Class for calculating properties of proteins and protein residues.
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__init__(self,
struct,
jobname,
cleanup=True,
nbcutoff=14.0,
residues=None,
lig_asl=None)
Construct a ProteinCalculator class from a structure
file and a jobname. |
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minimizer(self)
The minimizer used in energy calculations. |
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_prepInscode(self)
Private method to renumber residues with inscodes so that propka can
handle them. |
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runpKa(self)
Runs PROPKA to get the pKa of all residues in the
self.struct , then sets self.pka_data . |
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float
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getResiduepKa(self,
residue)
Returns the pKa for specified residue |
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float
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getTotalpKa(self)
Gets the sum of the pKa values for the protein. |
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setpKaData(self,
summary,
renum_map=None)
Compares residues from the PROPKA summary with the residues in
self.residues and when matches are found the summary's
pKa is set for that residue in self.pka_data |
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float
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float
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getPrimeEnergyByResidues(self,
residues)
Run Prime Minimization on self.struct only minimizing
the residues in residues . |
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float
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generator
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float
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getTotalPotentialEnergy(self)
Get the potential energy of self.struct which is
calculated using
schrodinger.structutils.minimize.Minimizer . |
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float
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generator
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_calculateEnergiesByResidue(self,
res) |
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float
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generator
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_calculateAtomicSasaList(self)
Calculate SASA for all atoms in the structure, and save them. |
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_sumSasaForAtoms(self,
atoms=None)
Sum up the pre-calculated SASAs for the given atoms. |
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float
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generator
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float
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generator
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float
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getResidueSASA(self,
residue,
sidechain=False)
Returns the SASA for residue. |
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generator
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float
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getTotalSASAPolar(self,
sidechain=False)
Returns the total approximate solvent accessible surface area for all
polar residues. |
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generator
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float
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getTotalSASANonPolar(self,
sidechain=False)
Returns the total approximate solvent accessible surface area for all
non-polar residues. |
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generator
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float
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getTotalSASA(self,
sidechain=False)
Returns the total approximate solvent accessible surface area for all
residues. |
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float
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generator
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float
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getTotalHydropathy(self,
sidechain=False)
Returns the total calculated hydropathy value for all residues. |
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int
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generator
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getRotatableBondsGenerator(self)
Returns a generator that yields the schrodinger.structure._Residue object
and its number of rotors for each residue in
self.struct . |
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float
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_calculateVDWSurfComp(self) |
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float
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getTotalSurfComp(self)
Returns:
Median of vdW surface complementarity values for all surface points
for all residues. |
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float
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getResidueSurfComp(self,
residue)
Returns:
Median of vdW surface complementarity values for all accounted points
on the surface of this residue. |
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generator
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calculateOverResidues(self,
*properties)
Helper method that returns a generator which will calculate multiple
properties for self.struct . |
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dict
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calculate(self,
*properties)
Helper method to calculate multiple properties for
self.struct . |
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getTotalAggregation(self) |
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getTotalComplementarity(self) |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__str__ ,
__subclasshook__
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