diff --git a/modules/index.rst b/modules/index.rst
index 8cc338a82b9480f516d927e48b3894b80b61e8d0..afc2142cfb81f0b06d9c83755207b29523132d7a 100644
--- a/modules/index.rst
+++ b/modules/index.rst
@@ -41,7 +41,9 @@ For Starters
Molecules
--------------------------------------------------------------------------------
-**Overview**: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>` | :doc:`queries <mol/base/query>`
+**Overview**: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>` | :doc:`queries <mol/base/query>` | :doc:`algorithms <mol/alg/molalg>`
+
+**Trajectories**: :doc:`basics <mol/base/traj>` | :ref:`analysis <traj-analysis>`
**Input/Output**: :ref:`loading and saving molecules <mol-io>`
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index fa3d676aeb593bb38f76857ef1e31a6cdb49195e..4730eec073af926ec47ef043930e75f1685515fb 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -82,6 +82,8 @@ The following function detects steric clashes in atomic structures. Two atoms ar
:returns: The filtered :class:`~ost.mol.EntityView`
+.. _traj-analysis:
+
Trajectory Analysis
--------------------------------------------------------------------------------
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 4520df521aa86b3f51c8e61bd59a03864903a76b..1ee9e6bdae35cce7abfe51d84e0315a354bc25da 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -583,7 +583,18 @@ The Handle Classes
.. attribute:: pos
- The atom's position in global coordinates. Also available as :meth:`GetPos`.
+ The atom's position in global coordinates, transformed by the entity
+ transformation. Also available as :meth:`GetPos`.
+
+ Read-only.
+
+ :type: :class:`~ost.geom.Vec3`
+
+ .. attribute:: original_pos
+
+ The atom's untransformed position in global coordinates. Also available as
+ :meth:`GetOriginalPos`.
+
Read-only.
:type: :class:`~ost.geom.Vec3`
diff --git a/modules/mol/base/doc/mol.rst b/modules/mol/base/doc/mol.rst
index 1ac7e3f2691b0a28cd299f7176ffa43e8bb4451b..976c2c8aa1ced240e5c461fb7f46745c60d0b36a 100644
--- a/modules/mol/base/doc/mol.rst
+++ b/modules/mol/base/doc/mol.rst
@@ -12,4 +12,5 @@ The mol module implements data structures to work with molecular datasets. At it
entity
editors
query
- surface
\ No newline at end of file
+ surface
+ traj
\ No newline at end of file
diff --git a/modules/mol/base/doc/traj.rst b/modules/mol/base/doc/traj.rst
new file mode 100644
index 0000000000000000000000000000000000000000..41730915f3efd9c94fc6fe59598f01f9a4125812
--- /dev/null
+++ b/modules/mol/base/doc/traj.rst
@@ -0,0 +1,220 @@
+Trajectories
+================================================================================
+
+.. currentmodule:: ost.mol
+
+
+.. function:: CreateCoordGroup(atoms)
+
+ :param atoms: List of atoms. All atoms must be from the same entity.
+ :type atoms: :class:`AtomHandleList`
+
+ :rtype: :class:`CoordGroupHandle`
+ :returns: A coord group with zero frames
+
+.. class:: CoordGroupHandle
+
+ A collection of coordinate frames, e.g. an MD trajectory. Create with
+ :func:`CreateCoordGroup`.
+
+
+ .. attribute:: entity
+
+ The attached entity.
+
+ :type: :class:`EntityHandle`
+
+ .. attribute:: atoms
+
+ The atoms of this coord group. The order of atoms is the same as the
+ positions in the coord frames. All atoms are from the same entity.
+
+ :type: :class:`AtomHandleList`
+ .. method:: AddFrames(frames)
+
+ Combine two trajectories by appending the frames of the second to the first
+ :param frames: a valid coord group
+ :type frames: :class:`CoordGroupHandle`
+
+ .. method:: Capture()
+
+ Record the atom positions of the entity attached to this coord group in a
+ new coordinate frame. Note that the atom positions transformed by the entity
+ transform will be stored. Only available for mutable coord groups.
+
+ :see: :attr:`AtomHandle.pos`
+
+ .. method:: CaptureInto(frame_index)
+
+ Same as :meth:`Capture`, but doesn't create a new frame and stores the
+ coordinates directly into frame with index *frame_index*. Only available for
+ mutable coord groups.
+
+ :param frame_index: index of the frame
+ :type frame_index: int
+
+ .. method:: CopyFrame(frame_index)
+
+ Copies the coordinates of frame with index *frame_index* to the attached
+ entity.
+
+ :param frame_index: index of the frame
+ :type frame_index: int
+
+ .. method:: Filter(view)
+
+ Returns a new trajectory containing only coordinates of the atoms in view.
+ Useful to remove water and other solvent molecules from a trajectory to
+ save memory.
+
+ :param view: a valid entity view
+ :type view: :class:`EntityView`
+ :rtype: :class:`CoordGroupHandle`
+
+ .. method:: GetAtomCount()
+
+ Returns the number of atoms in the coord group
+
+ :rtype: int
+
+
+ .. method:: GetAtomList()
+
+ Returns the atoms of the coord group in the same order they appear in the
+ coordinate frames.
+
+ :rtype: :class:`AtomHandleList`
+
+ .. method:: GetAtomPos(frame_index, atom)
+
+ Get position of *atom* in frame with index *frame_index*.
+
+
+ :param frame_index: frame index
+ :type frame_index: int
+ :param atom: A valid atom
+ :type atom: :class:`AtomHandle`
+ :rtype: :class:`Vec3`
+
+ .. method:: GetEntity()
+
+ Returns the attached entity
+
+ :rtype: :class:`EntityHandle`
+
+ .. method:: GetFrameCount()
+
+ Returns the number of frames of this coord group
+
+ :rtype: int
+
+ .. method:: IsValid()
+
+ Whether this coord group is valid
+
+ :rtype: bool
+
+ .. method:: SetAtomPos(frame_index, atom, pos)
+
+ Set position of *atom* in frame with index *frame_index* to *pos*
+
+ :param frame_index: index of the frame
+ :type frame_index: int
+ :param atom: a valid atom
+ :type atom: :class:`AtomHandle`
+ :param pos: new position of the atom
+ :type pos: :class:`Vec3`
+
+ .. method:: SetFramePositions(frame_index, positions)
+
+ Set the frame positions of frame with index *frame_index*. Order and count
+ of positions must match :attr:`atoms`.
+
+ :param frame_index: index of frame
+ :type frame_index: int
+ :param positions: list of positions
+ :type positions: :class:`~ost.geom.Vec3List`
+
+
+.. class:: CoordFrame
+
+ A single frame of coordinates in a :class:`CoordGroupHandle`.
+
+ .. method:: GetAngle(atom1, atom2, atom3)
+
+ :param atom1: first atom
+ :type atom1: :class:`AtomHandle`
+ :param atom2: second (central) atom
+ :type atom2: :class:`AtomHandle`
+ :param atom3: third atom
+ :type atom3: :class:`AtomHandle`
+
+ :returns: the angle in radians between the 3 atoms
+ :rtype: float
+
+ .. method:: GetAtomPos(atom)
+
+ Returns the position of the atom in the coord frame
+
+ :param atom: A valid atom handle
+ :type atom: :class:`AtomHandle`
+
+
+
+ :rtype: :class:`Vec3`
+
+ .. method:: GetCenterOfMassPos(view)
+
+
+ :param view: A valid entity view
+ :type view: :class:`EntityView`
+ :rtype: :class:`Vec3`
+
+ .. method:: GetDihedralAngle(atom1, atom2, atom3, atom4)
+
+ Get dihedral angle of the four atoms.
+
+ :param atom1: First atom. Must be valid
+ :type atom1: :class:`AtomHandle`
+ :param atom2: Second atom. Must be valid
+ :type atom2: :class:`AtomHandle`
+ :param atom3: Third atom. Must be valid
+ :type atom3: :class:`AtomHandle`
+ :param atom3: Fourth atom. Must be valid
+ :type atom3: :class:`AtomHandle`
+
+ :rtype: float
+
+ .. method:: GetDistanceBetwAtoms(atom1, atom2)
+
+ Get distance in (Angstroem) between *atom1* and *atom2* in coord frame.
+
+ :param atom1: First atom. Must be valid
+ :type atom1: :class:`AtomHandle`
+ :param atom2: Second atom. Must be valid
+ :type atom2: :class:`AtomHandle`
+ :rtype: float
+
+ .. method:: GetDistanceBetwCenterOfMass(view1, view2)
+
+ Get distance between center of mass of the first selection and the second.
+
+ :param view1: First view. Must be valid
+ :type view1: :class:`EntityView`
+ :param view2: Second view. Must be valid
+ :type view2: :class:`EntityView`
+ :rtype: float
+
+ .. method:: GetRMSD(view1, view2)
+
+ Get RMSD between two views in the coord frame. The coordinates of the views
+ are taken as is without superposition. The two views must have the same
+ number of atoms. Atoms are matches as they appear in
+ :attr:`EntityView.atoms`.
+
+ :param view1: First view. Must be valid
+ :type view1: :class:`EntityView`
+ :param view2: Second view. Must be valid
+ :type view2: :class:`EntityView`
+ :rtype: float
+
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index 42e18e0ce5f720e439429536192f10576608c5bd..f232d498cc3f52d61419d0c441c59e530470f737 100644
--- a/modules/mol/base/pymod/export_atom.cc
+++ b/modules/mol/base/pymod/export_atom.cc
@@ -53,6 +53,9 @@ void export_Atom()
.add_property("pos",
make_function(&AtomBase::GetPos,
return_value_policy<copy_const_reference>()))
+ .add_property("original_pos",
+ make_function(&AtomBase::GetOriginalPos,
+ return_value_policy<copy_const_reference>()))
.add_property("name",
make_function(&AtomBase::GetName,
return_value_policy<copy_const_reference>()),
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index ebd0f1f33daa0fc703d92f4e5351626741b52f61..794db5363c6ae050262e51c29608977ef83d569a 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -53,6 +53,7 @@ void export_CoordGroup()
.def("GetAtomPos",&CoordGroupHandle::GetAtomPos)
.def("CopyFrame",&CoordGroupHandle::CopyFrame)
.add_property("atoms", &CoordGroupHandle::GetAtomList)
+ .add_property("entity", &CoordGroupHandle::GetEntity)
.def("IsValid", &CoordGroupHandle::IsValid)
.def("Capture", capture1)
.def("Capture", capture2)