Accessing the results

class gorder.results.AnalysisResults

Class containing all the results of the analysis.

average_order(): Get the average order parameters calculated from all bond types of all molecule types.

average_ordermaps(): Get the average order parameter maps calculated from all bond types of all molecule types.

get_molecule(name): Get the results for a molecule with the specified name. Raises an exception if such molecule does not exist.

molecules(): Get the results for each individual molecule.

n_analyzed_frames(): Get the total number of analyzed frames.

write(): Write the results of the analysis into output files.

class gorder.results.AtomResults

Results of the analysis for a single atom type.

atom(): Get the type of the atom for which these results were calculated.

bonds(): Get the results for each bond of the atom.

get_bond(relative_index): Get the results for a bond between this heavy atom and the hydrogen atom with the specified relative index (AA) or get the results for a bond between this heavy atom and the virtual hydrogen atom with the specified index (UA).

molecule(): Get the name of the molecule type for which these results were calculated.

order(): Get the order parameters calculated for this atom.

ordermaps(): Get the ordermaps calculated for this atom.

class gorder.results.BondResults

Results of the analysis for a single bond type.

atoms(): Get the atom types involved in this bond type.

molecule(): Get the name of the molecule type for which these results were calculated.

order(): Get the order parameters calculated for this bond.

ordermaps(): Get the maps of order parameters calculated for this bond.

class gorder.results.Convergence

Stores information about the convergence of calculations, i.e. the average order parameter for this molecule collected in time.

frames(): Extract indices of trajectory frames where order parameters were calculated. The first analyzed frame is assigned an index of 1. For instance, if the analysis begins at 200 ns, the frame at or just after 200 ns is indexed as 1.

lower(): Extract cumulative average order parameters for this molecule, calculated only for the lower leaflet. Follows the same format and logic as total.

total()

Extract cumulative average order parameters for this molecule, calculated across the entire membrane.

Each value in the vector represents the cumulative average for a molecule up to a specific frame: The first element corresponds to the value from the first frame. The second element is the average from the first two frames. The third element is the average from the first three frames, and so on. The last element is the overall average across all frames.

upper(): Extract umulative average order parameters for this molecule, calculated only for the upper leaflet. Follows the same format and logic as total.

class gorder.results.Map

Map of order parameters.

extract()

Extract the order map into NumPy arrays.

Returns:: A tuple of NumPy arrays. The first array (1D) contains positions of the grid tiles along the x-axis. The second array (1D) contains positions of the grid tiles along the y-axis. The third array (2D) contains the calculated order parameters.
Return type:: Tuple[np.ndarray, np.ndarray, np.ndarray]

get_at(x, y): Get the value of the order parameter at the specified coordinates.

span_x(): Get the span of the map in the x-dimension.

span_y(): Get the span of the map along the y-dimension.

tile_dim(): Get the dimnesions of a single grid tile of the map.

class gorder.results.MoleculeResults

Results of the analysis for a single molecule type.

atoms(): Get the results for each atom of the molecule. Not available for coarse-grained order parameters, use bonds instead.

average_order(): Get the average order parameters calculated from all bond types of this molecule type.

average_ordermaps(): Get the average order parameter maps calculated from all bond types of this molecule type.

bonds(): Get the results for each bond of the molecule.

convergence(): Get data about the convergence of the calculated order parameters. Returns None if convergence is not available.

get_atom(relative_index): Get the results for a heavy atom with the specified relative index. Not available for coarse-grained order parameters, use get_bond instead.

get_bond(relative_index_1, relative_index_2): Get the results for a bond involving atoms with the specified relative indices. The order of the atom indices does not matter. Not available for united-atom order parameters.

molecule(): Get the name of the molecule for which these results were calculated.

class gorder.results.Order

Single order parameter value, optionally with its estimated error.

error(): Get the estimated error for this order parameter. Returns None if the error is not available.

value(): Get the value of the order parameter (mean from the analyzed frames).

class gorder.results.OrderCollection

Order parameters for a single object calculated for the full membrane, the upper leaflet, and the lower leaflet.

lower(): Get order parameter calculated from the lower leaflet. Returns None if the order parameter is not available.

total(): Get order parameter calculated from the whole membrane. Returns None if the order parameter is not available.

upper(): Get order parameter calculated from the upper leaflet. Returns None if the order parameter is not available.

class gorder.results.OrderMapsCollection

Ordermaps for a single object calculated for the full membrane, the upper leaflet, and the lower leaflet.

lower(): Get order parameter map calculated from the lower leaflet. Returns None if the ordermap is not available.

total(): Get order parameter map calculated from the whole membrane. Returns None if the ordermap is not available.

upper(): Get order parameter map calculated from the upper leaflet. Returns None if the ordermap is not available.