meshi.energy.solvate
Class SolvateParametersList
java.lang.Object
meshi.energy.solvate.SolvateParametersList
- All Implemented Interfaces:
- Parameters
public class SolvateParametersList
- extends java.lang.Object
- implements Parameters
The parameter class required for the SolvateEnergy class. This class reads the parameters from 14 different files.
The 14 file names are given as a String array to the constructor.
The first 10 files, are files that read parameters for the different sigmoid functions used in the calculations
of the carbon and HB indices in SolvateEnergy. See the documentation of the Sigma class to see what are the
parameters required to define a sigmoid. The formats of all these files are similar. Each file contains a
14x14 matrix of doubles (14 is the number of types in Tsai 99'. They are: 1-PRO-N ; 2-backbone-N ; 3-ASN-ND ; 4-LYS-NZ ;
5-backbone-O ; 6-ASP-OD ; 7-PHE-CG ; 8-PHE-CD ; 9-VAL-CB ; 10-backbone-CA ; 11-ALA-CB ; 12-MET-SD ; 13-CYS-SG ; 14-hydrogens).
Value i,j in the matrix, is the relevent sigmoid property of atom type j on atom type i. For example, the sixth value in the
second row, corresponds to a sigmoid of hydroxyl oxygen (type 6) on a backbone nitrogen (type 2).
The 13 file types:
------------------
1) SolvateExtResCend.dat - A 14x14 matrix of doubles. These values are the 'end' values in the sigmoid that
calculates the carbon index.
2) SolvateExtResCp1.dat - A 14x14 matrix of doubles. These values are the 'p1' values in the sigmoid that
calculates the carbon index.
3) SolvateExtResCp2.dat - A 14x14 matrix of doubles. These values are the 'p2' values in the sigmoid that
calculates the carbon index.
4) SolvateExtResCvalAtp1.dat - A 14x14 matrix of doubles. These values are the 'valAtp1' values in the sigmoid that
calculates the carbon index.
5) SolvateExtResCvalAtp2.dat - A 14x14 matrix of doubles. These values are the 'valAtp2' values in the sigmoid that
calculates the carbon index.
6) SolvateExtResHBend.dat - A 14x14 matrix of doubles. These values are the 'end' values in the sigmoid that
calculates the HB index.
7) SolvateExtResHBp1.dat - A 14x14 matrix of doubles. These values are the 'p1' values in the sigmoid that
calculates the HB index.
8) SolvateExtResHBp2.dat - A 14x14 matrix of doubles. These values are the 'p2' values in the sigmoid that
calculates the HB index.
9) SolvateExtResHBvalAtp1.dat - A 14x14 matrix of doubles. These values are the 'valAtp1' values in the sigmoid that
calculates the HB index.
10) SolvateExtResHBvalAtp2.dat - A 14x14 matrix of doubles. These values are the 'valAtp2' values in the sigmoid that
calculates the HB index.
11) SolvateMESHI2Tsai.dat - In MESHI there are 190 defined atom types. In the solvate energy, we sometime use
a reduce representation of 14 atom types as defined in Tsai et. al. 99'. The format of this file is:
{MESHI atom type (string)} {Tsai type number (int)}
{MESHI atom type (string)} {Tsai type number (int)}
{MESHI atom type (string)} {Tsai type number (int)}
...
{MESHI atom type (string)} {Tsai type number (int)}
12) SolvateSCpolarSplines.dat - 2D spline parameters for the solvation of side-chain polar atoms.
A spline is created for each of the of the 190 atom types, but it is a zero spline for those that are
not side-chain polar atoms. The format of this file is:
TRN {2D spline initialization string for TRN (see Spline2D.java)}
TRC {zero spline}
TRO {2D spline initialization string for TRO (see Spline2D.java)}
AH {zero spline)
AN {zero spline)
...
CSG {2D spline initialization string for CSG (see Spline2D.java)}
...
YOH {2D spline initialization string for YOH (see Spline2D.java)}
13) SolvateSCcarbonSplines.dat - 1D spline parameters for the solvation of side-chain NON-polar atoms.
A spline is created for each of the of the 190 atom types, but it is a zero spline for those that are
not side-chain NON-polar atoms. The format of this file is:
TRN {zero spline}
TRC {zero spline}
TRO {zero spline}
AH {zero spline}
...
DCG {1D spline initialization string for DCG (see Spline1D.java)}
...
YCZ {1D spline initialization string for YCZ (see Spline1D.java)}
YOH {zero spline}
14) SolvateBBpolarSplines.dat - 2D spline parameters for the solvation of backbone polar atoms.
A spline is created for each of the of the 190 atom types, but it is a zero spline for those that are
not backbone polar atoms. The format of this file is:
TRN {zero spline}
TRC {zero spline}
TRO {zero spline}
AH {zero spline)
AN {2D spline initialization string for AN (see Spline2D.java)}
...
AO {2D spline initialization string for AO (see Spline2D.java)}
...
YOH {zero spline}
|
Constructor Summary |
SolvateParametersList(java.lang.String[] parameterFiles)
The parameter to the constructor is an array of 14 Strings, giving the 14 files required as parameters. |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
N_TSAI
public static final int N_TSAI
- See Also:
- Constant Field Values
atomicTypeConverter
public final int[] atomicTypeConverter
maxEnd
public final double maxEnd
scPolarSplines
public final Spline2D[] scPolarSplines
bbSplines
public final Spline2D[] bbSplines
scCarbonSplines
public final Spline1D[] scCarbonSplines
cEnd
public final double[][] cEnd
cP1
public final double[][] cP1
cP2
public final double[][] cP2
cValAtp1
public final double[][] cValAtp1
cValAtp2
public final double[][] cValAtp2
hbEnd
public final double[][] hbEnd
hbP1
public final double[][] hbP1
hbP2
public final double[][] hbP2
hbValAtp1
public final double[][] hbValAtp1
hbValAtp2
public final double[][] hbValAtp2
sigmaParameters
public static final SigmaParameters[][] sigmaParameters
hbParameters
public static final SigmaParameters[][] hbParameters
SolvateParametersList
public SolvateParametersList(java.lang.String[] parameterFiles)
- The parameter to the constructor is an array of 14 Strings, giving the 14 files required as parameters.
See the MeshiPotential class for a detailed list.
createParameters
public Parameters createParameters(java.lang.String s)
parameters
public Parameters parameters(java.lang.Object obj)
readSigmoidValueFile
private void readSigmoidValueFile(double[][] ar,
java.lang.String filename)