Grantham Property Distance

Compute Grantham distance from caller-supplied residue composition, polarity, and volume properties.

Description

Grantham distance compares amino-acid properties through a weighted distance.

Grantham distance compares amino-acid properties through a weighted distance. Property units and order must match the declared model.

Compute Grantham distance from caller-supplied residue composition, polarity, and volume properties.

When to use Grantham Property Distance

Use this for the following task: Compute Grantham distance from caller-supplied residue composition, polarity, and volume properties.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Grantham Property Distance and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter originalProperties, replacementProperties, severityCutoff using the field table, then run the tool.
Read granthamDistance, aboveCutoff. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
originalProperties	Original properties	list of number; each entry: number	Required
replacementProperties	Replacement properties	list of number; each entry: number	Required
severityCutoff	Severity cutoff	number	Required

Supply composition/polarity/volume triples and a nonnegative severity cutoff. Compute the weighted distance and flag a result at or above the cutoff.^[1]

distance=50.723 sqrt(1.833Δcomposition²+0.1018Δpolarity²+0.000399Δvolume²)

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
granthamDistance	Grantham distance	number
aboveCutoff	Above cutoff	boolean

json

{
  "input": {
    "originalProperties": [
      1,
      2,
      3
    ],
    "replacementProperties": [
      1,
      2,
      3
    ],
    "severityCutoff": 100
  },
  "output": {
    "granthamDistance": 0,
    "aboveCutoff": false
  }
}

Limitations and assumptions

No residue property table is embedded. A large distance is not a pathogenicity classification.

The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose Synonymous Codon Sites for this operation: Count equally weighted synonymous single-base alternatives by codon position using the standard code. For a complementary task, use Premature Stop Position for this operation: Check a codon replacement for a new premature stop under the standard genetic code.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Grantham Property Distance — tool.io

Similar or alternative tools

Synonymous Codon Sites
Count equally weighted synonymous single-base alternatives by codon position using the standard code.
Premature Stop Position
Check a codon replacement for a new premature stop under the standard genetic code.