| Next changeset 1:8740338fdff4 (2021-07-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7d8024bb5f0c425b5a2b37e389802ac250b73c60" |
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added:
macros.xml test-data/small.dcd test-data/test.dcd test-data/test.gro test-data/test.pdb test-data/test.xtc test-data/test1.dcd traj_select_and_merge.xml |
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| diff -r 000000000000 -r f4a1e92ca3d2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 11 19:54:32 2021 +0000 |
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| @@ -0,0 +1,15 @@ +<macros> + <token name="@TOOL_VERSION@">1.9.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mdtraj</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.bpj.2015.08.015</citation> + <yield/> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r f4a1e92ca3d2 test-data/small.dcd |
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| Binary file test-data/small.dcd has changed |
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| diff -r 000000000000 -r f4a1e92ca3d2 test-data/test.dcd |
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| Binary file test-data/test.dcd has changed |
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| diff -r 000000000000 -r f4a1e92ca3d2 test-data/test.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.gro Thu Mar 11 19:54:32 2021 +0000 |
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| b'@@ -0,0 +1,1805 @@\n+Green Red Orange Magenta Azure Cyan Skyblue\n+ 1802\n+ 1BGLC C1 1 -0.078 0.146 0.038\n+ 1BGLC H1 2 -0.078 0.140 0.149\n+ 1BGLC O1 3 -0.134 0.271 0.005\n+ 1BGLC HO1 4 -0.126 0.281 -0.090\n+ 1BGLC C5 5 0.116 0.007 0.033\n+ 1BGLC H5 6 0.115 0.003 0.145\n+ 1BGLC O5 7 0.055 0.130 -0.011\n+ 1BGLC C2 8 -0.164 0.034 -0.017\n+ 1BGLC H2 9 -0.161 0.039 -0.129\n+ 1BGLC O2 10 -0.300 0.047 0.023\n+ 1BGLC HO2 11 -0.356 0.073 -0.051\n+ 1BGLC C3 12 -0.107 -0.100 0.026\n+ 1BGLC H3 13 -0.107 -0.103 0.137\n+ 1BGLC O3 14 -0.185 -0.208 -0.022\n+ 1BGLC HO3 15 -0.238 -0.241 0.052\n+ 1BGLC C4 16 0.036 -0.109 -0.022\n+ 1BGLC H4 17 0.037 -0.104 -0.134\n+ 1BGLC O4 18 0.095 -0.232 0.016\n+ 1BGLC HO4 19 0.066 -0.298 -0.049\n+ 1BGLC C6 20 0.260 0.008 -0.013\n+ 1BGLC H61 21 0.311 -0.086 0.018\n+ 1BGLC H62 22 0.265 0.014 -0.124\n+ 1BGLC O6 23 0.332 0.119 0.041\n+ 1BGLC HO6 24 0.295 0.199 0.002\n+ 1TIP3 OH2 25 -0.133 -0.342 -0.676\n+ 1TIP3 H1 26 -0.148 -0.245 -0.676\n+ 1TIP3 H2 27 -0.208 -0.372 -0.730\n+ 2TIP3 OH2 28 -0.275 -0.419 -0.266\n+ 2TIP3 H1 29 -0.241 -0.468 -0.188\n+ 2TIP3 H2 30 -0.319 -0.492 -0.315\n+ 3TIP3 OH2 31 -1.049 -0.481 -0.164\n+ 3TIP3 H1 32 -1.046 -0.555 -0.101\n+ 3TIP3 H2 33 -0.955 -0.470 -0.187\n+ 4TIP3 OH2 34 0.092 -0.139 -0.466\n+ 4TIP3 H1 35 0.055 -0.219 -0.425\n+ 4TIP3 H2 36 0.149 -0.107 -0.396\n+ 5TIP3 OH2 37 -0.942 0.021 -0.347\n+ 5TIP3 H1 38 -0.960 -0.072 -0.374\n+ 5TIP3 H2 39 -0.873 0.006 -0.281\n+ 6TIP3 OH2 40 -1.301 -0.677 -0.764\n+ 6TIP3 H1 41 -1.275 -0.593 -0.725\n+ 6TIP3 H2 42 -1.384 -0.696 -0.715\n+ 7TIP3 OH2 43 -1.191 -0.445 -0.529\n+ 7TIP3 H1 44 -1.148 -0.530 -0.507\n+ 7TIP3 H2 45 -1.116 -0.384 -0.532\n+ 8TIP3 OH2 46 -0.185 0.403 -0.441\n+ 8TIP3 H1 47 -0.148 0.326 -0.489\n+ 8TIP3 H2 48 -0.232 0.364 -0.366\n+ 9TIP3 OH2 49 -0.389 -0.168 -0.219\n+ 9TIP3 H1 50 -0.357 -0.252 -0.259\n+ 9TIP3 H2 51 -0.318 -0.156 -0.153\n+ 10TIP3 OH2 52 0.472 -1.028 -0.166\n+ 10TIP3 H1 53 0.486 -0.956 -0.102\n+ 10TIP3 H2 54 0.532 -1.002 -0.238\n+ 11TIP3 OH2 55 -0.108 -0.743 -0.254\n+ 11TIP3 H1 56 -0.100 -0.840 -0.239\n+ 11TIP3 H2 57 -0.131 -0.742 -0.349\n+ 12TIP3 OH2 58 -0.759 -0.942 -0.512\n+ 12TIP3 H1 59 -0.757 -0.855 -0.558\n+ 12TIP3 H2 60 -0.802 -0.997 -0.581\n+ 13TIP3 OH2 61 0.010 -0.901 -0.684\n+ 13TIP3 H1 62 0.058 -0.925 -0.601\n+ 13TIP3 H2 63 0.082 -0.857 -0.734\n+ 14TIP3 OH2 64 -1.087 -0.689 -0.462\n+ 14TIP3 H1 65 -1.035 -0.748 -0.405\n+ 14TIP3 H2 66 -1.075 -0.732 -0.549\n+ 15TIP3 OH2 67 -0.650 -0.546 -0.465\n+ 15TIP3 H1 68 -0.561 -0.579 -0.442\n+ 15TIP3 H2 69 -0.682 -0.615 -0.526\n+ 16TIP3 OH2 70 0.498 -0.853 0.055\n+ 16TIP3 H1 71 0.422 -0.796 0.031\n+ 16TIP3 H2 72 0.505 -0.834 0.150\n+ 17TIP3 OH2 73 -0.915 -1.025 -0.087\n+ 17TIP3 H1 74 -0.947 -0.972 -0.162\n+ 17TIP3 H2 75 -0.982 -1.002 -0.018\n+ 18TIP3 OH2 76 -0.183 -0.080 -0.751\n+ 18TIP3 H1 77 -0.207 -0.087 -0.845\n+ 18TIP3 H2 78 -0.233 -0.001 -0.725\n+ 19TIP3 OH2 79 -0.639 -0.251 -0.125\n+ 19TIP3 H1 80 -0.695 -0.177 -0.091\n+ 19TIP3 H2 81 -0.559 -0.202 -0.156\n+ 20TIP3 OH2 82 0.144 -0.946 -0.459\n+ 20TIP3 H1 83 0.144 -1.031 -0.411\n+ 20TIP3 H2 84 0.184 -0.886 -0.393\n+ 21TIP3 OH2 85 -0.936 -0.870 -0.316\n+ 21TIP3 H1 '..b'01 1.217\n+ 565TIP3 OH2 1717 0.242 0.897 0.515\n+ 565TIP3 H1 1718 0.281 0.849 0.591\n+ 565TIP3 H2 1719 0.148 0.872 0.520\n+ 566TIP3 OH2 1720 0.216 1.065 1.031\n+ 566TIP3 H1 1721 0.234 0.968 1.032\n+ 566TIP3 H2 1722 0.290 1.092 0.972\n+ 567TIP3 OH2 1723 0.281 0.800 1.037\n+ 567TIP3 H1 1724 0.301 0.749 1.119\n+ 567TIP3 H2 1725 0.213 0.742 0.998\n+ 568TIP3 OH2 1726 0.406 0.783 0.709\n+ 568TIP3 H1 1727 0.458 0.721 0.654\n+ 568TIP3 H2 1728 0.473 0.850 0.732\n+ 569TIP3 OH2 1729 -1.297 0.789 0.996\n+ 569TIP3 H1 1730 -1.302 0.837 1.081\n+ 569TIP3 H2 1731 -1.272 0.864 0.936\n+ 570TIP3 OH2 1732 0.367 0.662 1.253\n+ 570TIP3 H1 1733 0.434 0.592 1.242\n+ 570TIP3 H2 1734 0.426 0.734 1.282\n+ 571TIP3 OH2 1735 -1.078 0.633 1.186\n+ 571TIP3 H1 1736 -1.122 0.617 1.102\n+ 571TIP3 H2 1737 -1.040 0.545 1.205\n+ 572TIP3 OH2 1738 -1.188 0.612 0.815\n+ 572TIP3 H1 1739 -1.118 0.663 0.768\n+ 572TIP3 H2 1740 -1.224 0.680 0.876\n+ 573TIP3 OH2 1741 -0.611 0.608 1.207\n+ 573TIP3 H1 1742 -0.521 0.629 1.177\n+ 573TIP3 H2 1743 -0.609 0.512 1.217\n+ 574TIP3 OH2 1744 0.079 0.634 0.952\n+ 574TIP3 H1 1745 0.001 0.691 0.971\n+ 574TIP3 H2 1746 0.035 0.546 0.958\n+ 575TIP3 OH2 1747 -0.983 0.745 0.678\n+ 575TIP3 H1 1748 -0.931 0.693 0.613\n+ 575TIP3 H2 1749 -0.911 0.783 0.734\n+ 576TIP3 OH2 1750 -0.522 0.839 0.909\n+ 576TIP3 H1 1751 -0.482 0.760 0.949\n+ 576TIP3 H2 1752 -0.492 0.907 0.973\n+ 577TIP3 OH2 1753 0.622 1.274 1.078\n+ 577TIP3 H1 1754 0.608 1.356 1.027\n+ 577TIP3 H2 1755 0.561 1.214 1.032\n+ 578TIP3 OH2 1756 1.110 1.110 1.235\n+ 578TIP3 H1 1757 1.015 1.126 1.218\n+ 578TIP3 H2 1758 1.143 1.103 1.143\n+ 579TIP3 OH2 1759 1.248 1.001 0.562\n+ 579TIP3 H1 1760 1.218 0.937 0.629\n+ 579TIP3 H2 1761 1.177 0.997 0.497\n+ 580TIP3 OH2 1762 0.584 0.830 1.291\n+ 580TIP3 H1 1763 0.674 0.850 1.319\n+ 580TIP3 H2 1764 0.595 0.819 1.195\n+ 581TIP3 OH2 1765 0.597 0.971 0.794\n+ 581TIP3 H1 1766 0.667 1.028 0.756\n+ 581TIP3 H2 1767 0.538 1.040 0.830\n+ 582TIP3 OH2 1768 0.836 1.132 1.195\n+ 582TIP3 H1 1769 0.757 1.159 1.145\n+ 582TIP3 H2 1770 0.842 1.036 1.175\n+ 583TIP3 OH2 1771 1.199 1.095 0.971\n+ 583TIP3 H1 1772 1.284 1.141 0.966\n+ 583TIP3 H2 1773 1.152 1.137 0.895\n+ 584TIP3 OH2 1774 1.084 1.181 0.747\n+ 584TIP3 H1 1775 0.991 1.193 0.721\n+ 584TIP3 H2 1776 1.124 1.146 0.666\n+ 585TIP3 OH2 1777 0.895 0.866 1.164\n+ 585TIP3 H1 1778 0.862 0.774 1.177\n+ 585TIP3 H2 1779 0.984 0.849 1.134\n+ 586TIP3 OH2 1780 1.144 0.861 0.791\n+ 586TIP3 H1 1781 1.149 0.935 0.854\n+ 586TIP3 H2 1782 1.194 0.793 0.838\n+ 587TIP3 OH2 1783 0.748 1.190 0.704\n+ 587TIP3 H1 1784 0.740 1.273 0.755\n+ 587TIP3 H2 1785 0.725 1.220 0.616\n+ 588TIP3 OH2 1786 0.570 0.804 1.012\n+ 588TIP3 H1 1787 0.473 0.797 1.010\n+ 588TIP3 H2 1788 0.587 0.864 0.937\n+ 589TIP3 OH2 1789 0.812 0.616 1.222\n+ 589TIP3 H1 1790 0.719 0.585 1.215\n+ 589TIP3 H2 1791 0.858 0.530 1.213\n+ 590TIP3 OH2 1792 0.724 0.617 0.837\n+ 590TIP3 H1 1793 0.780 0.674 0.780\n+ 590TIP3 H2 1794 0.684 0.682 0.899\n+ 591TIP3 OH2 1795 1.267 0.567 1.239\n+ 591TIP3 H1 1796 1.345 0.614 1.208\n+ 591TIP3 H2 1797 1.290 0.542 1.330\n+ 592TIP3 OH2 1798 0.907 0.762 0.664\n+ 592TIP3 H1 1799 0.949 0.699 0.603\n+ 592TIP3 H2 1800 0.984 0.795 0.714\n+ 1SOD SOD 1801 -0.803 0.535 -0.778\n+ 1CLA CLA 1802 -0.538 0.247 0.749\n+ 0.00000 0.00000 0.00000\n' |
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| diff -r 000000000000 -r f4a1e92ca3d2 test-data/test.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.pdb Thu Mar 11 19:54:32 2021 +0000 |
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| b'@@ -0,0 +1,1811 @@\n+REMARK DIHEDRAL 6 0 7 11 $FC 60.0 \n+REMARK DIHEDRAL 0 7 11 15 $FC -60.0 \n+REMARK DIHEDRAL 7 11 15 4 $FC 60.0 \n+REMARK DIHEDRAL 11 15 4 6 $FC -60.0 \n+REMARK DIHEDRAL 15 4 6 0 $FC 60.0 \n+REMARK DIHEDRAL 4 6 0 7 $FC -60.0 \n+REMARK DATE: 10/24/19 2:43:11 CREATED BY USER: apache \n+ATOM 1 C1 BGLC 1 -0.782 1.463 0.380 1.00 1.00 CARB\n+ATOM 2 H1 BGLC 1 -0.775 1.400 1.492 1.00 0.00 CARB\n+ATOM 3 O1 BGLC 1 -1.337 2.710 0.046 1.00 0.50 CARB\n+ATOM 4 HO1 BGLC 1 -1.260 2.812 -0.905 1.00 0.00 CARB\n+ATOM 5 C5 BGLC 1 1.162 0.073 0.328 1.00 1.00 CARB\n+ATOM 6 H5 BGLC 1 1.149 0.033 1.445 1.00 0.00 CARB\n+ATOM 7 O5 BGLC 1 0.554 1.297 -0.113 1.00 1.00 CARB\n+ATOM 8 C2 BGLC 1 -1.643 0.339 -0.171 1.00 1.00 CARB\n+ATOM 9 H2 BGLC 1 -1.610 0.391 -1.286 1.00 0.00 CARB\n+ATOM 10 O2 BGLC 1 -3.001 0.466 0.233 1.00 0.50 CARB\n+ATOM 11 HO2 BGLC 1 -3.560 0.732 -0.506 1.00 0.00 CARB\n+ATOM 12 C3 BGLC 1 -1.070 -0.995 0.256 1.00 1.00 CARB\n+ATOM 13 H3 BGLC 1 -1.072 -1.034 1.374 1.00 0.00 CARB\n+ATOM 14 O3 BGLC 1 -1.854 -2.081 -0.221 1.00 0.50 CARB\n+ATOM 15 HO3 BGLC 1 -2.383 -2.412 0.516 1.00 0.00 CARB\n+ATOM 16 C4 BGLC 1 0.358 -1.094 -0.224 1.00 1.00 CARB\n+ATOM 17 H4 BGLC 1 0.373 -1.035 -1.339 1.00 0.00 CARB\n+ATOM 18 O4 BGLC 1 0.954 -2.322 0.160 1.00 0.50 CARB\n+ATOM 19 HO4 BGLC 1 0.664 -2.977 -0.495 1.00 0.00 CARB\n+ATOM 20 C6 BGLC 1 2.604 0.083 -0.133 1.00 1.00 CARB\n+ATOM 21 H61 BGLC 1 3.112 -0.856 0.180 1.00 0.00 CARB\n+ATOM 22 H62 BGLC 1 2.647 0.136 -1.245 1.00 0.00 CARB\n+ATOM 23 O6 BGLC 1 3.319 1.187 0.412 1.00 0.50 CARB\n+ATOM 24 HO6 BGLC 1 2.952 1.993 0.021 1.00 0.00 CARB\n+ATOM 25 OH2 TIP3 1 -1.328 -3.419 -6.761 1.00 0.00 SOLV\n+ATOM 26 H1 TIP3 1 -1.476 -2.452 -6.760 1.00 0.00 SOLV\n+ATOM 27 H2 TIP3 1 -2.081 -3.717 -7.300 1.00 0.00 SOLV\n+ATOM 28 OH2 TIP3 2 -2.751 -4.194 -2.655 1.00 0.00 SOLV\n+ATOM 29 H1 TIP3 2 -2.410 -4.676 -1.878 1.00 0.00 SOLV\n+ATOM 30 H2 TIP3 2 -3.191 -4.916 -3.149 1.00 0.00 SOLV\n+ATOM 31 OH2 TIP3 3 -10.493 -4.811 -1.639 1.00 0.00 SOLV\n+ATOM 32 H1 TIP3 3 -10.464 -5.550 -1.006 1.00 0.00 SOLV\n+ATOM 33 H2 TIP3 3 -9.554 -4.703 -1.869 1.00 0.00 SOLV\n+ATOM 34 OH2 TIP3 4 0.924 -1.390 -4.659 1.00 0.00 SOLV\n+ATOM 35 H1 TIP3 4 0.549 -2.192 -4.247 1.00 0.00 SOLV\n+ATOM 36 H2 TIP3 4 1.486 -1.067 -3.955 1.00 0.00 SOLV\n+ATOM 37 OH2 TIP3 5 -9.421 0.213 -3.466 1.00 0.00 SOLV\n+ATOM 38 H1 TIP3 5 -9.600 -0.715 -3.737 1.00 0.00 SOLV\n+ATOM 39 H2 TIP3 5 -8.730 0.063 -2.806 1.00 0.00 SOLV\n+ATOM 40 OH2 TIP3 6 -13.015 -6.771 -7.637 1.00 0.00 SOLV\n+ATOM 41 H1 TIP3 6 -12.753 -5.927 -7.249 1.00 0.00 SOLV\n+ATOM 42 H2 TIP3 6 -13.837 -6.959 -7.155 1.00 0.00 SOLV\n+ATOM 43 OH2 TIP3 7 -11.908 -4.446 -5.293 1.00 0.00 SOLV\n+ATOM '..b' H2 TIP3 576 -4.921 9.073 9.732 1.00 0.00 SOLV\n+ATOM 1753 OH2 TIP3 577 6.216 12.742 10.782 1.00 0.00 SOLV\n+ATOM 1754 H1 TIP3 577 6.083 13.556 10.272 1.00 0.00 SOLV\n+ATOM 1755 H2 TIP3 577 5.611 12.143 10.320 1.00 0.00 SOLV\n+ATOM 1756 OH2 TIP3 578 11.100 11.104 12.354 1.00 0.00 SOLV\n+ATOM 1757 H1 TIP3 578 10.148 11.262 12.182 1.00 0.00 SOLV\n+ATOM 1758 H2 TIP3 578 11.431 11.034 11.431 1.00 0.00 SOLV\n+ATOM 1759 OH2 TIP3 579 12.480 10.007 5.620 1.00 0.00 SOLV\n+ATOM 1760 H1 TIP3 579 12.183 9.366 6.294 1.00 0.00 SOLV\n+ATOM 1761 H2 TIP3 579 11.766 9.972 4.970 1.00 0.00 SOLV\n+ATOM 1762 OH2 TIP3 580 5.837 8.297 12.915 1.00 0.00 SOLV\n+ATOM 1763 H1 TIP3 580 6.740 8.502 13.187 1.00 0.00 SOLV\n+ATOM 1764 H2 TIP3 580 5.954 8.193 11.946 1.00 0.00 SOLV\n+ATOM 1765 OH2 TIP3 581 5.968 9.707 7.938 1.00 0.00 SOLV\n+ATOM 1766 H1 TIP3 581 6.666 10.282 7.561 1.00 0.00 SOLV\n+ATOM 1767 H2 TIP3 581 5.377 10.402 8.298 1.00 0.00 SOLV\n+ATOM 1768 OH2 TIP3 582 8.363 11.320 11.953 1.00 0.00 SOLV\n+ATOM 1769 H1 TIP3 582 7.566 11.591 11.455 1.00 0.00 SOLV\n+ATOM 1770 H2 TIP3 582 8.416 10.357 11.751 1.00 0.00 SOLV\n+ATOM 1771 OH2 TIP3 583 11.987 10.955 9.711 1.00 0.00 SOLV\n+ATOM 1772 H1 TIP3 583 12.840 11.411 9.660 1.00 0.00 SOLV\n+ATOM 1773 H2 TIP3 583 11.518 11.369 8.947 1.00 0.00 SOLV\n+ATOM 1774 OH2 TIP3 584 10.835 11.808 7.474 1.00 0.00 SOLV\n+ATOM 1775 H1 TIP3 584 9.912 11.929 7.210 1.00 0.00 SOLV\n+ATOM 1776 H2 TIP3 584 11.236 11.458 6.665 1.00 0.00 SOLV\n+ATOM 1777 OH2 TIP3 585 8.949 8.660 11.645 1.00 0.00 SOLV\n+ATOM 1778 H1 TIP3 585 8.618 7.740 11.768 1.00 0.00 SOLV\n+ATOM 1779 H2 TIP3 585 9.844 8.487 11.336 1.00 0.00 SOLV\n+ATOM 1780 OH2 TIP3 586 11.436 8.610 7.911 1.00 0.00 SOLV\n+ATOM 1781 H1 TIP3 586 11.493 9.350 8.543 1.00 0.00 SOLV\n+ATOM 1782 H2 TIP3 586 11.939 7.925 8.380 1.00 0.00 SOLV\n+ATOM 1783 OH2 TIP3 587 7.481 11.899 7.038 1.00 0.00 SOLV\n+ATOM 1784 H1 TIP3 587 7.396 12.734 7.553 1.00 0.00 SOLV\n+ATOM 1785 H2 TIP3 587 7.245 12.205 6.157 1.00 0.00 SOLV\n+ATOM 1786 OH2 TIP3 588 5.702 8.039 10.122 1.00 0.00 SOLV\n+ATOM 1787 H1 TIP3 588 4.729 7.972 10.101 1.00 0.00 SOLV\n+ATOM 1788 H2 TIP3 588 5.869 8.638 9.367 1.00 0.00 SOLV\n+ATOM 1789 OH2 TIP3 589 8.118 6.162 12.222 1.00 0.00 SOLV\n+ATOM 1790 H1 TIP3 589 7.194 5.847 12.150 1.00 0.00 SOLV\n+ATOM 1791 H2 TIP3 589 8.575 5.302 12.126 1.00 0.00 SOLV\n+ATOM 1792 OH2 TIP3 590 7.240 6.173 8.375 1.00 0.00 SOLV\n+ATOM 1793 H1 TIP3 590 7.795 6.735 7.801 1.00 0.00 SOLV\n+ATOM 1794 H2 TIP3 590 6.845 6.817 8.985 1.00 0.00 SOLV\n+ATOM 1795 OH2 TIP3 591 12.672 5.671 12.388 1.00 0.00 SOLV\n+ATOM 1796 H1 TIP3 591 13.455 6.140 12.084 1.00 0.00 SOLV\n+ATOM 1797 H2 TIP3 591 12.898 5.419 13.300 1.00 0.00 SOLV\n+ATOM 1798 OH2 TIP3 592 9.071 7.621 6.638 1.00 0.00 SOLV\n+ATOM 1799 H1 TIP3 592 9.494 6.987 6.028 1.00 0.00 SOLV\n+ATOM 1800 H2 TIP3 592 9.845 7.955 7.135 1.00 0.00 SOLV\n+ATOM 1801 SOD SOD 1 -8.032 5.354 -7.781 1.00 0.00 SOD \n+ATOM 1802 CLA CLA 1 -5.382 2.471 7.495 1.00 0.00 CLA \n+TER 1803 CLA 1\n+END\n' |
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| diff -r 000000000000 -r f4a1e92ca3d2 test-data/test.xtc |
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| Binary file test-data/test.xtc has changed |
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| diff -r 000000000000 -r f4a1e92ca3d2 test-data/test1.dcd |
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| Binary file test-data/test1.dcd has changed |
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| diff -r 000000000000 -r f4a1e92ca3d2 traj_select_and_merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/traj_select_and_merge.xml Thu Mar 11 19:54:32 2021 +0000 |
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| @@ -0,0 +1,166 @@ +<tool id="traj_selections_and_merge" name="Trajectory select and merge" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>- select specific molecules and merge multiple trajectories.</description> + <macros> + <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$strin' str.${strin.ext} && + #for $trj in $trajs: + ln -s '$trj' `basename '$trj'`.${select.traj_fmt} && + #end for + python '$mdtraj_script' + --istr str.${strin.ext} + --itraj *.${select.traj_fmt} + --isele '$selection' + --o_str output.${strin.ext} + --o_trj output.${select.traj_fmt} && + mv output.${strin.ext} '$outputstr' && + mv output.${select.traj_fmt} '$outputtraj' +]]></command> + <configfiles> + <configfile name="mdtraj_script"><![CDATA[ +import mdtraj as md +import sys +import argparse + +def parse_command_line(argv): + parser = argparse.ArgumentParser() + parser.add_argument('--istr', help='input str') + parser.add_argument('--itraj', nargs='+', help='input traj') + parser.add_argument('--isele', help='selection') + parser.add_argument('--o_str', help='MDA Ramachandran plot') + parser.add_argument('--o_trj', help='Seaborn Ramachandran plot') + return parser.parse_args() + +args = parse_command_line(sys.argv) +list_of_traj = [] +if args.itraj is not None: + list_of_traj.extend(args.itraj) + +try: + traj = md.load(list_of_traj, top=args.istr) +except Exception as einstance: + print(type(einstance)) + print(einstance.args) + print(einstance) +topology = traj.topology +try: + atoms_to_keep = topology.select(str(args.isele)) +except Exception as einstance: + print("Error: Check the selection is valid for the dataset chosen") + print(type(einstance)) + print(einstance.args) + print(einstance) +traj.restrict_atoms(atoms_to_keep) +newstruct = traj.slice(1) +newstruct.save(args.o_str) +traj.save(args.o_trj) +]]></configfile> + </configfiles> + <inputs> + <param format="pdb,gro" name="strin" type="data" label="PDB/GRO input" /> + <conditional name="select"> + <param name="traj_fmt" type="select" label="Trajectory format" help="Select the trajectory format to filter by"> + <option selected="True" value="dcd">dcd</option> + <option value="xtc">xtc</option> + <option value="netcdf">netcdf</option> + <option value="trr">trr</option> + </param> + <when value="dcd"> + <param name="trajs" multiple="True" type="data" format="dcd" label="trajectory file(s) input" /> + </when> + <when value="xtc"> + <param name="trajs" multiple="True" type="data" format="xtc" label="trajectory file(s) input" /> + </when> + <when value="netcdf"> + <param name="trajs" multiple="True" type="data" format="netcdf" label="trajectory file(s) input" /> + </when> + <when value="trr"> + <param name="trajs" multiple="True" type="data" format="trr" label="trajectory file(s) input" /> + </when> + </conditional> + <param name="selection" type="text" value="not water and not segname POT and not segname CLA" label="selection to keep" help="A valid mdtraj style selection string that selects atoms to keep in structure and trajectory file output"> + <validator type="regex" message="Maximum of 60 characters and space allowed.">^[a-zA-Z0-9 ]{1,60}$</validator> + </param> + </inputs> + <outputs> + <data name="outputstr" format_source="strin" /> + <data name="outputtraj" format_source="trajs" /> + </outputs> + <tests> + <test> + <param name="strin" value="test.pdb" ftype="pdb" /> + <conditional name="select"> + <param name="traj_fmt" value="dcd" /> + <param name="trajs" value="test.dcd" /> + </conditional> + <param name="selection" value="not water and not segname SOD and not segname CLA" /> + <output name="outputstr"> + <assert_contents> + <has_text text="ATOM 1 C1 BGL A 1 " /> + <has_text text="ATOM 24 HO6 BGL A 1" /> + </assert_contents> + </output> + <output name="outputtraj"> + <assert_contents> + <has_size value="4000" delta="100" /> + </assert_contents> + </output> + </test> + <test> + <param name="strin" value="test.gro" ftype="gro" /> + <conditional name="select"> + <param name="traj_fmt" value="xtc" /> + <param name="trajs" value="test.xtc" /> + </conditional> + <param name="selection" value="resname BGLC" /> + <output name="outputstr"> + <assert_contents> + <has_text text=" 1BGLC C1 1" /> + <has_text text=" 1BGLC HO6 24" /> + </assert_contents> + </output> + <output name="outputtraj"> + <assert_contents> + <has_size value="1940" delta="100" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +This tool is a filter and multijoin for trajectory files. You can select specific molecules (or atoms) and save out a new structure and trajectory file. If there are multiple trajectories selected, then these will all be combined into a single trajectory output. + +Use this tool to: + - reduce the size of trajectories for later analysis and help with selections where analysis tools may not have selection features that you need. + - combine trajectories for analysis, this is imperative for proper molecular dynamics analysis. + +_____ + + +.. class:: infomark + +**Input** + + - Structure file (pdb,gro) + - Choose a format of trajectory file (trr,xtc, dcd, netcdf) + - Trajectory file(s) (the files displayed are filtered by the trajectory type chosen). + - A valid mdtraj selection for the system under consideration. For example: not water and segname CARA and not type H + +_____ + + +.. class:: infomark + +**Output** + + - Structure file (same as input format) + - Trajectory file (same as input format) + ]]></help> + <expand macro="citations" /> +</tool> |