Author: | Oliver Beckstein |
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Year: | 2010 |
Copyright: | GNU Public License v3 |
One can use this information to identify
See example scripts in the examples/ directory on how to use LeafletFinder. The function optimize_cutoff() implements a (slow) heuristic method to find the best cut off for the LeafletFinder algorithm.
Identify atoms in the same leaflet of a lipid bilayer.
The components of the graph are stored in the list LeafletFinder.components; the atoms in each component are numbered consecutively, starting at 0. To obtain the atoms in the input structure use LeafletFinder.groups():
L = LeafletFinder(PDB, 'name P*')
leaflet0 = L.groups(0)
leaflet1 = L.groups(1)
The residues can be accessed through the standard MDAnalysis mechanism:
leaflet0.residues
provides a ResidueGroup instance. Similarly, all atoms in the first leaflet are then
leaflet0.residues.atoms
Initialize from a universe or pdb file.
Arguments : |
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Keywords : |
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Return a MDAnalysis.core.AtomGroup.AtomGroup for component_index.
Return a MDAnalysis.core.AtomGroup.AtomGroup for component_index.
If no argument is supplied, then a list of all leaflet groups is returned.
See also
Dict of component index with size of component.
Update components, possibly with a different cutoff
Write selections for the leaflets to filename.
The format is typically determined by the extension of filename (e.g. “vmd”, “pml”, or “ndx” for VMD, PyMol, or Gromacs).
See MDAnalysis.selections.base.SelectionWriter for all options.
Find cutoff that minimizes number of disconnected groups.
Applies heuristics to find best groups:
at least two groups (assumes that there are at least 2 leaflets)
reject any solutions for which:
|N0 - N1|/|N0 + N1| > *max_imbalance*
Ni = number of lipids in group i. This heuristic picks groups with balanced numbers of lipids.
Arguments : |
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Returns : | (cutoff,N) optimum cutoff and number of groups found |
Raises : | can die in various ways if really no appropriate number of groups can be found; needs to be made more robust |