Analysis types

class gorder.analysis_types.AAOrder(heavy_atoms, hydrogens)

Request the calculation of atomistic order parameters.

Parameters:

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

  • hydrogens (str) – 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.

Parameters:

beads (str) – 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.

Parameters:

  • saturated (Optional[str], default=None) – Selection query specifying saturated carbons which order parameters should be calculated.

  • unsaturated (Optional[str], default=None) – Selection query specifying unsaturated carbons which order parameters should be calculated.

  • ignore (Optional[str], default=None) – 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.