Index

A

AAOrder (class in gorder.analysis_types) Analysis (class in gorder) analysis_type (gorder.Analysis attribute) AnalysisError AnalysisResults (class in gorder.results) APIError atom() (gorder.results.AtomResults method) atom_name() (gorder.AtomType method)

AtomResults (class in gorder.results) atoms() (gorder.results.BondResults method) (gorder.results.MoleculeResults method) AtomType (class in gorder) average_order() (gorder.results.AnalysisResults method) (gorder.results.MoleculeResults method) average_ordermaps() (gorder.results.AnalysisResults method) (gorder.results.MoleculeResults method)

B

beads (gorder.analysis_types.CGOrder attribute) begin (gorder.Analysis attribute) bin_size (gorder.ordermap.OrderMap attribute)

BondResults (class in gorder.results) bonds (gorder.Analysis attribute) bonds() (gorder.results.AtomResults method) (gorder.results.MoleculeResults method)

C

CGOrder (class in gorder.analysis_types) ConfigError Convergence (class in gorder.results)

convergence() (gorder.results.MoleculeResults method) Cuboid (class in gorder.geometry) Cylinder (class in gorder.geometry)

D

dim (gorder.ordermap.OrderMap attribute)

DynamicNormal (class in gorder.membrane_normal)

E

end (gorder.Analysis attribute) error() (gorder.results.Order method) estimate_error (gorder.Analysis attribute)

EstimateError (class in gorder.estimate_error) every() (gorder.Frequency static method) extract() (gorder.results.Map method)

F

frames() (gorder.results.Convergence method) Frequency (class in gorder) frequency (gorder.leaflets.GlobalClassification attribute) (gorder.leaflets.IndividualClassification attribute) (gorder.leaflets.LocalClassification attribute) (gorder.leaflets.ManualClassification attribute) (gorder.leaflets.NdxClassification attribute)

from_file() (gorder.Analysis static method)

G

geometry (gorder.Analysis attribute) get_at() (gorder.results.Map method) get_atom() (gorder.results.MoleculeResults method) get_bond() (gorder.results.AtomResults method) (gorder.results.MoleculeResults method) get_molecule() (gorder.results.AnalysisResults method) GlobalClassification (class in gorder.leaflets) gorder module gorder.analysis_types module gorder.estimate_error module

gorder.exceptions module gorder.geometry module gorder.leaflets module gorder.membrane_normal module gorder.ordermap module gorder.results module

H

handle_pbc (gorder.Analysis attribute) heads (gorder.leaflets.GlobalClassification attribute) (gorder.leaflets.IndividualClassification attribute) (gorder.leaflets.LocalClassification attribute) (gorder.leaflets.NdxClassification attribute) (gorder.membrane_normal.DynamicNormal attribute)

heavy_atoms (gorder.analysis_types.AAOrder attribute) hydrogens (gorder.analysis_types.AAOrder attribute)

I

ignore (gorder.analysis_types.UAOrder attribute) index (gorder.Analysis attribute)

IndividualClassification (class in gorder.leaflets) input (gorder.leaflets.ManualClassification attribute)

L

leaflets (gorder.Analysis attribute) LocalClassification (class in gorder.leaflets) lower() (gorder.results.Convergence method) (gorder.results.OrderCollection method) (gorder.results.OrderMapsCollection method)

lower_leaflet (gorder.leaflets.NdxClassification attribute)

M

ManualClassification (class in gorder.leaflets) Map (class in gorder.results) membrane (gorder.leaflets.GlobalClassification attribute) (gorder.leaflets.LocalClassification attribute) membrane_normal (gorder.Analysis attribute) (gorder.leaflets.GlobalClassification attribute) (gorder.leaflets.IndividualClassification attribute) (gorder.leaflets.LocalClassification attribute) methyls (gorder.leaflets.IndividualClassification attribute) min_samples (gorder.Analysis attribute) (gorder.ordermap.OrderMap attribute) module gorder gorder.analysis_types gorder.estimate_error gorder.exceptions gorder.geometry gorder.leaflets gorder.membrane_normal gorder.ordermap gorder.results

molecule() (gorder.results.AtomResults method) (gorder.results.BondResults method) (gorder.results.MoleculeResults method) MoleculeResults (class in gorder.results) molecules() (gorder.results.AnalysisResults method)

N

n_analyzed_frames() (gorder.results.AnalysisResults method) n_blocks (gorder.estimate_error.EstimateError attribute)

n_threads (gorder.Analysis attribute) ndx (gorder.leaflets.NdxClassification attribute) NdxClassification (class in gorder.leaflets)

O

once() (gorder.Frequency static method) Order (class in gorder.results) order() (gorder.results.AtomResults method) (gorder.results.BondResults method) OrderCollection (class in gorder.results) OrderMap (class in gorder.ordermap) ordermap (gorder.Analysis attribute) ordermaps() (gorder.results.AtomResults method) (gorder.results.BondResults method)

OrderMapsCollection (class in gorder.results) orientation (gorder.geometry.Cylinder attribute) output_convergence (gorder.estimate_error.EstimateError attribute) output_csv (gorder.Analysis attribute) output_directory (gorder.ordermap.OrderMap attribute) output_tab (gorder.Analysis attribute) output_xvg (gorder.Analysis attribute) output_yaml (gorder.Analysis attribute) overwrite (gorder.Analysis attribute)

P

plane (gorder.ordermap.OrderMap attribute)

R

radius (gorder.geometry.Cylinder attribute) (gorder.geometry.Sphere attribute) (gorder.leaflets.LocalClassification attribute) (gorder.membrane_normal.DynamicNormal attribute) reference (gorder.geometry.Cuboid attribute) (gorder.geometry.Cylinder attribute) (gorder.geometry.Sphere attribute)

relative_index() (gorder.AtomType method) residue_name() (gorder.AtomType method) run() (gorder.Analysis method)

S

saturated (gorder.analysis_types.UAOrder attribute) silent (gorder.Analysis attribute) span (gorder.geometry.Cylinder attribute) span_x() (gorder.results.Map method)

span_y() (gorder.results.Map method) Sphere (class in gorder.geometry) step (gorder.Analysis attribute) structure (gorder.Analysis attribute)

T

tile_dim() (gorder.results.Map method) total() (gorder.results.Convergence method) (gorder.results.OrderCollection method) (gorder.results.OrderMapsCollection method)

trajectory (gorder.Analysis attribute)

U

UAOrder (class in gorder.analysis_types) unsaturated (gorder.analysis_types.UAOrder attribute) upper() (gorder.results.Convergence method) (gorder.results.OrderCollection method) (gorder.results.OrderMapsCollection method)

upper_leaflet (gorder.leaflets.NdxClassification attribute)

V

value() (gorder.results.Order method)

W

write() (gorder.results.AnalysisResults method)

WriteError

X

xdim (gorder.geometry.Cuboid attribute)

Y

ydim (gorder.geometry.Cuboid attribute)

Z

zdim (gorder.geometry.Cuboid attribute)