Package com.actelion.research.chem.conf
Class BondLengthSet
- java.lang.Object
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- com.actelion.research.chem.conf.BondLengthSet
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public class BondLengthSet extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static float
DEFAULT_BOND_LENGTH
static float
DEFAULT_BOND_STDDEV
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Constructor Summary
Constructors Constructor Description BondLengthSet(StereoMolecule mol)
Calculates and caches a list of bond length estimates from molecule.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static int
getAtomPi(StereoMolecule mol, int atom)
Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length.static float
getBondCount(int index)
static int
getBondID(StereoMolecule mol, int bond)
Constructs a bond classification index from a specific bond in a molecule.static java.lang.String
getBondIDString(int index)
static int
getBondIndex(int bondOrder, boolean isAromatic, boolean isDelocalized, int atomicNo1, int atomicNo2, int atomPi1, int atomPi2)
Constructs a bond classification ID from individual parameters and returns the ID's index in the sorted list of bond length information.static int
getBondIndex(StereoMolecule mol, int bond)
Constructs a bond classification ID from a specific bond in a molecule and returns the ID's index in the sorted list of bond length information.static float
getBondLength(int index)
Returns an estimate of the bond length based on atom and bond characteristics.static float
getBondLengthFromCovalentRadii(StereoMolecule mol, int bond)
Returns an estimate of the bond length based on atom and bond characteristics.static float
getBondStdDev(int index)
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.float
getLength(int bond)
float
getStdDev(int bond)
static float
getStdDevFromCovalentRadii(StereoMolecule mol, int bond)
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.static boolean
isPiConsidered(int atomicNo)
static float
lookupBondLength(StereoMolecule mol, int bond)
Returns an estimate of the bond length based on atom and bond characteristics.
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Field Detail
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DEFAULT_BOND_LENGTH
public static final float DEFAULT_BOND_LENGTH
- See Also:
- Constant Field Values
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DEFAULT_BOND_STDDEV
public static final float DEFAULT_BOND_STDDEV
- See Also:
- Constant Field Values
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Constructor Detail
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BondLengthSet
public BondLengthSet(StereoMolecule mol)
Calculates and caches a list of bond length estimates from molecule.- Parameters:
mol
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Method Detail
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getLength
public float getLength(int bond)
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getStdDev
public float getStdDev(int bond)
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getBondIDString
public static java.lang.String getBondIDString(int index)
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getBondIndex
public static int getBondIndex(int bondOrder, boolean isAromatic, boolean isDelocalized, int atomicNo1, int atomicNo2, int atomPi1, int atomPi2)
Constructs a bond classification ID from individual parameters and returns the ID's index in the sorted list of bond length information. The index can be used to get typical bond length and standard deviation.- Parameters:
bondOrder
-isAromatic
-isDelocalized
-atomicNo1
-atomicNo2
-atomPi1
-atomPi2
-- Returns:
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getBondIndex
public static int getBondIndex(StereoMolecule mol, int bond)
Constructs a bond classification ID from a specific bond in a molecule and returns the ID's index in the sorted list of bond length information. The index can be used to get typical bond length and standard deviation.- Parameters:
mol
-bond
-- Returns:
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getBondID
public static int getBondID(StereoMolecule mol, int bond)
Constructs a bond classification index from a specific bond in a molecule. The index can be used to get typical bond length and standard deviation.- Parameters:
mol
-bond
-- Returns:
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isPiConsidered
public static final boolean isPiConsidered(int atomicNo)
- Parameters:
atomicNo
-- Returns:
- whether this atomicNo uses the atom's pi count to further distinguish bond type cases
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getAtomPi
public static int getAtomPi(StereoMolecule mol, int atom)
Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length. The returned value may differ from the formal pi-electron count if the formal count does not represent the real mesomeric situation well.- Parameters:
mol
-atom
-- Returns:
- pi electron count
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lookupBondLength
public static float lookupBondLength(StereoMolecule mol, int bond)
Returns an estimate of the bond length based on atom and bond characteristics. The bond is classified based on its characteristics the returned value is the median of equally classified bonds within the COD database. Statistics of purely organic bonds (no metal atoms) are taken from the organic subset of the COD. Requires cHelperRings level of helper arrays.- Parameters:
mol
-bond
-- Returns:
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getBondLengthFromCovalentRadii
public static float getBondLengthFromCovalentRadii(StereoMolecule mol, int bond)
Returns an estimate of the bond length based on atom and bond characteristics. The bond is classified based on its characteristics the returned value is the median of equally classified bonds within the COD or CSD database. Statistics of purely organic bonds (no metal atoms) are taken from the organic subset of the COD/CSD. If there are no similar bond in the crystallographic data sets, the the bond length is estimated from the covalent radii, which if not available may be estimated from the van-der-waals radii.- Parameters:
mol
-bond
-- Returns:
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getStdDevFromCovalentRadii
public static float getStdDevFromCovalentRadii(StereoMolecule mol, int bond)
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data. If the estimate is based on covalent radii or van-der-waals radii, the standard deviation reflects that.- Parameters:
mol
-bond
-- Returns:
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getBondLength
public static float getBondLength(int index)
Returns an estimate of the bond length based on atom and bond characteristics. The bond is classified based on its characteristics the returned value is the median of equally classified bonds within the COD or CSD database. Statistics of purely organic bonds (no metal atoms) are taken from the organic subset of the COD/CSD.- Parameters:
index
- bond id index obtained with getBondIndex()- Returns:
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getBondCount
public static float getBondCount(int index)
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getBondStdDev
public static float getBondStdDev(int index)
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.- Parameters:
index
- bond id index obtained with getBondIndex()- Returns:
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