Package MolKit :: Module hydrogenBondBuilder :: Class HydrogenBondBuilder

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Class HydrogenBondBuilder

source code

object which can build hydrogen bonds between atoms according to their coords and atom type

Instance Methods

__init__(self, distCutoff=distCutoff, distCutoff2=distCutoff2, d2min=d2min, d2max=d2max, d3min=d3min, d3max=d3max, a2min=a2min, a2max=a2max, a3min=a3min, a3max=a3max, donorTypes=allDonors, acceptorTypes=allAcceptors, distOnly=False)

check_babel_types(self, ats)

reset(self, ats)

build(self, group1, group2=None, reset=True, paramDict=None)
atDict <- build(group1, group2, reset, paramDict=None, **kw): group1: atoms group2: atoms reset: remove all previous hbonds, default True!

checkForPossibleH(self, ats, blen)

getHBDonors(self, ats, donorList)

filterAcceptors(self, accAts)

getHBAcceptors(self, ats, acceptorList)

buildD(self, ats, paramDict=None)

getMat(self, ats)

process(self, dict1, dict2, paramDict)

makeBonds(self, pD, d2Ats, d3Ats, a2Ats, a3ats, paramDict)

filterBasedOnAngs(self, pD, d2Ats, d3Ats, a2Ats, a3ats, paramDict)

removeBadAts(self, atDict, badAtDict)

removeNeighbors(self, atDict)

getDonors(self, nodes, paramDict)

getAcceptors(self, nodes, paramDict)

Method Details

init(self, distCutoff=distCutoff, distCutoff2=distCutoff2, d2min=d2min, d2max=d2max, d3min=d3min, d3max=d3max, a2min=a2min, a2max=a2max, a3min=a3min, a3max=a3max, donorTypes=allDonors, acceptorTypes=allAcceptors, distOnly=False)
(Constructor)

None

check_babel_types(self, ats)

None

reset(self, ats)

None

build(self, group1, group2=None, reset=True, paramDict=None)

atDict <- build(group1, group2, reset, paramDict=None, **kw): group1: atoms group2: atoms reset: remove all previous hbonds, default True!

paramDict: a dictionary with these keys and default values distCutoff: 2.25 hydrogen--acceptor distance distCutoff2: 3.00 donor... acceptor distance d2min: 120 <min theta for sp2 hybridized donors> d2max: 180 <max theta for sp2 hybridized donors> d3min: 120 <min theta for sp3 hybridized donors> d3max: 170 <max theta for sp3 hybridized donors>

a2min: 120 <min phi for sp2 hybridized donors> a2max: 150 <max phi for sp2 hybridized donors> a3min: 100 <min phi for sp3 hybridized donors> a3max: 150 <max phi for sp3 hybridized donors> @@FIX THIS: these do not seem to be input here donorTypes = allDonors acceptorTypes = allAcceptors

checkForPossibleH(self, ats, blen)

None

getHBDonors(self, ats, donorList)

None

filterAcceptors(self, accAts)

None

getHBAcceptors(self, ats, acceptorList)

None

buildD(self, ats, paramDict=None)

None

getMat(self, ats)

None

process(self, dict1, dict2, paramDict)

None

makeBonds(self, pD, d2Ats, d3Ats, a2Ats, a3ats, paramDict)

None

filterBasedOnAngs(self, pD, d2Ats, d3Ats, a2Ats, a3ats, paramDict)

None

removeBadAts(self, atDict, badAtDict)

None

removeNeighbors(self, atDict)

None

getDonors(self, nodes, paramDict)

None

getAcceptors(self, nodes, paramDict)

None