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[FEATURE] improved/corrected pdb_selaltloc tool #156

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[FEATURE] improved/corrected pdb_selaltloc tool #156

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3c82825
first draft of solution to selaltloc bug
mgiulini Feb 8, 2023
e172b64
added test to selaltloc
mgiulini Feb 8, 2023
9669693
Working beta
joaomcteixeira Mar 29, 2023
580f292
added function to remove alt loc char
joaomcteixeira Mar 29, 2023
ac38e0f
pass all previous tests
joaomcteixeira Mar 30, 2023
ad4e66d
add missing test pdb
joaomcteixeira Mar 30, 2023
7f0f303
take tests from @mgiulini
joaomcteixeira Mar 30, 2023
ebcffea
add test from 3B9F suggested by @rvhonorato
joaomcteixeira Mar 30, 2023
66cec87
add MODEL test
joaomcteixeira Mar 30, 2023
6c29270
clean, docs, test the comments
joaomcteixeira Mar 30, 2023
6f37e82
test to flush on chains
joaomcteixeira Mar 30, 2023
dd27826
remove unnecessary prints
joaomcteixeira Mar 30, 2023
8196f07
Merge branch 'master' into selaltlocnew
joaomcteixeira Mar 31, 2023
0981c5a
remove strip
joaomcteixeira Apr 3, 2023
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452 changes: 163 additions & 289 deletions pdbtools/pdb_selaltloc.py
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133 changes: 133 additions & 0 deletions tests/data/altloc_3B9F.pdb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,133 @@
PDBTLS This file was edited to test pdb_selaltloc
PDBTLS Original PDB 3B9F
PDBTLS
HEADER HYDROLASE/HYDROLASE INHIBITOR 05-NOV-07 3B9F
TITLE 1.6 A STRUCTURE OF THE PCI-THROMBIN-HEPARIN COMPLEX
COMPND 21 ENGINEERED: YES
SOURCE MOL_ID: 1;
KEYWDS 4 PROTEASE, ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR W.LI,T.E.ADAMS,J.A.HUNTINGTON
REVDAT 1 22-APR-08 3B9F 0
JRNL AUTH W.LI,T.E.ADAMS,J.NANGALIA,C.T.ESMON,J.A.HUNTINGTON
REMARK 2
REMARK 999 NATURAL VARIANT AT THIS POSITION
DBREF 3B9F I 17 387 UNP P05154 IPSP_HUMAN 36 406
SEQADV 3B9F ALA H 195 UNP P00734 SER 568 ENGINEERED MUTATION
SEQRES 31 I 395 LYS VAL ASN ARG PRO
MODRES 3B9F ASN H 60G ASN GLYCOSYLATION SITE
HET NAG A 1 14
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 14 HOH *523(H2 O)
HELIX 1 1 ASN L 1K GLY L 1F 1 6
HELIX 20 20 SER I 305 THR I 309 5 5
SHEET 1 A 7 SER H 20 ASP H 21 0
SHEET 2 G 2 GLY I 340 ARG I 342 1 O THR I 341 N TRP I 190
SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.03
LINK O6 NAG A 1 C1 FUC A 2 1555 1555 1.40
CISPEP 2 LYS H 185 PRO H 186 0 0.28
CRYST1 44.055 48.825 97.850 78.72 81.52 77.69 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.022699 -0.004951 -0.002582 0.00000
SCALE2 0.000000 0.020963 -0.003616 0.00000
SCALE3 0.000000 0.000000 0.010485 0.00000
ATOM 16 N TYR L 1P -35.899 36.071 -57.146 1.00 24.40 N
ATOM 17 CA TYR L 1P -35.533 35.711 -55.782 1.00 22.98 C
ATOM 18 C TYR L 1P -35.689 36.923 -54.879 1.00 22.73 C
ATOM 19 O TYR L 1P -35.212 38.013 -55.199 1.00 24.86 O
ATOM 28 N AGLN L 1O -36.361 36.722 -53.750 0.20 22.43 N
ATOM 29 N BGLN L 1O -36.368 36.734 -53.754 0.80 21.82 N
ATOM 30 CA AGLN L 1O -36.584 37.781 -52.773 0.23 21.92 C
ATOM 31 CA BGLN L 1O -36.567 37.813 -52.796 0.77 21.45 C
ATOM 32 C AGLN L 1O -35.689 37.523 -51.567 0.25 21.18 C
ATOM 33 C BGLN L 1O -35.688 37.528 -51.586 0.65 20.57 C
ATOM 34 O AGLN L 1O -35.816 36.492 -50.908 0.23 20.76 O
ATOM 35 O BGLN L 1O -35.820 36.482 -50.950 0.77 19.47 O
ATOM 46 N THR L 1N -34.783 38.453 -51.279 1.00 20.45 N
ATOM 47 CA THR L 1N -33.885 38.283 -50.143 1.00 20.33 C
ATOM 48 C THR L 1N -34.665 38.284 -48.834 1.00 20.94 C
ATOM 49 O THR L 1N -35.715 38.926 -48.718 1.00 20.47 O
ATOM 101 N THR L 1H -25.711 41.829 -41.231 1.00 16.46 N
ATOM 102 CA THR L 1H -25.418 40.733 -40.321 1.00 14.66 C
ATOM 103 C THR L 1H -25.179 39.417 -41.051 1.00 15.08 C
ATOM 104 O THR L 1H -24.467 38.557 -40.552 1.00 14.35 O
ATOM 123 N ASER L 1E -22.556 39.135 -47.649 0.10 14.32 N
ATOM 124 N BSER L 1E -22.558 39.094 -47.639 0.85 13.30 N
ATOM 125 CA ASER L 1E -23.019 39.209 -49.032 0.16 13.53 C
ATOM 126 CA BSER L 1E -23.010 39.174 -49.023 0.84 12.40 C
ATOM 127 C ASER L 1E -23.259 37.839 -49.653 0.10 13.43 C
ATOM 128 C BSER L 1E -23.296 37.813 -49.635 0.82 12.51 C
ATOM 129 O ASER L 1E -22.829 36.818 -49.115 0.34 12.37 O
ATOM 130 O BSER L 1E -22.933 36.779 -49.072 0.42 11.68 O
ATOM 161 N CYS L 1 -27.779 33.791 -54.663 1.00 11.36 N
ATOM 162 CA CYS L 1 -27.645 32.429 -54.138 1.00 11.72 C
ATOM 163 C CYS L 1 -28.184 31.351 -55.065 1.00 12.46 C
ATOM 164 O CYS L 1 -29.066 31.597 -55.887 1.00 11.13 O
ATOM 167 N GLY L 2 -27.618 30.155 -54.931 1.00 11.94 N
ATOM 168 CA GLY L 2 -28.093 29.010 -55.681 1.00 13.42 C
ATOM 169 C GLY L 2 -27.920 28.936 -57.179 1.00 13.71 C
ATOM 170 O GLY L 2 -28.452 28.010 -57.799 1.00 12.21 O
ATOM 171 N LEU L 3 -27.207 29.893 -57.766 1.00 11.48 N
ATOM 172 CA LEU L 3 -26.960 29.891 -59.207 1.00 12.60 C
ATOM 173 C LEU L 3 -25.462 29.636 -59.346 1.00 13.82 C
ATOM 174 O LEU L 3 -24.649 30.462 -58.944 1.00 14.29 O
TER 378 LEU L 3
ATOM 498 N AMET H 32 -15.884 21.898 -46.134 0.03 13.63 N
ATOM 499 N BMET H 32 -15.886 21.863 -46.147 0.84 13.45 N
ATOM 500 CA AMET H 32 -15.223 20.827 -45.399 0.10 13.62 C
ATOM 501 CA BMET H 32 -15.262 20.752 -45.438 0.90 14.92 C
ATOM 502 C AMET H 32 -14.910 21.331 -44.004 0.01 14.47 C
ATOM 503 C BMET H 32 -14.862 21.255 -44.046 0.99 15.40 C
ATOM 504 O AMET H 32 -14.280 22.376 -43.844 0.10 14.26 O
ATOM 505 O BMET H 32 -14.125 22.236 -43.935 0.67 14.61 O
ATOM 514 N LEU H 33 -15.346 20.594 -42.992 1.00 15.12 N
ATOM 515 CA LEU H 33 -15.057 20.994 -41.613 1.00 17.37 C
ATOM 516 C LEU H 33 -13.966 20.110 -41.025 1.00 21.15 C
ATOM 517 O LEU H 33 -14.053 18.878 -41.092 1.00 21.77 O
ATOM 544 N LYS H 36 -8.375 20.177 -35.426 1.00 47.23 N
ATOM 545 CA LYS H 36 -6.948 20.457 -35.546 1.00 49.79 C
ATOM 546 C LYS H 36 -6.046 19.727 -34.564 1.00 51.19 C
ATOM 547 O LYS H 36 -6.501 19.201 -33.546 1.00 51.77 O
ATOM 553 N SER H 36A -4.757 19.702 -34.898 0.40 52.14 N
ATOM 554 CA SER H 36A -3.731 19.057 -34.087 0.40 52.58 C
ATOM 555 C SER H 36A -4.254 17.826 -33.356 0.40 52.69 C
ATOM 556 O SER H 36A -4.508 17.868 -32.151 0.40 54.21 O
ATOM 553 N BSER H 36A -4.757 19.702 -34.898 0.60 52.14 N
ATOM 554 CA BSER H 36A -3.731 19.057 -34.087 0.60 52.58 C
ATOM 555 C BSER H 36A -4.254 17.826 -33.356 0.60 52.69 C
ATOM 556 O BSER H 36A -4.508 17.868 -32.151 0.60 54.21 O
ATOM 583 N ALEU H 40 -10.561 15.413 -41.434 0.48 28.25 N
ATOM 584 N BLEU H 40 -10.564 15.370 -41.413 0.48 28.64 N
ATOM 585 CA ALEU H 40 -11.939 15.701 -41.811 0.03 25.33 C
ATOM 586 CA BLEU H 40 -11.952 15.605 -41.789 0.97 26.04 C
ATOM 587 C ALEU H 40 -12.927 15.248 -40.743 0.13 23.56 C
ATOM 588 C BLEU H 40 -12.860 15.301 -40.605 0.61 24.27 C
ATOM 589 O ALEU H 40 -12.964 14.075 -40.371 0.11 23.23 O
ATOM 590 O BLEU H 40 -12.739 14.255 -39.969 0.89 22.89 O
ATOM 599 N ALEU H 41 -13.727 16.191 -40.255 0.44 21.23 N
ATOM 600 N BLEU H 41 -13.774 16.219 -40.316 0.53 22.16 N
ATOM 601 CA ALEU H 41 -14.727 15.903 -39.235 0.04 18.81 C
ATOM 602 CA BLEU H 41 -14.696 16.049 -39.204 0.96 19.96 C
ATOM 603 C ALEU H 41 -16.114 15.742 -39.829 0.60 17.12 C
ATOM 604 C BLEU H 41 -16.124 15.865 -39.697 0.40 18.03 C
ATOM 605 O ALEU H 41 -16.804 14.756 -39.572 0.25 16.40 O
ATOM 606 O BLEU H 41 -16.844 14.976 -39.247 0.61 16.77 O
ATOM 615 N CYS H 42 -16.515 16.722 -40.632 1.00 15.17 N
ATOM 616 CA CYS H 42 -17.854 16.716 -41.198 1.00 14.43 C
ATOM 617 C CYS H 42 -17.965 17.557 -42.446 1.00 13.79 C
ATOM 618 O CYS H 42 -17.003 18.181 -42.892 1.00 13.66 O
ATOM 621 N GLY H 43 -19.183 17.574 -42.976 1.00 12.50 N
ATOM 622 CA GLY H 43 -19.506 18.388 -44.128 1.00 13.66 C
ATOM 623 C GLY H 43 -20.155 19.637 -43.546 1.00 12.41 C
ATOM 624 O GLY H 43 -20.400 19.711 -42.333 1.00 11.38 O
ATOM 625 N ALA H 44 -20.433 20.608 -44.408 1.00 12.66 N
ATOM 626 CA ALA H 44 -21.043 21.876 -44.015 1.00 12.16 C
ATOM 627 C ALA H 44 -21.446 22.558 -45.312 1.00 11.20 C
ATOM 628 O ALA H 44 -21.152 22.052 -46.394 1.00 11.04 O
TER 630 TER H 44
CONECT 5572 5571
MASTER 413 0 12 20 38 0 0 6 5736 3 109 55
END
113 changes: 113 additions & 0 deletions tests/data/altloc_3B9F_A.pdb
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Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,113 @@
PDBTLS This file was edited to test pdb_selaltloc
PDBTLS Original PDB 3B9F
PDBTLS
HEADER HYDROLASE/HYDROLASE INHIBITOR 05-NOV-07 3B9F
TITLE 1.6 A STRUCTURE OF THE PCI-THROMBIN-HEPARIN COMPLEX
COMPND 21 ENGINEERED: YES
SOURCE MOL_ID: 1;
KEYWDS 4 PROTEASE, ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR W.LI,T.E.ADAMS,J.A.HUNTINGTON
REVDAT 1 22-APR-08 3B9F 0
JRNL AUTH W.LI,T.E.ADAMS,J.NANGALIA,C.T.ESMON,J.A.HUNTINGTON
REMARK 2
REMARK 999 NATURAL VARIANT AT THIS POSITION
DBREF 3B9F I 17 387 UNP P05154 IPSP_HUMAN 36 406
SEQADV 3B9F ALA H 195 UNP P00734 SER 568 ENGINEERED MUTATION
SEQRES 31 I 395 LYS VAL ASN ARG PRO
MODRES 3B9F ASN H 60G ASN GLYCOSYLATION SITE
HET NAG A 1 14
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 14 HOH *523(H2 O)
HELIX 1 1 ASN L 1K GLY L 1F 1 6
HELIX 20 20 SER I 305 THR I 309 5 5
SHEET 1 A 7 SER H 20 ASP H 21 0
SHEET 2 G 2 GLY I 340 ARG I 342 1 O THR I 341 N TRP I 190
SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.03
LINK O6 NAG A 1 C1 FUC A 2 1555 1555 1.40
CISPEP 2 LYS H 185 PRO H 186 0 0.28
CRYST1 44.055 48.825 97.850 78.72 81.52 77.69 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.022699 -0.004951 -0.002582 0.00000
SCALE2 0.000000 0.020963 -0.003616 0.00000
SCALE3 0.000000 0.000000 0.010485 0.00000
ATOM 16 N TYR L 1P -35.899 36.071 -57.146 1.00 24.40 N
ATOM 17 CA TYR L 1P -35.533 35.711 -55.782 1.00 22.98 C
ATOM 18 C TYR L 1P -35.689 36.923 -54.879 1.00 22.73 C
ATOM 19 O TYR L 1P -35.212 38.013 -55.199 1.00 24.86 O
ATOM 28 N GLN L 1O -36.361 36.722 -53.750 0.20 22.43 N
ATOM 30 CA GLN L 1O -36.584 37.781 -52.773 0.23 21.92 C
ATOM 32 C GLN L 1O -35.689 37.523 -51.567 0.25 21.18 C
ATOM 34 O GLN L 1O -35.816 36.492 -50.908 0.23 20.76 O
ATOM 46 N THR L 1N -34.783 38.453 -51.279 1.00 20.45 N
ATOM 47 CA THR L 1N -33.885 38.283 -50.143 1.00 20.33 C
ATOM 48 C THR L 1N -34.665 38.284 -48.834 1.00 20.94 C
ATOM 49 O THR L 1N -35.715 38.926 -48.718 1.00 20.47 O
ATOM 101 N THR L 1H -25.711 41.829 -41.231 1.00 16.46 N
ATOM 102 CA THR L 1H -25.418 40.733 -40.321 1.00 14.66 C
ATOM 103 C THR L 1H -25.179 39.417 -41.051 1.00 15.08 C
ATOM 104 O THR L 1H -24.467 38.557 -40.552 1.00 14.35 O
ATOM 123 N SER L 1E -22.556 39.135 -47.649 0.10 14.32 N
ATOM 125 CA SER L 1E -23.019 39.209 -49.032 0.16 13.53 C
ATOM 127 C SER L 1E -23.259 37.839 -49.653 0.10 13.43 C
ATOM 129 O SER L 1E -22.829 36.818 -49.115 0.34 12.37 O
ATOM 161 N CYS L 1 -27.779 33.791 -54.663 1.00 11.36 N
ATOM 162 CA CYS L 1 -27.645 32.429 -54.138 1.00 11.72 C
ATOM 163 C CYS L 1 -28.184 31.351 -55.065 1.00 12.46 C
ATOM 164 O CYS L 1 -29.066 31.597 -55.887 1.00 11.13 O
ATOM 167 N GLY L 2 -27.618 30.155 -54.931 1.00 11.94 N
ATOM 168 CA GLY L 2 -28.093 29.010 -55.681 1.00 13.42 C
ATOM 169 C GLY L 2 -27.920 28.936 -57.179 1.00 13.71 C
ATOM 170 O GLY L 2 -28.452 28.010 -57.799 1.00 12.21 O
ATOM 171 N LEU L 3 -27.207 29.893 -57.766 1.00 11.48 N
ATOM 172 CA LEU L 3 -26.960 29.891 -59.207 1.00 12.60 C
ATOM 173 C LEU L 3 -25.462 29.636 -59.346 1.00 13.82 C
ATOM 174 O LEU L 3 -24.649 30.462 -58.944 1.00 14.29 O
TER 378 LEU L 3
ATOM 498 N MET H 32 -15.884 21.898 -46.134 0.03 13.63 N
ATOM 500 CA MET H 32 -15.223 20.827 -45.399 0.10 13.62 C
ATOM 502 C MET H 32 -14.910 21.331 -44.004 0.01 14.47 C
ATOM 504 O MET H 32 -14.280 22.376 -43.844 0.10 14.26 O
ATOM 514 N LEU H 33 -15.346 20.594 -42.992 1.00 15.12 N
ATOM 515 CA LEU H 33 -15.057 20.994 -41.613 1.00 17.37 C
ATOM 516 C LEU H 33 -13.966 20.110 -41.025 1.00 21.15 C
ATOM 517 O LEU H 33 -14.053 18.878 -41.092 1.00 21.77 O
ATOM 544 N LYS H 36 -8.375 20.177 -35.426 1.00 47.23 N
ATOM 545 CA LYS H 36 -6.948 20.457 -35.546 1.00 49.79 C
ATOM 546 C LYS H 36 -6.046 19.727 -34.564 1.00 51.19 C
ATOM 547 O LYS H 36 -6.501 19.201 -33.546 1.00 51.77 O
ATOM 553 N SER H 36A -4.757 19.702 -34.898 0.40 52.14 N
ATOM 554 CA SER H 36A -3.731 19.057 -34.087 0.40 52.58 C
ATOM 555 C SER H 36A -4.254 17.826 -33.356 0.40 52.69 C
ATOM 556 O SER H 36A -4.508 17.868 -32.151 0.40 54.21 O
ATOM 553 N BSER H 36A -4.757 19.702 -34.898 0.60 52.14 N
ATOM 554 CA BSER H 36A -3.731 19.057 -34.087 0.60 52.58 C
ATOM 555 C BSER H 36A -4.254 17.826 -33.356 0.60 52.69 C
ATOM 556 O BSER H 36A -4.508 17.868 -32.151 0.60 54.21 O
ATOM 583 N LEU H 40 -10.561 15.413 -41.434 0.48 28.25 N
ATOM 585 CA LEU H 40 -11.939 15.701 -41.811 0.03 25.33 C
ATOM 587 C LEU H 40 -12.927 15.248 -40.743 0.13 23.56 C
ATOM 589 O LEU H 40 -12.964 14.075 -40.371 0.11 23.23 O
ATOM 599 N LEU H 41 -13.727 16.191 -40.255 0.44 21.23 N
ATOM 601 CA LEU H 41 -14.727 15.903 -39.235 0.04 18.81 C
ATOM 603 C LEU H 41 -16.114 15.742 -39.829 0.60 17.12 C
ATOM 605 O LEU H 41 -16.804 14.756 -39.572 0.25 16.40 O
ATOM 615 N CYS H 42 -16.515 16.722 -40.632 1.00 15.17 N
ATOM 616 CA CYS H 42 -17.854 16.716 -41.198 1.00 14.43 C
ATOM 617 C CYS H 42 -17.965 17.557 -42.446 1.00 13.79 C
ATOM 618 O CYS H 42 -17.003 18.181 -42.892 1.00 13.66 O
ATOM 621 N GLY H 43 -19.183 17.574 -42.976 1.00 12.50 N
ATOM 622 CA GLY H 43 -19.506 18.388 -44.128 1.00 13.66 C
ATOM 623 C GLY H 43 -20.155 19.637 -43.546 1.00 12.41 C
ATOM 624 O GLY H 43 -20.400 19.711 -42.333 1.00 11.38 O
ATOM 625 N ALA H 44 -20.433 20.608 -44.408 1.00 12.66 N
ATOM 626 CA ALA H 44 -21.043 21.876 -44.015 1.00 12.16 C
ATOM 627 C ALA H 44 -21.446 22.558 -45.312 1.00 11.20 C
ATOM 628 O ALA H 44 -21.152 22.052 -46.394 1.00 11.04 O
TER 630 TER H 44
CONECT 5572 5571
MASTER 413 0 12 20 38 0 0 6 5736 3 109 55
END
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