Analysis types

class gorder.analysis_types.AAOrder(heavy_atoms, hydrogens)

Request the calculation of atomistic order parameters.

heavy_atoms

Selection query specifying the heavy atoms to be used in the analysis (typically carbon atoms in lipid tails).

hydrogens

Selection query specifiying the hydrogen atoms to be used in the analysis (only those bonded to heavy atoms will be considered).

Notes

Atoms should be specified using the groan selection language.
Order parameters are calculated for bonds between heavy_atoms and hydrogens. These bonds are detected automatically.
The order parameters for heavy atoms are determined by averaging the order parameters of the corresponding bonds.

class gorder.analysis_types.CGOrder(beads)

Request the calculation of coarse-grained order parameters.

beads

Selection query specifying the coarse-grained beads to be used in the analysis.

Notes

Beads should be specified using the groan selection language.
Order parameters are calculated for bonds between individual beads. These bonds are detected automatically.

class gorder.analysis_types.UAOrder(saturated=None, unsaturated=None, ignore=None)

Request the calculation of united-atom order parameters.

saturated

Selection query specifying saturated carbons which order parameters should be calculated.

unsaturated

Selection query specifying unsaturated carbons which order parameters should be calculated.

ignore

Selection query specifying atoms to be completely ignored when performing the analysis.

Notes

To specify atoms, use the groan selection language.
The positions of hydrogens will be predicted for the respective carbons and order parameters will be calculated for the individual carbon-hydrogen bonds.
Only carbons are supported. If you need to predict hydrogens for other elements, look elsewhere!
When calculating the number of bonds, gorder does not distinguish between single and double bonds. This means it will attempt to add one hydrogen to a carboxyl atom if specified. A simple solution to this issue is to exclude such atoms from the analysis.