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donor geometry testing functions
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Imported modules
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import base
from chimera import angle, sqdistance
from chimera.bondGeom import bondPositions
from chimera.idatm import typeInfo, geometry, planar, tetrahedral
from commonGeom import getPhiPlaneParams, testPhi, project, testTheta, sulphurCompensate
from hydpos import hydPositions
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Functions
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donGeneric
donThetaTau
donUpsilonTau
donWater
testUpsilonTauAcceptor
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donGeneric
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donGeneric (
donor,
donorHyds,
acceptor,
sp2Orp2,
sp3Orp2,
sp3Nrp2,
sp2Or2,
sp3Or2,
sp3Nr2,
genRp2,
genR2,
minHydAngle,
minBondedAngle,
)
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donThetaTau
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donThetaTau (
donor,
donorHyds,
acceptor,
sp2Orp2,
sp2Otheta,
sp3Orp2,
sp3Otheta,
sp3Ophi,
sp3Nrp2,
sp3Ntheta,
sp3Nupsilon,
genRp2,
genTheta,
isWater=0,
)
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donUpsilonTau
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donUpsilonTau (
donor,
donorHyds,
acceptor,
sp2Or2,
sp2OupsilonLow,
sp2OupsilonHigh,
sp2Otheta,
sp2Otau,
sp3Or2,
sp3OupsilonLow,
sp3OupsilonHigh,
sp3Otheta,
sp3Otau,
sp3Ophi,
sp3Nr2,
sp3NupsilonLow,
sp3NupsilonHigh,
sp3Ntheta,
sp3Ntau,
sp3NupsilonN,
genR2,
genUpsilonLow,
genUpsilonHigh,
genTheta,
tauSym,
)
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donWater
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donWater (
donor,
donorHyds,
acceptor,
sp2Orp2,
sp2Or2,
sp2Otheta,
sp3Orp2,
sp3Or2,
sp3Otheta,
sp3Ophi,
sp3Nrp2,
sp3Nr2,
sp3Ntheta,
sp3Nupsilon,
genRp2,
genR2,
genTheta,
)
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testUpsilonTauAcceptor
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testUpsilonTauAcceptor (
donor,
donorHyds,
acceptor,
r2,
upsilonLow,
upsilonHigh,
theta,
tau,
tauSym,
)
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Exceptions
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AssertionError, "Unexpected tau symmetry (%d," " should be %d) for donor %s" %(2 * len( bondedPos ), tauSym, donor.oslIdent() )
AssertionError, "upsilon tau donor (%s) not bonded to" " exactly one heavy atom" % donor.oslIdent()
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