DesignSeries.generate_mutant_variants(seqID, mutations, keep_scores=False)¶Expands selected decoy sequences generating all the provided mutant combinations.
For all the new mutations provided, it will generate all the possible combinations with
those mutations and annotate them with respect to the reference_sequence.
A mutation will be specified as a tuple of length=2. The first position will
be the sequence position to target (reference_shift aware) and the second will be a
string with all the desired residue types. Multiple positions can be provided in a
list():
mutants = [(20, "AIV"), (31, "EDQR")]
Lastly, when multiple changes are provided for a position, this will translate into an insertion.
Tip
The number of positions and mutations for position produce an exponential increment
of the generated sequences. Thus, the previous example will generate 3 * 4 new
sequences. Depending on the input this can explode pretty fast, be aware.
Tip
* will call all 20 regular amino acids for a given position.
Alters the names of the designs in description by adding a _v<number> suffix.
By providing multiple input decoys, sequence can be repeated. Thus, repeated sequences will be filtered; the provided copy will be the first instance of the sequence.
| Parameters: |
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|---|---|
| Returns: |
See also
DesignFrame.generate_mutants_from_matrix()
DesignFrame.make_resfile()
DesignSeries.generate_mutants_from_matrix()
DesignSeries.make_resfile()
Example
In [1]: from rstoolbox.io import parse_rosetta_file
...: import pandas as pd
...: pd.set_option('display.width', 1000)
...: pd.set_option('display.max_columns', 500)
...: df = parse_rosetta_file("../rstoolbox/tests/data/input_2seq.minisilent.gz",
...: {'scores': ['score', 'description'], 'sequence': 'B'})
...: df.add_reference_sequence('B', df.get_sequence('B').values[0])
...: mutants = [(20, "AIV"), (31, "EDQR")]
...: df.iloc[1].generate_mutant_variants('B', mutants)
...:
Out[1]:
sequence_B description mutants_B mutant_positions_B mutant_count_B
0 PKPEEAMREAYKLIKKYMLKAQKEAQEEWERMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,G21A,W22Q,E23K,H25A,E26Q,R27E,W31R,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 75
1 PKPEEAMREAYKLIKKYMLAAQKEAQEEWEEMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0001 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20A,G21A,W22Q,E23K,H25A,E26Q,R27E,W31E,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
2 PKPEEAMREAYKLIKKYMLAAQKEAQEEWEDMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0002 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20A,G21A,W22Q,E23K,H25A,E26Q,R27E,W31D,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
3 PKPEEAMREAYKLIKKYMLAAQKEAQEEWEQMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0003 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20A,G21A,W22Q,E23K,H25A,E26Q,R27E,W31Q,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
4 PKPEEAMREAYKLIKKYMLAAQKEAQEEWERMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0004 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20A,G21A,W22Q,E23K,H25A,E26Q,R27E,W31R,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
5 PKPEEAMREAYKLIKKYMLIAQKEAQEEWEEMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0005 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20I,G21A,W22Q,E23K,H25A,E26Q,R27E,W31E,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
6 PKPEEAMREAYKLIKKYMLIAQKEAQEEWEDMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0006 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20I,G21A,W22Q,E23K,H25A,E26Q,R27E,W31D,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
7 PKPEEAMREAYKLIKKYMLIAQKEAQEEWEQMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0007 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20I,G21A,W22Q,E23K,H25A,E26Q,R27E,W31Q,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
8 PKPEEAMREAYKLIKKYMLIAQKEAQEEWERMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0008 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20I,G21A,W22Q,E23K,H25A,E26Q,R27E,W31R,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
9 PKPEEAMREAYKLIKKYMLVAQKEAQEEWEEMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0009 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20V,G21A,W22Q,E23K,H25A,E26Q,R27E,W31E,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
10 PKPEEAMREAYKLIKKYMLVAQKEAQEEWEDMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0010 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20V,G21A,W22Q,E23K,H25A,E26Q,R27E,W31D,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
11 PKPEEAMREAYKLIKKYMLVAQKEAQEEWEQMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0011 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20V,G21A,W22Q,E23K,H25A,E26Q,R27E,W31Q,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76
12 PKPEEAMREAYKLIKKYMLVAQKEAQEEWERMRRTDGTKEEKDMFPEKMIAQALRAIGEIFNAYYWAFLKLQEFKKYPSVRWEEQEEARKRLKIMMKIGAEWAREIAREMKERIKR test_3lhp_binder_labeled_00002_v0012 T1P,R2K,R7M,E8R,R9E,W11Y,R12K,A14I,E15K,I16K,A17Y,R19L,K20V,G21A,W22Q,E23K,H25A,E26Q,R27E,W31R,W32M,K33R,A35T,S36D,K37G,G38T,R39K,R42K,L45F,R48K,A52Q,E64Y,W65Y,Q66W,M67A,R68F,E70K,M71L,E72Q,K73E,E74F,R75K,N77Y,N79S,A80V,G81R,E82W,K84E,M85Q,K86E,Q88A,K89R,E91R,A92L,W93K,K94I,I95M,A96M,Y97K,Y98I,W99G,G100A,L101E,M102W,A104R,Y105E,W106I,I107A,K108R,Q109E,H110M,R111K,K113R,E114I,R115K,K116R 1,2,7,8,9,11,12,14,15,16,17,19,20,21,22,23,25,26,27,31,32,33,35,36,37,38,39,42,45,48,52,64,65,66,67,68,70,71,72,73,74,75,77,79,80,81,82,84,85,86,88,89,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,113,114,115,116 76