diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst index d4ce787a4d5978de081643bdabe1c968bde1bd42..fc6ac170c8283343306325fa5f6a52bb82c50c00 100644 --- a/modules/mol/alg/doc/molalg.rst +++ b/modules/mol/alg/doc/molalg.rst @@ -636,6 +636,18 @@ The following function detects steric clashes in atomic structures. Two atoms ar :returns: true if the residue names are the same, false otherwise +.. autofunction:: ParseAtomNames + +.. autofunction:: MatchResidueByNum + +.. autofunction:: MatchResidueByIdx + +.. autofunction:: MatchResidueByLocalAln + +.. autofunction:: MatchResidueByGlobalAln + +.. autofunction:: Superpose + .. _traj-analysis: Trajectory Analysis @@ -651,6 +663,45 @@ All these functions have a "stride" argument that defaults to stride=1, which is used to skip frames in the analysis. +.. function:: SuperposeFrames(frames, sel, from=0, to=-1, ref=-1) + + This function superposes the frames of the given coord group and returns them + as a new coord group. + + :param frames: The source coord group. + :type frames: :class:`~ost.mol.CoordGroupHandle` + :param sel: An entity view containing the selection of atoms to be used for + superposition. If set to an invalid view, all atoms in the coord group are + used. + :type sel: :class:`ost.mol.EntityView` + :param from: index of the first frame + :param to: index of the last frame plus one. If set to -1, the value is set to + the number of frames in the coord group + :param ref: The index of the reference frame to use for superposition. If set + to -1, the each frame is superposed to the previous frame. + + :returns: A newly created coord group containing the superposed frames. + +.. function:: SuperposeFrames(frames, sel, ref_view, from=0, to=-1) + + Same as SuperposeFrames above, but the superposition is done on a reference + view and not on another frame of the trajectory. + + :param frames: The source coord group. + :type frames: :class:`~ost.mol.CoordGroupHandle` + :param sel: An entity view containing the selection of atoms of the frames to be used for + superposition. + :type sel: :class:`ost.mol.EntityView` + :param ref_view: The reference view on which the frames will be superposed. The number + of atoms in this reference view should be equal to the number of atoms in sel. + :type ref_view: :class:`ost.mol.EntityView` + :param from: index of the first frame + :param to: index of the last frame plus one. If set to -1, the value is set to + the number of frames in the coord group + + :returns: A newly created coord group containing the superposed frames. + + .. function:: AnalyzeAtomPos(traj, atom1, stride=1) This function extracts the position of an atom from a trajectory. It returns @@ -808,53 +859,7 @@ used to skip frames in the analysis. :param stride: Size of the increment of the frame's index between two consecutive frames analyzed. -.. function:: SuperposeFrames(frames, sel, from=0, to=-1, ref=-1) - - This function superposes the frames of the given coord group and returns them - as a new coord group. - - :param frames: The source coord group. - :type frames: :class:`~ost.mol.CoordGroupHandle` - :param sel: An entity view containing the selection of atoms to be used for - superposition. If set to an invalid view, all atoms in the coord group are - used. - :type sel: :class:`ost.mol.EntityView` - :param from: index of the first frame - :param to: index of the last frame plus one. If set to -1, the value is set to - the number of frames in the coord group - :param ref: The index of the reference frame to use for superposition. If set - to -1, the each frame is superposed to the previous frame. - - :returns: A newly created coord group containing the superposed frames. - -.. function:: SuperposeFrames(frames, sel, ref_view, from=0, to=-1) - - Same as SuperposeFrames above, but the superposition is done on a reference - view and not on another frame of the trajectory. - - :param frames: The source coord group. - :type frames: :class:`~ost.mol.CoordGroupHandle` - :param sel: An entity view containing the selection of atoms of the frames to be used for - superposition. - :type sel: :class:`ost.mol.EntityView` - :param ref_view: The reference view on which the frames will be superposed. The number - of atoms in this reference view should be equal to the number of atoms in sel. - :type ref_view: :class:`ost.mol.EntityView` - :param from: index of the first frame - :param to: index of the last frame plus one. If set to -1, the value is set to - the number of frames in the coord group - - :returns: A newly created coord group containing the superposed frames. - -.. autofunction:: ParseAtomNames - -.. autofunction:: MatchResidueByNum - -.. autofunction:: MatchResidueByIdx -.. autofunction:: MatchResidueByLocalAln -.. autofunction:: MatchResidueByGlobalAln -.. autofunction:: Superpose