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Running
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- pdbfixer/__init__.py +3 -0
- pdbfixer/__pycache__/__init__.cpython-310.pyc +0 -0
- pdbfixer/__pycache__/__init__.cpython-38.pyc +0 -0
- pdbfixer/__pycache__/pdbfixer.cpython-310.pyc +0 -0
- pdbfixer/__pycache__/pdbfixer.cpython-38.pyc +0 -0
- pdbfixer/__pycache__/ui.cpython-38.pyc +0 -0
- pdbfixer/__pycache__/uiserver.cpython-38.pyc +0 -0
- pdbfixer/html/addHeavyAtoms.html +15 -0
- pdbfixer/html/addHydrogens.html +197 -0
- pdbfixer/html/addResidues.html +16 -0
- pdbfixer/html/convertResidues.html +16 -0
- pdbfixer/html/error.html +9 -0
- pdbfixer/html/header.html +122 -0
- pdbfixer/html/quit.html +9 -0
- pdbfixer/html/removeChains.html +24 -0
- pdbfixer/html/saveFile.html +12 -0
- pdbfixer/html/start.html +39 -0
- pdbfixer/images/background.jpg +0 -0
- pdbfixer/images/logo.png +0 -0
- pdbfixer/images/logo.svg +388 -0
- pdbfixer/images/logo_small.png +0 -0
- pdbfixer/pdbfixer.py +1299 -0
- pdbfixer/setup.py +12 -0
- pdbfixer/soft.xml +0 -0
- pdbfixer/templates/A.pdb +24 -0
- pdbfixer/templates/ACE.pdb +5 -0
- pdbfixer/templates/ALA.pdb +7 -0
- pdbfixer/templates/ARG.pdb +13 -0
- pdbfixer/templates/ASN.pdb +10 -0
- pdbfixer/templates/ASP.pdb +10 -0
- pdbfixer/templates/C.pdb +22 -0
- pdbfixer/templates/CYS.pdb +8 -0
- pdbfixer/templates/DA.pdb +23 -0
- pdbfixer/templates/DC.pdb +21 -0
- pdbfixer/templates/DG.pdb +24 -0
- pdbfixer/templates/DT.pdb +22 -0
- pdbfixer/templates/G.pdb +25 -0
- pdbfixer/templates/GLN.pdb +11 -0
- pdbfixer/templates/GLU.pdb +11 -0
- pdbfixer/templates/GLY.pdb +6 -0
- pdbfixer/templates/HIS.pdb +12 -0
- pdbfixer/templates/ILE.pdb +10 -0
- pdbfixer/templates/LEU.pdb +10 -0
- pdbfixer/templates/LYS.pdb +11 -0
- pdbfixer/templates/MET.pdb +10 -0
- pdbfixer/templates/NME.pdb +4 -0
- pdbfixer/templates/PHE.pdb +13 -0
- pdbfixer/templates/PRO.pdb +9 -0
- pdbfixer/templates/SER.pdb +8 -0
- pdbfixer/templates/THR.pdb +9 -0
pdbfixer/__init__.py
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from __future__ import absolute_import
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from .pdbfixer import PDBFixer
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pdbfixer/__pycache__/__init__.cpython-310.pyc
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pdbfixer/__pycache__/__init__.cpython-38.pyc
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Binary file (235 Bytes). View file
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pdbfixer/__pycache__/pdbfixer.cpython-310.pyc
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Binary file (45 kB). View file
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pdbfixer/__pycache__/pdbfixer.cpython-38.pyc
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Binary file (44.2 kB). View file
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pdbfixer/__pycache__/ui.cpython-38.pyc
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Binary file (11.6 kB). View file
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pdbfixer/__pycache__/uiserver.cpython-38.pyc
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Binary file (3.16 kB). View file
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pdbfixer/html/addHeavyAtoms.html
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The following residues are missing heavy atoms, which will be added.
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<p>
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<form id="mainform" method="post" action="/">
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<table border="1">
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<tr><th>Chain</th><th>Residue</th><th>Missing Atoms</th></tr>
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%s
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</table>
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<p>
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<input type="button" value="Continue" onclick="submitWithSpinner()"/>
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</form>
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<script>
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setCurrentStep(5)
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</script>
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</body>
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<html>
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pdbfixer/html/addHydrogens.html
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<script>
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function validateForm() {
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if (document.getElementById("addHydrogensCheckbox").checked) {
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var ph = document.getElementById("phfield").value
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if (!(ph > 0 && ph < 14)) {
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alert("pH must be a number between 0 and 14.")
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return false
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}
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}
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if (document.getElementById("addWaterCheckbox").checked) {
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var custombox = document.getElementById("customBoxRadio").checked
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var xsize = document.getElementById("boxxfield").value
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var ysize = document.getElementById("boxyfield").value
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var zsize = document.getElementById("boxzfield").value
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if (custombox && !(xsize > 0 && ysize > 0 && zsize > 0)) {
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alert("Box dimensions must be positive numbers.")
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return false
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}
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var geombox = document.getElementById("geometricBoxRadio").checked
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var padsize = document.getElementById("geomPadding").value
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if (geombox && padsize < 0) {
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alert("Box padding cannot be negative.")
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return false
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}
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var strength = document.getElementById("ionicstrengthfield").value
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if (!(strength >= 0)) {
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alert("Ionic strength must be a nonnegative number.")
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return false
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}
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}
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if (document.getElementById("addMembraneCheckbox").checked) {
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var padsize = document.getElementById("membranePadding").value
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if (padsize < 0) {
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alert("Box padding cannot be negative.")
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return false
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}
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var strength = document.getElementById("ionicstrengthfield").value
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if (!(strength >= 0)) {
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alert("Ionic strength must be a nonnegative number.")
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return false
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}
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}
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return true
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}
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function applyPaddingToWaterBox(padding) {
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padding = parseFloat(padding);
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if(!padding || padding<0) padding = 0;
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if (document.getElementById('cubicPaddingCheckBox').checked){
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var maxAxis = Math.max.apply(Math, molxyz);
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for (var i = pbcxyz.length; i--;) {
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pbcxyz[i].value = Math.ceil((padding+maxAxis)*1000) / 1000;
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}
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}
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else {
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for (var i = pbcxyz.length; i--;) {
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pbcxyz[i].value = Math.ceil((padding+molxyz[i])*1000) / 1000;
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}
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| 58 |
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}
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}
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function waterBoxChanged() {
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checked = document.getElementById('addWaterCheckbox').checked;
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document.getElementById('addMembraneCheckbox').checked = false;
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| 63 |
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enableControls(document.getElementById('waterInputs'), checked);
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enableControls(document.getElementById('ionInputs'), checked);
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enableControls(document.getElementById('membraneInputs'), false);
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| 66 |
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}
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function membraneBoxChanged() {
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checked = document.getElementById('addMembraneCheckbox').checked;
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document.getElementById('addWaterCheckbox').checked = false;
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enableControls(document.getElementById('membraneInputs'), checked);
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enableControls(document.getElementById('ionInputs'), checked);
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enableControls(document.getElementById('waterInputs'), false);
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}
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</script>
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<style>
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| 76 |
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a.tooltip {
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display: inline;
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| 78 |
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position: relative;
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| 79 |
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color: #000;
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| 80 |
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border-bottom: 1px dotted #000;
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| 81 |
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text-decoration: none;
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}
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a.tooltip:hover:after {
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content: attr(rel);
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| 85 |
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text-align: center;
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| 86 |
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font-size: 80%%;
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| 87 |
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background: #000;
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color: #fff;
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width: 250px;
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bottom: 30px;
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left: -125px;
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padding: 10px 15px;
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position: absolute;
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| 94 |
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z-index: 100;
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/* Effects */
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| 96 |
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background: rgba(0,0,0,0.75);
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border-radius: 5px;
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box-shadow: 0 0 25px #333;
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}
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| 100 |
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/* Down arrow */
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| 101 |
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a.tooltip:hover:before {
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| 102 |
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border: solid;
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| 103 |
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border-color: #333 transparent;
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| 104 |
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border-width: 10px 10px 0 10px;
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| 105 |
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bottom: 20px;
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| 106 |
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left: -6px;
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| 107 |
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content: "";
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| 108 |
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position: absolute;
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| 109 |
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z-index: 99;
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| 110 |
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/* Effects */
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| 111 |
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border-color: rgba(0,0,0,0.75) transparent;
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| 112 |
+
}
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| 113 |
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</style>
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| 114 |
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<form id="mainform" method="post" action="/">
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| 115 |
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<h1>Add Missing Hydrogens</h1>
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| 116 |
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Add missing hydrogen atoms?
|
| 117 |
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<p>
|
| 118 |
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<input type="checkbox" id="addHydrogensCheckbox" name="addhydrogens" onchange="document.getElementById('phfield').disabled=!document.getElementById('addHydrogensCheckbox').checked" checked> Add hydrogens appropriate for pH <input type="text" id="phfield" name="ph" value="7.0" size="5">
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| 119 |
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<h1>Add Water/Membrane</h1>
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| 120 |
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Add a water box or membrane surrounding the model?
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| 121 |
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<p>
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| 122 |
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<input type="checkbox" id="addWaterCheckbox" name="addwater" onchange="waterBoxChanged()"> Add water box
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| 123 |
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<div id="waterInputs" style="margin-left:50px">
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| 124 |
+
<table style="text-align:right">
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| 125 |
+
<tr>
|
| 126 |
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<td style="text-align:left"><input id="customBoxRadio" type="radio" name="boxType" value="custom" checked>Custom box dimensions (in nm):</td>
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| 127 |
+
<div id="customBoxDimensions">
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| 128 |
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<td><input type="text" id="boxxfield" name="boxx" size="8"></td>
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| 129 |
+
<td><input type="text" id="boxyfield" name="boxy" size="8"></td>
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| 130 |
+
<td><input type="text" id="boxzfield" name="boxz" size="8"></td>
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| 131 |
+
</div>
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| 132 |
+
</tr>
|
| 133 |
+
|
| 134 |
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<tr>
|
| 135 |
+
<td style="text-align:left"><input id="geometricBoxRadio" type="radio" name="boxType" value="geometry">Geometry with padding (in nm):</td>
|
| 136 |
+
<div id="geometricBoxDimensions">
|
| 137 |
+
<td><input type="text" id="geomPadding" name="geomPadding" size="8">
|
| 138 |
+
</td>
|
| 139 |
+
<td colspan="2">
|
| 140 |
+
<select id="geometryDropdown" name="geometryDropdown">
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| 141 |
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<option value="cube" selected="selected">Cube</option>
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| 142 |
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<option value="truncatedOctahedron">Truncated octahedron</option>
|
| 143 |
+
<option value="rhombicDodecahedron">Rhombic dodecahedron</option>
|
| 144 |
+
</select>
|
| 145 |
+
<a href="#" rel="The specified padding will be applied on the largest molecular axis, while maintaining selected geometry." class="tooltip">?</a>
|
| 146 |
+
</div>
|
| 147 |
+
</td>
|
| 148 |
+
</tr>
|
| 149 |
+
%s
|
| 150 |
+
</table>
|
| 151 |
+
</div>
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| 152 |
+
<p>
|
| 153 |
+
<input type="checkbox" id="addMembraneCheckbox" name="addmembrane" onchange="membraneBoxChanged()"> Add membrane and water
|
| 154 |
+
<div id="membraneInputs" style="margin-left:50px">
|
| 155 |
+
The membrane will lie in the XY plane and be centered at Z=0. Make sure the protein is properly oriented and positioned.
|
| 156 |
+
When possible, it is easiest to use a PDB file from <a href="http://opm.phar.umich.edu/">OPM</a> since they are already properly positioned.
|
| 157 |
+
<p>
|
| 158 |
+
Lipid type:
|
| 159 |
+
<select id="lipidType" name="lipidType">
|
| 160 |
+
<option value="POPC" selected="selected">POPC</option>
|
| 161 |
+
<option value="POPE">POPE</option>
|
| 162 |
+
<option value="DLPC">DLPC</option>
|
| 163 |
+
<option value="DLPE">DLPE</option>
|
| 164 |
+
<option value="DMPC">DMPC</option>
|
| 165 |
+
<option value="DOPC">DOPC</option>
|
| 166 |
+
<option value="DPPC">DPPC</option>
|
| 167 |
+
</select>
|
| 168 |
+
<p>
|
| 169 |
+
Minimum padding around protein: <input type="text" id="membranePadding" name="membranePadding" value="1.0" size="5"> (nm)
|
| 170 |
+
</div>
|
| 171 |
+
<div id="ionInputs">
|
| 172 |
+
<p>
|
| 173 |
+
Ions will be added to neutralize the model. You can optionally add more ions based on a desired bulk ionic strength.
|
| 174 |
+
<p>
|
| 175 |
+
<table>
|
| 176 |
+
<tr><td style="text-align:right">Ionic strength (molar):</td><td><input type="text" id="ionicstrengthfield" name="ionicstrength" size="8" value="0.0"></td></tr>
|
| 177 |
+
<tr><td style="text-align:right">Positive ion:</td><td><select name="positiveion"><option value="Cs">Cs+</option><option value="K">K+</option><option value="Li">Li+</option><option value="Na" selected>Na+</option><option value="Rb">Rb+</option></select></td></tr>
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| 178 |
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<tr><td style="text-align:right">Negative ion:</td><td><select name="negativeion"><option value="Cl" selected>Cl-</option><option value="Br">Br-</option><option value="F">F-</option><option value="I">I-</option></select></td></tr>
|
| 179 |
+
</table>
|
| 180 |
+
</div>
|
| 181 |
+
<p>
|
| 182 |
+
<input type="button" value="Continue" onclick="if (validateForm()) submitWithSpinner()"/>
|
| 183 |
+
</form>
|
| 184 |
+
<script>
|
| 185 |
+
setCurrentStep(6);
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| 186 |
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enableControls(document.getElementById('waterInputs'), false);
|
| 187 |
+
enableControls(document.getElementById('membraneInputs'), false);
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| 188 |
+
enableControls(document.getElementById('ionInputs'), false);
|
| 189 |
+
var molxyz = [].slice.call(document.getElementById('boxContainingAllAtoms').getElementsByTagName('td')).splice(1,3).map(function(td){ return parseFloat(td.textContent)});
|
| 190 |
+
var hiddenInput = document.createElement("input");
|
| 191 |
+
hiddenInput.setAttribute("type", "hidden");
|
| 192 |
+
hiddenInput.setAttribute("name", "maxMolecularAxis");
|
| 193 |
+
hiddenInput.setAttribute("value", Math.max.apply(Math, molxyz));
|
| 194 |
+
document.getElementById("mainform").appendChild(hiddenInput);
|
| 195 |
+
</script>
|
| 196 |
+
</body>
|
| 197 |
+
<html>
|
pdbfixer/html/addResidues.html
ADDED
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|
| 1 |
+
The sequence records in this PDB file include residues that are missing from the atom data section. Do you want to add the missing residues?
|
| 2 |
+
<p>
|
| 3 |
+
<form id="mainform" method="post" action="/">
|
| 4 |
+
<table border="1" id="table">
|
| 5 |
+
<tr><th>Chain</th><th>Residue Positions</th><th>Sequence</th><th>Add?</th></tr>
|
| 6 |
+
%s
|
| 7 |
+
</table>
|
| 8 |
+
<input type="button" value="Select All" onclick="setCheckboxes(true);"/><input type="button" value="Select None" onclick="setCheckboxes(false);"/>
|
| 9 |
+
<p>
|
| 10 |
+
<input type="button" value="Continue" onclick="submitWithSpinner()"/>
|
| 11 |
+
</form>
|
| 12 |
+
<script>
|
| 13 |
+
setCurrentStep(3)
|
| 14 |
+
</script>
|
| 15 |
+
</body>
|
| 16 |
+
<html>
|
pdbfixer/html/convertResidues.html
ADDED
|
@@ -0,0 +1,16 @@
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|
| 1 |
+
This PDB file contains non-standard residues. Do you want to convert them to standard residues?
|
| 2 |
+
<p>
|
| 3 |
+
<form id="mainform" method="post" action="/">
|
| 4 |
+
<table border="1" id="table">
|
| 5 |
+
<tr><th>Chain</th><th>Residue</th><th>Convert To</th><th>Convert?</th></tr>
|
| 6 |
+
%s
|
| 7 |
+
</table>
|
| 8 |
+
<input type="button" value="Select All" onclick="setCheckboxes(true);"/><input type="button" value="Select None" onclick="setCheckboxes(false);"/>
|
| 9 |
+
<p>
|
| 10 |
+
<input type="button" value="Continue" onclick="submitWithSpinner()"/>
|
| 11 |
+
</form>
|
| 12 |
+
<script>
|
| 13 |
+
setCurrentStep(4)
|
| 14 |
+
</script>
|
| 15 |
+
</body>
|
| 16 |
+
<html>
|
pdbfixer/html/error.html
ADDED
|
@@ -0,0 +1,9 @@
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|
| 1 |
+
<p>
|
| 2 |
+
<form method="post" action="/controls">
|
| 3 |
+
<input type="submit" name="newfile" value="Start Over"/>
|
| 4 |
+
</form>
|
| 5 |
+
<script>
|
| 6 |
+
setCurrentStep(1)
|
| 7 |
+
</script>
|
| 8 |
+
</body>
|
| 9 |
+
<html>
|
pdbfixer/html/header.html
ADDED
|
@@ -0,0 +1,122 @@
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|
| 1 |
+
<html>
|
| 2 |
+
<head>
|
| 3 |
+
<title>PDBFixer</title>
|
| 4 |
+
<script>
|
| 5 |
+
function setCurrentStep(step) {
|
| 6 |
+
for (var i = 1; i < step; i++)
|
| 7 |
+
document.getElementById("step"+i).style.color="black"
|
| 8 |
+
document.getElementById("step"+step).style.color="red"
|
| 9 |
+
for (var i = step+1; i < 8; i++)
|
| 10 |
+
document.getElementById("step"+i).style.color="gray"
|
| 11 |
+
if (step == 1)
|
| 12 |
+
document.getElementById("newfile").disabled=true
|
| 13 |
+
}
|
| 14 |
+
function setCheckboxes(selected) {
|
| 15 |
+
checkboxes = document.getElementById("table").getElementsByTagName("input")
|
| 16 |
+
for (var i = 0; i < checkboxes.length; i++)
|
| 17 |
+
checkboxes[i].checked = selected
|
| 18 |
+
}
|
| 19 |
+
function enableControls(container, enabled) {
|
| 20 |
+
tags = ["input", "select"]
|
| 21 |
+
for (var i = 0; i < tags.length; i++) {
|
| 22 |
+
controls = container.getElementsByTagName(tags[i])
|
| 23 |
+
for (var j = 0; j < controls.length; j++)
|
| 24 |
+
controls[j].disabled = !enabled
|
| 25 |
+
}
|
| 26 |
+
}
|
| 27 |
+
function submitWithSpinner() {
|
| 28 |
+
animateSpinner.animateIndex = 0
|
| 29 |
+
setTimeout(function() {animateSpinner();document.getElementById('overlay').style.visibility='visible';}, 1500)
|
| 30 |
+
document.getElementById('mainform').submit()
|
| 31 |
+
}
|
| 32 |
+
function animateSpinner() {
|
| 33 |
+
for (var i = 0; i < 3; i++) {
|
| 34 |
+
var bar = document.getElementById("progress"+(i+1))
|
| 35 |
+
if (i == animateSpinner.animateIndex)
|
| 36 |
+
bar.style.backgroundColor = "black"
|
| 37 |
+
else
|
| 38 |
+
bar.style.backgroundColor = "lightgray"
|
| 39 |
+
}
|
| 40 |
+
animateSpinner.animateIndex = (animateSpinner.animateIndex+1)%3
|
| 41 |
+
setTimeout(function() {animateSpinner()}, 1000)
|
| 42 |
+
}
|
| 43 |
+
</script>
|
| 44 |
+
<style>
|
| 45 |
+
body {
|
| 46 |
+
margin-top: 0;
|
| 47 |
+
font-family:sans-serif;
|
| 48 |
+
background-color: rgb(217,217,217);
|
| 49 |
+
background-image: url("/image?name=background.jpg");
|
| 50 |
+
background-size: 80%;
|
| 51 |
+
background-repeat: repeat-y
|
| 52 |
+
}
|
| 53 |
+
input {
|
| 54 |
+
font-size: small
|
| 55 |
+
}
|
| 56 |
+
select {
|
| 57 |
+
font-size: small
|
| 58 |
+
}
|
| 59 |
+
table {
|
| 60 |
+
border-collapse: collapse;
|
| 61 |
+
margin: 7pt
|
| 62 |
+
}
|
| 63 |
+
th {
|
| 64 |
+
padding: 2pt;
|
| 65 |
+
background-color: lightgray
|
| 66 |
+
}
|
| 67 |
+
td {
|
| 68 |
+
padding: 2pt
|
| 69 |
+
}
|
| 70 |
+
#progressParent {
|
| 71 |
+
position: fixed;
|
| 72 |
+
top: 40%;
|
| 73 |
+
left: 50%;
|
| 74 |
+
margin-top: -75px;
|
| 75 |
+
margin-left: -125px
|
| 76 |
+
}
|
| 77 |
+
#overlay {
|
| 78 |
+
position: fixed;
|
| 79 |
+
width: 100%;
|
| 80 |
+
height: 100%;
|
| 81 |
+
top: 0px;
|
| 82 |
+
left: 0px;
|
| 83 |
+
background-color: rgba(255,255,255,0.75);
|
| 84 |
+
visibility:hidden;
|
| 85 |
+
}
|
| 86 |
+
#progressMessage {
|
| 87 |
+
width: 100%;
|
| 88 |
+
position: fixed;
|
| 89 |
+
top: 40%;
|
| 90 |
+
margin-top: 90px;
|
| 91 |
+
text-align: center
|
| 92 |
+
}
|
| 93 |
+
</style>
|
| 94 |
+
</head>
|
| 95 |
+
<body>
|
| 96 |
+
<div id="overlay">
|
| 97 |
+
<div id="progressParent">
|
| 98 |
+
<div id="progress1" style="width:50px;height:150px;position:absolute;left:0px"></div>
|
| 99 |
+
<div id="progress2" style="width:50px;height:150px;position:absolute;left:100px"></div>
|
| 100 |
+
<div id="progress3" style="width:50px;height:150px;position:absolute;left:200px"></div>
|
| 101 |
+
</div>
|
| 102 |
+
<div id="progressMessage">
|
| 103 |
+
<div style="font-size:xx-large">Processing</div>
|
| 104 |
+
This may take some time.
|
| 105 |
+
</div>
|
| 106 |
+
</div>
|
| 107 |
+
<span style="font-style:italic;font-size:large;float:right;position:relative;top:0;right:0;height:100%;padding:10px 10px">
|
| 108 |
+
<img src="/image?name=logo_small.png"/>
|
| 109 |
+
<p/>
|
| 110 |
+
<form method="post" action="/controls">
|
| 111 |
+
<input type="submit" name="newfile" value="New File" id="newfile"/>
|
| 112 |
+
<input type="submit" name="quit" value="Quit" style="float:right"/>
|
| 113 |
+
</form>
|
| 114 |
+
<p id="step1">Load File</p>
|
| 115 |
+
<p id="step2">Select Chains</p>
|
| 116 |
+
<p id="step3">Add Residues</p>
|
| 117 |
+
<p id="step4">Convert Residues</p>
|
| 118 |
+
<p id="step5">Add Heavy Atoms</p>
|
| 119 |
+
<p id="step6">Add Water/Hydrogens</p>
|
| 120 |
+
<p id="step7">Save File</p>
|
| 121 |
+
</span>
|
| 122 |
+
<p/>
|
pdbfixer/html/quit.html
ADDED
|
@@ -0,0 +1,9 @@
|
|
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|
| 1 |
+
<html>
|
| 2 |
+
<head>
|
| 3 |
+
<title>PDBFixer</title>
|
| 4 |
+
</head>
|
| 5 |
+
<body>
|
| 6 |
+
<h1 style="text-align:center">See You Again Soon!</h1>
|
| 7 |
+
PDBFixer has exited. You can close your browser window.
|
| 8 |
+
</body>
|
| 9 |
+
</html>
|
pdbfixer/html/removeChains.html
ADDED
|
@@ -0,0 +1,24 @@
|
|
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|
|
|
|
| 1 |
+
This PDB file contains %d chains. Select which ones to include.
|
| 2 |
+
<p>
|
| 3 |
+
<form id="mainform" method="post" action="/">
|
| 4 |
+
<table border="1" id="table">
|
| 5 |
+
<tr><th>Chain</th><th># Residues</th><th>Content</th><th>Include?</th></tr>
|
| 6 |
+
%s
|
| 7 |
+
</table>
|
| 8 |
+
<input type="button" value="Select All" onclick="setCheckboxes(true);"/><input type="button" value="Select None" onclick="setCheckboxes(false);"/>
|
| 9 |
+
<p>
|
| 10 |
+
A heterogen is any residue other than a standard amino acid or nucleotide. Do you want to delete heterogens?
|
| 11 |
+
<p>
|
| 12 |
+
<select name="heterogens">
|
| 13 |
+
<option value="all" selected>Keep all heterogens</option>
|
| 14 |
+
<option value="water">Delete heterogens except water</option>
|
| 15 |
+
<option value="none">Delete all heterogens</option>
|
| 16 |
+
</select>
|
| 17 |
+
<p>
|
| 18 |
+
<input type="button" value="Continue" onclick="submitWithSpinner()"/>
|
| 19 |
+
</form>
|
| 20 |
+
<script>
|
| 21 |
+
setCurrentStep(2)
|
| 22 |
+
</script>
|
| 23 |
+
</body>
|
| 24 |
+
<html>
|
pdbfixer/html/saveFile.html
ADDED
|
@@ -0,0 +1,12 @@
|
|
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|
|
|
|
|
|
|
|
|
|
| 1 |
+
The fixed PDB file is ready to save.
|
| 2 |
+
<p>
|
| 3 |
+
<form method="post" action="/">
|
| 4 |
+
<input type="submit" name="pdb" value="Save PDB File"/>
|
| 5 |
+
<input type="submit" name="pdbx" value="Save PDBx/mmCIF File"/>
|
| 6 |
+
<input type="submit" name="newfile" value="Process Another File"/>
|
| 7 |
+
</form>
|
| 8 |
+
<script>
|
| 9 |
+
setCurrentStep(7)
|
| 10 |
+
</script>
|
| 11 |
+
</body>
|
| 12 |
+
<html>
|
pdbfixer/html/start.html
ADDED
|
@@ -0,0 +1,39 @@
|
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|
| 1 |
+
<script>
|
| 2 |
+
function enableInputs() {
|
| 3 |
+
if (document.getElementById("localtype").checked) {
|
| 4 |
+
document.getElementById("pdbfile").disabled = false;
|
| 5 |
+
document.getElementById("pdbid").disabled = true;
|
| 6 |
+
document.getElementById("submitButton").disabled = (document.getElementById("pdbfile").value == "");
|
| 7 |
+
}
|
| 8 |
+
else {
|
| 9 |
+
document.getElementById("pdbfile").disabled = true;
|
| 10 |
+
document.getElementById("pdbid").disabled = false;
|
| 11 |
+
document.getElementById("submitButton").disabled = (document.getElementById("pdbid").value.length != 4);
|
| 12 |
+
}
|
| 13 |
+
}
|
| 14 |
+
</script>
|
| 15 |
+
<noscript>
|
| 16 |
+
<div style='color:red'>
|
| 17 |
+
<h1>Javascript Disabled</h1>
|
| 18 |
+
PDBFixer requires Javascript to operate. Please enable Javascript in your browser, then reload this page.
|
| 19 |
+
</div>
|
| 20 |
+
</noscript>
|
| 21 |
+
<h1>Welcome To PDBFixer!</h1>
|
| 22 |
+
Select a PDB file to load. It will be analyzed for problems.
|
| 23 |
+
<p>
|
| 24 |
+
<form id="mainform" method="post" action="/" enctype="multipart/form-data">
|
| 25 |
+
<input type="radio" name="type" id="localtype" value="local" onchange="enableInputs()" checked>Load a local file
|
| 26 |
+
<p style="margin-left:50px">
|
| 27 |
+
PDB File: <input type="file" id="pdbfile" name="pdbfile" onchange="enableInputs()"/>
|
| 28 |
+
</p>
|
| 29 |
+
<input type="radio" name="type" id="remotetype" value="remote" onchange="enableInputs()">Download a file from RCSB
|
| 30 |
+
<p style="margin-left:50px">
|
| 31 |
+
PDB Identifier: <input type="text" id="pdbid" name="pdbid" size="4" onchange="enableInputs()" onkeyup="enableInputs()" oninput="enableInputs()" disabled>
|
| 32 |
+
</p>
|
| 33 |
+
<input type="button" id="submitButton" value="Analyze File" onclick="submitWithSpinner()" disabled/>
|
| 34 |
+
</form>
|
| 35 |
+
<script>
|
| 36 |
+
setCurrentStep(1)
|
| 37 |
+
</script>
|
| 38 |
+
</body>
|
| 39 |
+
</html>
|
pdbfixer/images/background.jpg
ADDED
|
pdbfixer/images/logo.png
ADDED
|
pdbfixer/images/logo.svg
ADDED
|
pdbfixer/images/logo_small.png
ADDED
|
pdbfixer/pdbfixer.py
ADDED
|
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|
| 1 |
+
"""
|
| 2 |
+
pdbfixer.py: Fixes problems in PDB files
|
| 3 |
+
|
| 4 |
+
This is part of the OpenMM molecular simulation toolkit originating from
|
| 5 |
+
Simbios, the NIH National Center for Physics-Based Simulation of
|
| 6 |
+
Biological Structures at Stanford, funded under the NIH Roadmap for
|
| 7 |
+
Medical Research, grant U54 GM072970. See https://simtk.org.
|
| 8 |
+
|
| 9 |
+
Portions copyright (c) 2013-2023 Stanford University and the Authors.
|
| 10 |
+
Authors: Peter Eastman
|
| 11 |
+
Contributors:
|
| 12 |
+
|
| 13 |
+
Permission is hereby granted, free of charge, to any person obtaining a
|
| 14 |
+
copy of this software and associated documentation files (the "Software"),
|
| 15 |
+
to deal in the Software without restriction, including without limitation
|
| 16 |
+
the rights to use, copy, modify, merge, publish, distribute, sublicense,
|
| 17 |
+
and/or sell copies of the Software, and to permit persons to whom the
|
| 18 |
+
Software is furnished to do so, subject to the following conditions:
|
| 19 |
+
|
| 20 |
+
The above copyright notice and this permission notice shall be included in
|
| 21 |
+
all copies or substantial portions of the Software.
|
| 22 |
+
|
| 23 |
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
| 24 |
+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
| 25 |
+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
|
| 26 |
+
THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
|
| 27 |
+
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
|
| 28 |
+
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
|
| 29 |
+
USE OR OTHER DEALINGS IN THE SOFTWARE.
|
| 30 |
+
"""
|
| 31 |
+
from __future__ import absolute_import
|
| 32 |
+
__author__ = "Peter Eastman"
|
| 33 |
+
__version__ = "1.7"
|
| 34 |
+
|
| 35 |
+
import openmm as mm
|
| 36 |
+
import openmm.app as app
|
| 37 |
+
import openmm.unit as unit
|
| 38 |
+
from openmm.app.internal.pdbstructure import PdbStructure
|
| 39 |
+
from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
|
| 40 |
+
from openmm.app.element import hydrogen, oxygen
|
| 41 |
+
from openmm.app.forcefield import NonbondedGenerator
|
| 42 |
+
|
| 43 |
+
# Support Cythonized functions in OpenMM 7.3
|
| 44 |
+
# and also implementations in older versions.
|
| 45 |
+
try:
|
| 46 |
+
from openmm.app.internal import compiled
|
| 47 |
+
matchResidue = compiled.matchResidueToTemplate
|
| 48 |
+
except ImportError:
|
| 49 |
+
matchResidue = app.forcefield._matchResidue
|
| 50 |
+
|
| 51 |
+
import numpy as np
|
| 52 |
+
import numpy.linalg as lin
|
| 53 |
+
import sys
|
| 54 |
+
import os
|
| 55 |
+
import os.path
|
| 56 |
+
import math
|
| 57 |
+
|
| 58 |
+
from pkg_resources import resource_filename
|
| 59 |
+
|
| 60 |
+
if sys.version_info >= (3,0):
|
| 61 |
+
from urllib.request import urlopen
|
| 62 |
+
from io import StringIO
|
| 63 |
+
else:
|
| 64 |
+
from urllib2 import urlopen
|
| 65 |
+
from cStringIO import StringIO
|
| 66 |
+
|
| 67 |
+
substitutions = {
|
| 68 |
+
'2AS':'ASP', '3AH':'HIS', '5HP':'GLU', '5OW':'LYS', 'ACL':'ARG', 'AGM':'ARG', 'AIB':'ALA', 'ALM':'ALA', 'ALO':'THR', 'ALY':'LYS', 'ARM':'ARG',
|
| 69 |
+
'ASA':'ASP', 'ASB':'ASP', 'ASK':'ASP', 'ASL':'ASP', 'ASQ':'ASP', 'AYA':'ALA', 'BCS':'CYS', 'BHD':'ASP', 'BMT':'THR', 'BNN':'ALA',
|
| 70 |
+
'BUC':'CYS', 'BUG':'LEU', 'C5C':'CYS', 'C6C':'CYS', 'CAS':'CYS', 'CCS':'CYS', 'CEA':'CYS', 'CGU':'GLU', 'CHG':'ALA', 'CLE':'LEU', 'CME':'CYS',
|
| 71 |
+
'CSD':'ALA', 'CSO':'CYS', 'CSP':'CYS', 'CSS':'CYS', 'CSW':'CYS', 'CSX':'CYS', 'CXM':'MET', 'CY1':'CYS', 'CY3':'CYS', 'CYG':'CYS',
|
| 72 |
+
'CYM':'CYS', 'CYQ':'CYS', 'DAH':'PHE', 'DAL':'ALA', 'DAR':'ARG', 'DAS':'ASP', 'DCY':'CYS', 'DGL':'GLU', 'DGN':'GLN', 'DHA':'ALA',
|
| 73 |
+
'DHI':'HIS', 'DIL':'ILE', 'DIV':'VAL', 'DLE':'LEU', 'DLY':'LYS', 'DNP':'ALA', 'DPN':'PHE', 'DPR':'PRO', 'DSN':'SER', 'DSP':'ASP',
|
| 74 |
+
'DTH':'THR', 'DTR':'TRP', 'DTY':'TYR', 'DVA':'VAL', 'EFC':'CYS', 'FLA':'ALA', 'FME':'MET', 'GGL':'GLU', 'GL3':'GLY', 'GLZ':'GLY',
|
| 75 |
+
'GMA':'GLU', 'GSC':'GLY', 'HAC':'ALA', 'HAR':'ARG', 'HIC':'HIS', 'HIP':'HIS', 'HMR':'ARG', 'HPQ':'PHE', 'HTR':'TRP', 'HYP':'PRO',
|
| 76 |
+
'IAS':'ASP', 'IIL':'ILE', 'IYR':'TYR', 'KCX':'LYS', 'LLP':'LYS', 'LLY':'LYS', 'LTR':'TRP', 'LYM':'LYS', 'LYZ':'LYS', 'MAA':'ALA', 'MEN':'ASN',
|
| 77 |
+
'MHS':'HIS', 'MIS':'SER', 'MK8':'LEU', 'MLE':'LEU', 'MPQ':'GLY', 'MSA':'GLY', 'MSE':'MET', 'MVA':'VAL', 'NEM':'HIS', 'NEP':'HIS', 'NLE':'LEU',
|
| 78 |
+
'NLN':'LEU', 'NLP':'LEU', 'NMC':'GLY', 'OAS':'SER', 'OCS':'CYS', 'OMT':'MET', 'PAQ':'TYR', 'PCA':'GLU', 'PEC':'CYS', 'PHI':'PHE',
|
| 79 |
+
'PHL':'PHE', 'PR3':'CYS', 'PRR':'ALA', 'PTR':'TYR', 'PYX':'CYS', 'SAC':'SER', 'SAR':'GLY', 'SCH':'CYS', 'SCS':'CYS', 'SCY':'CYS',
|
| 80 |
+
'SEL':'SER', 'SEP':'SER', 'SET':'SER', 'SHC':'CYS', 'SHR':'LYS', 'SMC':'CYS', 'SOC':'CYS', 'STY':'TYR', 'SVA':'SER', 'TIH':'ALA',
|
| 81 |
+
'TPL':'TRP', 'TPO':'THR', 'TPQ':'ALA', 'TRG':'LYS', 'TRO':'TRP', 'TYB':'TYR', 'TYI':'TYR', 'TYQ':'TYR', 'TYS':'TYR', 'TYY':'TYR'
|
| 82 |
+
}
|
| 83 |
+
proteinResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR', 'ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL']
|
| 84 |
+
rnaResidues = ['A', 'G', 'C', 'U', 'I']
|
| 85 |
+
dnaResidues = ['DA', 'DG', 'DC', 'DT', 'DI']
|
| 86 |
+
|
| 87 |
+
class Sequence(object):
|
| 88 |
+
"""Sequence holds the sequence of a chain, as specified by SEQRES records."""
|
| 89 |
+
def __init__(self, chainId, residues):
|
| 90 |
+
self.chainId = chainId
|
| 91 |
+
self.residues = residues
|
| 92 |
+
|
| 93 |
+
class ModifiedResidue(object):
|
| 94 |
+
"""ModifiedResidue holds information about a modified residue, as specified by a MODRES record."""
|
| 95 |
+
def __init__(self, chainId, number, residueName, standardName):
|
| 96 |
+
self.chainId = chainId
|
| 97 |
+
self.number = number
|
| 98 |
+
self.residueName = residueName
|
| 99 |
+
self.standardName = standardName
|
| 100 |
+
|
| 101 |
+
def _guessFileFormat(file, filename):
|
| 102 |
+
"""Guess whether a file is PDB or PDBx/mmCIF based on its filename and contents."""
|
| 103 |
+
filename = filename.lower()
|
| 104 |
+
if '.pdbx' in filename or '.cif' in filename:
|
| 105 |
+
return 'pdbx'
|
| 106 |
+
if '.pdb' in filename:
|
| 107 |
+
return 'pdb'
|
| 108 |
+
for line in file:
|
| 109 |
+
if line.startswith('data_') or line.startswith('loop_'):
|
| 110 |
+
file.seek(0)
|
| 111 |
+
return 'pdbx'
|
| 112 |
+
if line.startswith('HEADER') or line.startswith('REMARK') or line.startswith('TITLE '):
|
| 113 |
+
file.seek(0)
|
| 114 |
+
return 'pdb'
|
| 115 |
+
|
| 116 |
+
# It's certainly not a valid PDBx/mmCIF. Guess that it's a PDB.
|
| 117 |
+
|
| 118 |
+
file.seek(0)
|
| 119 |
+
return 'pdb'
|
| 120 |
+
|
| 121 |
+
def _overlayPoints(points1, points2):
|
| 122 |
+
"""Given two sets of points, determine the translation and rotation that matches them as closely as possible.
|
| 123 |
+
|
| 124 |
+
Parameters
|
| 125 |
+
----------
|
| 126 |
+
points1 (numpy array of openmm.unit.Quantity with units compatible with distance) - reference set of coordinates
|
| 127 |
+
points2 (numpy array of openmm.unit.Quantity with units compatible with distance) - set of coordinates to be rotated
|
| 128 |
+
|
| 129 |
+
Returns
|
| 130 |
+
-------
|
| 131 |
+
translate2 - vector to translate points2 by in order to center it
|
| 132 |
+
rotate - rotation matrix to apply to centered points2 to map it on to points1
|
| 133 |
+
center1 - center of points1
|
| 134 |
+
|
| 135 |
+
Notes
|
| 136 |
+
-----
|
| 137 |
+
This is based on W. Kabsch, Acta Cryst., A34, pp. 828-829 (1978).
|
| 138 |
+
|
| 139 |
+
"""
|
| 140 |
+
|
| 141 |
+
if len(points1) == 0:
|
| 142 |
+
return (mm.Vec3(0, 0, 0), np.identity(3), mm.Vec3(0, 0, 0))
|
| 143 |
+
if len(points1) == 1:
|
| 144 |
+
return (points1[0], np.identity(3), -1*points2[0])
|
| 145 |
+
|
| 146 |
+
# Compute centroids.
|
| 147 |
+
|
| 148 |
+
center1 = unit.sum(points1)/float(len(points1))
|
| 149 |
+
center2 = unit.sum(points2)/float(len(points2))
|
| 150 |
+
|
| 151 |
+
# Compute R matrix.
|
| 152 |
+
|
| 153 |
+
R = np.zeros((3, 3))
|
| 154 |
+
for p1, p2 in zip(points1, points2):
|
| 155 |
+
x = p1-center1
|
| 156 |
+
y = p2-center2
|
| 157 |
+
for i in range(3):
|
| 158 |
+
for j in range(3):
|
| 159 |
+
R[i][j] += y[i]*x[j]
|
| 160 |
+
|
| 161 |
+
# Use an SVD to compute the rotation matrix.
|
| 162 |
+
|
| 163 |
+
(u, s, v) = lin.svd(R)
|
| 164 |
+
return (-1*center2, np.dot(u, v).transpose(), center1)
|
| 165 |
+
|
| 166 |
+
def _findUnoccupiedDirection(point, positions):
|
| 167 |
+
"""Given a point in space and a list of atom positions, find the direction in which the local density of atoms is lowest."""
|
| 168 |
+
|
| 169 |
+
point = point.value_in_unit(unit.nanometers)
|
| 170 |
+
direction = mm.Vec3(0, 0, 0)
|
| 171 |
+
for pos in positions.value_in_unit(unit.nanometers):
|
| 172 |
+
delta = pos-point
|
| 173 |
+
distance = unit.norm(delta)
|
| 174 |
+
if distance > 0.1:
|
| 175 |
+
distance2 = distance*distance
|
| 176 |
+
direction -= delta/(distance2*distance2)
|
| 177 |
+
direction /= unit.norm(direction)
|
| 178 |
+
return direction
|
| 179 |
+
|
| 180 |
+
class PDBFixer(object):
|
| 181 |
+
"""PDBFixer implements many tools for fixing problems in PDB and PDBx/mmCIF files.
|
| 182 |
+
"""
|
| 183 |
+
|
| 184 |
+
def __init__(self, filename=None, pdbfile=None, pdbxfile=None, url=None, pdbid=None):
|
| 185 |
+
"""Create a new PDBFixer instance to fix problems in a PDB or PDBx/mmCIF file.
|
| 186 |
+
|
| 187 |
+
Parameters
|
| 188 |
+
----------
|
| 189 |
+
filename : str, optional, default=None
|
| 190 |
+
The name of the file to read. The format is determined automatically based on the filename extension, or if
|
| 191 |
+
that is ambiguous, by looking at the file content.
|
| 192 |
+
pdbfile : file, optional, default=None
|
| 193 |
+
A file-like object from which the PDB file is to be read.
|
| 194 |
+
The file is not closed after reading.
|
| 195 |
+
pdbxfile : file, optional, default=None
|
| 196 |
+
A file-like object from which the PDBx/mmCIF file is to be read.
|
| 197 |
+
The file is not closed after reading.
|
| 198 |
+
url : str, optional, default=None
|
| 199 |
+
A URL specifying the internet location from which the file contents should be retrieved. The format is
|
| 200 |
+
determined automatically by looking for a filename extension in the URL, or if that is ambiguous, by looking
|
| 201 |
+
at the file content.
|
| 202 |
+
pdbid : str, optional, default=None
|
| 203 |
+
A four-letter PDB code specifying the structure to be retrieved from the RCSB.
|
| 204 |
+
|
| 205 |
+
Notes
|
| 206 |
+
-----
|
| 207 |
+
Only one of structure, filename, pdbfile, pdbxfile, url, or pdbid may be specified or an exception will be thrown.
|
| 208 |
+
|
| 209 |
+
Examples
|
| 210 |
+
--------
|
| 211 |
+
|
| 212 |
+
Start from a filename.
|
| 213 |
+
|
| 214 |
+
>>> filename = resource_filename('pdbfixer', 'tests/data/test.pdb')
|
| 215 |
+
>>> fixer = PDBFixer(filename=filename)
|
| 216 |
+
|
| 217 |
+
Start from a file object.
|
| 218 |
+
|
| 219 |
+
>>> with open(filename) as f:
|
| 220 |
+
... fixer = PDBFixer(pdbfile=f)
|
| 221 |
+
|
| 222 |
+
Start from a URL.
|
| 223 |
+
|
| 224 |
+
>>> fixer = PDBFixer(url='http://www.rcsb.org/pdb/files/1VII.pdb')
|
| 225 |
+
|
| 226 |
+
Start from a PDB code.
|
| 227 |
+
|
| 228 |
+
>>> fixer = PDBFixer(pdbid='1VII')
|
| 229 |
+
|
| 230 |
+
"""
|
| 231 |
+
|
| 232 |
+
# Check to make sure only one option has been specified.
|
| 233 |
+
if bool(filename) + bool(pdbfile) + bool(pdbxfile) + bool(url) + bool(pdbid) != 1:
|
| 234 |
+
raise Exception("Exactly one option [filename, pdbfile, pdbxfile, url, pdbid] must be specified.")
|
| 235 |
+
|
| 236 |
+
self.source = None
|
| 237 |
+
if pdbid:
|
| 238 |
+
# A PDB id has been specified.
|
| 239 |
+
url = 'http://www.rcsb.org/pdb/files/%s.pdb' % pdbid
|
| 240 |
+
if filename:
|
| 241 |
+
# A local file has been specified.
|
| 242 |
+
self.source = filename
|
| 243 |
+
file = open(filename, 'r')
|
| 244 |
+
if _guessFileFormat(file, filename) == 'pdbx':
|
| 245 |
+
self._initializeFromPDBx(file)
|
| 246 |
+
else:
|
| 247 |
+
self._initializeFromPDB(file)
|
| 248 |
+
file.close()
|
| 249 |
+
elif pdbfile:
|
| 250 |
+
# A file-like object has been specified.
|
| 251 |
+
self._initializeFromPDB(pdbfile)
|
| 252 |
+
elif pdbxfile:
|
| 253 |
+
# A file-like object has been specified.
|
| 254 |
+
self._initializeFromPDBx(pdbxfile)
|
| 255 |
+
elif url:
|
| 256 |
+
# A URL has been specified.
|
| 257 |
+
self.source = url
|
| 258 |
+
file = urlopen(url)
|
| 259 |
+
contents = file.read().decode('utf-8')
|
| 260 |
+
file.close()
|
| 261 |
+
file = StringIO(contents)
|
| 262 |
+
if _guessFileFormat(file, url) == 'pdbx':
|
| 263 |
+
self._initializeFromPDBx(contents)
|
| 264 |
+
else:
|
| 265 |
+
self._initializeFromPDB(StringIO(contents))
|
| 266 |
+
|
| 267 |
+
# Check the structure has some atoms in it.
|
| 268 |
+
atoms = list(self.topology.atoms())
|
| 269 |
+
if len(atoms) == 0:
|
| 270 |
+
raise Exception("Structure contains no atoms.")
|
| 271 |
+
|
| 272 |
+
# Load the templates.
|
| 273 |
+
|
| 274 |
+
self.templates = {}
|
| 275 |
+
templatesPath = os.path.join(os.path.dirname(__file__), 'templates')
|
| 276 |
+
for file in os.listdir(templatesPath):
|
| 277 |
+
templatePdb = app.PDBFile(os.path.join(templatesPath, file))
|
| 278 |
+
name = next(templatePdb.topology.residues()).name
|
| 279 |
+
self.templates[name] = templatePdb
|
| 280 |
+
|
| 281 |
+
def _initializeFromPDB(self, file):
|
| 282 |
+
"""Initialize this object by reading a PDB file."""
|
| 283 |
+
|
| 284 |
+
structure = PdbStructure(file)
|
| 285 |
+
pdb = app.PDBFile(structure)
|
| 286 |
+
self.topology = pdb.topology
|
| 287 |
+
self.positions = pdb.positions
|
| 288 |
+
self.sequences = [Sequence(s.chain_id, s.residues) for s in structure.sequences]
|
| 289 |
+
self.modifiedResidues = [ModifiedResidue(r.chain_id, r.number, r.residue_name, r.standard_name) for r in structure.modified_residues]
|
| 290 |
+
|
| 291 |
+
def _initializeFromPDBx(self, file):
|
| 292 |
+
"""Initialize this object by reading a PDBx/mmCIF file."""
|
| 293 |
+
|
| 294 |
+
pdbx = app.PDBxFile(file)
|
| 295 |
+
self.topology = pdbx.topology
|
| 296 |
+
self.positions = pdbx.positions
|
| 297 |
+
|
| 298 |
+
# PDBxFile doesn't record the information about sequence or modified residues, so we need to read them separately.
|
| 299 |
+
|
| 300 |
+
file.seek(0)
|
| 301 |
+
reader = PdbxReader(file)
|
| 302 |
+
data = []
|
| 303 |
+
reader.read(data)
|
| 304 |
+
block = data[0]
|
| 305 |
+
|
| 306 |
+
# Load the sequence data.
|
| 307 |
+
|
| 308 |
+
sequenceData = block.getObj('entity_poly_seq')
|
| 309 |
+
sequences = {}
|
| 310 |
+
if sequenceData is not None:
|
| 311 |
+
entityIdCol = sequenceData.getAttributeIndex('entity_id')
|
| 312 |
+
residueCol = sequenceData.getAttributeIndex('mon_id')
|
| 313 |
+
for row in sequenceData.getRowList():
|
| 314 |
+
entityId = row[entityIdCol]
|
| 315 |
+
residue = row[residueCol]
|
| 316 |
+
if entityId not in sequences:
|
| 317 |
+
sequences[entityId] = []
|
| 318 |
+
sequences[entityId].append(residue)
|
| 319 |
+
|
| 320 |
+
# Sequences are stored by "entity". There could be multiple chains that are all the same entity, so we need to
|
| 321 |
+
# convert from entities to chains.
|
| 322 |
+
|
| 323 |
+
asymData = block.getObj('struct_asym')
|
| 324 |
+
self.sequences = []
|
| 325 |
+
if asymData is not None:
|
| 326 |
+
asymIdCol = asymData.getAttributeIndex('id')
|
| 327 |
+
entityIdCol = asymData.getAttributeIndex('entity_id')
|
| 328 |
+
for row in asymData.getRowList():
|
| 329 |
+
asymId = row[asymIdCol]
|
| 330 |
+
entityId = row[entityIdCol]
|
| 331 |
+
if entityId in sequences:
|
| 332 |
+
self.sequences.append(Sequence(asymId, sequences[entityId]))
|
| 333 |
+
|
| 334 |
+
# Load the modified residues.
|
| 335 |
+
|
| 336 |
+
modData = block.getObj('pdbx_struct_mod_residue')
|
| 337 |
+
self.modifiedResidues = []
|
| 338 |
+
if modData is not None:
|
| 339 |
+
asymIdCol = modData.getAttributeIndex('label_asym_id')
|
| 340 |
+
resNameCol = modData.getAttributeIndex('label_comp_id')
|
| 341 |
+
resNumCol = modData.getAttributeIndex('auth_seq_id')
|
| 342 |
+
standardResCol = modData.getAttributeIndex('parent_comp_id')
|
| 343 |
+
if -1 not in (asymIdCol, resNameCol, resNumCol, standardResCol):
|
| 344 |
+
for row in modData.getRowList():
|
| 345 |
+
self.modifiedResidues.append(ModifiedResidue(row[asymIdCol], int(row[resNumCol]), row[resNameCol], row[standardResCol]))
|
| 346 |
+
|
| 347 |
+
def _addAtomsToTopology(self, heavyAtomsOnly, omitUnknownMolecules):
|
| 348 |
+
"""Create a new Topology in which missing atoms have been added.
|
| 349 |
+
|
| 350 |
+
Parameters
|
| 351 |
+
----------
|
| 352 |
+
heavyAtomsOnly : bool
|
| 353 |
+
If True, only heavy atoms will be added to the topology.
|
| 354 |
+
omitUnknownMolecules : bool
|
| 355 |
+
If True, unknown molecules will be omitted from the topology.
|
| 356 |
+
|
| 357 |
+
Returns
|
| 358 |
+
-------
|
| 359 |
+
newTopology : openmm.app.Topology
|
| 360 |
+
A new Topology object containing atoms from the old.
|
| 361 |
+
newPositions : list of openmm.unit.Quantity with units compatible with nanometers
|
| 362 |
+
Atom positions for the new Topology object.
|
| 363 |
+
newAtoms : openmm.app.Topology.Atom
|
| 364 |
+
New atom objects.
|
| 365 |
+
existingAtomMap : dict
|
| 366 |
+
Mapping from old atoms to new atoms.
|
| 367 |
+
|
| 368 |
+
"""
|
| 369 |
+
|
| 370 |
+
newTopology = app.Topology()
|
| 371 |
+
newPositions = []*unit.nanometer
|
| 372 |
+
newAtoms = []
|
| 373 |
+
existingAtomMap = {}
|
| 374 |
+
addedAtomMap = {}
|
| 375 |
+
addedOXT = []
|
| 376 |
+
residueCenters = [self._computeResidueCenter(res).value_in_unit(unit.nanometers) for res in self.topology.residues()]*unit.nanometers
|
| 377 |
+
for chain in self.topology.chains():
|
| 378 |
+
if omitUnknownMolecules and not any(residue.name in self.templates for residue in chain.residues()):
|
| 379 |
+
continue
|
| 380 |
+
chainResidues = list(chain.residues())
|
| 381 |
+
newChain = newTopology.addChain(chain.id)
|
| 382 |
+
for indexInChain, residue in enumerate(chain.residues()):
|
| 383 |
+
|
| 384 |
+
# Insert missing residues here.
|
| 385 |
+
|
| 386 |
+
if (chain.index, indexInChain) in self.missingResidues:
|
| 387 |
+
insertHere = self.missingResidues[(chain.index, indexInChain)]
|
| 388 |
+
endPosition = self._computeResidueCenter(residue)
|
| 389 |
+
if indexInChain > 0:
|
| 390 |
+
startPosition = self._computeResidueCenter(chainResidues[indexInChain-1])
|
| 391 |
+
loopDirection = _findUnoccupiedDirection((startPosition+endPosition)/2, residueCenters)
|
| 392 |
+
else:
|
| 393 |
+
outward = _findUnoccupiedDirection(endPosition, residueCenters)*unit.nanometers
|
| 394 |
+
norm = unit.norm(outward)
|
| 395 |
+
if norm > 0*unit.nanometer:
|
| 396 |
+
outward *= len(insertHere)*0.5*unit.nanometer/norm
|
| 397 |
+
startPosition = endPosition+outward
|
| 398 |
+
loopDirection = None
|
| 399 |
+
firstIndex = int(residue.id)-len(insertHere)
|
| 400 |
+
self._addMissingResiduesToChain(newChain, insertHere, startPosition, endPosition, loopDirection, residue, newAtoms, newPositions, firstIndex)
|
| 401 |
+
|
| 402 |
+
# Create the new residue and add existing heavy atoms.
|
| 403 |
+
|
| 404 |
+
newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
|
| 405 |
+
for atom in residue.atoms():
|
| 406 |
+
if not heavyAtomsOnly or (atom.element is not None and atom.element != hydrogen):
|
| 407 |
+
if atom.name == 'OXT' and (chain.index, indexInChain+1) in self.missingResidues:
|
| 408 |
+
continue # Remove terminal oxygen, since we'll add more residues after this one
|
| 409 |
+
newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
|
| 410 |
+
existingAtomMap[atom] = newAtom
|
| 411 |
+
newPositions.append(self.positions[atom.index])
|
| 412 |
+
if residue in self.missingAtoms:
|
| 413 |
+
|
| 414 |
+
# Find corresponding atoms in the residue and the template.
|
| 415 |
+
|
| 416 |
+
template = self.templates[residue.name]
|
| 417 |
+
atomPositions = dict((atom.name, self.positions[atom.index]) for atom in residue.atoms())
|
| 418 |
+
points1 = []
|
| 419 |
+
points2 = []
|
| 420 |
+
for atom in template.topology.atoms():
|
| 421 |
+
if atom.name in atomPositions:
|
| 422 |
+
points1.append(atomPositions[atom.name].value_in_unit(unit.nanometer))
|
| 423 |
+
points2.append(template.positions[atom.index].value_in_unit(unit.nanometer))
|
| 424 |
+
|
| 425 |
+
# Compute the optimal transform to overlay them.
|
| 426 |
+
|
| 427 |
+
(translate2, rotate, translate1) = _overlayPoints(points1, points2)
|
| 428 |
+
|
| 429 |
+
# Add the missing atoms.
|
| 430 |
+
|
| 431 |
+
addedAtomMap[residue] = {}
|
| 432 |
+
for atom in self.missingAtoms[residue]:
|
| 433 |
+
newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
|
| 434 |
+
newAtoms.append(newAtom)
|
| 435 |
+
addedAtomMap[residue][atom] = newAtom
|
| 436 |
+
templatePosition = template.positions[atom.index].value_in_unit(unit.nanometer)
|
| 437 |
+
newPositions.append((mm.Vec3(*np.dot(rotate, templatePosition+translate2))+translate1)*unit.nanometer)
|
| 438 |
+
if residue in self.missingTerminals:
|
| 439 |
+
terminalsToAdd = self.missingTerminals[residue]
|
| 440 |
+
else:
|
| 441 |
+
terminalsToAdd = None
|
| 442 |
+
|
| 443 |
+
# If this is the end of the chain, add any missing residues that come after it.
|
| 444 |
+
|
| 445 |
+
if residue == chainResidues[-1] and (chain.index, indexInChain+1) in self.missingResidues:
|
| 446 |
+
insertHere = self.missingResidues[(chain.index, indexInChain+1)]
|
| 447 |
+
if len(insertHere) > 0:
|
| 448 |
+
startPosition = self._computeResidueCenter(residue)
|
| 449 |
+
outward = _findUnoccupiedDirection(startPosition, residueCenters)*unit.nanometers
|
| 450 |
+
norm = unit.norm(outward)
|
| 451 |
+
if norm > 0*unit.nanometer:
|
| 452 |
+
outward *= len(insertHere)*0.5*unit.nanometer/norm
|
| 453 |
+
endPosition = startPosition+outward
|
| 454 |
+
firstIndex = int(residue.id)+1
|
| 455 |
+
self._addMissingResiduesToChain(newChain, insertHere, startPosition, endPosition, None, residue, newAtoms, newPositions, firstIndex)
|
| 456 |
+
newResidue = list(newChain.residues())[-1]
|
| 457 |
+
if newResidue.name in proteinResidues:
|
| 458 |
+
terminalsToAdd = ['OXT']
|
| 459 |
+
else:
|
| 460 |
+
terminalsToAdd = None
|
| 461 |
+
|
| 462 |
+
# If a terminal OXT is missing, add it.
|
| 463 |
+
|
| 464 |
+
if terminalsToAdd is not None:
|
| 465 |
+
atomPositions = dict((atom.name, newPositions[atom.index].value_in_unit(unit.nanometer)) for atom in newResidue.atoms())
|
| 466 |
+
if 'OXT' in terminalsToAdd:
|
| 467 |
+
newAtom = newTopology.addAtom('OXT', oxygen, newResidue)
|
| 468 |
+
newAtoms.append(newAtom)
|
| 469 |
+
addedOXT.append(newAtom)
|
| 470 |
+
d_ca_o = atomPositions['O']-atomPositions['CA']
|
| 471 |
+
d_ca_c = atomPositions['C']-atomPositions['CA']
|
| 472 |
+
d_ca_c /= unit.sqrt(unit.dot(d_ca_c, d_ca_c))
|
| 473 |
+
v = d_ca_o - d_ca_c*unit.dot(d_ca_c, d_ca_o)
|
| 474 |
+
newPositions.append((atomPositions['O']+2*v)*unit.nanometer)
|
| 475 |
+
newTopology.setUnitCellDimensions(self.topology.getUnitCellDimensions())
|
| 476 |
+
newTopology.createStandardBonds()
|
| 477 |
+
newTopology.createDisulfideBonds(newPositions)
|
| 478 |
+
|
| 479 |
+
# Add the bonds between atoms in heterogens.
|
| 480 |
+
|
| 481 |
+
for a1,a2 in self.topology.bonds():
|
| 482 |
+
if a1 in existingAtomMap and a2 in existingAtomMap and (a1.residue.name not in app.Topology._standardBonds or a2.residue.name not in app.Topology._standardBonds):
|
| 483 |
+
newTopology.addBond(existingAtomMap[a1], existingAtomMap[a2])
|
| 484 |
+
|
| 485 |
+
# Return the results.
|
| 486 |
+
|
| 487 |
+
return (newTopology, newPositions, newAtoms, existingAtomMap)
|
| 488 |
+
|
| 489 |
+
def _computeResidueCenter(self, residue):
|
| 490 |
+
"""Compute the centroid of a residue."""
|
| 491 |
+
return unit.sum([self.positions[atom.index] for atom in residue.atoms()])/len(list(residue.atoms()))
|
| 492 |
+
|
| 493 |
+
def _addMissingResiduesToChain(self, chain, residueNames, startPosition, endPosition, loopDirection, orientTo, newAtoms, newPositions, firstIndex):
|
| 494 |
+
"""Add a series of residues to a chain."""
|
| 495 |
+
orientToPositions = dict((atom.name, self.positions[atom.index]) for atom in orientTo.atoms())
|
| 496 |
+
if loopDirection is None:
|
| 497 |
+
loopDirection = mm.Vec3(0, 0, 0)
|
| 498 |
+
|
| 499 |
+
# We'll add the residues in an arc connecting the endpoints. Figure out the height of that arc.
|
| 500 |
+
|
| 501 |
+
length = unit.norm(endPosition-startPosition)
|
| 502 |
+
numResidues = len(residueNames)
|
| 503 |
+
if length > numResidues*0.3*unit.nanometers:
|
| 504 |
+
loopHeight = 0*unit.nanometers
|
| 505 |
+
else:
|
| 506 |
+
loopHeight = (numResidues*0.3*unit.nanometers-length)/2
|
| 507 |
+
|
| 508 |
+
# Add the residues.
|
| 509 |
+
|
| 510 |
+
for i, residueName in enumerate(residueNames):
|
| 511 |
+
template = self.templates[residueName]
|
| 512 |
+
|
| 513 |
+
# Find a translation that best matches the adjacent residue.
|
| 514 |
+
|
| 515 |
+
points1 = []
|
| 516 |
+
points2 = []
|
| 517 |
+
for atom in template.topology.atoms():
|
| 518 |
+
if atom.name in orientToPositions:
|
| 519 |
+
points1.append(orientToPositions[atom.name].value_in_unit(unit.nanometer))
|
| 520 |
+
points2.append(template.positions[atom.index].value_in_unit(unit.nanometer))
|
| 521 |
+
(translate2, rotate, translate1) = _overlayPoints(points1, points2)
|
| 522 |
+
|
| 523 |
+
# Create the new residue.
|
| 524 |
+
|
| 525 |
+
newResidue = chain.topology.addResidue(residueName, chain, "%d" % ((firstIndex+i)%10000))
|
| 526 |
+
fraction = (i+1.0)/(numResidues+1.0)
|
| 527 |
+
translate = startPosition + (endPosition-startPosition)*fraction + loopHeight*math.sin(fraction*math.pi)*loopDirection
|
| 528 |
+
templateAtoms = list(template.topology.atoms())
|
| 529 |
+
if newResidue == next(chain.residues()):
|
| 530 |
+
templateAtoms = [atom for atom in templateAtoms if atom.name not in ('P', 'OP1', 'OP2')]
|
| 531 |
+
for atom in templateAtoms:
|
| 532 |
+
newAtom = chain.topology.addAtom(atom.name, atom.element, newResidue)
|
| 533 |
+
newAtoms.append(newAtom)
|
| 534 |
+
templatePosition = template.positions[atom.index].value_in_unit(unit.nanometer)
|
| 535 |
+
newPositions.append(mm.Vec3(*np.dot(rotate, templatePosition))*unit.nanometer+translate)
|
| 536 |
+
|
| 537 |
+
def removeChains(self, chainIndices=None, chainIds=None):
|
| 538 |
+
"""Remove a set of chains from the structure.
|
| 539 |
+
|
| 540 |
+
Parameters
|
| 541 |
+
----------
|
| 542 |
+
chainIndices : list of int, optional, default=None
|
| 543 |
+
List of indices of chains to remove.
|
| 544 |
+
chainIds : list of str, optional, default=None
|
| 545 |
+
List of chain ids of chains to remove.
|
| 546 |
+
|
| 547 |
+
Examples
|
| 548 |
+
--------
|
| 549 |
+
|
| 550 |
+
Load a PDB file with two chains and eliminate the second chain.
|
| 551 |
+
|
| 552 |
+
>>> fixer = PDBFixer(pdbid='4J7F')
|
| 553 |
+
>>> fixer.removeChains(chainIndices=[1])
|
| 554 |
+
|
| 555 |
+
Load a PDB file with two chains and eliminate chains named 'B' and 'D'.
|
| 556 |
+
|
| 557 |
+
>>> fixer = PDBFixer(pdbid='4J7F')
|
| 558 |
+
>>> fixer.removeChains(chainIds=['B','D'])
|
| 559 |
+
|
| 560 |
+
"""
|
| 561 |
+
modeller = app.Modeller(self.topology, self.positions)
|
| 562 |
+
allChains = list(self.topology.chains())
|
| 563 |
+
|
| 564 |
+
if chainIndices == None:
|
| 565 |
+
chainIndices = list()
|
| 566 |
+
if chainIds != None:
|
| 567 |
+
# Add all chains that match the selection to the list.
|
| 568 |
+
for (chainNumber, chain) in enumerate(allChains):
|
| 569 |
+
if chain.id in chainIds:
|
| 570 |
+
chainIndices.append(chainNumber)
|
| 571 |
+
# Ensure only unique entries remain.
|
| 572 |
+
chainIndices = list(set(chainIndices))
|
| 573 |
+
|
| 574 |
+
# Do nothing if no chains will be deleted.
|
| 575 |
+
if len(chainIndices) == 0:
|
| 576 |
+
return
|
| 577 |
+
|
| 578 |
+
modeller.delete(allChains[i] for i in chainIndices)
|
| 579 |
+
self.topology = modeller.topology
|
| 580 |
+
self.positions = modeller.positions
|
| 581 |
+
|
| 582 |
+
return
|
| 583 |
+
|
| 584 |
+
def findMissingResidues(self):
|
| 585 |
+
"""Find residues that are missing from the structure.
|
| 586 |
+
|
| 587 |
+
The results are stored into the missingResidues field, which is a dict. Each key is a tuple consisting of
|
| 588 |
+
the index of a chain, and the residue index within that chain at which new residues should be inserted.
|
| 589 |
+
The corresponding value is a list of the names of residues to insert there.
|
| 590 |
+
|
| 591 |
+
Examples
|
| 592 |
+
--------
|
| 593 |
+
|
| 594 |
+
>>> fixer = PDBFixer(pdbid='1VII')
|
| 595 |
+
>>> fixer.findMissingResidues()
|
| 596 |
+
>>> missing_residues = fixer.missingResidues
|
| 597 |
+
|
| 598 |
+
"""
|
| 599 |
+
chains = [c for c in self.topology.chains() if len(list(c.residues())) > 0]
|
| 600 |
+
chainWithGaps = {}
|
| 601 |
+
|
| 602 |
+
# Find the sequence of each chain, with gaps for missing residues.
|
| 603 |
+
|
| 604 |
+
for chain in chains:
|
| 605 |
+
residues = list(chain.residues())
|
| 606 |
+
ids = [int(r.id) for r in residues]
|
| 607 |
+
for i, res in enumerate(residues):
|
| 608 |
+
if res.insertionCode not in ('', ' '):
|
| 609 |
+
for j in range(i, len(residues)):
|
| 610 |
+
ids[j] += 1
|
| 611 |
+
minResidue = min(ids)
|
| 612 |
+
maxResidue = max(ids)
|
| 613 |
+
chainWithGaps[chain] = [None]*(maxResidue-minResidue+1)
|
| 614 |
+
for r, id in zip(residues, ids):
|
| 615 |
+
chainWithGaps[chain][id-minResidue] = r.name
|
| 616 |
+
|
| 617 |
+
# Try to find the chain that matches each sequence.
|
| 618 |
+
|
| 619 |
+
chainSequence = {}
|
| 620 |
+
chainOffset = {}
|
| 621 |
+
for sequence in self.sequences:
|
| 622 |
+
for chain in chains:
|
| 623 |
+
if chain.id != sequence.chainId:
|
| 624 |
+
continue
|
| 625 |
+
if chain in chainSequence:
|
| 626 |
+
continue
|
| 627 |
+
for offset in range(len(sequence.residues)-len(chainWithGaps[chain])+1):
|
| 628 |
+
if all(a == b or b == None for a,b in zip(sequence.residues[offset:], chainWithGaps[chain])):
|
| 629 |
+
chainSequence[chain] = sequence
|
| 630 |
+
chainOffset[chain] = offset
|
| 631 |
+
break
|
| 632 |
+
if chain in chainSequence:
|
| 633 |
+
break
|
| 634 |
+
|
| 635 |
+
# Now build the list of residues to add.
|
| 636 |
+
|
| 637 |
+
self.missingResidues = {}
|
| 638 |
+
for chain in self.topology.chains():
|
| 639 |
+
if chain in chainSequence:
|
| 640 |
+
offset = chainOffset[chain]
|
| 641 |
+
sequence = chainSequence[chain].residues
|
| 642 |
+
gappedSequence = chainWithGaps[chain]
|
| 643 |
+
index = 0
|
| 644 |
+
for i in range(len(sequence)):
|
| 645 |
+
if i < offset or i >= len(gappedSequence)+offset or gappedSequence[i-offset] is None:
|
| 646 |
+
key = (chain.index, index)
|
| 647 |
+
if key not in self.missingResidues:
|
| 648 |
+
self.missingResidues[key] = []
|
| 649 |
+
residueName = sequence[i]
|
| 650 |
+
if residueName in substitutions:
|
| 651 |
+
residueName = substitutions[sequence[i]]
|
| 652 |
+
self.missingResidues[key].append(residueName)
|
| 653 |
+
else:
|
| 654 |
+
index += 1
|
| 655 |
+
|
| 656 |
+
def findNonstandardResidues(self):
|
| 657 |
+
"""Identify non-standard residues found in the structure, and select standard residues to replace them with.
|
| 658 |
+
|
| 659 |
+
The results are stored into the nonstandardResidues field, which is a map of Residue objects to the names
|
| 660 |
+
of suggested replacement residues.
|
| 661 |
+
|
| 662 |
+
Examples
|
| 663 |
+
--------
|
| 664 |
+
|
| 665 |
+
Find nonstandard residues.
|
| 666 |
+
|
| 667 |
+
>>> fixer = PDBFixer(pdbid='1YRI')
|
| 668 |
+
>>> fixer.findNonstandardResidues()
|
| 669 |
+
>>> nonstandard_residues = fixer.nonstandardResidues
|
| 670 |
+
|
| 671 |
+
"""
|
| 672 |
+
|
| 673 |
+
# First find residues based on our table of standard substitutions.
|
| 674 |
+
|
| 675 |
+
nonstandard = dict((r, substitutions[r.name]) for r in self.topology.residues() if r.name in substitutions)
|
| 676 |
+
|
| 677 |
+
# Now add ones based on MODRES records.
|
| 678 |
+
|
| 679 |
+
modres = dict(((m.chainId, str(m.number), m.residueName), m.standardName) for m in self.modifiedResidues)
|
| 680 |
+
for chain in self.topology.chains():
|
| 681 |
+
for residue in chain.residues():
|
| 682 |
+
key = (chain.id, residue.id, residue.name)
|
| 683 |
+
if key in modres:
|
| 684 |
+
replacement = modres[key]
|
| 685 |
+
if replacement == 'DU':
|
| 686 |
+
replacement = 'DT'
|
| 687 |
+
if replacement in self.templates:
|
| 688 |
+
nonstandard[residue] = replacement
|
| 689 |
+
self.nonstandardResidues = [(r, nonstandard[r]) for r in sorted(nonstandard, key=lambda r: r.index)]
|
| 690 |
+
|
| 691 |
+
def replaceNonstandardResidues(self):
|
| 692 |
+
"""Replace every residue listed in the nonstandardResidues field with the specified standard residue.
|
| 693 |
+
|
| 694 |
+
Notes
|
| 695 |
+
-----
|
| 696 |
+
You must have first called findNonstandardResidues() to identify nonstandard residues.
|
| 697 |
+
|
| 698 |
+
Examples
|
| 699 |
+
--------
|
| 700 |
+
|
| 701 |
+
Find and replace nonstandard residues using replacement templates stored in the 'templates' field of PDBFixer object.
|
| 702 |
+
|
| 703 |
+
>>> fixer = PDBFixer(pdbid='1YRI')
|
| 704 |
+
>>> fixer.findNonstandardResidues()
|
| 705 |
+
>>> fixer.replaceNonstandardResidues()
|
| 706 |
+
|
| 707 |
+
"""
|
| 708 |
+
if len(self.nonstandardResidues) > 0:
|
| 709 |
+
deleteAtoms = []
|
| 710 |
+
|
| 711 |
+
# Find atoms that should be deleted.
|
| 712 |
+
|
| 713 |
+
for residue, replaceWith in self.nonstandardResidues:
|
| 714 |
+
residue.name = replaceWith
|
| 715 |
+
template = self.templates[replaceWith]
|
| 716 |
+
standardAtoms = set(atom.name for atom in template.topology.atoms())
|
| 717 |
+
for atom in residue.atoms():
|
| 718 |
+
if atom.element in (None, hydrogen) or atom.name not in standardAtoms:
|
| 719 |
+
deleteAtoms.append(atom)
|
| 720 |
+
|
| 721 |
+
# Delete them.
|
| 722 |
+
|
| 723 |
+
modeller = app.Modeller(self.topology, self.positions)
|
| 724 |
+
modeller.delete(deleteAtoms)
|
| 725 |
+
self.topology = modeller.topology
|
| 726 |
+
self.positions = modeller.positions
|
| 727 |
+
|
| 728 |
+
|
| 729 |
+
def applyMutations(self, mutations, chain_id):
|
| 730 |
+
"""Apply a list of amino acid substitutions to make a mutant protein.
|
| 731 |
+
|
| 732 |
+
Parameters
|
| 733 |
+
----------
|
| 734 |
+
mutations : list of strings
|
| 735 |
+
Each string must include the resName (original), index,
|
| 736 |
+
and resName (target). For example, ALA-133-GLY will mutate
|
| 737 |
+
alanine 133 to glycine.
|
| 738 |
+
chain_id : str
|
| 739 |
+
String based chain ID of the single chain you wish to mutate.
|
| 740 |
+
|
| 741 |
+
Notes
|
| 742 |
+
-----
|
| 743 |
+
|
| 744 |
+
We require three letter codes to avoid possible ambiguitities.
|
| 745 |
+
We can't guarantee that the resulting model is a good one; for
|
| 746 |
+
significant changes in sequence, you should probably be using
|
| 747 |
+
a standalone homology modelling tool.
|
| 748 |
+
|
| 749 |
+
Examples
|
| 750 |
+
--------
|
| 751 |
+
|
| 752 |
+
Find nonstandard residues.
|
| 753 |
+
|
| 754 |
+
>>> fixer = PDBFixer(pdbid='1VII')
|
| 755 |
+
>>> fixer.applyMutations(["ALA-57-GLY"], "A")
|
| 756 |
+
>>> fixer.findMissingResidues()
|
| 757 |
+
>>> fixer.findMissingAtoms()
|
| 758 |
+
>>> fixer.addMissingAtoms()
|
| 759 |
+
>>> fixer.addMissingHydrogens(7.0)
|
| 760 |
+
|
| 761 |
+
"""
|
| 762 |
+
# Retrieve all residues that match the specified chain_id.
|
| 763 |
+
# NOTE: Multiple chains may have the same chainid, but must have unique resSeq entries.
|
| 764 |
+
resSeq_to_residue = dict() # resSeq_to_residue[resid] is the residue in the requested chain corresponding to residue identifier 'resid'
|
| 765 |
+
for chain in self.topology.chains():
|
| 766 |
+
if chain.id == chain_id:
|
| 767 |
+
for residue in chain.residues():
|
| 768 |
+
resSeq_to_residue[int(residue.id)] = residue
|
| 769 |
+
|
| 770 |
+
# Make a map of residues to mutate based on requested mutation list.
|
| 771 |
+
residue_map = dict() # residue_map[residue] is the name of the new residue to mutate to, if a mutation is desired
|
| 772 |
+
for mut_str in mutations:
|
| 773 |
+
old_name, resSeq, new_name = mut_str.split("-")
|
| 774 |
+
resSeq = int(resSeq)
|
| 775 |
+
|
| 776 |
+
if resSeq not in resSeq_to_residue:
|
| 777 |
+
raise(KeyError("Cannot find chain %s residue %d in system!" % (chain_id, resSeq)))
|
| 778 |
+
|
| 779 |
+
residue = resSeq_to_residue[resSeq] # retrieve the requested residue
|
| 780 |
+
|
| 781 |
+
if residue.name != old_name:
|
| 782 |
+
raise(ValueError("You asked to mutate chain %s residue %d name %s, but that residue is actually %s!" % (chain_id, resSeq, old_name, residue.name)))
|
| 783 |
+
|
| 784 |
+
try:
|
| 785 |
+
template = self.templates[new_name]
|
| 786 |
+
except KeyError:
|
| 787 |
+
raise(KeyError("Cannot find residue %s in template library!" % new_name))
|
| 788 |
+
|
| 789 |
+
# Store mutation
|
| 790 |
+
residue_map[residue] = new_name
|
| 791 |
+
|
| 792 |
+
# If there are mutations to be made, make them.
|
| 793 |
+
if len(residue_map) > 0:
|
| 794 |
+
deleteAtoms = [] # list of atoms to delete
|
| 795 |
+
|
| 796 |
+
# Find atoms that should be deleted.
|
| 797 |
+
for residue in residue_map.keys():
|
| 798 |
+
replaceWith = residue_map[residue]
|
| 799 |
+
residue.name = replaceWith
|
| 800 |
+
template = self.templates[replaceWith]
|
| 801 |
+
standardAtoms = set(atom.name for atom in template.topology.atoms())
|
| 802 |
+
for atom in residue.atoms():
|
| 803 |
+
if atom.element in (None, hydrogen) or atom.name not in standardAtoms:
|
| 804 |
+
deleteAtoms.append(atom)
|
| 805 |
+
|
| 806 |
+
# Delete atoms queued to be deleted.
|
| 807 |
+
modeller = app.Modeller(self.topology, self.positions)
|
| 808 |
+
modeller.delete(deleteAtoms)
|
| 809 |
+
self.topology = modeller.topology
|
| 810 |
+
self.positions = modeller.positions
|
| 811 |
+
|
| 812 |
+
|
| 813 |
+
def findMissingAtoms(self):
|
| 814 |
+
"""Find heavy atoms that are missing from the structure.
|
| 815 |
+
|
| 816 |
+
The results are stored into two fields: missingAtoms and missingTerminals. Each of these is a dict whose keys
|
| 817 |
+
are Residue objects and whose values are lists of atom names. missingAtoms contains standard atoms that should
|
| 818 |
+
be present in any residue of that type. missingTerminals contains terminal atoms that should be present at the
|
| 819 |
+
start or end of a chain.
|
| 820 |
+
|
| 821 |
+
Notes
|
| 822 |
+
-----
|
| 823 |
+
You must have first called findMissingResidues().
|
| 824 |
+
|
| 825 |
+
Examples
|
| 826 |
+
--------
|
| 827 |
+
|
| 828 |
+
Find missing heavy atoms in Abl kinase structure.
|
| 829 |
+
|
| 830 |
+
>>> fixer = PDBFixer(pdbid='2F4J')
|
| 831 |
+
>>> fixer.findMissingResidues()
|
| 832 |
+
>>> fixer.findMissingAtoms()
|
| 833 |
+
>>> # Retrieve missing atoms.
|
| 834 |
+
>>> missingAtoms = fixer.missingAtoms
|
| 835 |
+
>>> # Retrieve missing terminal atoms.
|
| 836 |
+
>>> missingTerminals = fixer.missingTerminals
|
| 837 |
+
|
| 838 |
+
"""
|
| 839 |
+
missingAtoms = {}
|
| 840 |
+
missingTerminals = {}
|
| 841 |
+
|
| 842 |
+
# Loop over residues.
|
| 843 |
+
|
| 844 |
+
for chain in self.topology.chains():
|
| 845 |
+
chainResidues = list(chain.residues())
|
| 846 |
+
for residue in chain.residues():
|
| 847 |
+
if residue.name in self.templates:
|
| 848 |
+
template = self.templates[residue.name]
|
| 849 |
+
atomNames = set(atom.name for atom in residue.atoms())
|
| 850 |
+
templateAtoms = list(template.topology.atoms())
|
| 851 |
+
if residue == chainResidues[0] and (chain.index, 0) not in self.missingResidues:
|
| 852 |
+
templateAtoms = [atom for atom in templateAtoms if atom.name not in ('P', 'OP1', 'OP2')]
|
| 853 |
+
|
| 854 |
+
# Add atoms from the template that are missing.
|
| 855 |
+
|
| 856 |
+
missing = []
|
| 857 |
+
for atom in templateAtoms:
|
| 858 |
+
if atom.name not in atomNames:
|
| 859 |
+
missing.append(atom)
|
| 860 |
+
if len(missing) > 0:
|
| 861 |
+
missingAtoms[residue] = missing
|
| 862 |
+
|
| 863 |
+
# Add missing terminal atoms.
|
| 864 |
+
|
| 865 |
+
terminals = []
|
| 866 |
+
if residue == chainResidues[-1] and (chain.index, len(chainResidues)) not in self.missingResidues:
|
| 867 |
+
templateNames = set(atom.name for atom in template.topology.atoms())
|
| 868 |
+
if 'OXT' not in atomNames and all(name in templateNames for name in ['C', 'O', 'CA']):
|
| 869 |
+
terminals.append('OXT')
|
| 870 |
+
if len(terminals) > 0:
|
| 871 |
+
missingTerminals[residue] = terminals
|
| 872 |
+
self.missingAtoms = missingAtoms
|
| 873 |
+
self.missingTerminals = missingTerminals
|
| 874 |
+
|
| 875 |
+
def addMissingAtoms(self, seed=None):
|
| 876 |
+
"""Add all missing heavy atoms, as specified by the missingAtoms, missingTerminals, and missingResidues fields.
|
| 877 |
+
|
| 878 |
+
Parameters
|
| 879 |
+
----------
|
| 880 |
+
seed : int
|
| 881 |
+
Integer to set the random seed number of the integrator used in the minimization of the
|
| 882 |
+
coordinates of the newly-added atoms.
|
| 883 |
+
|
| 884 |
+
Notes
|
| 885 |
+
-----
|
| 886 |
+
You must already have called findMissingAtoms() to have identified atoms to be added.
|
| 887 |
+
|
| 888 |
+
Examples
|
| 889 |
+
--------
|
| 890 |
+
|
| 891 |
+
Find missing heavy atoms in Abl kinase structure.
|
| 892 |
+
|
| 893 |
+
>>> fixer = PDBFixer(pdbid='2F4J')
|
| 894 |
+
>>> fixer.findMissingResidues()
|
| 895 |
+
>>> fixer.findMissingAtoms()
|
| 896 |
+
>>> fixer.addMissingAtoms()
|
| 897 |
+
|
| 898 |
+
"""
|
| 899 |
+
|
| 900 |
+
# Create a Topology that 1) adds missing atoms, 2) removes all hydrogens, and 3) removes unknown molecules.
|
| 901 |
+
|
| 902 |
+
(newTopology, newPositions, newAtoms, existingAtomMap) = self._addAtomsToTopology(True, True)
|
| 903 |
+
if len(newAtoms) == 0:
|
| 904 |
+
|
| 905 |
+
# No atoms were added, but new bonds might have been created.
|
| 906 |
+
|
| 907 |
+
newBonds = set(newTopology.bonds())
|
| 908 |
+
for atom1, atom2 in self.topology.bonds():
|
| 909 |
+
if atom1 in existingAtomMap and atom2 in existingAtomMap:
|
| 910 |
+
a1 = existingAtomMap[atom1]
|
| 911 |
+
a2 = existingAtomMap[atom2]
|
| 912 |
+
if (a1, a2) in newBonds:
|
| 913 |
+
newBonds.remove((a1, a2))
|
| 914 |
+
elif (a2, a1) in newBonds:
|
| 915 |
+
newBonds.remove((a2, a1))
|
| 916 |
+
|
| 917 |
+
# Add the new bonds to the original Topology.
|
| 918 |
+
|
| 919 |
+
inverseAtomMap = dict((y,x) for (x,y) in existingAtomMap.items())
|
| 920 |
+
for atom1, atom2 in newBonds:
|
| 921 |
+
self.topology.addBond(inverseAtomMap[atom1], inverseAtomMap[atom2])
|
| 922 |
+
else:
|
| 923 |
+
|
| 924 |
+
# Create a System for energy minimizing it.
|
| 925 |
+
|
| 926 |
+
forcefield = self._createForceField(newTopology, False)
|
| 927 |
+
system = forcefield.createSystem(newTopology)
|
| 928 |
+
|
| 929 |
+
# Set any previously existing atoms to be massless, they so won't move.
|
| 930 |
+
|
| 931 |
+
for atom in existingAtomMap.values():
|
| 932 |
+
system.setParticleMass(atom.index, 0.0)
|
| 933 |
+
|
| 934 |
+
# If any heavy atoms were omitted, add them back to avoid steric clashes.
|
| 935 |
+
|
| 936 |
+
nonbonded = [f for f in system.getForces() if isinstance(f, mm.CustomNonbondedForce)][0]
|
| 937 |
+
for atom in self.topology.atoms():
|
| 938 |
+
if atom.element not in (None, hydrogen) and atom not in existingAtomMap:
|
| 939 |
+
system.addParticle(0.0)
|
| 940 |
+
nonbonded.addParticle([])
|
| 941 |
+
newPositions.append(self.positions[atom.index])
|
| 942 |
+
|
| 943 |
+
# For efficiency, only compute interactions that involve a new atom.
|
| 944 |
+
|
| 945 |
+
nonbonded.addInteractionGroup([atom.index for atom in newAtoms], range(system.getNumParticles()))
|
| 946 |
+
|
| 947 |
+
# Do an energy minimization.
|
| 948 |
+
|
| 949 |
+
integrator = mm.LangevinIntegrator(300*unit.kelvin, 10/unit.picosecond, 5*unit.femtosecond)
|
| 950 |
+
if seed is not None:
|
| 951 |
+
integrator.setRandomNumberSeed(seed)
|
| 952 |
+
context = mm.Context(system, integrator)
|
| 953 |
+
context.setPositions(newPositions)
|
| 954 |
+
mm.LocalEnergyMinimizer.minimize(context)
|
| 955 |
+
state = context.getState(getPositions=True)
|
| 956 |
+
if newTopology.getNumResidues() > 1:
|
| 957 |
+
# When looking for pairs of atoms that are too close to each other, exclude pairs that
|
| 958 |
+
# are in the same residue or are directly bonded to each other.
|
| 959 |
+
|
| 960 |
+
exclusions = dict((atom, {a.index for a in atom.residue.atoms()}) for atom in newAtoms)
|
| 961 |
+
for a1, a2 in newTopology.bonds():
|
| 962 |
+
if a1 in exclusions:
|
| 963 |
+
exclusions[a1].add(a2.index)
|
| 964 |
+
if a2 in exclusions:
|
| 965 |
+
exclusions[a2].add(a1.index)
|
| 966 |
+
cutoff = 0.13
|
| 967 |
+
nearest = self._findNearestDistance(context, newAtoms, cutoff, exclusions)
|
| 968 |
+
if nearest < cutoff:
|
| 969 |
+
|
| 970 |
+
# Some atoms are very close together. Run some dynamics while slowly increasing the strength of the
|
| 971 |
+
# repulsive interaction to try to improve the result.
|
| 972 |
+
|
| 973 |
+
for i in range(10):
|
| 974 |
+
context.setParameter('C', 0.15*(i+1))
|
| 975 |
+
integrator.step(200)
|
| 976 |
+
d = self._findNearestDistance(context, newAtoms, cutoff, exclusions)
|
| 977 |
+
if d > nearest:
|
| 978 |
+
nearest = d
|
| 979 |
+
state = context.getState(getPositions=True)
|
| 980 |
+
if nearest >= cutoff:
|
| 981 |
+
break
|
| 982 |
+
context.setState(state)
|
| 983 |
+
context.setParameter('C', 1.0)
|
| 984 |
+
mm.LocalEnergyMinimizer.minimize(context)
|
| 985 |
+
state = context.getState(getPositions=True)
|
| 986 |
+
|
| 987 |
+
# Now create a new Topology, including all atoms from the original one and adding the missing atoms.
|
| 988 |
+
|
| 989 |
+
(newTopology2, newPositions2, newAtoms2, existingAtomMap2) = self._addAtomsToTopology(False, False)
|
| 990 |
+
|
| 991 |
+
# Copy over the minimized positions for the new atoms.
|
| 992 |
+
|
| 993 |
+
for a1, a2 in zip(newAtoms, newAtoms2):
|
| 994 |
+
newPositions2[a2.index] = state.getPositions()[a1.index]
|
| 995 |
+
self.topology = newTopology2
|
| 996 |
+
self.positions = newPositions2
|
| 997 |
+
|
| 998 |
+
def removeHeterogens(self, keepWater=True):
|
| 999 |
+
"""Remove all heterogens from the structure.
|
| 1000 |
+
|
| 1001 |
+
Parameters
|
| 1002 |
+
----------
|
| 1003 |
+
keepWater : bool, optional, default=True
|
| 1004 |
+
If True, water molecules will not be removed.
|
| 1005 |
+
|
| 1006 |
+
Examples
|
| 1007 |
+
--------
|
| 1008 |
+
|
| 1009 |
+
Remove heterogens in Abl structure complexed with imatinib.
|
| 1010 |
+
|
| 1011 |
+
>>> fixer = PDBFixer(pdbid='2F4J')
|
| 1012 |
+
>>> fixer.removeHeterogens(keepWater=False)
|
| 1013 |
+
|
| 1014 |
+
"""
|
| 1015 |
+
|
| 1016 |
+
keep = set(proteinResidues).union(dnaResidues).union(rnaResidues)
|
| 1017 |
+
keep.add('N')
|
| 1018 |
+
keep.add('UNK')
|
| 1019 |
+
if keepWater:
|
| 1020 |
+
keep.add('HOH')
|
| 1021 |
+
toDelete = []
|
| 1022 |
+
for residue in self.topology.residues():
|
| 1023 |
+
if residue.name not in keep:
|
| 1024 |
+
toDelete.append(residue)
|
| 1025 |
+
modeller = app.Modeller(self.topology, self.positions)
|
| 1026 |
+
modeller.delete(toDelete)
|
| 1027 |
+
self.topology = modeller.topology
|
| 1028 |
+
self.positions = modeller.positions
|
| 1029 |
+
|
| 1030 |
+
def addMissingHydrogens(self, pH=7.0, forcefield=None):
|
| 1031 |
+
"""Add missing hydrogen atoms to the structure.
|
| 1032 |
+
|
| 1033 |
+
Parameters
|
| 1034 |
+
----------
|
| 1035 |
+
pH : float, optional, default=7.0
|
| 1036 |
+
The pH based on which to select hydrogens.
|
| 1037 |
+
forcefield : ForceField, optional, default=None
|
| 1038 |
+
The forcefield used when adding and minimizing hydrogens. If None, a default forcefield is used.
|
| 1039 |
+
|
| 1040 |
+
Notes
|
| 1041 |
+
-----
|
| 1042 |
+
No extensive electrostatic analysis is performed; only default residue pKas are used.
|
| 1043 |
+
|
| 1044 |
+
Examples
|
| 1045 |
+
--------
|
| 1046 |
+
|
| 1047 |
+
Examples
|
| 1048 |
+
--------
|
| 1049 |
+
|
| 1050 |
+
Add missing hydrogens appropriate for pH 8.
|
| 1051 |
+
|
| 1052 |
+
>>> fixer = PDBFixer(pdbid='1VII')
|
| 1053 |
+
>>> fixer.addMissingHydrogens(pH=8.0)
|
| 1054 |
+
|
| 1055 |
+
"""
|
| 1056 |
+
modeller = app.Modeller(self.topology, self.positions)
|
| 1057 |
+
modeller.addHydrogens(pH=pH, forcefield=forcefield)
|
| 1058 |
+
self.topology = modeller.topology
|
| 1059 |
+
self.positions = modeller.positions
|
| 1060 |
+
|
| 1061 |
+
def addSolvent(self, boxSize=None, padding=None, boxVectors=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*unit.molar, boxShape='cube'):
|
| 1062 |
+
"""Add a solvent box surrounding the structure.
|
| 1063 |
+
|
| 1064 |
+
Parameters
|
| 1065 |
+
----------
|
| 1066 |
+
boxSize : openmm.Vec3, optional, default=None
|
| 1067 |
+
The size of the box to fill with water. If specified, padding and boxVectors must not be specified.
|
| 1068 |
+
padding : openmm.unit.Quantity compatible with nanometers, optional, default=None
|
| 1069 |
+
Padding around macromolecule for filling box with water. If specified, boxSize and boxVectors must not be specified.
|
| 1070 |
+
boxVectors : 3-tuple of openmm.Vec3, optional, default=None
|
| 1071 |
+
Three vectors specifying the geometry of the box. If specified, padding and boxSize must not be specified.
|
| 1072 |
+
positiveIon : str, optional, default='Na+'
|
| 1073 |
+
The type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'.
|
| 1074 |
+
negativeIon : str, optional, default='Cl-'
|
| 1075 |
+
The type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'.
|
| 1076 |
+
ionicStrength : openmm.unit.Quantity with units compatible with molar, optional, default=0*molar
|
| 1077 |
+
The total concentration of ions (both positive and negative) to add. This does not include ions that are added to neutralize the system.
|
| 1078 |
+
boxShape: str='cube'
|
| 1079 |
+
the box shape to use. Allowed values are 'cube', 'dodecahedron', and 'octahedron'. If padding is None, this is ignored.
|
| 1080 |
+
|
| 1081 |
+
Examples
|
| 1082 |
+
--------
|
| 1083 |
+
|
| 1084 |
+
Add missing residues, heavy atoms, and hydrogens, and then solvate with 10 A padding.
|
| 1085 |
+
|
| 1086 |
+
>>> fixer = PDBFixer(pdbid='1VII')
|
| 1087 |
+
>>> fixer.findMissingResidues()
|
| 1088 |
+
>>> fixer.findMissingAtoms()
|
| 1089 |
+
>>> fixer.addMissingAtoms()
|
| 1090 |
+
>>> fixer.addMissingHydrogens(pH=8.0)
|
| 1091 |
+
>>> fixer.addSolvent(padding=10*unit.angstrom, ionicStrength=0.050*unit.molar)
|
| 1092 |
+
|
| 1093 |
+
"""
|
| 1094 |
+
|
| 1095 |
+
modeller = app.Modeller(self.topology, self.positions)
|
| 1096 |
+
forcefield = self._createForceField(self.topology, True)
|
| 1097 |
+
modeller.addSolvent(forcefield, padding=padding, boxSize=boxSize, boxVectors=boxVectors, boxShape=boxShape, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength)
|
| 1098 |
+
chains = list(modeller.topology.chains())
|
| 1099 |
+
if len(chains) == 1:
|
| 1100 |
+
chains[0].id = 'A'
|
| 1101 |
+
else:
|
| 1102 |
+
chains[-1].id = chr(ord(chains[-2].id)+1)
|
| 1103 |
+
self.topology = modeller.topology
|
| 1104 |
+
self.positions = modeller.positions
|
| 1105 |
+
|
| 1106 |
+
def addMembrane(self, lipidType='POPC', membraneCenterZ=0*unit.nanometer, minimumPadding=1*unit.nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*unit.molar):
|
| 1107 |
+
"""Add a lipid membrane to the structure.
|
| 1108 |
+
|
| 1109 |
+
This method adds both lipids and water, so you should call either addSolvent() or addMembrane(),
|
| 1110 |
+
but not both. See Modeller.addMembrane() for more details.
|
| 1111 |
+
|
| 1112 |
+
Parameters
|
| 1113 |
+
----------
|
| 1114 |
+
lipidType : string='POPC'
|
| 1115 |
+
the type of lipid to use. Supported values are 'POPC', 'POPE', 'DLPC', 'DLPE', 'DMPC', 'DOPC', and 'DPPC'.
|
| 1116 |
+
membraneCenterZ: distance=0*nanometer
|
| 1117 |
+
the position along the Z axis of the center of the membrane
|
| 1118 |
+
minimumPadding : distance=1*nanometer
|
| 1119 |
+
the padding distance to use
|
| 1120 |
+
positiveIon : str, optional, default='Na+'
|
| 1121 |
+
The type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'.
|
| 1122 |
+
negativeIon : str, optional, default='Cl-'
|
| 1123 |
+
The type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'.
|
| 1124 |
+
ionicStrength : openmm.unit.Quantity with units compatible with molar, optional, default=0*molar
|
| 1125 |
+
The total concentration of ions (both positive and negative) to add. This does not include ions that are added to neutralize the system.
|
| 1126 |
+
"""
|
| 1127 |
+
modeller = app.Modeller(self.topology, self.positions)
|
| 1128 |
+
forcefield = self._createForceField(self.topology, True)
|
| 1129 |
+
modeller.addMembrane(forcefield, lipidType=lipidType, minimumPadding=minimumPadding, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength)
|
| 1130 |
+
chains = list(modeller.topology.chains())
|
| 1131 |
+
if len(chains) == 1:
|
| 1132 |
+
chains[0].id = 'A'
|
| 1133 |
+
else:
|
| 1134 |
+
chains[-1].id = chr(ord(chains[-2].id)+1)
|
| 1135 |
+
self.topology = modeller.topology
|
| 1136 |
+
self.positions = modeller.positions
|
| 1137 |
+
|
| 1138 |
+
def _createForceField(self, newTopology, water):
|
| 1139 |
+
"""Create a force field to use for optimizing the positions of newly added atoms."""
|
| 1140 |
+
|
| 1141 |
+
if water:
|
| 1142 |
+
forcefield = app.ForceField('amber14-all.xml', 'amber14/tip3p.xml')
|
| 1143 |
+
nonbonded = [f for f in forcefield._forces if isinstance(f, NonbondedGenerator)][0]
|
| 1144 |
+
radii = {'H':0.198, 'Li':0.203, 'C':0.340, 'N':0.325, 'O':0.299, 'F':0.312, 'Na':0.333, 'Mg':0.141,
|
| 1145 |
+
'P':0.374, 'S':0.356, 'Cl':0.347, 'K':0.474, 'Br':0.396, 'Rb':0.527, 'I':0.419, 'Cs':0.605}
|
| 1146 |
+
else:
|
| 1147 |
+
forcefield = app.ForceField(os.path.join(os.path.dirname(__file__), 'soft.xml'))
|
| 1148 |
+
|
| 1149 |
+
# The Topology may contain residues for which the ForceField does not have a template.
|
| 1150 |
+
# If so, we need to create new templates for them.
|
| 1151 |
+
|
| 1152 |
+
atomTypes = {}
|
| 1153 |
+
bondedToAtom = []
|
| 1154 |
+
for atom in newTopology.atoms():
|
| 1155 |
+
bondedToAtom.append(set())
|
| 1156 |
+
for atom1, atom2 in newTopology.bonds():
|
| 1157 |
+
bondedToAtom[atom1.index].add(atom2.index)
|
| 1158 |
+
bondedToAtom[atom2.index].add(atom1.index)
|
| 1159 |
+
for residue in newTopology.residues():
|
| 1160 |
+
|
| 1161 |
+
# Make sure the ForceField has a template for this residue.
|
| 1162 |
+
|
| 1163 |
+
signature = app.forcefield._createResidueSignature([atom.element for atom in residue.atoms()])
|
| 1164 |
+
if signature in forcefield._templateSignatures:
|
| 1165 |
+
if any(matchResidue(residue, t, bondedToAtom) is not None for t in forcefield._templateSignatures[signature]):
|
| 1166 |
+
continue
|
| 1167 |
+
|
| 1168 |
+
# Create a new template.
|
| 1169 |
+
|
| 1170 |
+
resName = "extra_"+residue.name
|
| 1171 |
+
template = app.ForceField._TemplateData(resName)
|
| 1172 |
+
forcefield._templates[resName] = template
|
| 1173 |
+
indexInResidue = {}
|
| 1174 |
+
for atom in residue.atoms():
|
| 1175 |
+
element = atom.element
|
| 1176 |
+
typeName = 'extra_'+element.symbol
|
| 1177 |
+
if element not in atomTypes:
|
| 1178 |
+
atomTypes[element] = app.ForceField._AtomType(typeName, '', 0.0, element)
|
| 1179 |
+
forcefield._atomTypes[typeName] = atomTypes[element]
|
| 1180 |
+
if water:
|
| 1181 |
+
# Select a reasonable vdW radius for this atom type.
|
| 1182 |
+
|
| 1183 |
+
if element.symbol in radii:
|
| 1184 |
+
sigma = radii[element.symbol]
|
| 1185 |
+
else:
|
| 1186 |
+
sigma = 0.5
|
| 1187 |
+
nonbonded.registerAtom({'type':typeName, 'charge':'0', 'sigma':str(sigma), 'epsilon':'0'})
|
| 1188 |
+
indexInResidue[atom.index] = len(template.atoms)
|
| 1189 |
+
template.atoms.append(app.ForceField._TemplateAtomData(atom.name, typeName, element))
|
| 1190 |
+
for atom in residue.atoms():
|
| 1191 |
+
for bondedTo in bondedToAtom[atom.index]:
|
| 1192 |
+
if bondedTo in indexInResidue:
|
| 1193 |
+
b = (indexInResidue[atom.index], indexInResidue[bondedTo])
|
| 1194 |
+
if b[0] < b[1]:
|
| 1195 |
+
template.bonds.append(b)
|
| 1196 |
+
template.atoms[b[0]].bondedTo.append(b[1])
|
| 1197 |
+
template.atoms[b[1]].bondedTo.append(b[0])
|
| 1198 |
+
else:
|
| 1199 |
+
b = indexInResidue[atom.index]
|
| 1200 |
+
template.externalBonds.append(b)
|
| 1201 |
+
template.atoms[b].externalBonds += 1
|
| 1202 |
+
if signature in forcefield._templateSignatures:
|
| 1203 |
+
forcefield._templateSignatures[signature].append(template)
|
| 1204 |
+
else:
|
| 1205 |
+
forcefield._templateSignatures[signature] = [template]
|
| 1206 |
+
return forcefield
|
| 1207 |
+
|
| 1208 |
+
def _findNearestDistance(self, context, newAtoms, cutoff, exclusions):
|
| 1209 |
+
"""Given a set of newly added atoms, find the closest distance between one of those atoms and another atom."""
|
| 1210 |
+
|
| 1211 |
+
positions = context.getState(getPositions=True).getPositions(asNumpy=True).value_in_unit(unit.nanometer)
|
| 1212 |
+
boxSize = np.max(positions, axis=0)-np.min(positions, axis=0)
|
| 1213 |
+
boxVectors = [(boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2])]
|
| 1214 |
+
cells = app.modeller._CellList(positions, cutoff, boxVectors, False)
|
| 1215 |
+
nearest_squared = sys.float_info.max
|
| 1216 |
+
for atom in newAtoms:
|
| 1217 |
+
excluded = exclusions[atom]
|
| 1218 |
+
for i in cells.neighbors(positions[atom.index]):
|
| 1219 |
+
if i not in excluded:
|
| 1220 |
+
p = positions[atom.index]-positions[i]
|
| 1221 |
+
dist_squared = np.dot(p, p)
|
| 1222 |
+
if dist_squared < nearest_squared:
|
| 1223 |
+
nearest_squared = dist_squared
|
| 1224 |
+
return np.sqrt(nearest_squared)
|
| 1225 |
+
|
| 1226 |
+
|
| 1227 |
+
def main():
|
| 1228 |
+
if len(sys.argv) < 2:
|
| 1229 |
+
# Display the UI.
|
| 1230 |
+
from . import ui
|
| 1231 |
+
ui.launchUI()
|
| 1232 |
+
else:
|
| 1233 |
+
# Run in command line mode.
|
| 1234 |
+
|
| 1235 |
+
from optparse import OptionParser
|
| 1236 |
+
parser = OptionParser(usage="Usage: %prog\n %prog filename [options] \n\nWhen run with no arguments, it launches the user interface. If any arguments are specified, it runs in command line mode.")
|
| 1237 |
+
parser.add_option('--pdbid', default=None, dest='pdbid', metavar='PDBID', help='PDB id to retrieve from RCSB [default: None]')
|
| 1238 |
+
parser.add_option('--url', default=None, dest='url', metavar='URL', help='URL to retrieve PDB from [default: None]')
|
| 1239 |
+
parser.add_option('--output', default='output.pdb', dest='output', metavar='FILENAME', help='output pdb file [default: output.pdb]')
|
| 1240 |
+
parser.add_option('--add-atoms', default='all', dest='atoms', choices=('all', 'heavy', 'hydrogen', 'none'), help='which missing atoms to add: all, heavy, hydrogen, or none [default: all]')
|
| 1241 |
+
parser.add_option('--keep-heterogens', default='all', dest='heterogens', choices=('all', 'water', 'none'), metavar='OPTION', help='which heterogens to keep: all, water, or none [default: all]')
|
| 1242 |
+
parser.add_option('--replace-nonstandard', action='store_true', default=False, dest='nonstandard', help='replace nonstandard residues with standard equivalents')
|
| 1243 |
+
parser.add_option('--add-residues', action='store_true', default=False, dest='residues', help='add missing residues')
|
| 1244 |
+
parser.add_option('--water-box', dest='box', type='float', nargs=3, metavar='X Y Z', help='add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]')
|
| 1245 |
+
parser.add_option('--ph', type='float', default=7.0, dest='ph', help='the pH to use for adding missing hydrogens [default: 7.0]')
|
| 1246 |
+
parser.add_option('--positive-ion', default='Na+', dest='positiveIon', choices=('Cs+', 'K+', 'Li+', 'Na+', 'Rb+'), metavar='ION', help='positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]')
|
| 1247 |
+
parser.add_option('--negative-ion', default='Cl-', dest='negativeIon', choices=('Cl-', 'Br-', 'F-', 'I-'), metavar='ION', help='negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]')
|
| 1248 |
+
parser.add_option('--ionic-strength', type='float', default=0.0, dest='ionic', metavar='STRENGTH', help='molar concentration of ions to add to the water box [default: 0.0]')
|
| 1249 |
+
parser.add_option('--verbose', default=False, action='store_true', dest='verbose', metavar='VERBOSE', help='Print verbose output')
|
| 1250 |
+
(options, args) = parser.parse_args()
|
| 1251 |
+
if (len(args) == 0) and (options.pdbid==None) and (options.url==None):
|
| 1252 |
+
parser.error('No filename specified')
|
| 1253 |
+
if len(args) > 1:
|
| 1254 |
+
parser.error('Must specify a single filename or --pdbid or --url')
|
| 1255 |
+
if options.pdbid != None:
|
| 1256 |
+
if options.verbose: print('Retrieving PDB "' + options.pdbid + '" from RCSB...')
|
| 1257 |
+
fixer = PDBFixer(pdbid=options.pdbid)
|
| 1258 |
+
elif options.url != None:
|
| 1259 |
+
if options.verbose: print('Retrieving PDB from URL "' + options.url + '"...')
|
| 1260 |
+
fixer = PDBFixer(url=options.url)
|
| 1261 |
+
else:
|
| 1262 |
+
fixer = PDBFixer(filename=sys.argv[1])
|
| 1263 |
+
if options.residues:
|
| 1264 |
+
if options.verbose: print('Finding missing residues...')
|
| 1265 |
+
fixer.findMissingResidues()
|
| 1266 |
+
else:
|
| 1267 |
+
fixer.missingResidues = {}
|
| 1268 |
+
if options.nonstandard:
|
| 1269 |
+
if options.verbose: print('Finding nonstandard residues...')
|
| 1270 |
+
fixer.findNonstandardResidues()
|
| 1271 |
+
if options.verbose: print('Replacing nonstandard residues...')
|
| 1272 |
+
fixer.replaceNonstandardResidues()
|
| 1273 |
+
if options.heterogens == 'none':
|
| 1274 |
+
fixer.removeHeterogens(False)
|
| 1275 |
+
elif options.heterogens == 'water':
|
| 1276 |
+
fixer.removeHeterogens(True)
|
| 1277 |
+
if options.verbose: print('Finding missing atoms...')
|
| 1278 |
+
fixer.findMissingAtoms()
|
| 1279 |
+
if options.atoms not in ('all', 'heavy'):
|
| 1280 |
+
fixer.missingAtoms = {}
|
| 1281 |
+
fixer.missingTerminals = {}
|
| 1282 |
+
if options.verbose: print('Adding missing atoms...')
|
| 1283 |
+
fixer.addMissingAtoms()
|
| 1284 |
+
if options.atoms in ('all', 'hydrogen'):
|
| 1285 |
+
if options.verbose: print('Adding missing hydrogens...')
|
| 1286 |
+
fixer.addMissingHydrogens(options.ph)
|
| 1287 |
+
if options.box is not None:
|
| 1288 |
+
if options.verbose: print('Adding solvent...')
|
| 1289 |
+
fixer.addSolvent(boxSize=options.box*unit.nanometer, positiveIon=options.positiveIon,
|
| 1290 |
+
negativeIon=options.negativeIon, ionicStrength=options.ionic*unit.molar)
|
| 1291 |
+
with open(options.output, 'w') as f:
|
| 1292 |
+
if options.verbose: print('Writing output...')
|
| 1293 |
+
if fixer.source is not None:
|
| 1294 |
+
f.write("REMARK 1 PDBFIXER FROM: %s\n" % fixer.source)
|
| 1295 |
+
app.PDBFile.writeFile(fixer.topology, fixer.positions, f, True)
|
| 1296 |
+
if options.verbose: print('Done.')
|
| 1297 |
+
|
| 1298 |
+
if __name__ == '__main__':
|
| 1299 |
+
main()
|
pdbfixer/setup.py
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from setuptools import setup, find_packages
|
| 2 |
+
|
| 3 |
+
setup(
|
| 4 |
+
name="pdbfixer",
|
| 5 |
+
version="1.9.0",
|
| 6 |
+
packages=find_packages(),
|
| 7 |
+
include_package_data=True,
|
| 8 |
+
package_data={
|
| 9 |
+
"pdbfixer": ["templates/*", "*.py", "**/*.py"],
|
| 10 |
+
},
|
| 11 |
+
install_requires=["numpy", "openmm>=7.1"],
|
| 12 |
+
)
|
pdbfixer/soft.xml
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
pdbfixer/templates/A.pdb
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 P A A 1 -2.114 -1.179 3.781 1.00 0.00
|
| 2 |
+
ATOM 2 OP1 A A 1 -1.822 -1.633 5.165 1.00 0.00
|
| 3 |
+
ATOM 3 OP2 A A 1 -3.263 -0.267 3.555 1.00 0.00
|
| 4 |
+
ATOM 4 O5' A A 1 -0.800 -0.568 3.129 1.00 0.00
|
| 5 |
+
ATOM 5 C5' A A 1 0.456 -1.202 3.303 1.00 0.00
|
| 6 |
+
ATOM 6 C4' A A 1 1.422 -0.825 2.211 1.00 0.00
|
| 7 |
+
ATOM 7 O4' A A 1 0.959 -1.348 0.941 1.00 0.00
|
| 8 |
+
ATOM 8 C3' A A 1 1.591 0.662 1.951 1.00 0.00
|
| 9 |
+
ATOM 9 O3' A A 1 2.443 1.298 2.889 1.00 0.00
|
| 10 |
+
ATOM 10 C2' A A 1 2.123 0.687 0.523 1.00 0.00
|
| 11 |
+
ATOM 11 O2' A A 1 3.512 0.395 0.500 1.00 0.00
|
| 12 |
+
ATOM 12 C1' A A 1 1.371 -0.491 -0.105 1.00 0.00
|
| 13 |
+
ATOM 13 N9 A A 1 0.184 -0.049 -0.863 1.00 0.00
|
| 14 |
+
ATOM 14 C8 A A 1 -1.080 0.283 -0.428 1.00 0.00
|
| 15 |
+
ATOM 15 N7 A A 1 -1.892 0.655 -1.393 1.00 0.00
|
| 16 |
+
ATOM 16 C5 A A 1 -1.105 0.569 -2.537 1.00 0.00
|
| 17 |
+
ATOM 17 C6 A A 1 -1.360 0.829 -3.900 1.00 0.00
|
| 18 |
+
ATOM 18 N6 A A 1 -2.535 1.248 -4.391 1.00 0.00
|
| 19 |
+
ATOM 19 N1 A A 1 -0.337 0.635 -4.764 1.00 0.00
|
| 20 |
+
ATOM 20 C2 A A 1 0.851 0.217 -4.302 1.00 0.00
|
| 21 |
+
ATOM 21 N3 A A 1 1.212 -0.058 -3.054 1.00 0.00
|
| 22 |
+
ATOM 22 C4 A A 1 0.177 0.144 -2.219 1.00 0.00
|
| 23 |
+
TER 23 A A 1
|
| 24 |
+
END
|
pdbfixer/templates/ACE.pdb
ADDED
|
@@ -0,0 +1,5 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 C ACE A 1 0.336 0.267 -0.194 1.00 0.00
|
| 2 |
+
ATOM 2 O ACE A 1 -0.134 -0.667 -0.918 1.00 0.00
|
| 3 |
+
ATOM 3 CH3 ACE A 1 -0.201 0.401 1.112 1.00 0.00
|
| 4 |
+
TER 4 ACE A 1
|
| 5 |
+
END
|
pdbfixer/templates/ALA.pdb
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N ALA A 1 -1.444 -0.596 0.968 1.00 0.00
|
| 2 |
+
ATOM 2 CA ALA A 1 -0.194 -0.546 0.198 1.00 0.00
|
| 3 |
+
ATOM 3 CB ALA A 1 -0.584 -0.626 -1.282 1.00 0.00
|
| 4 |
+
ATOM 4 C ALA A 1 0.716 0.684 0.478 1.00 0.00
|
| 5 |
+
ATOM 5 O ALA A 1 1.506 1.084 -0.362 1.00 0.00
|
| 6 |
+
TER 6 ALA A 1
|
| 7 |
+
END
|
pdbfixer/templates/ARG.pdb
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N ARG A 1 -0.592 -1.491 -3.605 1.00 0.00
|
| 2 |
+
ATOM 2 CA ARG A 1 -0.082 -1.191 -2.255 1.00 0.00
|
| 3 |
+
ATOM 3 CB ARG A 1 -1.242 -0.801 -1.315 1.00 0.00
|
| 4 |
+
ATOM 4 CG ARG A 1 -0.782 -0.301 0.075 1.00 0.00
|
| 5 |
+
ATOM 5 CD ARG A 1 -0.102 1.079 0.035 1.00 0.00
|
| 6 |
+
ATOM 6 NE ARG A 1 0.598 1.429 1.295 1.00 0.00
|
| 7 |
+
ATOM 7 CZ ARG A 1 0.068 1.769 2.455 1.00 0.00
|
| 8 |
+
ATOM 8 NH1 ARG A 1 -1.212 1.659 2.695 1.00 0.00
|
| 9 |
+
ATOM 9 NH2 ARG A 1 0.808 2.279 3.405 1.00 0.00
|
| 10 |
+
ATOM 10 C ARG A 1 0.748 -2.351 -1.695 1.00 0.00
|
| 11 |
+
ATOM 11 O ARG A 1 1.788 -2.081 -1.095 1.00 0.00
|
| 12 |
+
TER 12 ARG A 1
|
| 13 |
+
END
|
pdbfixer/templates/ASN.pdb
ADDED
|
@@ -0,0 +1,10 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N ASN A 1 -0.065 -1.086 -1.454 1.00 0.00
|
| 2 |
+
ATOM 2 CA ASN A 1 0.635 -0.556 -0.284 1.00 0.00
|
| 3 |
+
ATOM 3 CB ASN A 1 -0.375 0.064 0.696 1.00 0.00
|
| 4 |
+
ATOM 4 CG ASN A 1 -1.175 1.204 0.086 1.00 0.00
|
| 5 |
+
ATOM 5 OD1 ASN A 1 -0.665 2.274 -0.194 1.00 0.00
|
| 6 |
+
ATOM 6 ND2 ASN A 1 -2.455 1.024 -0.124 1.00 0.00
|
| 7 |
+
ATOM 7 C ASN A 1 1.495 -1.616 0.426 1.00 0.00
|
| 8 |
+
ATOM 8 O ASN A 1 2.605 -1.306 0.846 1.00 0.00
|
| 9 |
+
TER 9 ASN A 1
|
| 10 |
+
END
|
pdbfixer/templates/ASP.pdb
ADDED
|
@@ -0,0 +1,10 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N ASP A 1 -0.296 1.560 1.112 1.00 0.00
|
| 2 |
+
ATOM 2 CA ASP A 1 0.554 0.380 1.103 1.00 0.00
|
| 3 |
+
ATOM 3 CB ASP A 1 -0.246 -0.830 0.562 1.00 0.00
|
| 4 |
+
ATOM 4 CG ASP A 1 -1.176 -0.590 -0.648 1.00 0.00
|
| 5 |
+
ATOM 5 OD1 ASP A 1 -0.926 0.310 -1.478 1.00 0.00
|
| 6 |
+
ATOM 6 OD2 ASP A 1 -2.206 -1.310 -0.667 1.00 0.00
|
| 7 |
+
ATOM 7 C ASP A 1 1.894 0.660 0.383 1.00 0.00
|
| 8 |
+
ATOM 8 O ASP A 1 2.404 -0.180 -0.368 1.00 0.00
|
| 9 |
+
TER 9 ASP A 1
|
| 10 |
+
END
|
pdbfixer/templates/C.pdb
ADDED
|
@@ -0,0 +1,22 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 P C A 1 -2.563 1.193 2.810 1.00 0.00
|
| 2 |
+
ATOM 2 OP1 C A 1 -2.884 2.401 2.011 1.00 0.00
|
| 3 |
+
ATOM 3 OP2 C A 1 -2.477 1.317 4.283 1.00 0.00
|
| 4 |
+
ATOM 4 O5' C A 1 -1.243 0.497 2.246 1.00 0.00
|
| 5 |
+
ATOM 5 C5' C A 1 -0.850 -0.791 2.702 1.00 0.00
|
| 6 |
+
ATOM 6 C4' C A 1 0.199 -1.413 1.809 1.00 0.00
|
| 7 |
+
ATOM 7 O4' C A 1 -0.344 -1.649 0.484 1.00 0.00
|
| 8 |
+
ATOM 8 C3' C A 1 1.442 -0.581 1.550 1.00 0.00
|
| 9 |
+
ATOM 9 O3' C A 1 2.367 -0.613 2.625 1.00 0.00
|
| 10 |
+
ATOM 10 C2' C A 1 1.975 -1.189 0.255 1.00 0.00
|
| 11 |
+
ATOM 11 O2' C A 1 2.641 -2.418 0.508 1.00 0.00
|
| 12 |
+
ATOM 12 C1' C A 1 0.675 -1.498 -0.484 1.00 0.00
|
| 13 |
+
ATOM 13 N1 C A 1 0.289 -0.415 -1.415 1.00 0.00
|
| 14 |
+
ATOM 14 C2 C A 1 0.999 -0.291 -2.603 1.00 0.00
|
| 15 |
+
ATOM 15 O2 C A 1 1.926 -1.086 -2.824 1.00 0.00
|
| 16 |
+
ATOM 16 N3 C A 1 0.659 0.687 -3.476 1.00 0.00
|
| 17 |
+
ATOM 17 C4 C A 1 -0.344 1.523 -3.212 1.00 0.00
|
| 18 |
+
ATOM 18 N4 C A 1 -0.627 2.463 -4.117 1.00 0.00
|
| 19 |
+
ATOM 19 C5 C A 1 -1.092 1.422 -2.008 1.00 0.00
|
| 20 |
+
ATOM 20 C6 C A 1 -0.741 0.447 -1.154 1.00 0.00
|
| 21 |
+
TER 21 C A 1
|
| 22 |
+
END
|
pdbfixer/templates/CYS.pdb
ADDED
|
@@ -0,0 +1,8 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N CYS A 1 0.155 0.347 1.678 1.00 0.00
|
| 2 |
+
ATOM 2 CA CYS A 1 -0.145 0.107 0.268 1.00 0.00
|
| 3 |
+
ATOM 3 CB CYS A 1 1.135 0.017 -0.562 1.00 0.00
|
| 4 |
+
ATOM 4 SG CYS A 1 1.895 1.667 -0.722 1.00 0.00
|
| 5 |
+
ATOM 5 C CYS A 1 -1.045 -1.123 0.048 1.00 0.00
|
| 6 |
+
ATOM 6 O CYS A 1 -1.995 -1.013 -0.712 1.00 0.00
|
| 7 |
+
TER 7 CYS A 1
|
| 8 |
+
END
|
pdbfixer/templates/DA.pdb
ADDED
|
@@ -0,0 +1,23 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 P DA A 1 3.455 -3.048 -0.447 1.00 0.00
|
| 2 |
+
ATOM 2 OP1 DA A 1 3.367 -2.804 -1.906 1.00 0.00
|
| 3 |
+
ATOM 3 OP2 DA A 1 3.853 -4.386 0.047 1.00 0.00
|
| 4 |
+
ATOM 4 O5' DA A 1 2.057 -2.670 0.231 1.00 0.00
|
| 5 |
+
ATOM 5 C5' DA A 1 1.984 -2.545 1.646 1.00 0.00
|
| 6 |
+
ATOM 6 C4' DA A 1 0.732 -1.793 2.062 1.00 0.00
|
| 7 |
+
ATOM 7 O4' DA A 1 0.860 -0.386 1.748 1.00 0.00
|
| 8 |
+
ATOM 8 C3' DA A 1 -0.540 -2.217 1.345 1.00 0.00
|
| 9 |
+
ATOM 9 O3' DA A 1 -1.083 -3.380 1.961 1.00 0.00
|
| 10 |
+
ATOM 10 C2' DA A 1 -1.428 -0.996 1.557 1.00 0.00
|
| 11 |
+
ATOM 11 C1' DA A 1 -0.430 0.158 1.535 1.00 0.00
|
| 12 |
+
ATOM 12 N9 DA A 1 -0.431 0.892 0.273 1.00 0.00
|
| 13 |
+
ATOM 13 C8 DA A 1 0.420 0.716 -0.781 1.00 0.00
|
| 14 |
+
ATOM 14 N7 DA A 1 0.190 1.518 -1.793 1.00 0.00
|
| 15 |
+
ATOM 15 C5 DA A 1 -0.891 2.276 -1.375 1.00 0.00
|
| 16 |
+
ATOM 16 C6 DA A 1 -1.617 3.311 -1.997 1.00 0.00
|
| 17 |
+
ATOM 17 N6 DA A 1 -1.340 3.769 -3.223 1.00 0.00
|
| 18 |
+
ATOM 18 N1 DA A 1 -2.641 3.854 -1.304 1.00 0.00
|
| 19 |
+
ATOM 19 C2 DA A 1 -2.916 3.391 -0.077 1.00 0.00
|
| 20 |
+
ATOM 20 N3 DA A 1 -2.303 2.427 0.609 1.00 0.00
|
| 21 |
+
ATOM 21 C4 DA A 1 -1.289 1.903 -0.103 1.00 0.00
|
| 22 |
+
TER 22 DA A 1
|
| 23 |
+
END
|
pdbfixer/templates/DC.pdb
ADDED
|
@@ -0,0 +1,21 @@
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 P DC A 1 0.295 -2.226 -3.343 1.00 0.00
|
| 2 |
+
ATOM 2 OP1 DC A 1 1.043 -3.343 -3.965 1.00 0.00
|
| 3 |
+
ATOM 3 OP2 DC A 1 -1.169 -2.387 -3.225 1.00 0.00
|
| 4 |
+
ATOM 4 O5' DC A 1 0.883 -1.865 -1.892 1.00 0.00
|
| 5 |
+
ATOM 5 C5' DC A 1 2.189 -1.294 -1.719 1.00 0.00
|
| 6 |
+
ATOM 6 C4' DC A 1 2.331 -0.489 -0.428 1.00 0.00
|
| 7 |
+
ATOM 7 O4' DC A 1 1.384 0.603 -0.437 1.00 0.00
|
| 8 |
+
ATOM 8 C3' DC A 1 2.062 -1.218 0.887 1.00 0.00
|
| 9 |
+
ATOM 9 O3' DC A 1 3.255 -1.815 1.397 1.00 0.00
|
| 10 |
+
ATOM 10 C2' DC A 1 1.590 -0.107 1.824 1.00 0.00
|
| 11 |
+
ATOM 11 C1' DC A 1 1.067 0.976 0.890 1.00 0.00
|
| 12 |
+
ATOM 12 N1 DC A 1 -0.402 1.178 0.991 1.00 0.00
|
| 13 |
+
ATOM 13 C2 DC A 1 -0.894 2.298 1.673 1.00 0.00
|
| 14 |
+
ATOM 14 O2 DC A 1 -0.091 3.098 2.179 1.00 0.00
|
| 15 |
+
ATOM 15 N3 DC A 1 -2.241 2.473 1.753 1.00 0.00
|
| 16 |
+
ATOM 16 C4 DC A 1 -3.071 1.588 1.193 1.00 0.00
|
| 17 |
+
ATOM 17 N4 DC A 1 -4.387 1.805 1.302 1.00 0.00
|
| 18 |
+
ATOM 18 C5 DC A 1 -2.582 0.441 0.498 1.00 0.00
|
| 19 |
+
ATOM 19 C6 DC A 1 -1.255 0.277 0.423 1.00 0.00
|
| 20 |
+
TER 20 DC A 1
|
| 21 |
+
END
|
pdbfixer/templates/DG.pdb
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 P DG A 1 1.161 1.329 -4.498 1.00 0.00
|
| 2 |
+
ATOM 2 OP1 DG A 1 1.796 0.851 -5.745 1.00 0.00
|
| 3 |
+
ATOM 3 OP2 DG A 1 -0.048 2.176 -4.567 1.00 0.00
|
| 4 |
+
ATOM 4 O5' DG A 1 0.805 0.084 -3.560 1.00 0.00
|
| 5 |
+
ATOM 5 C5' DG A 1 1.762 -0.946 -3.341 1.00 0.00
|
| 6 |
+
ATOM 6 C4' DG A 1 1.846 -1.326 -1.871 1.00 0.00
|
| 7 |
+
ATOM 7 O4' DG A 1 1.636 -0.145 -1.058 1.00 0.00
|
| 8 |
+
ATOM 8 C3' DG A 1 0.791 -2.290 -1.343 1.00 0.00
|
| 9 |
+
ATOM 9 O3' DG A 1 1.106 -3.631 -1.683 1.00 0.00
|
| 10 |
+
ATOM 10 C2' DG A 1 0.949 -2.063 0.154 1.00 0.00
|
| 11 |
+
ATOM 11 C1' DG A 1 1.187 -0.555 0.219 1.00 0.00
|
| 12 |
+
ATOM 12 N9 DG A 1 -0.028 0.159 0.606 1.00 0.00
|
| 13 |
+
ATOM 13 C8 DG A 1 -0.940 0.835 -0.171 1.00 0.00
|
| 14 |
+
ATOM 14 N7 DG A 1 -1.931 1.350 0.512 1.00 0.00
|
| 15 |
+
ATOM 15 C5 DG A 1 -1.657 0.985 1.826 1.00 0.00
|
| 16 |
+
ATOM 16 C6 DG A 1 -2.358 1.244 3.030 1.00 0.00
|
| 17 |
+
ATOM 17 O6 DG A 1 -3.413 1.875 3.205 1.00 0.00
|
| 18 |
+
ATOM 18 N1 DG A 1 -1.704 0.676 4.123 1.00 0.00
|
| 19 |
+
ATOM 19 C2 DG A 1 -0.533 -0.046 4.077 1.00 0.00
|
| 20 |
+
ATOM 20 N2 DG A 1 -0.051 -0.517 5.237 1.00 0.00
|
| 21 |
+
ATOM 21 N3 DG A 1 0.126 -0.294 2.961 1.00 0.00
|
| 22 |
+
ATOM 22 C4 DG A 1 -0.493 0.251 1.889 1.00 0.00
|
| 23 |
+
TER 23 DG A 1
|
| 24 |
+
END
|
pdbfixer/templates/DT.pdb
ADDED
|
@@ -0,0 +1,22 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 P DT A 1 -1.137 0.745 4.665 1.00 0.00
|
| 2 |
+
ATOM 2 OP1 DT A 1 -2.403 1.211 5.278 1.00 0.00
|
| 3 |
+
ATOM 3 OP2 DT A 1 -0.705 -0.655 4.875 1.00 0.00
|
| 4 |
+
ATOM 4 O5' DT A 1 -1.190 1.013 3.082 1.00 0.00
|
| 5 |
+
ATOM 5 C5' DT A 1 -1.958 0.196 2.186 1.00 0.00
|
| 6 |
+
ATOM 6 C4' DT A 1 -2.031 0.805 0.789 1.00 0.00
|
| 7 |
+
ATOM 7 O4' DT A 1 -0.707 0.882 0.198 1.00 0.00
|
| 8 |
+
ATOM 8 C3' DT A 1 -2.890 0.053 -0.226 1.00 0.00
|
| 9 |
+
ATOM 9 O3' DT A 1 -3.701 0.978 -0.945 1.00 0.00
|
| 10 |
+
ATOM 10 C2' DT A 1 -1.866 -0.623 -1.137 1.00 0.00
|
| 11 |
+
ATOM 11 C1' DT A 1 -0.766 0.430 -1.140 1.00 0.00
|
| 12 |
+
ATOM 12 N1 DT A 1 0.603 -0.035 -1.562 1.00 0.00
|
| 13 |
+
ATOM 13 C2 DT A 1 0.971 0.054 -2.892 1.00 0.00
|
| 14 |
+
ATOM 14 O2 DT A 1 0.235 0.484 -3.765 1.00 0.00
|
| 15 |
+
ATOM 15 N3 DT A 1 2.244 -0.389 -3.167 1.00 0.00
|
| 16 |
+
ATOM 16 C4 DT A 1 3.169 -0.897 -2.270 1.00 0.00
|
| 17 |
+
ATOM 17 O4 DT A 1 4.288 -1.269 -2.619 1.00 0.00
|
| 18 |
+
ATOM 18 C5 DT A 1 2.725 -0.959 -0.899 1.00 0.00
|
| 19 |
+
ATOM 19 C7 DT A 1 3.643 -1.492 0.163 1.00 0.00
|
| 20 |
+
ATOM 20 C6 DT A 1 1.484 -0.529 -0.617 1.00 0.00
|
| 21 |
+
TER 21 DT A 1
|
| 22 |
+
END
|
pdbfixer/templates/G.pdb
ADDED
|
@@ -0,0 +1,25 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 P G A 1 -3.890 3.026 0.738 1.00 0.00
|
| 2 |
+
ATOM 2 OP1 G A 1 -3.347 3.996 -0.254 1.00 0.00
|
| 3 |
+
ATOM 3 OP2 G A 1 -4.455 3.555 2.014 1.00 0.00
|
| 4 |
+
ATOM 4 O5' G A 1 -2.795 1.882 1.048 1.00 0.00
|
| 5 |
+
ATOM 5 C5' G A 1 -2.835 1.119 2.259 1.00 0.00
|
| 6 |
+
ATOM 6 C4' G A 1 -1.720 0.091 2.340 1.00 0.00
|
| 7 |
+
ATOM 7 O4' G A 1 -1.679 -0.704 1.121 1.00 0.00
|
| 8 |
+
ATOM 8 C3' G A 1 -0.295 0.626 2.465 1.00 0.00
|
| 9 |
+
ATOM 9 O3' G A 1 0.046 1.086 3.774 1.00 0.00
|
| 10 |
+
ATOM 10 C2' G A 1 0.547 -0.561 1.985 1.00 0.00
|
| 11 |
+
ATOM 11 O2' G A 1 0.709 -1.536 3.011 1.00 0.00
|
| 12 |
+
ATOM 12 C1' G A 1 -0.344 -1.143 0.879 1.00 0.00
|
| 13 |
+
ATOM 13 N9 G A 1 0.102 -0.691 -0.466 1.00 0.00
|
| 14 |
+
ATOM 14 C8 G A 1 -0.447 0.259 -1.306 1.00 0.00
|
| 15 |
+
ATOM 15 N7 G A 1 0.226 0.442 -2.421 1.00 0.00
|
| 16 |
+
ATOM 16 C5 G A 1 1.309 -0.426 -2.320 1.00 0.00
|
| 17 |
+
ATOM 17 C6 G A 1 2.388 -0.666 -3.222 1.00 0.00
|
| 18 |
+
ATOM 18 O6 G A 1 2.613 -0.146 -4.319 1.00 0.00
|
| 19 |
+
ATOM 19 N1 G A 1 3.267 -1.620 -2.739 1.00 0.00
|
| 20 |
+
ATOM 20 C2 G A 1 3.122 -2.258 -1.538 1.00 0.00
|
| 21 |
+
ATOM 21 N2 G A 1 4.078 -3.144 -1.251 1.00 0.00
|
| 22 |
+
ATOM 22 N3 G A 1 2.135 -2.053 -0.678 1.00 0.00
|
| 23 |
+
ATOM 23 C4 G A 1 1.254 -1.125 -1.124 1.00 0.00
|
| 24 |
+
TER 24 G A 1
|
| 25 |
+
END
|
pdbfixer/templates/GLN.pdb
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N GLN A 1 -0.269 -2.647 0.620 1.00 0.00
|
| 2 |
+
ATOM 2 CA GLN A 1 0.731 -1.587 0.440 1.00 0.00
|
| 3 |
+
ATOM 3 CB GLN A 1 0.271 -0.507 -0.570 1.00 0.00
|
| 4 |
+
ATOM 4 CG GLN A 1 -0.889 0.383 -0.120 1.00 0.00
|
| 5 |
+
ATOM 5 CD GLN A 1 -1.129 1.583 -1.050 1.00 0.00
|
| 6 |
+
ATOM 6 OE1 GLN A 1 -1.969 1.563 -1.940 1.00 0.00
|
| 7 |
+
ATOM 7 NE2 GLN A 1 -0.409 2.673 -0.880 1.00 0.00
|
| 8 |
+
ATOM 8 C GLN A 1 1.271 -0.987 1.750 1.00 0.00
|
| 9 |
+
ATOM 9 O GLN A 1 2.391 -0.477 1.750 1.00 0.00
|
| 10 |
+
TER 10 GLN A 1
|
| 11 |
+
END
|
pdbfixer/templates/GLU.pdb
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N GLU A 1 -1.989 -1.946 0.778 1.00 0.00
|
| 2 |
+
ATOM 2 CA GLU A 1 -0.599 -1.546 0.468 1.00 0.00
|
| 3 |
+
ATOM 3 CB GLU A 1 -0.599 -0.126 -0.142 1.00 0.00
|
| 4 |
+
ATOM 4 CG GLU A 1 0.761 0.324 -0.712 1.00 0.00
|
| 5 |
+
ATOM 5 CD GLU A 1 0.731 1.684 -1.442 1.00 0.00
|
| 6 |
+
ATOM 6 OE1 GLU A 1 1.141 2.704 -0.822 1.00 0.00
|
| 7 |
+
ATOM 7 OE2 GLU A 1 0.371 1.724 -2.642 1.00 0.00
|
| 8 |
+
ATOM 8 C GLU A 1 0.301 -1.656 1.718 1.00 0.00
|
| 9 |
+
ATOM 9 O GLU A 1 -0.119 -1.166 2.798 1.00 0.00
|
| 10 |
+
TER 10 GLU A 1
|
| 11 |
+
END
|
pdbfixer/templates/GLY.pdb
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N GLY A 1 -1.452 -0.970 -0.205 1.00 0.00
|
| 2 |
+
ATOM 2 CA GLY A 1 -0.522 0.060 -0.665 1.00 0.00
|
| 3 |
+
ATOM 3 C GLY A 1 0.388 0.570 0.455 1.00 0.00
|
| 4 |
+
ATOM 4 O GLY A 1 1.587 0.340 0.415 1.00 0.00
|
| 5 |
+
TER 5 GLY A 1
|
| 6 |
+
END
|
pdbfixer/templates/HIS.pdb
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N HIS A 1 -0.532 -1.545 -1.177 1.00 0.00
|
| 2 |
+
ATOM 2 CA HIS A 1 0.668 -0.725 -1.257 1.00 0.00
|
| 3 |
+
ATOM 3 CB HIS A 1 0.958 -0.235 0.173 1.00 0.00
|
| 4 |
+
ATOM 4 CG HIS A 1 -0.222 0.485 0.783 1.00 0.00
|
| 5 |
+
ATOM 5 ND1 HIS A 1 -1.102 -0.065 1.713 1.00 0.00
|
| 6 |
+
ATOM 6 CE1 HIS A 1 -2.082 0.835 1.883 1.00 0.00
|
| 7 |
+
ATOM 7 NE2 HIS A 1 -1.862 1.915 1.113 1.00 0.00
|
| 8 |
+
ATOM 8 CD2 HIS A 1 -0.682 1.725 0.413 1.00 0.00
|
| 9 |
+
ATOM 9 C HIS A 1 1.868 -1.425 -1.927 1.00 0.00
|
| 10 |
+
ATOM 10 O HIS A 1 2.988 -0.965 -1.717 1.00 0.00
|
| 11 |
+
TER 11 HIS A 1
|
| 12 |
+
END
|
pdbfixer/templates/ILE.pdb
ADDED
|
@@ -0,0 +1,10 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N ILE A 1 -0.264 1.893 -0.670 1.00 0.00
|
| 2 |
+
ATOM 2 CA ILE A 1 0.446 0.733 -0.110 1.00 0.00
|
| 3 |
+
ATOM 3 CB ILE A 1 -0.494 -0.498 -0.030 1.00 0.00
|
| 4 |
+
ATOM 4 CG2 ILE A 1 0.276 -1.757 0.420 1.00 0.00
|
| 5 |
+
ATOM 5 CG1 ILE A 1 -1.674 -0.238 0.930 1.00 0.00
|
| 6 |
+
ATOM 6 CD1 ILE A 1 -2.864 -1.177 0.730 1.00 0.00
|
| 7 |
+
ATOM 7 C ILE A 1 1.736 0.483 -0.910 1.00 0.00
|
| 8 |
+
ATOM 8 O ILE A 1 2.836 0.562 -0.360 1.00 0.00
|
| 9 |
+
TER 9 ILE A 1
|
| 10 |
+
END
|
pdbfixer/templates/LEU.pdb
ADDED
|
@@ -0,0 +1,10 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N LEU A 1 0.876 0.196 -1.980 1.00 0.00
|
| 2 |
+
ATOM 2 CA LEU A 1 0.876 -0.194 -0.560 1.00 0.00
|
| 3 |
+
ATOM 3 CB LEU A 1 -0.574 -0.304 -0.040 1.00 0.00
|
| 4 |
+
ATOM 4 CG LEU A 1 -1.294 1.036 0.190 1.00 0.00
|
| 5 |
+
ATOM 5 CD1 LEU A 1 -2.774 0.796 0.500 1.00 0.00
|
| 6 |
+
ATOM 6 CD2 LEU A 1 -0.694 1.786 1.380 1.00 0.00
|
| 7 |
+
ATOM 7 C LEU A 1 1.616 -1.514 -0.320 1.00 0.00
|
| 8 |
+
ATOM 8 O LEU A 1 1.966 -1.804 0.830 1.00 0.00
|
| 9 |
+
TER 9 LEU A 1
|
| 10 |
+
END
|
pdbfixer/templates/LYS.pdb
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 1 N LYS A 1 -0.320 -2.683 0.169 1.00 0.00
|
| 2 |
+
ATOM 2 CA LYS A 1 0.500 -1.623 0.779 1.00 0.00
|
| 3 |
+
ATOM 3 CB LYS A 1 -0.150 -0.253 0.479 1.00 0.00
|
| 4 |
+
ATOM 4 CG LYS A 1 -0.110 0.217 -0.971 1.00 0.00
|
| 5 |
+
ATOM 5 CD LYS A 1 -0.990 1.467 -1.121 1.00 0.00
|
| 6 |
+
ATOM 6 CE LYS A 1 -0.730 2.197 -2.431 1.00 0.00
|
| 7 |
+
ATOM 7 NZ LYS A 1 0.120 3.387 -2.231 1.00 0.00
|
| 8 |
+
ATOM 8 C LYS A 1 0.640 -1.813 2.309 1.00 0.00
|
| 9 |
+
ATOM 9 O LYS A 1 1.040 -0.893 3.019 1.00 0.00
|
| 10 |
+
TER 10 LYS A 1
|
| 11 |
+
END
|
pdbfixer/templates/MET.pdb
ADDED
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ATOM 1 N MET A 1 -0.356 2.184 0.403 1.00 0.00
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ATOM 2 CA MET A 1 0.594 1.064 0.333 1.00 0.00
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ATOM 3 CB MET A 1 -0.076 -0.216 -0.208 1.00 0.00
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ATOM 4 CG MET A 1 -1.146 -0.756 0.753 1.00 0.00
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ATOM 5 SD MET A 1 -1.606 -2.486 0.483 1.00 0.00
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ATOM 6 CE MET A 1 -2.216 -2.456 -1.228 1.00 0.00
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ATOM 7 C MET A 1 1.844 1.434 -0.497 1.00 0.00
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ATOM 8 O MET A 1 2.964 1.234 -0.038 1.00 0.00
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TER 9 MET A 1
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END
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pdbfixer/templates/NME.pdb
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ATOM 1 N NME A 1 -0.237 0.562 -0.354 1.00 0.00
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ATOM 2 C NME A 1 0.237 -0.562 0.354 1.00 0.00
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TER 3 NME A 1
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END
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pdbfixer/templates/PHE.pdb
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ATOM 1 N PHE A 1 0.069 -0.545 3.506 1.00 0.00
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ATOM 2 CA PHE A 1 -0.321 -0.545 2.096 1.00 0.00
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ATOM 3 CB PHE A 1 0.809 0.085 1.266 1.00 0.00
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ATOM 4 CG PHE A 1 0.519 0.445 -0.194 1.00 0.00
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ATOM 5 CD1 PHE A 1 -0.791 0.565 -0.704 1.00 0.00
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ATOM 6 CE1 PHE A 1 -1.001 0.935 -2.044 1.00 0.00
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ATOM 7 CZ PHE A 1 0.099 1.185 -2.884 1.00 0.00
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ATOM 8 CE2 PHE A 1 1.399 1.085 -2.374 1.00 0.00
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ATOM 9 CD2 PHE A 1 1.609 0.715 -1.044 1.00 0.00
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ATOM 10 C PHE A 1 -0.721 -1.925 1.566 1.00 0.00
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ATOM 11 O PHE A 1 -1.671 -1.995 0.806 1.00 0.00
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TER 12 PHE A 1
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END
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pdbfixer/templates/PRO.pdb
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ATOM 1 N PRO A 1 1.094 0.154 -0.780 1.00 0.00
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ATOM 2 CD PRO A 1 1.964 0.224 0.390 1.00 0.00
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ATOM 3 CG PRO A 1 1.284 -0.636 1.450 1.00 0.00
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ATOM 4 CB PRO A 1 -0.196 -0.386 1.170 1.00 0.00
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ATOM 5 CA PRO A 1 -0.256 -0.246 -0.350 1.00 0.00
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ATOM 6 C PRO A 1 -1.406 0.684 -0.790 1.00 0.00
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ATOM 7 O PRO A 1 -2.486 0.204 -1.090 1.00 0.00
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TER 8 PRO A 1
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END
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pdbfixer/templates/SER.pdb
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ATOM 1 N SER A 1 -1.192 -0.063 1.270 1.00 0.00
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ATOM 2 CA SER A 1 -0.052 -0.153 0.330 1.00 0.00
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ATOM 3 CB SER A 1 -0.512 -0.243 -1.130 1.00 0.00
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ATOM 4 OG SER A 1 -1.332 -1.373 -1.370 1.00 0.00
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ATOM 5 C SER A 1 0.938 1.017 0.460 1.00 0.00
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ATOM 6 O SER A 1 2.148 0.817 0.440 1.00 0.00
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TER 7 SER A 1
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END
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pdbfixer/templates/THR.pdb
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ATOM 1 N THR A 1 -1.233 0.087 1.536 1.00 0.00
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ATOM 2 CA THR A 1 -0.113 -0.063 0.586 1.00 0.00
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ATOM 3 CB THR A 1 -0.633 -0.183 -0.854 1.00 0.00
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ATOM 4 CG2 THR A 1 0.457 -0.443 -1.884 1.00 0.00
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ATOM 5 OG1 THR A 1 -1.493 -1.293 -0.954 1.00 0.00
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ATOM 6 C THR A 1 0.907 1.067 0.716 1.00 0.00
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ATOM 7 O THR A 1 2.107 0.827 0.856 1.00 0.00
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TER 8 THR A 1
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END
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