_symmops_P3121(), protocols::cryst::get_symmops_P31c(), protocols::cryst::get_symmops_P31m(), protocols::cryst::get_symmops_P32(), protocols::cryst::get_symmops_P321(), protocols::cryst::get_symmops_P3212(), protocols::cryst::get_symmops_P3221(), protocols::cryst::get_symmops_P3c1(), protocols::cryst::get_symmops_P3m1(), protocols::cryst::get_symmops_P4(), protocols::cryst::get_symmops_P41(), protocols::cryst::get_symmops_P41212(), protocols::cryst::get_symmops_P4122(), protocols::cryst::get_symmops_P4132(), protocols::cryst::get_symmops_P42(), protocols::cryst::get_symmops_P4212(), protocols::cryst::get_symmops_P422(), protocols::cryst::get_symmops_P42212(), protocols::cryst::get_symmops_P4222(), protocols::cryst::get_symmops_P4232(), protocols::cryst::get_symmops_P42bc(), protocols::cryst::get_symmops_P42cm(), protocols::cryst::get_symmops_P42mc(), protocols::cryst::get_symmops_P42nm(), protocols::cryst::get_symmops_P42slashm(), protocols::cryst::get_symmops_P42slashmbc(), protocols::cryst::get_symmops_P42slashmcm(), protocols::cryst::get_symmops_P42slashmmc(), protocols::cryst::get_symmops_P42slashmnm(), protocols::cryst::get_symmops_P42slashn__2(), protocols::cryst::get_symmops_P42slashnbc__2(), protocols::cryst::get_symmops_P42slashncm__2(), protocols::cryst::get_symmops_P42slashnmc__2(), protocols::cryst::get_symmops_P42slashnnm__2(), protocols::cryst::get_symmops_P43(), protocols::cryst::get_symmops_P432(), protocols::cryst::get_symmops_P43212(), protocols::cryst::get_symmops_P4322(), protocols::cryst::get_symmops_P4332(), protocols::cryst::get_symmops_P4bm(), protocols::cryst::get_symmops_P4cc(), protocols::cryst::get_symmops_P4mm(), protocols::cryst::get_symmops_P4nc(), protocols::cryst::get_symmops_P4slashm(), protocols::cryst::get_symmops_P4slashmbm(), protocols::cryst::get_symmops_P4slashmcc(), protocols::cryst::get_symmops_P4slashmmm(), protocols::cryst::get_symmops_P4slashmnc(), protocols::cryst::get_symmops_P4slashn__2(), protocols::cryst::get_symmops_P4slashnbm__2(), protocols::cryst::get_symmops_P4slashncc__2(), protocols::cryst::get_symmops_P4slashnmm__2(), protocols::cryst::get_symmops_P4slashnnc__2(), protocols::cryst::get_symmops_P6(), protocols::cryst::get_symmops_P61(), protocols::cryst::get_symmops_P6122(), protocols::cryst::get_symmops_P62(), protocols::cryst::get_symmops_P622(), protocols::cryst::get_symmops_P6222(), protocols::cryst::get_symmops_P63(), protocols::cryst::get_symmops_P6322(), protocols::cryst::get_symmops_P63cm(), protocols::cryst::get_symmops_P63mc(), protocols::cryst::get_symmops_P63slashm(), protocols::cryst::get_symmops_P63slashmcm(), protocols::cryst::get_symmops_P63slashmmc(), protocols::cryst::get_symmops_P64(), protocols::cryst::get_symmops_P6422(), protocols::cryst::get_symmops_P65(), protocols::cryst::get_symmops_P6522(), protocols::cryst::get_symmops_P6cc(), protocols::cryst::get_symmops_P6mm(), protocols::cryst::get_symmops_P6slashm(), protocols::cryst::get_symmops_P6slashmcc(), protocols::cryst::get_symmops_P6slashmmm(), protocols::cryst::get_symmops_Paminus3(), protocols::cryst::get_symmops_Pba2(), protocols::cryst::get_symmops_Pbam(), protocols::cryst::get_symmops_Pban__2(), protocols::cryst::get_symmops_Pbca(), protocols::cryst::get_symmops_Pbcm(), protocols::cryst::get_symmops_Pbcn(), protocols::cryst::get_symmops_Pca21(), protocols::cryst::get_symmops_Pcc2(), protocols::cryst::get_symmops_Pcca(), protocols::cryst::get_symmops_Pccm(), protocols::cryst::get_symmops_Pccn(), protocols::cryst::get_symmops_Pma2(), protocols::cryst::get_symmops_Pmc21(), protocols::cryst::get_symmops_Pminus1(), protocols::cryst::get_symmops_Pminus3(), protocols::cryst::get_symmops_Pminus31c(), protocols::cryst::get_symmops_Pminus31m(), protocols::cryst::get_symmops_Pminus3c1(), protocols::cryst::get_symmops_Pminus3m1(), protocols::cryst::get_symmops_Pminus4(), protocols::cryst::get_symmops_Pminus421c(), protocols::cryst::get_symmops_Pminus421m(), protocols::cryst::get_symmops_Pminus42c(), protocols::cryst::get_symmops_Pminus42m(), protocols::cryst::get_symmops_Pminus43m(), protocols::cryst::get_symmops_Pminus43n(), protocols::cryst::get_symmops_Pminus4b2(), protocols::cryst::get_symmops_Pminus4c2(), protocols::cryst::get_symmops_Pminus4m2(), protocols::cryst::get_symmops_Pminus4n2(), protocols::cryst::get_symmops_Pminus6(), protocols::cryst::get_symmops_Pminus62c(), protocols::cryst::get_symmops_Pminus62m(), protocols::cryst::get_symmops_Pminus6c2(), protocols::cryst::get_symmops_Pminus6m2(), protocols::cryst::get_symmops_Pmm2(), protocols::cryst::get_symmops_Pmma(), protocols::cryst::get_symmops_Pmminus3(), protocols::cryst::get_symmops_Pmminus3m(), protocols::cryst::get_symmops_Pmminus3n(), protocols::cryst::get_symmops_Pmmm(), protocols::cryst::get_symmops_Pmmn__2(), protocols::cryst::get_symmops_Pmn21(), protocols::cryst::get_symmops_Pmna(), protocols::cryst::get_symmops_Pna21(), protocols::cryst::get_symmops_Pnc2(), protocols::cryst::get_symmops_Pnma(), protocols::cryst::get_symmops_Pnminus3__2(), protocols::cryst::get_symmops_Pnminus3m__2(), protocols::cryst::get_symmops_Pnminus3n__2(), protocols::cryst::get_symmops_Pnn2(), protocols::cryst::get_symmops_Pnna(), protocols::cryst::get_symmops_Pnnm(), protocols::cryst::get_symmops_Pnnn__2(), protocols::cryst::get_symmops_R32__H(), protocols::cryst::get_symmops_R3__H(), protocols::cryst::get_symmops_R3c__H(), protocols::cryst::get_symmops_R3m__H(), protocols::cryst::get_symmops_Rminus3__H(), protocols::cryst::get_symmops_Rminus3c__H(), protocols::cryst::get_symmops_Rminus3m__H(), and name_.

Referenced by get_moveable_dofs(), and set_spacegroup().

numeric::xyzVector<core::Size> protocols::cryst::Spacegroup::get_trans_dofs ( )
inline

References protocols::cryst::CUBIC, protocols::cryst::HEXAGONAL, protocols::cryst::MONOCLINIC, protocols::cryst::ORTHORHOMBIC, setting_, protocols::cryst::TETRAGONAL, and protocols::cryst::TRICLINIC.

core::Size protocols::cryst::Spacegroup::minmult ( ) const
inline

References protocols::cryst::CUBIC, protocols::cryst::HEXAGONAL, protocols::cryst::MONOCLINIC, protocols::cryst::ORTHORHOMBIC, setting_, protocols::cryst::TETRAGONAL, and protocols::cryst::TRICLINIC.

std::string protocols::cryst::Spacegroup::name ( ) const
inline

References name_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

core::Size protocols::cryst::Spacegroup::nsymmops ( ) const
inline

References symmops_.

Referenced by protocols::cryst::crystRMSfast(), get_nsubdivisions(), and protocols::cryst::DockLatticeMover::initialize().

std::string protocols::cryst::Spacegroup::pdbname ( ) const

References name_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

void protocols::cryst::Spacegroup::set_parameters ( core::Real  a_in,
core::Real  b_in,
core::Real  c_in,
core::Real  alpha_in,
core::Real  beta_in,
core::Real  gamma_in 
)

References a_, alpha_, b_, beta_, c2f_, c_, protocols::cryst::CUBIC, DEG2RAD, f2c_, gamma_, protocols::cryst::HEXAGONAL, protocols::cryst::MONOCLINIC, protocols::cryst::ORTHORHOMBIC, setting_, core::scoring::electron_density::square(), protocols::cryst::TETRAGONAL, protocols::cryst::TRICLINIC, protocols::cryst::TSG(), and V_.

Referenced by protocols::cryst::crystRMSfast(), and protocols::cryst::DockLatticeMover::initialize().

void protocols::cryst::Spacegroup::set_spacegroup ( std::string  name_in)

References a_, alpha_, b_, beta_, c_, cc_, protocols::cryst::CUBIC, gamma_, get_symmops(), protocols::cryst::HEXAGONAL, protocols::cryst::MONOCLINIC, name_, ncopies_, protocols::cryst::ORTHORHOMBIC, setting_, symmops_, protocols::cryst::TETRAGONAL, protocols::cryst::TRICLINIC, and V_.

Referenced by protocols::cryst::UpdateCrystInfo::apply(), protocols::cryst::crystRMSfast(), protocols::cryst::DockLatticeMover::initialize(), and Spacegroup().

SpacegroupSetting protocols::cryst::Spacegroup::setting ( ) const
inline

References setting_.

Referenced by protocols::cryst::UpdateCrystInfo::apply().

core::kinematics::RT protocols::cryst::Spacegroup::symmop ( core::Size  i) const
inline

References symmops_.

Referenced by protocols::cryst::crystRMSfast().

utility::vector1<core::kinematics::RT> const& protocols::cryst::Spacegroup::symmops ( ) const
inline

References symmops_.

Referenced by protocols::cryst::MakeLatticeMover::symmops().

core::Real protocols::cryst::Spacegroup::volume ( ) const
inline

References V_.

Referenced by protocols::cryst::DockLatticeMover::initialize().

Member Data Documentation

core::Real protocols::cryst::Spacegroup::a_
private

Referenced by A(), set_parameters(), set_spacegroup(), and Spacegroup().

core::Real protocols::cryst::Spacegroup::alpha_
private

Referenced by alpha(), set_parameters(), set_spacegroup(), and Spacegroup().

core::Real protocols::cryst::Spacegroup::b_
private

Referenced by B(), set_parameters(), set_spacegroup(), and Spacegroup().

core::Real protocols::cryst::Spacegroup::beta_
private

Referenced by beta(), set_parameters(), set_spacegroup(), and Spacegroup().

numeric::xyzMatrix<core::Real> protocols::cryst::Spacegroup::c2f_
private

Referenced by c2f(), and set_parameters().

core::Real protocols::cryst::Spacegroup::c_
private

Referenced by C(), set_parameters(), set_spacegroup(), and Spacegroup().

CheshireCell protocols::cryst::Spacegroup::cc_
private

Referenced by cheshire_cell(), and set_spacegroup().

numeric::xyzMatrix<core::Real> protocols::cryst::Spacegroup::f2c_
private

Referenced by f2c(), and set_parameters().

core::Real protocols::cryst::Spacegroup::gamma_
private

Referenced by gamma(), set_parameters(), set_spacegroup(), and Spacegroup().

std::string protocols::cryst::Spacegroup::name_
private

Referenced by get_symmops(), name(), pdbname(), set_spacegroup(), and Spacegroup().

core::Size protocols::cryst::Spacegroup::ncopies_
private

Referenced by set_spacegroup(), and Spacegroup().

SpacegroupSetting protocols::cryst::Spacegroup::setting_
private

Referenced by get_nrot_dofs(), get_trans_dofs(), minmult(), set_parameters(), set_spacegroup(), setting(), and Spacegroup().

utility::vector1<core::kinematics::RT> protocols::cryst::Spacegroup::symmops_
private

Referenced by get_nsubdivisions(), nsymmops(), set_spacegroup(), symmop(), and symmops().

core::Real protocols::cryst::Spacegroup::V_
private

Referenced by set_parameters(), set_spacegroup(), Spacegroup(), and volume().

The documentation for this class was generated from the following files:
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