Mercurial > repos > chemteam > pdbfixer
changeset 0:24bf162ef74b draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
| author | chemteam |
|---|---|
| date | Wed, 13 Apr 2022 16:21:56 +0000 |
| parents | |
| children | |
| files | pdbfixer.xml test-data/broken.pdb |
| diffstat | 2 files changed, 337 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pdbfixer.xml Wed Apr 13 16:21:56 2022 +0000 @@ -0,0 +1,189 @@ +<tool id="pdbfixer" name="PDBFixer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>to automatically fix a PDB file before performing molecular dynamics simulation</description> + <macros> + <token name="@TOOL_VERSION@">1.8.1</token> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pdbfixer</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + pdbfixer + '$pdb_input' + ## --pdbid and --url not implemented here, users can use the get_pdb tool + --output '$output' + --add-atoms='$add_atoms' ## which missing atoms to add: all, heavy, hydrogen, or none [default: all] + --keep-heterogens='$keep_heterogens' ## which heterogens to keep: all, water, or none [default: all] + $replace_nonstandard ## replace nonstandard residues with standard equivalents + $add_residues ## add missing residues + --ph='$ph' ## the pH to use for adding missing hydrogens [default: 7.0] + + #if $solvent.box.water_box == "true": + --water-box=$solvent.box.x $solvent.box.y $solvent.box.z ## add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0] + --positive-ion='$solvent.positive_ion' ## positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+] + --negative-ion='$solvent.negative_ion' ## negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-] + --ionic-strength='$solvent.ionic_strength' ## molar concentration of ions to add to the water box [default: 0.0] + #end if + --verbose + + ]]></command> + <inputs> + <param format="pdb" name="pdb_input" type="data" label="PDB input file"/> + <param name="add_atoms" type="select" label="Missing atoms to be added"> + <option value="all" selected="true">All</option> + <option value="heavy">Heavy atoms only</option> + <option value="hydrogen">Hydrogen atoms only</option> + <option value="none">None</option> + </param> + <param name="keep_heterogens" type="select" label="Which heterogens to keep"> + <option value="all" selected="true">All</option> + <option value="water">Only water</option> + <option value="none">None</option> + </param> + <param name="replace_nonstandard" type="boolean" label="Replace nonstandard residues with standard equivalents?" truevalue="--replace-nonstandard" falsevalue="" value=""/> + <param name="add_residues" type="boolean" label="Add missing residues?" truevalue="--add-residues" falsevalue="" value=""/> + <param name="ph" type="float" min="0" max="14" value="7" label="pH" help="Ignored if not adding hydrogen atoms"/> + <section name="solvent" title="Solvent parameters" help="Note that you may prefer to modify solvent parameters using other tools."> + <conditional name="box"> + <param name="water_box" type="select" label="Add a water box?" help="Dimensions in nanometers"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="x" type="float" min="0" value="0" label="Size in X dimension"/> + <param name="y" type="float" min="0" value="0" label="Size in Y dimension"/> + <param name="z" type="float" min="0" value="0" label="Size in Z dimension"/> + </when> + <when value="false" /> + </conditional> + <param name="positive_ion" type="select" label="Type of positive ion to add"> + <option value="Li+">Lithium (Li+)</option> + <option value="Na+" selected="true">Sodium (Na+)</option> + <option value="K+">Potassium (K+)</option> + <option value="Rb+">Rubidium (Rb+)</option> + <option value="Cs+">Cesium (Cs+)</option> + </param> + <param name="negative_ion" type="select" label="Type of negative ion to add"> + <option value="Cl-" selected="true">Chloride (Cl-)</option> + <option value="Br-">Bromide (Br-)</option> + <option value="F-">Fluoride (F-)</option> + <option value="I-">Iodide (I-)</option> + </param> + <param name="ionic_strength" type="float" min="0" max="10" value="0" label="Ionic strength" help="Molar concentration of ions to add to the water box"/> + </section> + </inputs> + <outputs> + <data name="output" format="pdb"/> + </outputs> + <tests> + <!-- pdbfixer test-data/broken.pdb -add-atoms=all -keep-heterogens=all -replace-nonstandard --> + <test> + <param name="pdb_input" value="broken.pdb"/> + <param name="add_atoms" value="all"/> + <param name="keep_heterogens" value="all"/> + <param name="replace_nonstandard" value="true"/> + <param name="add_residues" value="false"/> + <param name="ph" value="7"/> + <output name="output"> + <assert_contents> + <has_n_lines n="162"/> + <!-- check LYS8 is fixed --> + <has_text text="CD LYS A 8"/> + <has_text text="CE LYS A 8"/> + <!-- check hydration --> + <has_text_matching expression="H \n" n="81"/> + </assert_contents> + </output> + </test> + <!-- pdbfixer test-data/broken.pdb -add-atoms=heavy -keep-heterogens=all -replace-nonstandard -add-residues --> + <test> + <param name="pdb_input" value="broken.pdb"/> + <param name="add_atoms" value="heavy"/> + <param name="keep_heterogens" value="all"/> + <param name="replace_nonstandard" value="true"/> + <param name="add_residues" value="false"/> + <output name="output"> + <assert_contents> + <has_n_lines n="81"/> + <!-- check LYS8 is fixed --> + <has_text text="CD LYS A 8"/> + <has_text text="CE LYS A 8"/> + <!-- check no hydration --> + <has_text_matching expression="H \n" negate="true"/> + </assert_contents> + </output> + </test> + <test> + <param name="pdb_input" value="broken.pdb"/> + <param name="add_atoms" value="all"/> + <param name="keep_heterogens" value="all"/> + <param name="replace_nonstandard" value="true"/> + <param name="add_residues" value="false"/> + <param name="ph" value="14"/> + <param name="water_box" value="true"/> + <param name="x" value="5"/> + <param name="y" value="5"/> + <param name="z" value="5"/> + <param name="positive_ion" value="Li+"/> + <param name="negative_ion" value="I-"/> + <param name="ionic_strength" value="2"/> + <output name="output"> + <assert_contents> + <!-- seems insertion of water is random and not fully reproducible --> + <has_n_lines n="11482" delta="100"/> + <!-- check LYS8 is fixed --> + <has_text text="CD LYS A 8"/> + <has_text text="CE LYS A 8"/> + <!-- check hydration one less due to raised pH --> + <has_text_matching expression="ATOM.* H \n" n="80"/> + <!-- check water and ions --> + <has_text_matching expression="HOH" n="11041" delta="100"/> + <has_text_matching expression=" I .*\n" n="144"/> + <has_text_matching expression=" Li .*\n" n="144"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Fixes any issues in a PDB file (for example, adding missing residues, or missing atoms) prior to performing molecular dynamics simulations. + +PDBFixer can do any or all of the following: + + - Add missing heavy atoms. + - Add missing hydrogen atoms. + - Build missing loops. + - Convert non-standard residues to their standard equivalents. + - Select a single position for atoms with multiple alternate positions listed. + - Delete unwanted chains from the model. + - Delete unwanted heterogens. + - Build a water box for explicit solvent simulations. + +_____ + + +.. class:: infomark + +**Input** + + - PDB file + +_____ + + +.. class:: infomark + +**Output** + + - PDB file + + ]]></help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1005659</citation> + <citation type="bibtex">@misc{pdbfixer, author = {{Peter Eastman et al.}}, title = {PDBFixer}, url={https://github.com/openmm/PDBFixer}, abstract = {PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them.}, urldate = {2022-03-25}, publisher = {GitHub}, year = {2022}, month = mar, }</citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/broken.pdb Wed Apr 13 16:21:56 2022 +0000 @@ -0,0 +1,148 @@ +COMPND /data/dnb05/galaxy_db/files/a/e/1/dataset_ae125e29-1e3c-4170-98b3-b4bfa9ea44ab.dat +AUTHOR GENERATED BY OPEN BABEL 3.1.0 +ATOM 1 N MET A 1 -1.471 35.518 -6.691 1.00 0.00 N +ATOM 2 CA MET A 1 -1.910 34.141 -6.485 1.00 0.00 C +ATOM 3 C MET A 1 -2.164 33.409 -7.811 1.00 0.00 C +ATOM 4 O MET A 1 -3.080 33.757 -8.560 1.00 0.00 O +ATOM 5 CB MET A 1 -3.164 34.104 -5.599 1.00 0.00 C +ATOM 6 CG MET A 1 -3.723 32.707 -5.358 1.00 0.00 C +ATOM 7 SD MET A 1 -5.149 32.703 -4.256 1.00 0.00 S +ATOM 8 CE MET A 1 -5.972 34.205 -4.783 1.00 0.00 C +ATOM 9 N LEU A 2 -1.342 32.398 -8.090 1.00 0.00 N +ATOM 10 CA LEU A 2 -1.526 31.550 -9.263 1.00 0.00 C +ATOM 11 C LEU A 2 -2.804 30.743 -9.107 1.00 0.00 C +ATOM 12 O LEU A 2 -2.963 30.014 -8.134 1.00 0.00 O +ATOM 13 CB LEU A 2 -0.324 30.624 -9.448 1.00 0.00 C +ATOM 14 CG LEU A 2 1.001 31.349 -9.723 1.00 0.00 C +ATOM 15 CD1 LEU A 2 2.173 30.375 -9.719 1.00 0.00 C +ATOM 16 CD2 LEU A 2 0.952 32.131 -11.039 1.00 0.00 C +ATOM 17 N ASP A 3 -3.717 30.888 -10.062 1.00 0.00 N +ATOM 18 CA ASP A 3 -5.063 30.335 -9.928 1.00 0.00 C +ATOM 19 C ASP A 3 -5.073 28.812 -9.891 1.00 0.00 C +ATOM 20 O ASP A 3 -4.491 28.155 -10.748 1.00 0.00 O +ATOM 21 CB ASP A 3 -5.977 30.843 -11.046 1.00 0.00 C +ATOM 22 CG ASP A 3 -7.366 30.238 -10.982 1.00 0.00 C +ATOM 23 OD1 ASP A 3 -8.026 30.358 -9.929 1.00 0.00 O +ATOM 24 OD2 ASP A 3 -7.805 29.641 -11.988 1.00 0.00 O +ATOM 25 N ALA A 4 -5.745 28.263 -8.886 1.00 0.00 N +ATOM 26 CA ALA A 4 -5.828 26.821 -8.702 1.00 0.00 C +ATOM 27 C ALA A 4 -5.989 26.064 -10.024 1.00 0.00 C +ATOM 28 O ALA A 4 -5.329 25.051 -10.250 1.00 0.00 O +ATOM 29 CB ALA A 4 -6.966 26.483 -7.755 1.00 0.00 C +ATOM 30 N GLU A 5 -6.859 26.566 -10.895 1.00 0.00 N +ATOM 31 CA GLU A 5 -7.238 25.852 -12.112 1.00 0.00 C +ATOM 32 C GLU A 5 -6.055 25.641 -13.052 1.00 0.00 C +ATOM 33 O GLU A 5 -6.076 24.755 -13.902 1.00 0.00 O +ATOM 34 CB GLU A 5 -8.361 26.594 -12.840 1.00 0.00 C +ATOM 35 CG GLU A 5 -9.491 25.689 -13.296 1.00 0.00 C +ATOM 36 CD GLU A 5 -10.466 25.372 -12.172 1.00 0.00 C +ATOM 37 OE1 GLU A 5 -10.799 26.295 -11.396 1.00 0.00 O +ATOM 38 OE2 GLU A 5 -10.905 24.205 -12.067 1.00 0.00 O +ATOM 39 N ARG A 6 -5.023 26.457 -12.887 1.00 0.00 N +ATOM 40 CA ARG A 6 -3.821 26.365 -13.708 1.00 0.00 C +ATOM 41 C ARG A 6 -2.815 25.349 -13.160 1.00 0.00 C +ATOM 42 O ARG A 6 -1.684 25.263 -13.639 1.00 0.00 O +ATOM 43 CB ARG A 6 -3.150 27.737 -13.778 1.00 0.00 C +ATOM 44 CG ARG A 6 -3.941 28.787 -14.536 1.00 0.00 C +ATOM 45 CD ARG A 6 -3.495 28.859 -15.983 1.00 0.00 C +ATOM 46 NE ARG A 6 -4.209 29.895 -16.722 1.00 0.00 N +ATOM 47 CZ ARG A 6 -3.682 30.592 -17.723 1.00 0.00 C +ATOM 48 NH1 ARG A 6 -2.424 30.376 -18.098 1.00 0.00 N +ATOM 49 NH2 ARG A 6 -4.407 31.513 -18.342 1.00 0.00 N +ATOM 50 N LEU A 7 -3.216 24.583 -12.152 1.00 0.00 N +ATOM 51 CA LEU A 7 -2.263 23.726 -11.457 1.00 0.00 C +ATOM 52 C LEU A 7 -2.667 22.264 -11.491 1.00 0.00 C +ATOM 53 O LEU A 7 -1.975 21.419 -10.930 1.00 0.00 O +ATOM 54 CB LEU A 7 -2.102 24.177 -9.997 1.00 0.00 C +ATOM 55 CG LEU A 7 -1.945 25.680 -9.749 1.00 0.00 C +ATOM 56 CD1 LEU A 7 -2.124 26.012 -8.270 1.00 0.00 C +ATOM 57 CD2 LEU A 7 -0.611 26.185 -10.257 1.00 0.00 C +ATOM 58 N LYS A 8 -3.791 21.963 -12.132 1.00 0.00 N +ATOM 59 CA LYS A 8 -4.302 20.595 -12.151 1.00 0.00 C +ATOM 60 C LYS A 8 -3.234 19.587 -12.586 1.00 0.00 C +ATOM 61 O LYS A 8 -3.277 18.417 -12.186 1.00 0.00 O +ATOM 62 CB LYS A 8 -5.543 20.491 -13.049 1.00 0.00 C +ATOM 63 N HIS A 9 -2.276 20.055 -13.390 1.00 0.00 N +ATOM 64 CA HIS A 9 -1.222 19.210 -13.959 1.00 0.00 C +ATOM 65 C HIS A 9 -0.085 18.862 -12.995 1.00 0.00 C +ATOM 66 O HIS A 9 0.712 17.970 -13.281 1.00 0.00 O +ATOM 67 CB HIS A 9 -0.609 19.900 -15.181 1.00 0.00 C +ATOM 68 CG HIS A 9 0.182 21.125 -14.839 1.00 0.00 C +ATOM 69 ND1 HIS A 9 -0.411 22.328 -14.524 1.00 0.00 N +ATOM 70 CD2 HIS A 9 1.516 21.327 -14.740 1.00 0.00 C +ATOM 71 CE1 HIS A 9 0.522 23.224 -14.256 1.00 0.00 C +ATOM 72 NE2 HIS A 9 1.702 22.642 -14.381 1.00 0.00 N +CONECT 1 2 +CONECT 2 3 1 5 +CONECT 3 4 4 9 2 +CONECT 4 3 3 +CONECT 5 2 6 +CONECT 6 5 7 +CONECT 7 6 8 +CONECT 8 7 +CONECT 9 10 3 +CONECT 10 13 11 9 +CONECT 11 17 10 12 12 +CONECT 12 11 11 +CONECT 13 14 10 +CONECT 14 16 15 13 +CONECT 15 14 +CONECT 16 14 +CONECT 17 18 11 +CONECT 18 21 17 19 +CONECT 19 20 20 18 25 +CONECT 20 19 19 +CONECT 21 22 18 +CONECT 22 24 24 21 23 +CONECT 23 22 +CONECT 24 22 22 +CONECT 25 19 26 +CONECT 26 27 25 29 +CONECT 27 30 28 28 26 +CONECT 28 27 27 +CONECT 29 26 +CONECT 30 31 27 +CONECT 31 32 34 30 +CONECT 32 33 33 39 31 +CONECT 33 32 32 +CONECT 34 35 31 +CONECT 35 34 36 +CONECT 36 35 38 38 37 +CONECT 37 36 +CONECT 38 36 36 +CONECT 39 40 32 +CONECT 40 43 41 39 +CONECT 41 40 42 42 50 +CONECT 42 41 41 +CONECT 43 44 40 +CONECT 44 45 43 +CONECT 45 46 44 +CONECT 46 47 47 45 +CONECT 47 49 48 46 46 +CONECT 48 47 +CONECT 49 47 +CONECT 50 41 51 +CONECT 51 50 52 54 +CONECT 52 58 51 53 53 +CONECT 53 52 52 +CONECT 54 51 55 +CONECT 55 57 54 56 +CONECT 56 55 +CONECT 57 55 +CONECT 58 59 52 +CONECT 59 62 60 58 +CONECT 60 63 61 61 59 +CONECT 61 60 60 +CONECT 62 59 +CONECT 63 64 60 +CONECT 64 67 63 65 +CONECT 65 64 66 66 +CONECT 66 65 65 +CONECT 67 68 64 +CONECT 68 67 70 70 69 +CONECT 69 68 71 +CONECT 70 68 68 72 +CONECT 71 69 72 72 +CONECT 72 70 71 71 +MASTER 0 0 0 0 0 0 0 0 72 0 72 0 +END