Class Bond
- java.lang.Object
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- com.actelion.research.chem.forcefield.mmff.table.Bond
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- All Implemented Interfaces:
Searchable
public final class Bond extends java.lang.Object implements Searchable
Bond table, corresponds to the MMFFBOND.PAR parameters table provided in the MMFF literature. This table holds parameters for bond stretching interactions.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
get(int row, int col)
This should get an integer value given a column and row.double
kb(int index)
Returns the 'kb' value at the given index from the Bond table.double
kb(MMFFMolecule mol, int atom1, int atom2)
Returns 'kb' given a molecule and two atoms in that molecule that form a bond.int
length()
This function should return the total number of rows in a searchable table.double
r0(int index)
Returns the 'r0' value at the given index from the Bond table.double
r0(MMFFMolecule mol, int atom1, int atom2)
Returns 'r0' given a molecule and two atoms in that molecule that form a bond.
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Constructor Detail
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Bond
public Bond(Tables t, java.lang.String csvpath)
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Method Detail
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get
public int get(int row, int col)
Description copied from interface:Searchable
This should get an integer value given a column and row. The binary search function only searches columns containing integers for a value.- Specified by:
get
in interfaceSearchable
- Parameters:
row
- The row in the table.col
- The column in the row to return.- Returns:
- The value at 'col' in 'row'.
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length
public int length()
Description copied from interface:Searchable
This function should return the total number of rows in a searchable table. This is normally just the length of the array.- Specified by:
length
in interfaceSearchable
- Returns:
- The number of elements that can be searched.
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r0
public double r0(int index)
Returns the 'r0' value at the given index from the Bond table.- Parameters:
index
- The table index for the row.- Returns:
- 'r0' for that index.
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kb
public double kb(int index)
Returns the 'kb' value at the given index from the Bond table.- Parameters:
index
- The table index for the row.- Returns:
- 'kb' for that index.
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r0
public double r0(MMFFMolecule mol, int atom1, int atom2)
Returns 'r0' given a molecule and two atoms in that molecule that form a bond.- Parameters:
mol
- The molecule containing the bond.atom1
- The first atom of the bond.atom2
- The second atom of the bond.- Returns:
- 'r0' for that bond.
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kb
public double kb(MMFFMolecule mol, int atom1, int atom2)
Returns 'kb' given a molecule and two atoms in that molecule that form a bond.- Parameters:
mol
- The molecule containing the bond.atom1
- The first atom of the bond.atom2
- The second atom of the bond.- Returns:
- 'kb' for that bond.
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