@@ -36,11 +36,12 @@ class FramesConfigurator(RangeConfigurator):
"""
This configurator allows to input a frame selection for the analysis.
The frame selection can be be input as:
#. a 3-tuple where the 1st, 2nd will corresponds respectively to the indexes of the first and last (excluded) frames to be selected while the 3rd element
The frame selection can be input as:
* a 3-tuple where the 1st, 2nd will corresponds respectively to the indexes of the first and last (excluded) frames to be selected while the 3rd element
will correspond to the step number between two frames. For example (1,11,3) will give 1,4,7,10
#. 'all' keyword, in such case, all the frames of the trajectory are selected
#. None keyword, in such case, all the frames of the trajectory are selected
* 'all' keyword, in such case, all the frames of the trajectory are selected
* None keyword, in such case, all the frames of the trajectory are selected
:note: this configurator depends on 'trajectory' configurator to be configured
@@ -46,18 +45,16 @@ class GroupingLevelConfigurator(SingleChoiceConfigurator):
"""
This configurator allows to choose the level of granularity in the atom selection.
The level of granularity will be applied, when reading the trajectory, by grouping the atoms of the selection according to
their level of granularity to a single dummy-atoms located on the center of gravity of those atoms.
When reading the trajectory, the level of granularity will be applied by grouping the atoms of the selection
to a single dummy-atoms located on the center of gravity of those atoms.
The level of granularity currently supported are:
#. 'atom': no grouping will be performed
#. 'group': the atoms that belongs to a MMTK AtomCluster object will be grouped as a single atom per object while the ones that belongs to a MMTK Molecule,
NucleotideChain, PeptideChain and Protein object will be grouped according to the chemical group they belong to (e.g. peptide group, methyl group ...).
#. 'residue': the atoms that belongs to a MMTK AtomCluster or Molecule object will be grouped as a single atom per object while the ones thta belongs to a
MMTK NucleotideChain, PeptideChain or Protein object will be grouped according to the residue to which they belong to (e.g. Histidine, Cytosyl ...)
#. 'chain': the atoms that belongs to a MMTK AtomCluster or Molecule object will be grouped as a single atom per object while the ones that belongs to a
MMTK NucleotideChain, PeptideChain or Protein object will be grouped according to the chain they belong to
#. 'molecule': the atoms that belongs to any MMTK chemical object will be grouped as a single atom per object
* 'atom': no grouping will be performed
* 'group': the atoms that belongs to a MMTK AtomCluster object will be grouped as a single atom per object while the ones that belongs to a MMTK Molecule, NucleotideChain, PeptideChain and Protein object will be grouped according to the chemical group they belong to (e.g. peptide group, methyl group ...)
* 'residue': the atoms that belongs to a MMTK AtomCluster or Molecule object will be grouped as a single atom per object while the ones thta belongs to a MMTK NucleotideChain, PeptideChain or Protein object will be grouped according to the residue to which they belong to (e.g. Histidine, Cytosyl ...)
* 'chain': the atoms that belongs to a MMTK AtomCluster or Molecule object will be grouped as a single atom per object while the ones that belongs to a MMTK NucleotideChain, PeptideChain or Protein object will be grouped according to the chain they belong to
* 'molecule': the atoms that belongs to any MMTK chemical object will be grouped as a single atom per object