ost::mol::alg::hbond Namespace Reference

Data Structures
class	HBondableAtoms
class	HBondDonor
class	HBondAcceptor
class	HBond
Functions
def	BuildCHARMMHBondDonorAcceptorDict
def	BuildCHARMMHBondDonorEquivalenceDict
def	BuildCHARMMHBondAcceptorEquivalenceDict
def	ListEquivalentDonors
def	ListEquivalentAcceptors
def	AreHBonded
def	GetHbondDonorAcceptorList
def	GetHbondListFromDonorAcceptorLists
def	GetHbondListFromView
def	GetHbondListFromTraj
def	GetHbondListBetweenViews
def	GetEquivalentHBonds
def	CalculateHBondScore
def	AnalyzeHBondScore
def	GetHBondListIntersection
Variables
tuple	__all__

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Function Documentation

def ost::mol::alg::hbond::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
	)

Returns the same score as CalculateHBondScore, but for a trajectory.

Definition at line 389 of file hbond.py.

def ost::mol::alg::hbond::AreHBonded	(		donor,
			acceptor,
			da_dist = 3.9,
			ha_dist = 2.5,
			dha_angle = 1.57,
			daaa_angle = 1.57,
			haaa_angle = 1.57
	)

determines if a donor/acceptor pair is hydrogen bonded or not

Definition at line 203 of file hbond.py.

def ost::mol::alg::hbond::BuildCHARMMHBondAcceptorEquivalenceDict

(

)

Definition at line 97 of file hbond.py.

def ost::mol::alg::hbond::BuildCHARMMHBondDonorAcceptorDict

(

)

Definition at line 23 of file hbond.py.

def ost::mol::alg::hbond::BuildCHARMMHBondDonorEquivalenceDict

(

)

Definition at line 89 of file hbond.py.

def ost::mol::alg::hbond::CalculateHBondScore	(		ref_eh,
			eh2,
			ref_eh2 = None,
			hbond_donor_acceptor_dict = {},
			swap = False,
			donor_swap_dict = {},
			acceptor_swap_dict = {},
			verbose = True
	)

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.

def ost::mol::alg::hbond::GetEquivalentHBonds	(		ref_hbond_list,
			eh,
			swap = False,
			donor_swap_dict = {},
			acceptor_swap_dict = {},
			verbose = True
	)

Definition at line 331 of file hbond.py.

def ost::mol::alg::hbond::GetHbondDonorAcceptorList	(		eh,
			hbond_donor_acceptor_dict = {},
			verbose = True
	)

returns a list of hydrogen-bond donors and acceptors from an Entity or EntityView.
It 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.

Definition at line 219 of file hbond.py.

def ost::mol::alg::hbond::GetHbondListBetweenViews	(		eh1,
			eh2,
			hbond_donor_acceptor_dict = {},
			verbose = True
	)

return the list of hydrogen bonds formed between two Entity or EntityView.
if no dictionary for the hbond donors and acceptors is specified
it will use the standard CHARMM names to determine them

Definition at line 308 of file hbond.py.

def ost::mol::alg::hbond::GetHbondListFromDonorAcceptorLists	(		donor_list,
			acceptor_list
	)

return a list of hydrogen bonds between donors and acceptors from
a list of donors and a list of acceptors.

Definition at line 244 of file hbond.py.

def ost::mol::alg::hbond::GetHbondListFromTraj	(		t,
			eh,
			cutoff = 0.7,
			stride = 1,
			swap = False,
			donor_swap_dict = {},
			acceptor_swap_dict = {},
			hbond_donor_acceptor_dict = {},
			verbose = True
	)

return a list of hydrogen bonds from an Entity or EntityView that are
present in a fraction of the frames larger than *cutoff*.
if no dictionary for the hbond donors and acceptors is specified
it will use the standard CHARMM names to determine them

Definition at line 268 of file hbond.py.

def ost::mol::alg::hbond::GetHbondListFromView	(		eh,
			hbond_donor_acceptor_dict = {},
			verbose = True
	)

return a list of hydrogen bonds from an Entity or EntityView.
if no dictionary for the hbond donors and acceptors is specified
it will use the standard CHARMM names to determine them

Definition at line 255 of file hbond.py.

def ost::mol::alg::hbond::GetHBondListIntersection	(		ref_hbond_list,
			ref_eh,
			hbond_list,
			swap = False,
			donor_swap_dict = {},
			acceptor_swap_dict = {}
	)

Definition at line 423 of file hbond.py.

def ost::mol::alg::hbond::ListEquivalentAcceptors	(		acceptor,
			acceptor_swap_dict
	)

Definition at line 115 of file hbond.py.

def ost::mol::alg::hbond::ListEquivalentDonors	(		donor,
			donor_swap_dict
	)

Definition at line 103 of file hbond.py.

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Variable Documentation

tuple __all__

Initial value:

('HBondDonor','HBondAcceptor','BuildCHARMMHBondDonorAcceptorDict','AreHBonded','GetHbondDonorAcceptorList',\
         'GetHbondListFromDonorAcceptorLists','GetHbondListFromView','GetHbondListFromTraj','GetHbondListBetweenViews'\
         'CalculateHBondScore','AnalyzeHBondScore')

Definition at line 13 of file hbond.py.