Order parameters for individual leaflets

class gorder.leaflets.GlobalClassification(membrane, heads, frequency=None, membrane_normal=None)

Assign lipids into leaflets based on the global membrane center of geometry.

Generally reliable and fast. The best option for analyzing disrupted membranes.

membrane

Selection query specifying all lipids forming the membrane.

Type:: str

heads

Selection query specifying reference atoms representing lipid headgroups (typically phosphorus atoms or phosphate beads). There must be exactly one such atom/bead per lipid molecule.

Type:: str

frequency

Frequency of classification. Defaults to every frame.

Type:: Optional[Frequency]

membrane_normal

Membrane normal used for leaflet classification. Defaults to the membrane normal specified for the entire Analysis.

Type:: Optional[str]

class gorder.leaflets.IndividualClassification(heads, methyls, frequency=None, membrane_normal=None)

Assign lipids into leaflets based on the orientation of acyl chains.

Less reliable but computationally fast.

heads

Selection query specifying reference atoms representing lipid headgroups (typically phosphorus atoms or phosphate beads). There must be exactly one such atom/bead per lipid molecule.

Type:: str

methyls

Selection query specifying reference atoms representing methyl groups at the ends of lipid tails. There should be exactly one such atom/bead per acyl chain (e.g., two for lipids with two acyl chains).

Type:: str

frequency

Frequency of classification. Defaults to every frame.

Type:: Optional[Frequency]

membrane_normal

Membrane normal used for leaflet classification. Defaults to the membrane normal specified for the entire Analysis.

Type:: Optional[str]

class gorder.leaflets.LocalClassification(membrane, heads, radius, frequency=None, membrane_normal=None)

Assign lipids into leaflets based on the local membrane center of geometry.

Useful for curved membranes but computationally slow.

membrane

Selection query specifying all lipids forming the membrane.

Type:: str

heads

Selection query specifying reference atoms representing lipid headgroups (typically phosphorus atoms or phosphate beads). There must be exactly one such atom/bead per lipid molecule.

Type:: str

radius

Radius of a cylinder used to calculate the local membrane center of geometry (in nm).

Type:: float

frequency

Frequency of classification. Defaults to every frame.

Type:: Optional[Frequency]

membrane_normal

Membrane normal used for leaflet classification. Defaults to the membrane normal specified for the entire Analysis.

Type:: Optional[str]

class gorder.leaflets.ManualClassification(input, frequency=None)

Get leaflet assignment from an external YAML file or a dictionary.

input

Path to the input YAML file containing the leaflet assignment or a dictionary specifying the leaflet assignment.

Type:: Union[str, dict]

frequency

Frequency of classification. Defaults to every frame.

Type:: Optional[Frequency]

class gorder.leaflets.NdxClassification(ndx, heads, upper_leaflet, lower_leaflet, frequency=None)

Get leaflet assignment from NDX file(s).

ndx

A list of NDX files to read.

Type:: List[str]

heads

Selection query specifying reference atoms representing lipid headgroups (typically phosphorus atoms or phosphate beads). There must be exactly one such atom/bead per lipid molecule.

Type:: str

upper_leaflet

Name of the group in the NDX file(s) specifying the atoms of the upper leaflet.

Type:: str

lower_leaflet

Name of the group in the NDX file(s) specifying the atoms of the lower leaflet.

Type:: str

frequency

Frequency of classification. Defaults to every frame.

Type:: Optional[Frequency]

Notes

No glob expansion is performed for the NDX files.