Class Charge
- java.lang.Object
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- com.actelion.research.chem.forcefield.mmff.table.Charge
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public class Charge extends java.lang.Object
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
bci_binary_search(int col, int val, int lo, int hi, boolean findlow)
Binary search in the bci table.double
get_bci_f(int row, int col)
int
get_bci_len()
int
get_bci_n(int row, int col)
double
getFcadj(int type)
Returns the formal charge adjustment for a given atom type.double
getPartial(int bondt, int a1t, int a2t)
Gets the partial charge of a bond type and its two atom types.double
getPbci(int type)
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Constructor Detail
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Charge
public Charge(Tables t, java.lang.String csv_pbci, java.lang.String csv_bci)
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Method Detail
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getFcadj
public double getFcadj(int type)
Returns the formal charge adjustment for a given atom type.- Parameters:
type
- The MMFF atom type for an atom.- Returns:
- The formal charge adjustment as a double.
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getPbci
public double getPbci(int type)
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getPartial
public double getPartial(int bondt, int a1t, int a2t)
Gets the partial charge of a bond type and its two atom types.- Parameters:
bondt
- The MMFF bond type.a1t
- The MMFF atom type of atom 1.a2t
- The MMFF atom type of atom 2.- Returns:
- The partial charge.
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bci_binary_search
public int bci_binary_search(int col, int val, int lo, int hi, boolean findlow)
Binary search in the bci table. This is a wrapper function around 'binary_search' which just passes a SearchArray object for bci.- Parameters:
col
- The column in the array to search, it should be an integer value.val
- The value to be searched for.lo
- The starting low index to begin searching from. This index is included in the search.hi
- The ending high index to end searching in. This index is EXCLUDED in the search, with the value below it being searched.findlow
- True if the binary search should find the lowest value if there are duplicates, False if the binary search should find the highest value if there are duplicates.- Returns:
- The lowest/highest index to the value.
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get_bci_f
public double get_bci_f(int row, int col)
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get_bci_n
public int get_bci_n(int row, int col)
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get_bci_len
public int get_bci_len()
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