19 #ifndef OST_MOL_COORD_FRAME_HH
20 #define OST_MOL_COORD_FRAME_HH
26 #include <boost/shared_ptr.hpp>
32 namespace ost {
namespace mol {
62 ucell_angles_=box_angles;
70 return this->ucell_size_;
78 return this->ucell_angles_;
86 Real GetDistanceBetwAtoms(
int atom1_index,
int atom2_index)
const;
102 Real GetAngle(
int atom1_index,
int atom2_index,
int atom3_index)
const;
108 Real GetDihedralAngle(
int a1_index,
int a2_index,
int a3_index,
int a4_index)
const;
118 geom::Vec3 GetCenterOfMassPos(std::vector<unsigned long>& indices,
119 std::vector<Real>& masses)
const;
130 std::vector<unsigned long>& indices2, std::vector<Real>& masses2)
const;
136 Real GetRMSD(
const std::vector<geom::Vec3>& ref_pos,
137 const std::vector<unsigned long>& indices_sele)
const;
152 Real GetMinDistance(std::vector<unsigned long>& index_list1,
153 std::vector<unsigned long>& index_list2)
const;
164 std::vector<Real>& masses_cm,
165 std::vector<unsigned long>& indices_atoms)
const;
171 geom::Line3 GetODRLine(std::vector<unsigned long>& indices_ca)
const;
174 geom::Plane GetODRPlane(std::vector<unsigned long>& indices_ca)
const;
185 std::pair<geom::Line3, Real> FitCylinder(std::vector<unsigned long>& indices_ca)
const;
188 std::pair<geom::Line3, Real> FitCylinder(
const mol::EntityView& view1)
const;
198 std::vector<unsigned long>& indices_c,
199 std::vector<unsigned long>& indices_o,
200 std::vector<unsigned long>& indices_n)
const;
232 std::vector<unsigned long>& indices,
233 std::vector<Real>& masses);
243 std::vector<unsigned long>& indices_ca,
244 std::vector<unsigned long>& indices_c,
245 std::vector<unsigned long>& indices_o,
246 std::vector<unsigned long>& indices_n);
DLLEXPORT_OST_MOL void GetIndices(const EntityView &sele, std::vector< unsigned long > &indices)
CoordFrame(const base_type &rhs)
geom::Vec3 GetCellAngles() const
void SetCellSize(const geom::Vec3 &s)
CoordFrame(size_t size, const geom::Vec3 &value=geom::Vec3())
std::vector< Vec3 > base_type
boost::shared_ptr< CoordFrame > CoordFramePtr
CoordFrame(const std::vector< geom::Vec3 > &rhs)
geom::Vec3 GetCellSize() const
void SetCellAngles(const geom::Vec3 &a)
def GetMinDistBetwCenterOfMassAndView
DLLEXPORT_OST_MOL void GetIndicesAndMasses(const EntityView &sele, std::vector< unsigned long > &indices, std::vector< Real > &masses)
conveniece for GetIndices and GetMasses in one call
CoordFrame(base_type::iterator b, base_type::iterator e)
Three dimensional vector class, using Real precision.
#define DLLEXPORT_OST_MOL
DLLEXPORT_OST_MOL void GetCaCONIndices(const EntityView &segment, std::vector< unsigned long > &indices_ca, std::vector< unsigned long > &indices_c, std::vector< unsigned long > &indices_o, std::vector< unsigned long > &indices_n)
Writes the backbone indices of all residues in the EntityView into the provided list.
DLLEXPORT_OST_MOL void GetPositions(const EntityView &sele, std::vector< geom::Vec3 > &ref_pos)
Writes the positions of all atoms in the EntityView into the provided vec3 list.
std::vector< CoordFramePtr > CoordFrameList
DLLEXPORT_OST_MOL void GetMasses(const EntityView &sele, std::vector< Real > &masses)
DLLEXPORT_OST_MOL void GetCaIndices(const EntityView &segment, std::vector< unsigned long > &indices_ca)
Writes the indices of all atoms in the EntityView into the provided list.
def GetDistanceBetwCenterOfMass
DLLEXPORT_OST_MOL CoordFrame CreateCoordFrame(const geom::Vec3List &atom_pos, const geom::Vec3 &cell_size=geom::Vec3(), const geom::Vec3 &cell_angles=geom::Vec3())
CoordFrame(const std::vector< geom::Vec3 > &rhs, const geom::Vec3 box_size, const geom::Vec3 box_angles)