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Basic implementation of molecular_weight function #341

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1b6acc7
add molecular_weight function
Alessio-Agustini Sep 1, 2025
d13ab69
include molecular weights file
BeastyBlacksmith Sep 1, 2025
937f83e
Merge pull request #1 from BeastyBlacksmith/patch-1
Alessio-Agustini Sep 1, 2025
9123983
edit function to accept any AA_seq
Alessio-Agustini Sep 1, 2025
45441a3
Adding implementation for ssDNA and ssRNA
Alessio-Agustini Sep 1, 2025
86fdba3
Changing implemnetation for AASeq's
Alessio-Agustini Sep 2, 2025
85702be
fixed typo
Alessio-Agustini Sep 2, 2025
0085cc9
fixed typo
Alessio-Agustini Sep 2, 2025
8eea91b
Changing and expanding upon the implementation for nucseq
Alessio-Agustini Sep 2, 2025
31f2221
Implementing changes to function molecular weight,in accordance to fe…
Alessio-Agustini Sep 3, 2025
015fea5
added lost of water weight
Alessio-Agustini Sep 3, 2025
3e22148
Changing function for DNA/RNA in accordance to feedback
Alessio-Agustini Sep 4, 2025
336f8c6
adding docstring,creating
Alessio-Agustini Sep 4, 2025
a0ffd5f
creating weights.jl
Alessio-Agustini Sep 4, 2025
6b94455
Adding basic tests to weight.jl + corrections in fuction for phosphat…
Alessio-Agustini Sep 5, 2025
9204c96
Change formatting
jakobnissen Sep 5, 2025
d7a6641
Make water weight a constant
jakobnissen Sep 5, 2025
04a8477
Move weight to its own variable
jakobnissen Sep 5, 2025
2ecf3bc
Change signatures of functions
jakobnissen Sep 5, 2025
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1 change: 1 addition & 0 deletions src/BioSequences.jl
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Expand Up @@ -223,6 +223,7 @@ include("longsequences/randseq.jl")
include("longsequences/find.jl")

include("counting.jl")
include("molecular-weight.jl")

include("geneticcode.jl")

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260 changes: 260 additions & 0 deletions src/molecular-weight.jl
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@@ -0,0 +1,260 @@
# Definning const of molecular weight of canonical amino acids in g/mol
const AA_A_MW = 89.09 # Alanine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/5950
const AA_R_MW = 174.20 # Arginine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6322
const AA_N_MW = 132.12 # Asparagine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6267
const AA_D_MW = 133.10 # Aspartate -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/5960
const AA_C_MW = 121.16 # Cysteine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/5862
const AA_Q_MW = 146.14 # Glutamine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/5961
const AA_E_MW = 147.13 # Glutamate -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/33032
const AA_G_MW = 75.07 # Glycine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/750
const AA_H_MW = 155.15 # Histidine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6274
const AA_I_MW = 131.17 # Isoleucine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6306
const AA_L_MW = 131.17 # Leucine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6106
const AA_K_MW = 146.19 # Lysine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/5962
const AA_M_MW = 149.21 # Methionine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6137
const AA_F_MW = 165.19 # Phenylalanine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6140
const AA_P_MW = 115.13 # Proline -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/145742
const AA_S_MW = 105.09 # Serine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/5951
const AA_T_MW = 119.12 # Threonine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6288
const AA_W_MW = 204.22 # Tryptophan -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6305
const AA_Y_MW = 181.19 # Tyrosine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6057
const AA_V_MW = 117.15 # Valine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6287
# Defining water molecular weight (required for calculation of water lost)
const WATER_MW = 18.02 # Water -> Source = https://www.cmu.edu/gelfand/k12-educational-resources/polymers/what-is-polymer/molecular-weight-calculation.html

# Non canonical / not defined amino acids in g/mol
const AA_O_MW_MW = 255.31 # Pyrrolysine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/21873141
const AA_U_MW_MW = 168.06 # Selenocysteine -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/25076
const AA_B_MW_MW = (AA_N_MW + AA_D_MW)/2 # Aspartate or Asparagine -> Average between Aspartic acid and Asparagine
const AA_J_MW_MW = 131.17 # Leucine or Isoleucine -> Both have the same molecular weight
const AA_Z_MW_MW = (AA_Q_MW + AA_D_MW)/2 # Glutamine or Glutamine -> Average between Glutamine and Glutamine
const AA_X_MW_MW = 110 # Any amino acid (average) -> Source = http://thermofisher.com/de/de/home/references/ambion-tech-support/rna-tools-and-calculators/proteins-and-amino-acids.html
const AA_O_Gap_MW = 0 # Consider gap as 0

# Defining the function molecular_weight, which accepts a AA sequence and units ("gmol", "KDa") as input and return molecular weight in either g/mol or kDa. If not specified it returns in g/mol
function molecular_weight(aa_seq::AASeq, unit=:"gmol")
AA_vector = Vector{Float64}(undef, 0)
i = 1
while i <= length(aa_seq)
if aa_seq[i] == AA_A
push!(AA_vector, AA_A_MW)
elseif aa_seq[i] == AA_R
push!(AA_vector, AA_R_MW)
elseif aa_seq[i] == AA_N
push!(AA_vector, AA_N_MW)
elseif aa_seq[i] == AA_D
push!(AA_vector, AA_D_MW)
elseif aa_seq[i] == AA_C
push!(AA_vector, AA_C_MW)
elseif aa_seq[i] == AA_Q
push!(AA_vector, AA_Q_MW)
elseif aa_seq[i] == AA_E
push!(AA_vector, AA_E_MW)
elseif aa_seq[i] == AA_G
push!(AA_vector, AA_G_MW)
elseif aa_seq[i] == AA_H
push!(AA_vector, AA_H_MW)
elseif aa_seq[i] == AA_I
push!(AA_vector, AA_I_MW)
elseif aa_seq[i] == AA_L
push!(AA_vector, AA_L_MW)
elseif aa_seq[i] == AA_K
push!(AA_vector, AA_K_MW)
elseif aa_seq[i] == AA_M
push!(AA_vector, AA_M_MW)
elseif aa_seq[i] == AA_F
push!(AA_vector, AA_F_MW)
elseif aa_seq[i] == AA_P
push!(AA_vector, AA_P_MW)
elseif aa_seq[i] == AA_S
push!(AA_vector, AA_S_MW)
elseif aa_seq[i] == AA_T
push!(AA_vector, AA_T_MW)
elseif aa_seq[i] == AA_W
push!(AA_vector, AA_W_MW)
elseif aa_seq[i] == AA_Y
push!(AA_vector, AA_Y_MW)
elseif aa_seq[i] == AA_V
push!(AA_vector, AA_V_MW)
elseif aa_seq[i] == AA_O
push!(AA_vector, AA_O_MW_MW)
elseif aa_seq[i] == AA_U
push!(AA_vector, AA_U_MW_MW)
elseif aa_seq[i] == AA_B
push!(AA_vector, AA_B_MW_MW)
elseif aa_seq[i] == AA_J
push!(AA_vector, AA_J_MW_MW)
elseif aa_seq[i] == AA_Z
push!(AA_vector, AA_Z_MW_MW)
elseif aa_seq[i] == AA_X
push!(AA_vector, AA_X_MW_MW)
elseif aa_seq[i] == AA_O_Gap
push!(AA_vector, AA_O_Gap_MW)
else
println("Error due to unknown amino acid at $i position")
return nothing
end
i = i+1
end
if unit == "gmol"
return round(sum(AA_vector) - ((length(aa_seq) - 1) * WATER_MW); digits = 3)
elseif unit == "kDa"
return round(((sum(AA_vector) - ((length(aa_seq) - 1) * WATER_MW))/1000); digits = 3)
else
return nothing
end
end

# Defining a function, which accepts a AA sequence and print the molecular weight in g/mol and kDa from a given n_start position in the sequence until a n_end given position in the sequence
function molecular_weight(aa_seq::AASeq, n_start::Integer, n_end::Integer)
AA_vector = Vector{Float64}(undef, 0)
i = n_start
while i <= n_end
if aa_seq[i] == AA_A
push!(AA_vector, AA_A_MW)
elseif aa_seq[i] == AA_R
push!(AA_vector, AA_R_MW)
elseif aa_seq[i] == AA_N
push!(AA_vector, AA_N_MW)
elseif aa_seq[i] == AA_D
push!(AA_vector, AA_D_MW)
elseif aa_seq[i] == AA_C
push!(AA_vector, AA_C_MW)
elseif aa_seq[i] == AA_Q
push!(AA_vector, AA_Q_MW)
elseif aa_seq[i] == AA_E
push!(AA_vector, AA_E_MW)
elseif aa_seq[i] == AA_G
push!(AA_vector, AA_G_MW)
elseif aa_seq[i] == AA_H
push!(AA_vector, AA_H_MW)
elseif aa_seq[i] == AA_I
push!(AA_vector, AA_I_MW)
elseif aa_seq[i] == AA_L
push!(AA_vector, AA_L_MW)
elseif aa_seq[i] == AA_K
push!(AA_vector, AA_K_MW)
elseif aa_seq[i] == AA_M
push!(AA_vector, AA_M_MW)
elseif aa_seq[i] == AA_F
push!(AA_vector, AA_F_MW)
elseif aa_seq[i] == AA_P
push!(AA_vector, AA_P_MW)
elseif aa_seq[i] == AA_S
push!(AA_vector, AA_S_MW)
elseif aa_seq[i] == AA_T
push!(AA_vector, AA_T_MW)
elseif aa_seq[i] == AA_W
push!(AA_vector, AA_W_MW)
elseif aa_seq[i] == AA_Y
push!(AA_vector, AA_Y_MW)
elseif aa_seq[i] == AA_V
push!(AA_vector, AA_V_MW)
elseif aa_seq[i] == AA_O
push!(AA_vector, AA_O_MW_MW)
elseif aa_seq[i] == AA_U
push!(AA_vector, AA_U_MW_MW)
elseif aa_seq[i] == AA_B
push!(AA_vector, AA_B_MW_MW)
elseif aa_seq[i] == AA_J
push!(AA_vector, AA_J_MW_MW)
elseif aa_seq[i] == AA_Z
push!(AA_vector, AA_Z_MW_MW)
elseif aa_seq[i] == AA_X
push!(AA_vector, AA_X_MW_MW)
elseif aa_seq[i] == AA_O_Gap
push!(AA_vector, AA_O_Gap_MW)
else
println("Error due to unknown amino acid at $i position")
return nothing
end
i = i+1
end
println("$(round(sum(AA_vector) - ((n_end - n_start - 1) * WATER_MW); digits = 3)) g/mol")
println("$(round(((sum(AA_vector) - ((n_end - n_start - 1) * WATER_MW))/1000); digits = 3)) kDa")
end

# Definning const of molecular weight of monophosphate in g/mol to account for the loss of water and PPi during synthesis
const DNA_A_MW = 331.22 - WATER_MW # DNA Adenine dAMP -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/12599
const RNA_A_MW = 347.22 - WATER_MW # RNA Adenine AMP -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6083
const DNA_C_MW = 307.20 - WATER_MW # DNA Cytosine dCMP -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/13945
const RNA_C_MW = 323.20 - WATER_MW # RNA Cytosine CMP -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6131
const DNA_G_MW = 347.22 - WATER_MW # DNA Guanine dGMP -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/1135398597
const RNA_G_MW = 363.22 - WATER_MW # RNA Guanine GMP -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/135398631
const DNA_T_MW = 322.21 - WATER_MW # DNA Thymine dTMP -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/9700
const RNA_U_MW = 324.18 - WATER_MW # RNA Uracil UMP -> Source = https://pubchem.ncbi.nlm.nih.gov/compound/6030

# Calculations following the following guidelines: https://ymc.eu/files/imported/publications/556/documents/YMC-Expert-Tip---How-to-calculate-the-MW-of-nucleic-acids.pdf
# Defining a function, which accepts DNA sequences
function molecular_weight(aa_seq::NucSeq{4, DNAAlphabet{4}}, unit=:"gmol", five_terminal_state=:"Hydroxyl")
AA_vector = Vector{Float64}(undef, 0)
i = 1
while i <= length(aa_seq)
if aa_seq[i] == DNA_A
push!(AA_vector, DNA_A_MW)
elseif aa_seq[i] == DNA_C
push!(AA_vector, DNA_C_MW)
elseif aa_seq[i] == DNA_G
push!(AA_vector, DNA_G_MW)
elseif aa_seq[i] == DNA_T
push!(AA_vector, DNA_T_MW)
else
println("Error due to unknown nucleotide at $i position")
return nothing
end
i = i+1
end
if unit == "gmol" && five_terminal_state == "Phosphate"
return round(sum(AA_vector) + 79; digits = 3)
elseif unit == "gmol" && five_terminal_state == "Hydroxyl"
return round(sum(AA_vector) - 62; digits = 3)
elseif unit == "gmol" && five_terminal_state == "Triphosphate"
return round(sum(AA_vector) + 178; digits = 3)
elseif unit == "kDa" && five_terminal_state == "Phosphate"
return (round(sum(AA_vector) + 79; digits = 3))/1000
elseif unit == "kDa" && five_terminal_state == "Hydroxyl"
return (round(sum(AA_vector) - 62; digits = 3))/1000
elseif unit == "kDa" && five_terminal_state == "Triphosphate"
return (round(sum(AA_vector) + 178; digits = 3))/1000
else
println("Error")
return nothing
end
end

# Defining a function, which accepts a RNA sequences
function molecular_weight(aa_seq::NucSeq{4, RNAAlphabet{4}}, unit=:"gmol", five_terminal_state=:"Triphosphate")
AA_vector = Vector{Float64}(undef, 0)
i = 1
while i <= length(aa_seq)
if aa_seq[i] == RNA_A
push!(AA_vector, RNA_A_MW)
elseif aa_seq[i] == RNA_C
push!(AA_vector, RNA_C_MW)
elseif aa_seq[i] == RNA_G
push!(AA_vector, RNA_G_MW)
elseif aa_seq[i] == RNA_U
push!(AA_vector, RNA_U_MW)
else
println("Error due to unknown nucleotide at $i position")
return nothing
end
i = i+1
end
if unit == "gmol" && five_terminal_state == "Triphosphate"
return round(sum(AA_vector) + 178; digits = 3)
elseif unit == "gmol" && five_terminal_state == "Phosphate"
return round(sum(AA_vector) + 79; digits = 3)
elseif unit == "gmol" && five_terminal_state == "Hydroxyl"
return round(sum(AA_vector) - 62; digits = 3)
elseif unit == "kDa" && five_terminal_state == "Triphosphate"
return (round(sum(AA_vector) - 62; digits = 3))/1000
elseif unit == "kDa" && five_terminal_state == "Phosphate"
return (round(sum(AA_vector) + 79; digits = 3))/1000
elseif unit == "kDa" && five_terminal_state == "Hydroxyl"
return (round(sum(AA_vector) - 62; digits = 3))/1000
else
println("Error")
return nothing
end
end
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