OpenStructure
trajectory_analysis.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2020 by the OpenStructure authors
5 //
6 // This library is free software; you can redistribute it and/or modify it under
7 // the terms of the GNU Lesser General Public License as published by the Free
8 // Software Foundation; either version 3.0 of the License, or (at your option)
9 // any later version.
10 // This library is distributed in the hope that it will be useful, but WITHOUT
11 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
15 // You should have received a copy of the GNU Lesser General Public License
16 // along with this library; if not, write to the Free Software Foundation, Inc.,
17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 
20 /*
21  * Niklaus Johner
22  */
23 #ifndef OST_TRAJECTORY_ANALYSIS_HH
24 #define OST_TRAJECTORY_ANALYSIS_HH
25 
27 
28 #include <ost/base.hh>
29 #include <ost/geom/geom.hh>
30 #include <ost/mol/entity_view.hh>
31 #include <ost/mol/coord_group.hh>
32 
33 
34 namespace ost { namespace mol { namespace alg {
35 
36  geom::Vec3List DLLEXPORT_OST_MOL_ALG AnalyzeAtomPos(const CoordGroupHandle& traj, const AtomHandle& a1,unsigned int stride=1);
38  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeDistanceBetwAtoms(const CoordGroupHandle& traj, const AtomHandle& a1, const AtomHandle& a2,unsigned int stride=1);
39  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeAngle(const CoordGroupHandle& traj, const AtomHandle& a1, const AtomHandle& a2, const AtomHandle& a3,unsigned int stride=1);
40  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeDistanceBetwCenterOfMass(const CoordGroupHandle& traj, const EntityView& sele1, const EntityView& sele2,unsigned int stride=1);
41  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeDihedralAngle(const CoordGroupHandle& traj, const AtomHandle& a1, const AtomHandle& a2, const AtomHandle& a3, const AtomHandle& a4,unsigned int stride=1);
42  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeRMSD(const CoordGroupHandle& traj, const EntityView& reference_view, const EntityView& sele,unsigned int stride=1);
43  Real DLLEXPORT_OST_MOL_ALG AnalyzeRMSF(const CoordGroupHandle& traj, const EntityView& selection,int from=0, int to=-1, unsigned int stride=1);
44  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeMinDistance(const CoordGroupHandle& traj, const EntityView& view1, const EntityView& view2,unsigned int stride=1);
45  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeMinDistanceBetwCenterOfMassAndView(const CoordGroupHandle& traj, const EntityView& view_cm, const EntityView& view_atoms,unsigned int stride=1);
46  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, const EntityView& view_ring1, const EntityView& view_ring2,unsigned int stride=1);
47  void DLLEXPORT_OST_MOL_ALG AnalyzeAlphaHelixAxis(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& directions, geom::Vec3List& centers, unsigned int stride=1);
48  void DLLEXPORT_OST_MOL_ALG AnalyzeBestFitLine(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& directions, geom::Vec3List& centers, unsigned int stride=1);
49  void DLLEXPORT_OST_MOL_ALG AnalyzeBestFitPlane(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& normals, geom::Vec3List& origins, unsigned int stride=1);
50  EntityHandle DLLEXPORT_OST_MOL_ALG CreateMeanStructure(const CoordGroupHandle& traj, const EntityView& selection, int from=0, int to=-1, unsigned int stride=1);
51  std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeHelicity(const CoordGroupHandle& traj, const EntityView& prot_seg, unsigned int stride=1);
52 }}}//ns
53 #endif
Handle to atom datatype.
Definition: atom_handle.hh:37
coordinate group, for trajectories and such
Definition: coord_group.hh:39
Protein or molecule.
definition of EntityView
Definition: entity_view.hh:86
float Real
Definition: base.hh:44
#define DLLEXPORT_OST_MOL_ALG
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeDistanceBetwCenterOfMass(const CoordGroupHandle &traj, const EntityView &sele1, const EntityView &sele2, unsigned int stride=1)
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeAngle(const CoordGroupHandle &traj, const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, unsigned int stride=1)
Real DLLEXPORT_OST_MOL_ALG AnalyzeRMSF(const CoordGroupHandle &traj, const EntityView &selection, int from=0, int to=-1, unsigned int stride=1)
EntityHandle DLLEXPORT_OST_MOL_ALG CreateMeanStructure(const CoordGroupHandle &traj, const EntityView &selection, int from=0, int to=-1, unsigned int stride=1)
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeDistanceBetwAtoms(const CoordGroupHandle &traj, const AtomHandle &a1, const AtomHandle &a2, unsigned int stride=1)
void DLLEXPORT_OST_MOL_ALG AnalyzeAlphaHelixAxis(const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &directions, geom::Vec3List &centers, unsigned int stride=1)
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeMinDistance(const CoordGroupHandle &traj, const EntityView &view1, const EntityView &view2, unsigned int stride=1)
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeHelicity(const CoordGroupHandle &traj, const EntityView &prot_seg, unsigned int stride=1)
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeDihedralAngle(const CoordGroupHandle &traj, const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, const AtomHandle &a4, unsigned int stride=1)
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeMinDistanceBetwCenterOfMassAndView(const CoordGroupHandle &traj, const EntityView &view_cm, const EntityView &view_atoms, unsigned int stride=1)
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeRMSD(const CoordGroupHandle &traj, const EntityView &reference_view, const EntityView &sele, unsigned int stride=1)
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeAromaticRingInteraction(const CoordGroupHandle &traj, const EntityView &view_ring1, const EntityView &view_ring2, unsigned int stride=1)
geom::Vec3List DLLEXPORT_OST_MOL_ALG AnalyzeCenterOfMassPos(const CoordGroupHandle &traj, const EntityView &sele, unsigned int stride=1)
void DLLEXPORT_OST_MOL_ALG AnalyzeBestFitPlane(const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &normals, geom::Vec3List &origins, unsigned int stride=1)
geom::Vec3List DLLEXPORT_OST_MOL_ALG AnalyzeAtomPos(const CoordGroupHandle &traj, const AtomHandle &a1, unsigned int stride=1)
void DLLEXPORT_OST_MOL_ALG AnalyzeBestFitLine(const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &directions, geom::Vec3List &centers, unsigned int stride=1)
Definition: base.dox:1