How can I compute physico-chemical properties using Command Prompt?

1) Download biojava3-aa-prop-3.0.2-SNAPSHOT-jar-with-dependencies.jar and rename it to AAProperties.jar
2) Study the Manual section below
Note: Test.fasta is available if you would need sample fasta sequences.



An executable to generate physico-chemical properties of protein sequences.


java -jar AAProperties.jar -i test.fasta -a
    Generates all possible properties.

java -jar AAProperties.jar -i test.fasta -1 -3 -7
    Generates only molecular weight, extinction coefficient and isoelectric point.

java -jar AAProperties.jar -i test.fasta -0 A -0 N -1
    Generates composition of two specific amino acid symbol and molecular weight.


    -i location of input FASTA file

    -o location of output file [standard output (default)]
    -f output format [csv (default) or tsv]
    -x location of Amino Acid Composition XML file for defining amino acid composition
    -y location of Element Mass XML file for defining mass of elements
    -d number of decimals (int) [4 (default)]

Provide at least one of them
    -a compute properties of option 1-9
    -1 compute molecular weight
    -2 compute absorbance
    -3 compute extinction coefficient
    -4 compute instability index
    -5 compute apliphatic index
    -6 compute average hydropathy value
    -7 compute isoelectric point
    -8 compute net charge at pH 7
    -9 compute composition of 20 standard amino acid (A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V)
    -0 compute composition of specific amino acid symbol