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| def | BuildCHARMMHBondDonorAcceptorDict () |
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| def | BuildCHARMMHBondDonorEquivalenceDict () |
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| def | BuildCHARMMHBondAcceptorEquivalenceDict () |
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| def | ListEquivalentDonors (donor, donor_swap_dict) |
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| def | ListEquivalentAcceptors (acceptor, acceptor_swap_dict) |
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| def | AreHBonded (donor, acceptor, da_dist=3.9, ha_dist=2.5, dha_angle=1.57, daaa_angle=1.57, haaa_angle=1.57) |
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| def | GetHbondDonorAcceptorList (eh, hbond_donor_acceptor_dict={}, verbose=True) |
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| def | GetHbondListFromDonorAcceptorLists (donor_list, acceptor_list) |
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| def | GetHbondListFromView (eh, hbond_donor_acceptor_dict={}, verbose=True) |
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| def | GetHbondListFromTraj (t, eh, cutoff=0.7, stride=1, swap=False, donor_swap_dict={}, acceptor_swap_dict={}, hbond_donor_acceptor_dict={}, verbose=True) |
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| def | GetHbondListBetweenViews (eh1, eh2, hbond_donor_acceptor_dict={}, verbose=True) |
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| def | GetEquivalentHBonds (ref_hbond_list, eh, swap=False, donor_swap_dict={}, acceptor_swap_dict={}, verbose=True) |
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| def | CalculateHBondScore (ref_eh, eh2, ref_eh2=None, hbond_donor_acceptor_dict={}, swap=False, donor_swap_dict={}, acceptor_swap_dict={}, verbose=True) |
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| def | AnalyzeHBondScore (ref_eh, t, eh2, ref_eh2=None, hbond_donor_acceptor_dict={}, swap=False, donor_swap_dict={}, acceptor_swap_dict={}, first=0, last=-1, stride=1, verbose=True) |
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| def | GetHBondListIntersection (ref_hbond_list, ref_eh, hbond_list, swap=False, donor_swap_dict={}, acceptor_swap_dict={}) |
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| def ost.mol.alg.hbond.CalculateHBondScore |
( |
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ref_eh, |
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eh2, |
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ref_eh2 = None, |
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hbond_donor_acceptor_dict = {}, |
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swap = False, |
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donor_swap_dict = {}, |
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acceptor_swap_dict = {}, |
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verbose = True |
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) |
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Returns the fraction of H-bonds from ref_eh that are also present in eh2.
If ref_eh2 is specified, it uses as reference the Hbonds between ref_eh and ref_eh2.
This allows to look at H-bonds between specific parts of proteins or so.
Alternatively ref_eh can be a list of H-bonds.
This function relies on atom names to determine the list of H-bond donors and acceptors.
These names are given in a dictionary, which defaults to CHARMM.
If swap is set to True, a dictionary for equivalent donors and one for equivalent acceptors
(defaults to CHARMM) is used to check for equivalent HBonds in eh2.
If swap is set to True, if two equivalent hydrogen bonds are present in the reference entity
(for example both oxygens of ASP H-bonding the same atom), it suffices that on of these bonds is
present in eh2 for both of them to be counted as present in eh2.
Definition at line 358 of file hbond.py.
