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stage
include
ost
mol
alg
trajectory_analysis.hh
Go to the documentation of this file.
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//------------------------------------------------------------------------------
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// This file is part of the OpenStructure project <www.openstructure.org>
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//
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// Copyright (C) 2008-2011 by the OpenStructure authors
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//
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// This library is free software; you can redistribute it and/or modify it under
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// the terms of the GNU Lesser General Public License as published by the Free
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// Software Foundation; either version 3.0 of the License, or (at your option)
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// any later version.
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// This library is distributed in the hope that it will be useful, but WITHOUT
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// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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// details.
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//
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// You should have received a copy of the GNU Lesser General Public License
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// along with this library; if not, write to the Free Software Foundation, Inc.,
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// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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//------------------------------------------------------------------------------
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/*
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* Niklaus Johner
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*/
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#ifndef OST_TRAJECTORY_ANALYSIS_HH
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#define OST_TRAJECTORY_ANALYSIS_HH
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#include <
ost/mol/alg/module_config.hh
>
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#include <
ost/base.hh
>
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#include <
ost/geom/geom.hh
>
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#include <
ost/mol/entity_view.hh
>
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#include <
ost/mol/coord_group.hh
>
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namespace
ost {
namespace
mol {
namespace
alg {
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geom::Vec3List
DLLEXPORT_OST_MOL_ALG
AnalyzeAtomPos
(
const
CoordGroupHandle& traj,
const
AtomHandle& a1,
unsigned
int
stride=1);
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geom::Vec3List
DLLEXPORT_OST_MOL_ALG
AnalyzeCenterOfMassPos
(
const
CoordGroupHandle& traj,
const
EntityView& sele,
unsigned
int
stride=1);
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std::vector<Real>
DLLEXPORT_OST_MOL_ALG
AnalyzeDistanceBetwAtoms
(
const
CoordGroupHandle& traj,
const
AtomHandle& a1,
const
AtomHandle& a2,
unsigned
int
stride=1);
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std::vector<Real>
DLLEXPORT_OST_MOL_ALG
AnalyzeAngle
(
const
CoordGroupHandle& traj,
const
AtomHandle& a1,
const
AtomHandle& a2,
const
AtomHandle& a3,
unsigned
int
stride=1);
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std::vector<Real>
DLLEXPORT_OST_MOL_ALG
AnalyzeDistanceBetwCenterOfMass
(
const
CoordGroupHandle& traj,
const
EntityView& sele1,
const
EntityView& sele2,
unsigned
int
stride=1);
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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);
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std::vector<Real>
DLLEXPORT_OST_MOL_ALG
AnalyzeRMSD
(
const
CoordGroupHandle& traj,
const
EntityView& reference_view,
const
EntityView& sele,
unsigned
int
stride=1);
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Real
DLLEXPORT_OST_MOL_ALG
AnalyzeRMSF
(
const
CoordGroupHandle& traj,
const
EntityView& selection,
int
from=0,
int
to=-1,
unsigned
int
stride=1);
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std::vector<Real>
DLLEXPORT_OST_MOL_ALG
AnalyzeMinDistance
(
const
CoordGroupHandle& traj,
const
EntityView& view1,
const
EntityView& view2,
unsigned
int
stride=1);
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std::vector<Real>
DLLEXPORT_OST_MOL_ALG
AnalyzeMinDistanceBetwCenterOfMassAndView
(
const
CoordGroupHandle& traj,
const
EntityView& view_cm,
const
EntityView& view_atoms,
unsigned
int
stride=1);
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std::vector<Real>
DLLEXPORT_OST_MOL_ALG
AnalyzeAromaticRingInteraction
(
const
CoordGroupHandle& traj,
const
EntityView& view_ring1,
const
EntityView& view_ring2,
unsigned
int
stride=1);
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void
DLLEXPORT_OST_MOL_ALG
AnalyzeAlphaHelixAxis
(
const
CoordGroupHandle& traj,
const
EntityView& prot_seg,
geom::Vec3List
& directions,
geom::Vec3List
& centers,
unsigned
int
stride=1);
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void
DLLEXPORT_OST_MOL_ALG
AnalyzeBestFitLine
(
const
CoordGroupHandle& traj,
const
EntityView& prot_seg,
geom::Vec3List
& directions,
geom::Vec3List
& centers,
unsigned
int
stride=1);
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void
DLLEXPORT_OST_MOL_ALG
AnalyzeBestFitPlane
(
const
CoordGroupHandle& traj,
const
EntityView& prot_seg,
geom::Vec3List
& normals,
geom::Vec3List
& origins,
unsigned
int
stride=1);
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EntityHandle
DLLEXPORT_OST_MOL_ALG
CreateMeanStructure
(
const
CoordGroupHandle& traj,
const
EntityView& selection,
int
from=0,
int
to=-1,
unsigned
int
stride=1);
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std::vector<Real>
DLLEXPORT_OST_MOL_ALG
AnalyzeHelicity
(
const
CoordGroupHandle& traj,
const
EntityView& prot_seg,
unsigned
int
stride=1);
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}}}
//ns
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#endif
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