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Victor
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Victor
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Includes methods that allow to calculate solvation, energy and propensity. More...
Inheritance diagram for SolvationPotential: Collaboration diagram for SolvationPotential:Public Member Functions | |
| SolvationPotential (unsigned int _resol=1) | |
| virtual long double | calculateEnergy (Spacer &sp, unsigned int index1, unsigned int index2) |
| long double | calculateSolvation (Spacer &sp) |
| long double | calculateSolvation (AminoAcid &aa, Spacer &sp, unsigned int start=0, unsigned int end=9999) |
| long double | calculateSolvation (AminoAcid &resid, AminoAcidCode type, Spacer &sp) |
| long double | pReturnMaxPropensity (const AminoAcidCode type) const |
| long double | pReturnMinPropensity (const AminoAcidCode type) const |
Includes methods that allow to calculate solvation, energy and propensity.
A simple solvation potential is derived in analogy to the one described for GenTHREADER (Jones, 1999). The likelihood for each of the 20 amino acids to adopt a given relative solvent accessibility is used to derive the pseudo-energy. The relative solvent accessibility is estimated as the number of other Cβ atoms within a sphere of radius 10 Å centered on the residue’s Cβ atom. This computationally simple measure was reported to correlate very well (cc > 0.85) with the accessible surface of the residue (Jones, 1999). Since up to 40 surrounding Cβ atoms were encountered in the database, individual propensity bins were chosen for each number i of surrounding Cβ atoms (i = 0,..., 40). The energy for a given structure is calculated by summing the individual energies over all residues in the protein.
| SolvationPotential | ( | unsigned int | _resol = 1 | ) |
Basic constructor, allocate information from the "solv.par" file, and set the min and max propensities values.
| _resol | is the number of bins to calculate the statistics. 1 = max resulution. |
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virtual |
calculates the total energy for a portion of a residue in the spacer
| reference | of a Spacer(Spacer&), index for the beginning and ending position of the residue portion(unsigned int) |
Implements Potential.
| long double calculateSolvation | ( | Spacer & | sp | ) |
calculates the total solvation potential for the residue in the spacer
| reference | of a Spacer(Spacer&) |
| long double calculateSolvation | ( | AminoAcid & | aa, |
| Spacer & | sp, | ||
| unsigned int | start = 0, |
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| unsigned int | end = 9999 |
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calculates the total solvation potential for a portion of residues in the spacer, and an specific residue. the relation between them should be minor to SOLVATION_CUTOFF_DISTANCE and not identical
| reference | of a residue (AminoAcid&), reference of a Spacer(Spacer&), index for the beginning and ending position of the residues portion(unsigned int) |
solvation potential of the residue, considering a given amino acid type.
| reference | of a residue (AminoAcid&), amino acid type (aminoacidCode) ,reference of a Spacer(Spacer&) |
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virtual |
returns the maximum propensity for an amino acid type
| the | amino acid type(AminoAcidCode) |
Reimplemented from Potential.
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returns the minimum propensity for an amino acid type
| the | amino acid type(AminoAcidCode) |
Reimplemented from Potential.
1.8.6 
