htmd.membranebuilder.ringpenetration module#

htmd.membranebuilder.ringpenetration.getAllNeighbours(lipids, idx)#
Return type:

list

htmd.membranebuilder.ringpenetration.least_square_fit_plane(coords)#
htmd.membranebuilder.ringpenetration.moveLipidToPos(mol, lip)#
htmd.membranebuilder.ringpenetration.resolveRingPenetrations(lipids, box, max_iterations=50)#

Iteratively resolve ring penetrations between neighboring lipids.

Detects pairs of lipids where one lipid’s chain atoms thread through another’s aromatic or aliphatic ring (e.g. cholesterol). When a penetration is found, the offending lipid is rotated by 10 degrees around the Z-axis and the check is repeated. If all penetrations are resolved before max_iterations, the function returns normally; otherwise a warning is logged.

Parameters:

  • lipids (list) – List of _Lipid objects with mol, xyz, rot, headname, rings, and neighbours attributes.

  • box (list | ndarray) – Periodic box dimensions (XY) used for minimum-image wrapping when checking neighbor distances.

  • max_iterations (int) – Maximum number of rotation-and-recheck cycles before giving up.

htmd.membranebuilder.ringpenetration.wrap(coor, com2, box)#
Return type:

ndarray