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secondary-structure.validation

secondary-structure.validation 6.3 KB
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  1. compares Mol* port of DSSP (with default parameters) to the BioJava implementation
    2. 

  2. 

  3. ### pdb:1pga ###
    4. 

  4. # turns #
    5. 

  5. Mol*: ----------------------TTTTTTTTTTTTTTTT--------TTTT------
    6. 

  6. 53 turns, 18 openings
    7. 

  7. DSSP: ----------------------TTTTTTTTTTTTTTTT--------TTTT------
    8. 

  8. 53 turns, 18 openings
    9. 

  9. 

  10. # bends #
    11. 

  11. Mol*: ---------SS---------SSSSSSSSSSSSSSSSSS--------SSS-------
    12. 

  12. 23 bends
    13. 

  13. DSSP: ---------SS---------SSSSSSSSSSSSSSSSSS--------SSS-------
    14. 

  14. 23 bends
    15. 

  15. 

  16. # helices #
    17. 

  17. Mol*: ----------------------HHHHHHHHHHHHHHTT--------TTTT------
    18. 

  18. 44 helix elements - 0 3-10, 44 alpha, 0 pi
    19. 

  19. DSSP: ----------------------HHHHHHHHHHHHHHTT--------TTTT------
    20. 

  20. 44 helix elements - 0 3-10, 44 alpha, 0 pi
    21. 

  21. 

  22. # all #
    23. 

  23. Mol*: -EEEEEEE-SS-EEEEEEE-SSHHHHHHHHHHHHHHTT---EEEEETTTTEEEEE-
    24. 

  24. DSSP: -EEEEEEE-SS-EEEEEEE-SSHHHHHHHHHHHHHHTT---EEEEETTTTEEEEE-
    25. 

  25. 

  26. 

  27. ### pdb:1bta ###
    28. 

  28. # turns #
    29. 

  29. Mol*: ------TTT---TTTTTTTTTTTTT--TT----TTTTTTTTTTT-----------TTTTTTTTT--TTTTTTTTTTTTTTT--------
    30. 

  30. 127 turns, 44 openings
    31. 

  31. DSSP: ------TTT---TTTTTTTTTTTTT--TT----TTTTTTTTTTT-----------TTTTTTTTT--TTTTTTTTTTTTTTT--------
    32. 

  32. 127 turns, 44 openings
    33. 

  33. 

  34. # bends #
    35. 

  35. Mol*: ------SSS--SSSSSSSSSSSSS---SS---SSSSSSSSSSSSS-SS------SSSSSSSSSSSSSSSSSSSSSSSSSSS--------
    36. 

  36. 60 bends
    37. 

  37. DSSP: ------SSS--SSSSSSSSSSSSS---SS---SSSSSSSSSSSSS-SS------SSSSSSSSSSSSSSSSSSSSSSSSSSS--------
    38. 

  38. 60 bends
    39. 

  39. 

  40. # helices #
    41. 

  41. Mol*: ------TTT---HHHHHHHHHHHHT--TT----HHHHHHHHTTT-----------TTHHHHTTT--HHHHHHHHHHHHHTT--------
    42. 

  42. 100 helix elements - 0 3-10, 100 alpha, 0 pi
    43. 

  43. DSSP: ------TTT---HHHHHHHHHHHHT--TT----HHHHHHHHTTT-----------TTHHHHTTT--HHHHHHHHHHHHHTT--------
    44. 

  44. 100 helix elements - 0 3-10, 100 alpha, 0 pi
    45. 

  45. 

  46. # all #
    47. 

  47. Mol*: -EEEEETTT--SHHHHHHHHHHHHT--TT---SHHHHHHHHTTTS-SSEEEEEESTTHHHHTTTSSHHHHHHHHHHHHHTT--EEEEE-
    48. 

  48. DSSP: -EEEEETTT--SHHHHHHHHHHHHT--TT---SHHHHHHHHTTTS-SSEEEEEESTTHHHHTTTSSHHHHHHHHHHHHHTT--EEEEE-
    49. 

  49. 

  50. 

  51. ### pdb:1acj ###
    52. 

  52. # turns #
    53. 

  53. Mol*: -------TT----------TT----------------TTTTT----------------------------TTTT-TTTTTT----------------------------------TTT------TTT-TTTTTTTTT-----------TTTT---TT-------TTTTTTTTTTTTTTTTTTTTT--TT-------TTTTTTTTTTTT-TTTTTT----------TT-TT----TTTTTTTTTTTTTTTT-----TTTTTTTTTT--TTTTTTTTTTT-----------------------TTTTTTTT----------------TTTTTTT-TT--TT------TTTTTTTTTTTTTT--TTTTTTTTTTT--TTTTT-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-------------TT----TTT---TTTTTTTTTTTTT-TTT---TTTTTTTTTTTTTTTTTTTT--------------------------------TTTTTTTTTTTTTTTTTTT-
    54. 

  54. 614 turns, 223 openings
    55. 

  55. DSSP: -------TT----------TT----------------TTTTT------------------------------TT-TTTTTT----------------------------------TTT------TTT-TTTTTTTTT-----------TTTT---TT-------TTTTTTTTTTTTTTTTTTTTT--TT-------TTTTTTTTTTTT-TTTTTT----------TT-TT----TTTTTTTTTTTTTTTT-----TTTTTTTTTT--TTTTTTTTTTT-----------------------TTTTTTTT----------------TTTTTTT-TT--TT------TTTTTTTTTTT-TT--TTTTTTTTTTT--TTTTT-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-------------TT----TTT---TTTTTTTTTTTTT-TTT---TTTTTTTTTTTTTTTTTTTT--------------------------------TTTTTTTTTTTTTTTTTTT-
    56. 

  56. 606 turns, 220 openings
    57. 

  57. 

  58. # bends #
    59. 

  59. Mol*: --S----SS----------SSS----------S----SS-SSS--------SS-----S-----------SSSS-SSSSSSS--S---S----------SS--SS---------SSSS---S-SSSS--SSSSSSS-----------SSSS----SS-SSS-S-SSSSSSSSSSSSSSSSSSSSS--SSS------SSSSSSSSSSSS-SSSSSS-S----SS--SSSSSS---SSSSSSSSSSSSSSS----S-SSSSSSSSSSS-SSSSSSSSSS--SS--SS--S------SSSSSS-SSSSSSS--S--S-------S--SSSSSSSSSSS--SSS-----SSSSSSSSSSS-SS--SSSSSSSSSSS--SSSSS-SSSSSSSSSSSSSSSSS----SSSSSSSSSSSS-----------SS--S-SSS-S-SS-SSSSSS--SS-SSS---SSSSSSSSSSSSSSSSSSSSSSSS---------SSS------SSSS----SSSS-S----SSSSSSSSSS--
    60. 

  60. 305 bends
    61. 

  61. DSSP: --S----SS----------SSS----------S----SS-SSS--------SS-----S-----------SSSS-SSSSSSS--S---S----------SS--SS---------SSSS---S-SSSS--SSSSSSS-----------SSSS----SS-SSS-S-SSSSSSSSSSSSSSSSSSSSS--SSS------SSSSSSSSSSSS-SSSSSS-S----SS--SSSSSS---SSSSSSSSSSSSSSS----S-SSSSSSSSSSS-SSSSSSSSSS--SS--SS--S------SSSSSS-SSSSSSS--S--S-------S--SSSSSSSSSSS--SSS-----SSSSSSSSSSS-SS--SSSSSSSSSSS--SSSSS-SSSSSSSSSSSSSSSSS----SSSSSSSSSSSS-----------SS--S-SSS-S-SS-SSSSSS--SS-SSS---SSSSSSSSSSSSSSSSSSSSSSSS---------SSS------SSSS----SSSS-S----SSSSSSSSSS--
    62. 

  62. 305 bends
    63. 

  63. 

  64. # helices #
    65. 

  65. Mol*: -------TT----------TT----------------GGGTT----------------------------TTTT-HHHHTT----------------------------------TTT------GGG-THHHHHHHT-----------HHHH---TT-------HHHHHHHHHHHHHHHHGGGGT--TT-------THHHHHHHHHHH-HHHHTT----------TT-TT----HHHHHHHHHHHHHHTT-----HHHHHHHHHH--HHHHHHHHGGG-----------------------HHHHHHHT----------------HHHHHHH-TT--TT------HHHHHHHHHHHTTT--HHHHHHHHHHH--GGGTT-HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTT-------------TT----GGG---TTTTHHHHTTGGG-GGG---HHHHHHHHHHHHHHHHHHHT--------------------------------TTHHHHHHHHTHHHHHHHH-
    66. 

  66. 523 helix elements - 27 3-10, 496 alpha, 0 pi
    67. 

  67. DSSP: -------TT----------TT----------------GGGTT------------------------------TT-HHHHTT----------------------------------TTT------GGG-THHHHHHHT-----------HHHH---TT-------HHHHHHHHHHHHHHHHGGGGT--TT-------THHHHHHHHHHH-HHHHTT----------TT-TT----HHHHHHHHHHHHHHTT-----HHHHHHHHHH--HHHHHHHHGGG-----------------------HHHHHHHT----------------HHHHHHH-TT--TT------HHHHHHHHHHH-TT--HHHHHHHHHHH--GGGTT-HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTT-------------TT----GGG---TTTTHHHHTTGGG-GGG---HHHHHHHHHHHHHHHHHHHT--------------------------------TTHHHHHHHHTHHHHHHHH-
    68. 

  68. 523 helix elements - 27 3-10, 496 alpha, 0 pi
    69. 

  69. 

  70. # all #
    71. 

  71. Mol*: --SEEEETTEEEE-EEEEETTEEEEEEEEEE-EE---GGGTTS--EE----SSEEE--S---B-------TTTT-HHHHTTS--S-B-S---EEEEEE-SS--SSEEEEEEE--STTT---S-SGGG-THHHHHHHT-EEEE-----SHHHH---TT-SSS-S-HHHHHHHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHH-HHHHTT-SEEEEES--TTSTTSEEEHHHHHHHHHHHHHHTT---S-HHHHHHHHHHS-HHHHHHHHGGG-SS--SS--S--EEE-SSSSSS-HHHHHHHT-S--S-EEEEEESB-SHHHHHHHSTT--TTS-----HHHHHHHHHHHTTT--HHHHHHHHHHH--GGGTT-HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTTSS-EEEEEE----TT--S-GGG-SBTTTTHHHHTTGGG-GGG---HHHHHHHHHHHHHHHHHHHTSSSS---------SSS-EEEEESSSS--EEESTTHHHHHHHHTHHHHHHHH-
    72. 

  72. DSSP: --SEEEETTEEEE-EEEEETTEEEEEEEEEE-EE---GGGTTS--EE----SSEEE--S---B-------SSTT-HHHHTTS--S-B-S---EEEEEE-SS--SSEEEEEEE--STTT---S-SGGG-THHHHHHHT-EEEE-----SHHHH---TT-SSS-S-HHHHHHHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHH-HHHHTT-SEEEEES--TTSTTS-EEHHHHHHHHHHHHHHTT---S-HHHHHHHHHHS-HHHHHHHHGGG-SS--SS--S---EE-SSSSSS-HHHHHHHT-S--S-EEEEEESB-SHHHHHHHSTT--TTS-----HHHHHHHHHHH-TT--HHHHHHHHHHH--GGGTT-HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTTSS-EEEEEE----TT--S-GGG-SBTTTTHHHHTTGGG-GGG---HHHHHHHHHHHHHHHHHHHTSSSS---------SSS-EEEEESSSS--EEESTTHHHHHHHHTHHHHHHHH-
    73. 

  73. 

  74. TODO fix mismatches                                                   e.g. here
    75. 

  75. TODO move to spec.ts once tests are running
    76.