Class HydrogenBondFinder

object --+
         |
        HydrogenBondFinder

Find candidate hydrogen bonds.

More hbonds will be found than are "realistic"; further filtering may be performed using the energy attribute of the returned hbonds. A reasonable filter seems to be around -1.0 (more negative is stronger); i.e. energies greater than that are more likely than not to be spurious.

The HydrogenBond class can also be used directly to compute hydrogen bond geometry and energies by supplying donor, acceptor and hydrogen positions.

Instance Methods

[hide private]

__init__(self, system, donors, acceptors, cutoff=3.5)
Args: system (System): msys system donors: selection string, list of ids, or list of Atoms acceptors: selection string, list of ids, or list of Atoms cutoff (float): distance cutoff for donor and acceptor

find(self, pos=None)
Find hydrogen bonds for the given positions, defaulting to the current positions of the input system.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, system, donors, acceptors, cutoff=3.5)
(Constructor)


Args:
    system (System): msys system
    donors: selection string, list of ids, or list of Atoms
    acceptors: selection string, list of ids, or list of Atoms
    cutoff (float): distance cutoff for donor and acceptor

Note:
    If Atoms are provided, they must be members of system.

Overrides: object.__init__

Class HydrogenBondFinder

__init__(self, system, donors, acceptors, cutoff=3.5) (Constructor)

init(self, system, donors, acceptors, cutoff=3.5)
(Constructor)