upadte files

cabsflex_visualization.py

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+import pandas as pd

heatmap_free_energies.py

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+import pandas as pd
+import seaborn as sns
+import numpy as np
+
+matrix = pd.read_csv(r"C:\Users\nilsh\OneDrive\Desktop\protein_modelling\energies.csv")
+sns_matrix = matrix.iloc[:, 3:]
+aa_wild = matrix.iloc[:, 0].tolist()
+residues_var = list(sns_matrix.columns)
+residues_wild = list((np.array(matrix.iloc[:, 2].tolist()) +318)) # 318 because from homology modelling the residue positions were set to 0.
+merged_wild = list(zip(aa_wild, residues_wild))
+sns_matrix = sns_matrix.drop(5, axis=0)
+residue_aa_heat = sns.heatmap(sns_matrix,
+                              cmap = "seismic",
+                              center = 0,
+                              xticklabels = residues_var,
+                              yticklabels=merged_wild)
+residue_aa_heat.set_xlabel('Amino Acid', fontsize = 16)
+residue_aa_heat.set_ylabel('Residues', fontsize = 16)
+colorbar = residue_aa_heat.collections[0].colorbar
+colorbar.set_label('Free Energy in kcal/mol', fontsize=16)

mutatex/individual_list.txt

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+

mutatex/mutatex_input.txt

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+417 A
+417 C
+417 D
+417 E
+417 F
+417 G
+417 H
+417 I
+417 K
+417 L
+417 M
+417 N
+417 P
+417 Q
+417 R
+417 S
+417 T
+417 V
+417 W
+417 Y
+486 A
+486 C
+486 D
+486 E
+486 F
+486 G
+486 H
+486 I
+486 K
+486 L
+486 M
+486 N
+486 P
+486 Q
+486 R
+486 S
+486 T
+486 V
+486 W
+486 Y
+501 A
+501 C
+501 D
+501 E
+501 F
+501 G
+501 H
+501 I
+501 K
+501 L
+501 M
+501 N
+501 P
+501 Q
+501 R
+501 S
+501 T
+501 V
+501 W
+501 Y
+505 A
+505 C
+505 D
+505 E
+505 F
+505 G
+505 H
+505 I
+505 K
+505 L
+505 M
+505 N
+505 P
+505 Q
+505 R
+505 S
+505 T
+505 V
+505 W
+505 Y
+497 A
+497 C
+497 D
+497 E
+497 F
+497 G
+497 H
+497 I
+497 K
+497 L
+497 M
+497 N
+497 P
+497 Q
+497 R
+497 S
+497 T
+497 V
+497 W
+497 Y
+445 A
+445 C
+445 D
+445 E
+445 F
+445 G
+445 H
+445 I
+445 K
+445 L
+445 M
+445 N
+445 P
+445 Q
+445 R
+445 S
+445 T
+445 V
+445 W
+445 Y
+498 A
+498 C
+498 D
+498 E
+498 F
+498 G
+498 H
+498 I
+498 K
+498 L
+498 M
+498 N
+498 P
+498 Q
+498 R
+498 S
+498 T
+498 V
+498 W
+498 Y
+493 A
+493 C
+493 D
+493 E
+493 F
+493 G
+493 H
+493 I
+493 K
+493 L
+493 M
+493 N
+493 P
+493 Q
+493 R
+493 S
+493 T
+493 V
+493 W
+493 Y
+449 A
+449 C
+449 D
+449 E
+449 F
+449 G
+449 H
+449 I
+449 K
+449 L
+449 M
+449 N
+449 P
+449 Q
+449 R
+449 S
+449 T
+449 V
+449 W
+449 Y

not_used_scripts/create_mut_txt.py

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+import itertools
+
+def generate_mutatex_input(residues, output_file, chain = False):
+    amino_acids = "ACDEFGHIKLMNPQRSTVWY"
+    mutations = []
+
+    for residue in residues:
+        for aa in amino_acids:
+            if residue[1] != aa:
+                if chain==True:
+                    mutations.append(f"{residue[1]}{residue[2]}{residue[0]}"+";")
+                else:
+                    mutations.append(f"{residue[1]}{residue[0]}"+";")
+
+    with open(output_file, "w") as f:
+        for mutation in mutations:
+            f.write(f"{mutation}\n")
+
+# Example usage
+def generate_mutatex_input(residues, output_file, chain = False):
+    amino_acids = "ACDEFGHIKLMNPQRSTVWY"
+    mutations = []
+
+    for residue in residues:
+        if chain==True:
+            mutations.append(f"{residue[1]}{residue[2]}{residue[0]}"+";")
+        else:
+            mutations.append(f"{residue[1]}{residue[0]}"+";")
+
+    with open(output_file, "w") as f:
+        for mutation in mutations:
+            f.write(f"{mutation}\n")
+
+
+# Example usage
+residues = [("417", "N", "X"), ("486", "P", "X"), ("501", "Y", "X"), ("505", "H", "X"), ("497", "F", "X"), ("445", "P", "X"), ("498", "R", "X"), ("493", "Q", "X"), ("449", "Y", "X")]
+output_file = "../mutatex/individual_list.txt"
+
+generate_mutatex_input(residues, output_file)

not_used_scripts/pairwise_alignment.py

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+from Bio import pairwise2
+
+# Define your three sequences
+seq1 = "CPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRLFRKSNLKPFERDISTEIYQAGSTPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELT-----VCG"
+seq2 = "CPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNRPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCG"
+seq3 = "CPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG"
+
+
+
+# Perform pairwise sequence alignments
+alignments12 = pairwise2.align.globalxx(seq1, seq2)
+alignments13 = pairwise2.align.globalxx(seq1, seq3)
+alignments23 = pairwise2.align.globalxx(seq2, seq3)
+
+# Print the alignment scores and aligned sequences
+print("Alignment 1-2 score:", alignments12[0][2])
+print(pairwise2.format_alignment(*alignments12[0]))
+
+print("Alignment 1-3 score:", alignments13[0][2])
+print(pairwise2.format_alignment(*alignments13[0]))
+
+print("Alignment 2-3 score:", alignments23[0][2])
+print(pairwise2.format_alignment(*alignments23[0]))
+