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Merge pull request #112 from martimunicoy/add_elements_to_PDB
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PDB fixer
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@martimunicoy
martimunicoy committed Nov 27, 2020
2 parents d5c20f8 + 1ca6b8c commit a81f60a
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2 changes: 2 additions & 0 deletions docs/releasehistory.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ New features
- `PR #92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New parameter to skip the stereochemistry assignment (and the checking from the OpenFF toolkit).
- `PR #100 <https://github.com/martimunicoy/peleffy/pull/100>`_: New writer for the OPLS OBC parameters.
- `PR #106 <https://github.com/martimunicoy/peleffy/pull/106>`_: New method to initialize a Molecule object directly from an RDKit and OpenFF molecular representations.
- `PR #112 <https://github.com/martimunicoy/peleffy/pull/112>`_: New method to fix an input PDB file with no atomic element identifiers.

Bugfixes
""""""""
Expand All @@ -41,6 +42,7 @@ Tests added
- `PR #97 <https://github.com/martimunicoy/peleffy/pull/97>`_: Includes tests for the new Topology container class.
- `PR #100 <https://github.com/martimunicoy/peleffy/pull/100>`_: Adds tests to validate the solvent template writers.
- `PR #106 <https://github.com/martimunicoy/peleffy/pull/106>`_: Adds tests to check the RDKit and OpenFF molecular initializers.
- `PR #112 <https://github.com/martimunicoy/peleffy/pull/112>`_: Adds one test to check the new PDB fixer method.


1.0.0 - Full compatibility for OPLS2005 and OpenFF dihedrals and rotamer library improvements
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85 changes: 85 additions & 0 deletions peleffy/data/tests/ligSUV_fixed.pdb
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@@ -0,0 +1,85 @@
ATOM 1 C LIG 1 22.986 39.636 19.856 1.00 0.00 C
ATOM 2 C1 LIG 1 24.246 39.226 20.646 1.00 0.00 C
ATOM 3 H LIG 1 24.396 40.036 21.286 1.00 0.00 H
ATOM 4 C2 LIG 1 25.436 38.996 19.716 1.00 0.00 C
ATOM 5 C3 LIG 1 25.356 37.706 18.746 1.00 0.00 C
ATOM 6 N LIG 1 25.506 36.516 19.656 1.00 0.00 N
ATOM 7 C4 LIG 1 24.306 35.866 20.276 1.00 0.00 C
ATOM 8 C5 LIG 1 23.306 36.896 20.806 1.00 0.00 C
ATOM 9 N1 LIG 1 24.006 38.046 21.476 1.00 0.00 N
ATOM 10 C6 LIG 1 24.526 37.806 22.726 1.00 0.00 C
ATOM 11 O LIG 1 24.436 36.716 23.296 1.00 0.00 O
ATOM 12 C7 LIG 1 25.306 38.916 23.346 1.00 0.00 C
ATOM 13 C8 LIG 1 26.706 38.796 23.236 1.00 0.00 C
ATOM 14 C9 LIG 1 27.546 39.796 23.726 1.00 0.00 C
ATOM 15 C10 LIG 1 29.096 39.576 23.486 1.00 0.00 C
ATOM 16 C11 LIG 1 27.006 40.896 24.456 1.00 0.00 C
ATOM 17 C12 LIG 1 25.596 40.876 24.676 1.00 0.00 C
ATOM 18 C13 LIG 1 24.756 39.916 24.136 1.00 0.00 C
ATOM 19 N2 LIG 1 23.406 39.986 24.426 1.00 0.00 N
ATOM 20 N3 LIG 1 22.726 40.996 23.856 1.00 0.00 N
ATOM 21 C14 LIG 1 21.556 40.796 24.466 1.00 0.00 C
ATOM 22 C15 LIG 1 21.496 39.446 25.006 1.00 0.00 C
ATOM 23 N4 LIG 1 22.746 38.976 25.056 1.00 0.00 N
ATOM 24 C16 LIG 1 26.766 36.196 20.086 1.00 0.00 C
ATOM 25 N5 LIG 1 27.876 36.586 19.446 1.00 0.00 N
ATOM 26 C17 LIG 1 28.826 35.996 20.176 1.00 0.00 C
ATOM 27 C18 LIG 1 30.226 36.276 20.126 1.00 0.00 C
ATOM 28 C19 LIG 1 31.076 35.706 21.086 1.00 0.00 C
ATOM 29 CL LIG 1 32.816 35.986 21.036 1.00 0.00 Cl
ATOM 30 C20 LIG 1 30.496 34.796 22.066 1.00 0.00 C
ATOM 31 C21 LIG 1 29.106 34.546 22.066 1.00 0.00 C
ATOM 32 C22 LIG 1 28.296 35.186 21.166 1.00 0.00 C
ATOM 33 O1 LIG 1 26.946 35.236 21.076 1.00 0.00 O
ATOM 34 H1 LIG 1 23.106 40.666 19.576 1.00 0.00 H
ATOM 35 H2 LIG 1 22.116 39.526 20.486 1.00 0.00 H
ATOM 36 H3 LIG 1 22.876 39.076 18.986 1.00 0.00 H
ATOM 37 H4 LIG 1 26.336 38.916 20.236 1.00 0.00 H
ATOM 38 H5 LIG 1 25.536 39.886 19.116 1.00 0.00 H
ATOM 39 H6 LIG 1 26.246 37.726 18.126 1.00 0.00 H
ATOM 40 H7 LIG 1 24.476 37.666 18.136 1.00 0.00 H
ATOM 41 H8 LIG 1 24.616 35.326 21.136 1.00 0.00 H
ATOM 42 H9 LIG 1 23.776 35.196 19.606 1.00 0.00 H
ATOM 43 H10 LIG 1 22.606 36.456 21.466 1.00 0.00 H
ATOM 44 H11 LIG 1 22.646 37.186 19.926 1.00 0.00 H
ATOM 45 H12 LIG 1 27.136 37.926 22.796 1.00 0.00 H
ATOM 46 H13 LIG 1 29.506 40.436 22.956 1.00 0.00 H
ATOM 47 H14 LIG 1 29.336 38.636 23.036 1.00 0.00 H
ATOM 48 H15 LIG 1 29.616 39.566 24.486 1.00 0.00 H
ATOM 49 H16 LIG 1 27.666 41.666 24.886 1.00 0.00 H
ATOM 50 H17 LIG 1 25.156 41.676 25.266 1.00 0.00 H
ATOM 51 H18 LIG 1 20.726 41.526 24.306 1.00 0.00 H
ATOM 52 H19 LIG 1 20.636 38.916 25.516 1.00 0.00 H
ATOM 53 H20 LIG 1 30.696 36.886 19.386 1.00 0.00 H
ATOM 54 H21 LIG 1 31.196 34.286 22.766 1.00 0.00 H
ATOM 55 H22 LIG 1 28.626 33.916 22.836 1.00 0.00 H
CONECT 1 2 34 35 36
CONECT 2 3 4 9
CONECT 4 5 37 38
CONECT 5 6 39 40
CONECT 6 7 24
CONECT 7 8 41 42
CONECT 8 9 43 44
CONECT 9 10
CONECT 10 11 11 12
CONECT 12 13 13 18
CONECT 13 14 45
CONECT 14 15 16 16
CONECT 15 46 47 48
CONECT 16 17 49
CONECT 17 18 18 50
CONECT 18 19
CONECT 19 20 23
CONECT 20 21 21
CONECT 21 22 51
CONECT 22 23 23 52
CONECT 24 25 25 33
CONECT 25 26
CONECT 26 27 27 32
CONECT 27 28 53
CONECT 28 29 30 30
CONECT 30 31 54
CONECT 31 32 32 55
CONECT 32 33
END

62 changes: 62 additions & 0 deletions peleffy/data/tests/ligSUV_no_elements1.pdb
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@@ -0,0 +1,62 @@
REMARK GENERATED BY TRJCONV
TITLE 4S0V-LIG in water t= 7842.00000
REMARK THIS IS A SIMULATION BOX
CRYST1 53.451 53.451 53.451 70.53 109.47 70.53 P 1 1
MODEL 1
ATOM 1 C LIG 1 22.986 39.636 19.856 1.00 0.00
ATOM 2 C1 LIG 1 24.246 39.226 20.646 1.00 0.00
ATOM 3 H LIG 1 24.396 40.036 21.286 1.00 0.00
ATOM 4 C2 LIG 1 25.436 38.996 19.716 1.00 0.00
ATOM 5 C3 LIG 1 25.356 37.706 18.746 1.00 0.00
ATOM 6 N LIG 1 25.506 36.516 19.656 1.00 0.00
ATOM 7 C4 LIG 1 24.306 35.866 20.276 1.00 0.00
ATOM 8 C5 LIG 1 23.306 36.896 20.806 1.00 0.00
ATOM 9 N1 LIG 1 24.006 38.046 21.476 1.00 0.00
ATOM 10 C6 LIG 1 24.526 37.806 22.726 1.00 0.00
ATOM 11 O LIG 1 24.436 36.716 23.296 1.00 0.00
ATOM 12 C7 LIG 1 25.306 38.916 23.346 1.00 0.00
ATOM 13 C8 LIG 1 26.706 38.796 23.236 1.00 0.00
ATOM 14 C9 LIG 1 27.546 39.796 23.726 1.00 0.00
ATOM 15 C10 LIG 1 29.096 39.576 23.486 1.00 0.00
ATOM 16 C11 LIG 1 27.006 40.896 24.456 1.00 0.00
ATOM 17 C12 LIG 1 25.596 40.876 24.676 1.00 0.00
ATOM 18 C13 LIG 1 24.756 39.916 24.136 1.00 0.00
ATOM 19 N2 LIG 1 23.406 39.986 24.426 1.00 0.00
ATOM 20 N3 LIG 1 22.726 40.996 23.856 1.00 0.00
ATOM 21 C14 LIG 1 21.556 40.796 24.466 1.00 0.00
ATOM 22 C15 LIG 1 21.496 39.446 25.006 1.00 0.00
ATOM 23 N4 LIG 1 22.746 38.976 25.056 1.00 0.00
ATOM 24 C16 LIG 1 26.766 36.196 20.086 1.00 0.00
ATOM 25 N5 LIG 1 27.876 36.586 19.446 1.00 0.00
ATOM 26 C17 LIG 1 28.826 35.996 20.176 1.00 0.00
ATOM 27 C18 LIG 1 30.226 36.276 20.126 1.00 0.00
ATOM 28 C19 LIG 1 31.076 35.706 21.086 1.00 0.00
ATOM 29 CL LIG 1 32.816 35.986 21.036 1.00 0.00
ATOM 30 C20 LIG 1 30.496 34.796 22.066 1.00 0.00
ATOM 31 C21 LIG 1 29.106 34.546 22.066 1.00 0.00
ATOM 32 C22 LIG 1 28.296 35.186 21.166 1.00 0.00
ATOM 33 O1 LIG 1 26.946 35.236 21.076 1.00 0.00
ATOM 34 H1 LIG 1 23.106 40.666 19.576 1.00 0.00
ATOM 35 H2 LIG 1 22.116 39.526 20.486 1.00 0.00
ATOM 36 H3 LIG 1 22.876 39.076 18.986 1.00 0.00
ATOM 37 H4 LIG 1 26.336 38.916 20.236 1.00 0.00
ATOM 38 H5 LIG 1 25.536 39.886 19.116 1.00 0.00
ATOM 39 H6 LIG 1 26.246 37.726 18.126 1.00 0.00
ATOM 40 H7 LIG 1 24.476 37.666 18.136 1.00 0.00
ATOM 41 H8 LIG 1 24.616 35.326 21.136 1.00 0.00
ATOM 42 H9 LIG 1 23.776 35.196 19.606 1.00 0.00
ATOM 43 H10 LIG 1 22.606 36.456 21.466 1.00 0.00
ATOM 44 H11 LIG 1 22.646 37.186 19.926 1.00 0.00
ATOM 45 H12 LIG 1 27.136 37.926 22.796 1.00 0.00
ATOM 46 H13 LIG 1 29.506 40.436 22.956 1.00 0.00
ATOM 47 H14 LIG 1 29.336 38.636 23.036 1.00 0.00
ATOM 48 H15 LIG 1 29.616 39.566 24.486 1.00 0.00
ATOM 49 H16 LIG 1 27.666 41.666 24.886 1.00 0.00
ATOM 50 H17 LIG 1 25.156 41.676 25.266 1.00 0.00
ATOM 51 H18 LIG 1 20.726 41.526 24.306 1.00 0.00
ATOM 52 H19 LIG 1 20.636 38.916 25.516 1.00 0.00
ATOM 53 H20 LIG 1 30.696 36.886 19.386 1.00 0.00
ATOM 54 H21 LIG 1 31.196 34.286 22.766 1.00 0.00
ATOM 55 H22 LIG 1 28.626 33.916 22.836 1.00 0.00
TER
ENDMDL
62 changes: 62 additions & 0 deletions peleffy/data/tests/ligSUV_no_elements2.pdb
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@@ -0,0 +1,62 @@
REMARK GENERATED BY TRJCONV
TITLE 4S0V-LIG in water t= 7842.00000
REMARK THIS IS A SIMULATION BOX
CRYST1 53.451 53.451 53.451 70.53 109.47 70.53 P 1 1
MODEL 1
ATOM 1 C LIG 1 22.986 39.636 19.856 1.00 0.00
ATOM 2 C1 LIG 1 24.246 39.226 20.646 1.00 0.00
ATOM 3 H LIG 1 24.396 40.036 21.286 1.00 0.00
ATOM 4 C2 LIG 1 25.436 38.996 19.716 1.00 0.00
ATOM 5 C3 LIG 1 25.356 37.706 18.746 1.00 0.00
ATOM 6 N LIG 1 25.506 36.516 19.656 1.00 0.00
ATOM 7 C4 LIG 1 24.306 35.866 20.276 1.00 0.00
ATOM 8 C5 LIG 1 23.306 36.896 20.806 1.00 0.00
ATOM 9 N1 LIG 1 24.006 38.046 21.476 1.00 0.00
ATOM 10 C6 LIG 1 24.526 37.806 22.726 1.00 0.00
ATOM 11 O LIG 1 24.436 36.716 23.296 1.00 0.00
ATOM 12 C7 LIG 1 25.306 38.916 23.346 1.00 0.00
ATOM 13 C8 LIG 1 26.706 38.796 23.236 1.00 0.00
ATOM 14 C9 LIG 1 27.546 39.796 23.726 1.00 0.00
ATOM 15 C10 LIG 1 29.096 39.576 23.486 1.00 0.00
ATOM 16 C11 LIG 1 27.006 40.896 24.456 1.00 0.00
ATOM 17 C12 LIG 1 25.596 40.876 24.676 1.00 0.00
ATOM 18 C13 LIG 1 24.756 39.916 24.136 1.00 0.00
ATOM 19 N2 LIG 1 23.406 39.986 24.426 1.00 0.00
ATOM 20 N3 LIG 1 22.726 40.996 23.856 1.00 0.00
ATOM 21 C14 LIG 1 21.556 40.796 24.466 1.00 0.00
ATOM 22 C15 LIG 1 21.496 39.446 25.006 1.00 0.00
ATOM 23 N4 LIG 1 22.746 38.976 25.056 1.00 0.00
ATOM 24 C16 LIG 1 26.766 36.196 20.086 1.00 0.00
ATOM 25 N5 LIG 1 27.876 36.586 19.446 1.00 0.00
ATOM 26 C17 LIG 1 28.826 35.996 20.176 1.00 0.00
ATOM 27 C18 LIG 1 30.226 36.276 20.126 1.00 0.00
ATOM 28 C19 LIG 1 31.076 35.706 21.086 1.00 0.00
ATOM 29 CL LIG 1 32.816 35.986 21.036 1.00 0.00
ATOM 30 C20 LIG 1 30.496 34.796 22.066 1.00 0.00
ATOM 31 C21 LIG 1 29.106 34.546 22.066 1.00 0.00
ATOM 32 C22 LIG 1 28.296 35.186 21.166 1.00 0.00
ATOM 33 O1 LIG 1 26.946 35.236 21.076 1.00 0.00
ATOM 34 H1 LIG 1 23.106 40.666 19.576 1.00 0.00
ATOM 35 H2 LIG 1 22.116 39.526 20.486 1.00 0.00
ATOM 36 H3 LIG 1 22.876 39.076 18.986 1.00 0.00
ATOM 37 H4 LIG 1 26.336 38.916 20.236 1.00 0.00
ATOM 38 H5 LIG 1 25.536 39.886 19.116 1.00 0.00
ATOM 39 H6 LIG 1 26.246 37.726 18.126 1.00 0.00
ATOM 40 H7 LIG 1 24.476 37.666 18.136 1.00 0.00
ATOM 41 H8 LIG 1 24.616 35.326 21.136 1.00 0.00
ATOM 42 H9 LIG 1 23.776 35.196 19.606 1.00 0.00
ATOM 43 H10 LIG 1 22.606 36.456 21.466 1.00 0.00
ATOM 44 H11 LIG 1 22.646 37.186 19.926 1.00 0.00
ATOM 45 H12 LIG 1 27.136 37.926 22.796 1.00 0.00
ATOM 46 H13 LIG 1 29.506 40.436 22.956 1.00 0.00
ATOM 47 H14 LIG 1 29.336 38.636 23.036 1.00 0.00
ATOM 48 H15 LIG 1 29.616 39.566 24.486 1.00 0.00
ATOM 49 H16 LIG 1 27.666 41.666 24.886 1.00 0.00
ATOM 50 H17 LIG 1 25.156 41.676 25.266 1.00 0.00
ATOM 51 H18 LIG 1 20.726 41.526 24.306 1.00 0.00
ATOM 52 H19 LIG 1 20.636 38.916 25.516 1.00 0.00
ATOM 53 H20 LIG 1 30.696 36.886 19.386 1.00 0.00
ATOM 54 H21 LIG 1 31.196 34.286 22.766 1.00 0.00
ATOM 55 H22 LIG 1 28.626 33.916 22.836 1.00 0.00
TER
ENDMDL
62 changes: 62 additions & 0 deletions peleffy/data/tests/ligSUV_no_elements3.pdb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,62 @@
REMARK GENERATED BY TRJCONV
TITLE 4S0V-LIG in water t= 7842.00000
REMARK THIS IS A SIMULATION BOX
CRYST1 53.451 53.451 53.451 70.53 109.47 70.53 P 1 1
MODEL 1
ATOM 1 C LIG 1 22.986 39.636 19.856 1.00 0.00
ATOM 2 C1 LIG 1 24.246 39.226 20.646 1.00 0.00
ATOM 3 H LIG 1 24.396 40.036 21.286 1.00 0.00
ATOM 4 C2 LIG 1 25.436 38.996 19.716 1.00 0.00
ATOM 5 C3 LIG 1 25.356 37.706 18.746 1.00 0.00
ATOM 6 N LIG 1 25.506 36.516 19.656 1.00 0.00
ATOM 7 C4 LIG 1 24.306 35.866 20.276 1.00 0.00
ATOM 8 C5 LIG 1 23.306 36.896 20.806 1.00 0.00
ATOM 9 N1 LIG 1 24.006 38.046 21.476 1.00 0.00
ATOM 10 C6 LIG 1 24.526 37.806 22.726 1.00 0.00
ATOM 11 OXX LIG 1 24.436 36.716 23.296 1.00 0.00
ATOM 12 C7 LIG 1 25.306 38.916 23.346 1.00 0.00
ATOM 13 C8 LIG 1 26.706 38.796 23.236 1.00 0.00
ATOM 14 C9 LIG 1 27.546 39.796 23.726 1.00 0.00
ATOM 15 C10 LIG 1 29.096 39.576 23.486 1.00 0.00
ATOM 16 C11 LIG 1 27.006 40.896 24.456 1.00 0.00
ATOM 17 C12 LIG 1 25.596 40.876 24.676 1.00 0.00
ATOM 18 C13 LIG 1 24.756 39.916 24.136 1.00 0.00
ATOM 19 N2 LIG 1 23.406 39.986 24.426 1.00 0.00
ATOM 20 N3 LIG 1 22.726 40.996 23.856 1.00 0.00
ATOM 21 C14 LIG 1 21.556 40.796 24.466 1.00 0.00
ATOM 22 C15 LIG 1 21.496 39.446 25.006 1.00 0.00
ATOM 23 N4 LIG 1 22.746 38.976 25.056 1.00 0.00
ATOM 24 C16 LIG 1 26.766 36.196 20.086 1.00 0.00
ATOM 25 N5 LIG 1 27.876 36.586 19.446 1.00 0.00
ATOM 26 C17 LIG 1 28.826 35.996 20.176 1.00 0.00
ATOM 27 C18 LIG 1 30.226 36.276 20.126 1.00 0.00
ATOM 28 C19 LIG 1 31.076 35.706 21.086 1.00 0.00
ATOM 29 CL LIG 1 32.816 35.986 21.036 1.00 0.00
ATOM 30 C20 LIG 1 30.496 34.796 22.066 1.00 0.00
ATOM 31 C21 LIG 1 29.106 34.546 22.066 1.00 0.00
ATOM 32 C22 LIG 1 28.296 35.186 21.166 1.00 0.00
ATOM 33 O1 LIG 1 26.946 35.236 21.076 1.00 0.00
ATOM 34 H1 LIG 1 23.106 40.666 19.576 1.00 0.00
ATOM 35 H2 LIG 1 22.116 39.526 20.486 1.00 0.00
ATOM 36 H3 LIG 1 22.876 39.076 18.986 1.00 0.00
ATOM 37 H4 LIG 1 26.336 38.916 20.236 1.00 0.00
ATOM 38 H5 LIG 1 25.536 39.886 19.116 1.00 0.00
ATOM 39 H6 LIG 1 26.246 37.726 18.126 1.00 0.00
ATOM 40 H7 LIG 1 24.476 37.666 18.136 1.00 0.00
ATOM 41 H8 LIG 1 24.616 35.326 21.136 1.00 0.00
ATOM 42 H9 LIG 1 23.776 35.196 19.606 1.00 0.00
ATOM 43 H10 LIG 1 22.606 36.456 21.466 1.00 0.00
ATOM 44 H11 LIG 1 22.646 37.186 19.926 1.00 0.00
ATOM 45 H12 LIG 1 27.136 37.926 22.796 1.00 0.00
ATOM 46 H13 LIG 1 29.506 40.436 22.956 1.00 0.00
ATOM 47 H14 LIG 1 29.336 38.636 23.036 1.00 0.00
ATOM 48 H15 LIG 1 29.616 39.566 24.486 1.00 0.00
ATOM 49 H16 LIG 1 27.666 41.666 24.886 1.00 0.00
ATOM 50 H17 LIG 1 25.156 41.676 25.266 1.00 0.00
ATOM 51 H18 LIG 1 20.726 41.526 24.306 1.00 0.00
ATOM 52 H19 LIG 1 20.636 38.916 25.516 1.00 0.00
ATOM 53 H20 LIG 1 30.696 36.886 19.386 1.00 0.00
ATOM 54 H21 LIG 1 31.196 34.286 22.766 1.00 0.00
ATOM 55 H22 LIG 1 28.626 33.916 22.836 1.00 0.00
TER
ENDMDL
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