| Next changeset 1:f40eb1f8536f (2019-10-07) |
|
Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 8aeaf3f199cccb1bbb26a29628e7bb75abaf189d |
|
added:
md_converter.xml test-data/str.gro test-data/str.pdb test-data/str2.pdb test-data/traj.dcd test-data/traj.trr test-data/traj.xtc |
| b |
| diff -r 000000000000 -r acce5039ece7 md_converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/md_converter.xml Sun Oct 14 05:31:36 2018 -0400 |
| [ |
| @@ -0,0 +1,115 @@ +<tool id="md_converter" name="MDTraj file converter" version="1.9.1"> + + <description>- interconvert between MD trajectory or structure file formats.</description> + + <requirements> + <requirement type="package" version="1.9.1">mdtraj</requirement> + <requirement type="package" version="2018.2">gromacs</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + + #if $input.conversion == 'str': + ln -s '$input_file' ./input.$input_file.ext && + gmx editconf -f ./input.$input_file.ext -o ./output.${input.output_format} && + cp ./output.${input.output_format} $output + #end if + + #if $input.conversion == 'traj': + ln -s '$input_file' ./input.$input_file.ext && + mdconvert ./input.$input_file.ext -o ./output.${input.output_format} && + cp ./output.${input.output_format} $output + + #end if + + ]]></command> + <inputs> + <conditional name="input"> + <param argument="conversion" type="select" label="Type of conversion"> + <option value="traj">Trajectory file</option> + <option value="str">Structure file</option> + </param> + <when value="traj"> + <param argument="input_file" type="data" format='xtc, trr, dcd' label="Input file for conversion"/> + <param argument="output_format" type="select" label="Output format"> + <option value="trr">TRR file</option> + <option value="xtc">XTC file</option> + <option value="dcd">DCD file</option> + </param> + </when> + <when value="str"> + <param argument="input_file" type="data" format='gro, pdb' label="Input file for conversion"/> + <param argument="output_format" type="select" label="Output format"> + <option value="gro">GRO file</option> + <option value="pdb">PDB file</option> + </param> + </when> + </conditional> + </inputs> + + <outputs> + <data name="output" format="text"> + <change_format> + <when input="output_format" value="gro" format="gro"/> + <when input="output_format" value="pdb" format="pdb"/> + <when input="output_format" value="trr" format="trr"/> + <when input="output_format" value="xtc" format="xtc"/> + <when input="output_format" value="dcd" format="dcd"/> + </change_format> + </data> + </outputs> + + <tests> + <test> + <param name="conversion" value="traj" /> + <param name="output_format" value="dcd" /> + <param name="input_file" value="traj.xtc" /> + <output name="output" file="traj.dcd" compare="sim_size"/> + </test> + <test> + <param name="conversion" value="traj" /> + <param name="output_format" value="trr" /> + <param name="input_file" value="traj.dcd" /> + <output name="output" file="traj.trr"/> + </test> + <test> + <param name="conversion" value="str" /> + <param name="output_format" value="gro" /> + <param name="input_file" value="str.pdb" ftype="pdb"/> + <output name="output" file="str.gro" compare="sim_size"/> + </test> + <test> + <param name="conversion" value="str" /> + <param name="output_format" value="pdb" /> + <param name="input_file" value="str.gro" ftype="gro"/> + <output name="output" file="str2.pdb" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool interconverts between MD file formats: xtc, trr and dcd (trajectory formats) and pdb and gro (structure formats). + +_____ + + +.. class:: infomark + +**Input** + + - Trajectory file (trr, xtc, dcd) or structure file (pdb, gro) + +_____ + + +.. class:: infomark + +**Output** + + - Trajectory file (trr, xtc, dcd) or structure file (pdb, gro) + ]]></help> + <citations> + <citation type="doi">10.1016/j.bpj.2015.08.015</citation> + <citation type="doi">10.1016/j.softx.2015.06.001</citation> + </citations> +</tool> \ No newline at end of file |
| b |
| diff -r 000000000000 -r acce5039ece7 test-data/str.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/str.gro Sun Oct 14 05:31:36 2018 -0400 |
| b |
| b'@@ -0,0 +1,734 @@\n+VILLIN\n+ 731\n+ 42LEU N 1 -0.740 0.981 0.791\n+ 42LEU CA 2 -0.643 0.930 0.699\n+ 42LEU C 3 -0.500 0.953 0.746\n+ 42LEU O 4 -0.481 1.044 0.827\n+ 42LEU CB 5 -0.659 1.007 0.564\n+ 42LEU CG 6 -0.788 0.986 0.487\n+ 42LEU CD1 7 -0.795 1.079 0.365\n+ 42LEU CD2 8 -0.797 0.842 0.442\n+ 42LEU H1 9 -0.822 0.966 0.760\n+ 42LEU H2 10 -0.727 1.069 0.802\n+ 42LEU H3 11 -0.730 0.940 0.870\n+ 42LEU HA 12 -0.658 0.834 0.685\n+ 42LEU HB2 13 -0.650 1.101 0.582\n+ 42LEU HB3 14 -0.586 0.981 0.506\n+ 42LEU HG 15 -0.864 1.006 0.546\n+ 42LEU HD11 16 -0.790 1.170 0.394\n+ 42LEU HD12 17 -0.878 1.065 0.319\n+ 42LEU HD13 18 -0.722 1.060 0.306\n+ 42LEU HD21 19 -0.879 0.828 0.394\n+ 42LEU HD22 20 -0.795 0.784 0.519\n+ 42LEU HD23 21 -0.723 0.822 0.385\n+ 43SER N 22 -0.403 0.881 0.699\n+ 43SER CA 23 -0.263 0.912 0.722\n+ 43SER C 24 -0.233 1.045 0.654\n+ 43SER O 25 -0.305 1.093 0.565\n+ 43SER CB 26 -0.173 0.802 0.664\n+ 43SER OG 27 -0.181 0.807 0.525\n+ 43SER H 28 -0.423 0.812 0.652\n+ 43SER HA 29 -0.247 0.920 0.818\n+ 43SER HB2 30 -0.081 0.816 0.693\n+ 43SER HB3 31 -0.202 0.715 0.696\n+ 43SER HG 32 -0.133 0.749 0.493\n+ 44ASP N 33 -0.121 1.103 0.695\n+ 44ASP CA 34 -0.081 1.231 0.640\n+ 44ASP C 35 -0.048 1.212 0.492\n+ 44ASP O 36 -0.073 1.299 0.410\n+ 44ASP CB 37 0.029 1.300 0.719\n+ 44ASP CG 38 -0.016 1.358 0.853\n+ 44ASP OD1 39 -0.138 1.354 0.874\n+ 44ASP OD2 40 0.074 1.401 0.928\n+ 44ASP H 41 -0.072 1.064 0.754\n+ 44ASP HA 42 -0.160 1.290 0.644\n+ 44ASP HB2 43 0.100 1.236 0.736\n+ 44ASP HB3 44 0.066 1.372 0.665\n+ 45GLU N 45 0.010 1.094 0.461\n+ 45GLU CA 46 0.038 1.065 0.322\n+ 45GLU C 47 -0.089 1.054 0.238\n+ 45GLU O 48 -0.097 1.106 0.126\n+ 45GLU CB 49 0.125 0.938 0.310\n+ 45GLU CB 50 0.118 0.932 0.316\n+ 45GLU CG 51 0.273 0.969 0.327\n+ 45GLU CG 52 0.248 0.934 0.389\n+ 45GLU CD 53 0.328 1.060 0.220\n+ 45GLU CD 54 0.260 0.919 0.537\n+ 45GLU OE1 55 0.336 1.020 0.101\n+ 45GLU OE1 56 0.381 0.911 0.577\n+ 45GLU OE2 57 0.367 1.175 0.251\n+ 45GLU OE2 58 0.163 0.915 0.615\n+ 45GLU H 59 0.030 1.038 0.522\n+ 45GLU HA 60 0.090 1.140 0.286\n+ 45GLU HB2 61 0.098 0.874 0.377\n+ 45GLU HB2 62 0.063 0.861 0.354\n+ 45GLU HB3 63 0.111 0.897 0.223\n+ 45GLU HB3 64 0.134 0.909 0.223\n+ 45GLU HG2 65 0.287 1.010 0.414\n+ 45GLU HG2 66 0.302 0.863 0.349\n+ 45GLU HG3 67 0.323 0.886 0.326\n+ 45GLU HG3 68 0.291 1.018 0.366\n+ 46ASP N 69 -0.190 0.980 0.287\n+ 46ASP CA 70 -0.314 0.971 0.217\n+ 46ASP C 71 -0.381 1.107 0.204\n+ 46ASP O 72 -0.443 1.134 0.101\n+ 46ASP CB 73 -0.409 0.871 0.278\n+ 46ASP CG 74 -0.376 0.725 0.265\n+ 46ASP OD1 75 -0.276 0.696 0.195\n+ 46ASP OD2 76 -0.446 0.636 0.321\n+ 46ASP H 77 -0.180 0.938 0.362\n+ 46ASP HA 78 -0.294 0.940 0.126\n+ 46ASP HB2 79 -0.416 0.891 0.373\n+ 46ASP HB3 80 -0.497 0.885 0.240\n+ 47PHE N 81 -0.378 1.187 0.307\n+ 47PHE CA 82 -0.440 1.319 0.299\n+ 47PHE C 83 -0.382 1.400 0.186\n+ 47PHE O 84 -0.452 1.463 0.108\n+ 47PHE CB 85 -0.419 1.391 0.436\n+ 47PHE CG 86 -0.489 1.527 0.443\n+ 47PHE '..b' 77SO4 O3 647 -0.964 1.303 0.543\n+ 77SO4 O4 648 -0.865 1.509 0.769\n+ 77SO4 O4 649 -0.849 1.286 0.759\n+ 80ACT C 650 -1.490 3.344 0.474\n+ 80ACT C 651 -1.442 3.117 0.691\n+ 80ACT C 652 -1.454 3.103 0.688\n+ 80ACT O 653 -1.613 3.390 0.473\n+ 80ACT O 654 -1.319 3.082 0.738\n+ 80ACT O 655 -1.499 3.224 0.684\n+ 80ACT OXT 656 -1.413 3.389 0.387\n+ 80ACT OXT 657 -1.528 3.116 0.780\n+ 80ACT OXT 658 -1.334 3.079 0.707\n+ 80ACT CH3 659 -1.442 3.256 0.585\n+ 80ACT CH3 660 -1.485 3.025 0.576\n+ 80ACT CH3 661 -1.556 2.990 0.706\n+ 80ACT H1 662 -1.516 3.233 0.642\n+ 80ACT H1 663 -1.417 3.024 0.508\n+ 80ACT H1 664 -1.644 3.023 0.687\n+ 80ACT H2 665 -1.376 3.303 0.637\n+ 80ACT H2 666 -1.567 3.057 0.538\n+ 80ACT H2 667 -1.553 2.959 0.797\n+ 80ACT H3 668 -1.404 3.176 0.549\n+ 80ACT H3 669 -1.497 2.936 0.609\n+ 80ACT H3 670 -1.535 2.918 0.646\n+ 1001HOH O 671 -0.055 0.588 0.430\n+ 1002HOH O 672 -1.160 3.046 0.794\n+ 1002HOH O 673 -1.510 3.330 0.181\n+ 1003HOH O 674 0.082 1.887 0.748\n+ 1004HOH O 675 -1.409 2.327 0.827\n+ 1005HOH O 676 -0.969 1.884 -0.349\n+ 1006HOH O 677 -0.601 2.026 0.755\n+ 1007HOH O 678 -1.508 1.347 -0.543\n+ 1008HOH O 679 -0.043 1.588 0.497\n+ 1009HOH O 680 -1.224 1.832 -0.298\n+ 1010HOH O 681 -0.825 2.924 0.792\n+ 1011HOH O 682 -1.985 1.374 0.127\n+ 1012HOH O 683 -0.019 1.894 -0.528\n+ 1013HOH O 684 -0.062 0.704 0.040\n+ 1014HOH O 685 -1.648 1.857 0.744\n+ 1015HOH O 686 -0.811 3.159 0.420\n+ 1016HOH O 687 -0.495 0.642 0.563\n+ 1017HOH O 688 0.107 1.130 -0.070\n+ 1018HOH O 689 -0.788 2.018 -0.184\n+ 1019HOH O 690 -0.879 3.255 0.161\n+ 1020HOH O 691 -0.796 2.573 0.996\n+ 1021HOH O 692 -0.230 1.267 1.124\n+ 1022HOH O 693 -0.168 2.595 0.883\n+ 1023HOH O 694 -0.300 0.431 0.586\n+ 1024HOH O 695 -1.908 1.350 0.400\n+ 1025HOH O 696 0.028 1.014 0.922\n+ 1026HOH O 697 -1.242 1.445 1.006\n+ 1027HOH O 698 0.125 2.829 0.709\n+ 1028HOH O 699 -1.359 1.529 -0.622\n+ 1029HOH O 700 -0.785 2.240 -0.343\n+ 1030HOH O 701 -1.340 1.939 -0.520\n+ 1031HOH O 702 0.025 1.710 0.943\n+ 1032HOH O 703 0.104 1.276 -0.315\n+ 1033HOH O 704 0.343 1.985 0.760\n+ 1034HOH O 705 -1.476 2.066 0.833\n+ 1035HOH O 706 0.057 2.125 -0.683\n+ 1036HOH O 707 -0.053 1.495 -0.354\n+ 1037HOH O 708 -0.761 1.705 -0.466\n+ 1038HOH O 709 -0.899 2.464 -0.315\n+ 1039HOH O 710 -2.142 2.447 0.746\n+ 1040HOH O 711 -1.817 0.921 0.386\n+ 1041HOH O 712 -0.969 3.221 0.629\n+ 1042HOH O 713 -1.110 2.071 0.799\n+ 1043HOH O 714 -0.590 0.576 0.769\n+ 1044HOH O 715 -1.603 1.958 -0.612\n+ 1045HOH O 716 -1.987 1.820 -0.149\n+ 1046HOH O 717 -0.549 2.104 -0.459\n+ 1047HOH O 718 -2.020 1.331 -0.271\n+ 1048HOH O 719 -0.945 2.071 -0.555\n+ 1049HOH O 720 -1.675 2.901 0.948\n+ 1050HOH O 721 -0.138 2.966 0.948\n+ 1051HOH O 722 -2.125 1.827 0.836\n+ 1052HOH O 723 -1.884 1.674 -0.680\n+ 1053HOH O 724 -1.102 3.425 0.199\n+ 1054HOH O 725 -1.145 2.519 -0.516\n+ 1055HOH O 726 -1.854 1.485 -0.426\n+ 1056HOH O 727 -1.414 3.478 0.821\n+ 1057HOH O 728 -0.549 3.134 0.688\n+ 1058HOH O 729 -0.869 3.014 0.998\n+ 1059HOH O 730 -0.186 2.259 -0.680\n+ 1060HOH O 731 -1.300 3.317 0.000\n+ 3.21550 2.78470 5.68630 0.00000 0.00000 -1.60775 0.00000 0.00000 0.00000\n' |
| b |
| diff -r 000000000000 -r acce5039ece7 test-data/str.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/str.pdb Sun Oct 14 05:31:36 2018 -0400 |
| b |
| b'@@ -0,0 +1,1465 @@\n+HEADER STRUCTURAL PROTEIN 03-FEB-05 1YRF \n+TITLE CHICKEN VILLIN SUBDOMAIN HP-35, N68H, PH6.7 \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: VILLIN; \n+COMPND 3 CHAIN: A; \n+COMPND 4 FRAGMENT: VHP; \n+COMPND 5 ENGINEERED: YES; \n+COMPND 6 MUTATION: YES \n+SOURCE MOL_ID: 1; \n+SOURCE 2 SYNTHETIC: YES; \n+SOURCE 3 OTHER_DETAILS: SEQUENCE CORRESPONDS TO CHICKEN VILLIN RESIDUES 792- \n+SOURCE 4 826 \n+KEYWDS VILLIN HEADPIECE SUBDOMAIN, STRUCTURAL PROTEIN \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR T.K.CHIU,J.KUBELKA,R.HERBST-IRMER,W.A.EATON,J.HOFRICHTER,D.R.DAVIES \n+REVDAT 5 11-OCT-17 1YRF 1 REMARK \n+REVDAT 4 24-FEB-09 1YRF 1 VERSN \n+REVDAT 3 21-JUN-05 1YRF 1 JRNL \n+REVDAT 2 31-MAY-05 1YRF 1 JRNL \n+REVDAT 1 03-MAY-05 1YRF 0 \n+JRNL AUTH T.K.CHIU,J.KUBELKA,R.HERBST-IRMER,W.A.EATON,J.HOFRICHTER, \n+JRNL AUTH 2 D.R.DAVIES \n+JRNL TITL HIGH-RESOLUTION X-RAY CRYSTAL STRUCTURES OF THE VILLIN \n+JRNL TITL 2 HEADPIECE SUBDOMAIN, AN ULTRAFAST FOLDING PROTEIN. \n+JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 7517 2005 \n+JRNL REFN ISSN 0027-8424 \n+JRNL PMID 15894611 \n+JRNL DOI 10.1073/PNAS.0502495102 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 1.07 ANGSTROMS. \n+REMARK 3 \n+REMARK 3 REFINEMENT. \n+REMARK 3 PROGRAM : SHELXL-97 \n+REMARK 3 AUTHORS : G.M.SHELDRICK \n+REMARK 3 \n+REMARK 3 DATA USED IN REFINEMENT. \n+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.07 \n+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 \n+REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL \n+REMARK 3 COMPLETENESS FOR RANGE (%) : NULL \n+REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT \n+REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM \n+REMARK 3 \n+REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). \n+REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL \n+REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.155 \n+REMARK 3 FREE R VALUE (NO CUTOFF) : 0.161 \n+REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL \n+REMARK 3 FREE R VALUE TEST SET COUNT '..b'OH A1053 -11.018 34.254 1.994 1.00 31.47 O \n+ANISOU 725 O HOH A1053 3679 3661 4617 534 -509 912 O \n+HETATM 726 O HOH A1054 -11.454 25.194 -5.155 1.00 45.64 O \n+ANISOU 726 O HOH A1054 5771 5709 5860 -183 -290 89 O \n+HETATM 727 O HOH A1055 -18.538 14.850 -4.264 1.00 43.27 O \n+ANISOU 727 O HOH A1055 5026 5467 5948 406 -273 241 O \n+HETATM 728 O HOH A1056 -14.137 34.778 8.213 1.00 43.04 O \n+ANISOU 728 O HOH A1056 5010 5550 5794 -37 -415 -153 O \n+HETATM 729 O HOH A1057 -5.495 31.337 6.878 1.00 33.39 O \n+ANISOU 729 O HOH A1057 4755 3450 4483 13 64 -794 O \n+HETATM 730 O HOH A1058 -8.694 30.139 9.984 1.00 39.11 O \n+ANISOU 730 O HOH A1058 5749 4866 4244 -435 383 -267 O \n+HETATM 731 O HOH A1059 -1.857 22.585 -6.796 1.00 31.37 O \n+ANISOU 731 O HOH A1059 3530 4123 4264 364 738 -69 O \n+HETATM 732 O HOH A1060 -13.004 33.171 0.000 0.50 43.97 O \n+ANISOU 732 O HOH A1060 5472 5539 5694 58 -638 368 O \n+CONECT 641 643 645 647 649 \n+CONECT 642 644 646 648 650 \n+CONECT 643 641 \n+CONECT 644 642 \n+CONECT 645 641 \n+CONECT 646 642 \n+CONECT 647 641 \n+CONECT 648 642 \n+CONECT 649 641 \n+CONECT 650 642 \n+CONECT 651 654 657 660 \n+CONECT 652 655 658 661 \n+CONECT 653 656 659 662 \n+CONECT 654 651 \n+CONECT 655 652 \n+CONECT 656 653 \n+CONECT 657 651 \n+CONECT 658 652 \n+CONECT 659 653 \n+CONECT 660 651 663 666 669 \n+CONECT 661 652 664 667 670 \n+CONECT 662 653 665 668 671 \n+CONECT 663 660 \n+CONECT 664 661 \n+CONECT 665 662 \n+CONECT 666 660 \n+CONECT 667 661 \n+CONECT 668 662 \n+CONECT 669 660 \n+CONECT 670 661 \n+CONECT 671 662 \n+MASTER 243 0 2 3 0 0 5 6 358 1 31 3 \n+END \n' |
| b |
| diff -r 000000000000 -r acce5039ece7 test-data/str2.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/str2.pdb Sun Oct 14 05:31:36 2018 -0400 |
| b |
| b'@@ -0,0 +1,737 @@\n+TITLE VILLIN\n+REMARK THIS IS A SIMULATION BOX\n+CRYST1 32.155 32.155 56.863 90.00 90.00 120.00 P 1 1\n+MODEL 1\n+ATOM 1 N LEU 42 -7.400 9.810 7.910 1.00 0.00 \n+ATOM 2 CA LEU 42 -6.430 9.300 6.990 1.00 0.00 \n+ATOM 3 C LEU 42 -5.000 9.530 7.460 1.00 0.00 \n+ATOM 4 O LEU 42 -4.810 10.440 8.270 1.00 0.00 \n+ATOM 5 CB LEU 42 -6.590 10.070 5.640 1.00 0.00 \n+ATOM 6 CG LEU 42 -7.880 9.860 4.870 1.00 0.00 \n+ATOM 7 CD1 LEU 42 -7.950 10.790 3.650 1.00 0.00 \n+ATOM 8 CD2 LEU 42 -7.970 8.420 4.420 1.00 0.00 \n+ATOM 9 H1 LEU 42 -8.220 9.660 7.600 1.00 0.00 \n+ATOM 10 H2 LEU 42 -7.270 10.690 8.020 1.00 0.00 \n+ATOM 11 H3 LEU 42 -7.300 9.400 8.700 1.00 0.00 \n+ATOM 12 HA LEU 42 -6.580 8.340 6.850 1.00 0.00 \n+ATOM 13 HB2 LEU 42 -6.500 11.010 5.820 1.00 0.00 \n+ATOM 14 HB3 LEU 42 -5.860 9.810 5.060 1.00 0.00 \n+ATOM 15 HG LEU 42 -8.640 10.060 5.460 1.00 0.00 \n+ATOM 16 1HD1 LEU 42 -7.900 11.700 3.940 1.00 0.00 \n+ATOM 17 2HD1 LEU 42 -8.780 10.650 3.190 1.00 0.00 \n+ATOM 18 3HD1 LEU 42 -7.220 10.600 3.060 1.00 0.00 \n+ATOM 19 1HD2 LEU 42 -8.790 8.280 3.940 1.00 0.00 \n+ATOM 20 2HD2 LEU 42 -7.950 7.840 5.190 1.00 0.00 \n+ATOM 21 3HD2 LEU 42 -7.230 8.220 3.850 1.00 0.00 \n+ATOM 22 N SER 43 -4.030 8.810 6.990 1.00 0.00 \n+ATOM 23 CA SER 43 -2.630 9.120 7.220 1.00 0.00 \n+ATOM 24 C SER 43 -2.330 10.450 6.540 1.00 0.00 \n+ATOM 25 O SER 43 -3.050 10.930 5.650 1.00 0.00 \n+ATOM 26 CB SER 43 -1.730 8.020 6.640 1.00 0.00 \n+ATOM 27 OG SER 43 -1.810 8.070 5.250 1.00 0.00 \n+ATOM 28 H SER 43 -4.230 8.120 6.520 1.00 0.00 \n+ATOM 29 HA SER 43 -2.470 9.200 8.180 1.00 0.00 \n+ATOM 30 HB2 SER 43 -0.810 8.160 6.930 1.00 0.00 \n+ATOM 31 HB3 SER 43 -2.020 7.150 6.960 1.00 0.00 \n+ATOM 32 HG SER 43 -1.330 7.490 4.930 1.00 0.00 \n+ATOM 33 N ASP 44 -1.210 11.030 6.950 1.00 0.00 \n+ATOM 34 CA ASP 44 -0.810 12.310 6.400 1.00 0.00 \n+ATOM 35 C ASP 44 -0.480 12.120 4.920 1.00 0.00 \n+ATOM 36 O ASP 44 -0.730 12.990 4.100 1.00 0.00 \n+ATOM 37 CB ASP 44 0.290 13.000 7.190 1.00 0.00 \n+ATOM 38 CG ASP 44 -0.160 13.580 8.530 1.00 0.00 \n+ATOM 39 OD1 ASP 44 -1.380 13.540 8.740 1.00 0.00 \n+ATOM 40 OD2 ASP 44 0.740 14.010 9.280 1.00 0.00 \n+ATOM 41 H ASP 44 -0.720 10.640 7.540 1.00 0.00 \n+ATOM 42 HA ASP 44 -1.600 12.900 6.440 1.00 0.00 \n+ATOM 43 HB2 ASP 44 1.000 12.360 7.360 1.00 0.00 \n+ATOM 44 HB3 ASP 44 0.660 13.720 6.650 1.00 0.00 \n+ATOM 45 N GLU 45 0.100 10.940 4.610 1.00 0.00 \n+ATOM 46 CA GLU 45 0.380 10.650 3.220 1.00 0.00 \n+ATOM 47 C GLU 45 -0.890 10.540 2.380 1.00 0.00 \n+ATOM 48 O GLU 45 -0.970 11.060 1.260 1.00 0.00 '..b'O HOH 1011 -19.850 13.740 1.270 1.00 0.00 \n+ATOM 683 O HOH 1012 -0.190 18.940 -5.280 1.00 0.00 \n+ATOM 684 O HOH 1013 -0.620 7.040 0.400 1.00 0.00 \n+ATOM 685 O HOH 1014 -16.480 18.570 7.440 1.00 0.00 \n+ATOM 686 O HOH 1015 -8.110 31.590 4.200 1.00 0.00 \n+ATOM 687 O HOH 1016 -4.950 6.420 5.630 1.00 0.00 \n+ATOM 688 O HOH 1017 1.070 11.300 -0.700 1.00 0.00 \n+ATOM 689 O HOH 1018 -7.880 20.180 -1.840 1.00 0.00 \n+ATOM 690 O HOH 1019 -8.790 32.550 1.610 1.00 0.00 \n+ATOM 691 O HOH 1020 -7.960 25.730 9.960 1.00 0.00 \n+ATOM 692 O HOH 1021 -2.300 12.670 11.240 1.00 0.00 \n+ATOM 693 O HOH 1022 -1.680 25.950 8.830 1.00 0.00 \n+ATOM 694 O HOH 1023 -3.000 4.310 5.860 1.00 0.00 \n+ATOM 695 O HOH 1024 -19.080 13.500 4.000 1.00 0.00 \n+ATOM 696 O HOH 1025 0.280 10.140 9.220 1.00 0.00 \n+ATOM 697 O HOH 1026 -12.420 14.450 10.060 1.00 0.00 \n+ATOM 698 O HOH 1027 1.250 28.290 7.090 1.00 0.00 \n+ATOM 699 O HOH 1028 -13.590 15.290 -6.220 1.00 0.00 \n+ATOM 700 O HOH 1029 -7.850 22.400 -3.430 1.00 0.00 \n+ATOM 701 O HOH 1030 -13.400 19.390 -5.200 1.00 0.00 \n+ATOM 702 O HOH 1031 0.250 17.100 9.430 1.00 0.00 \n+ATOM 703 O HOH 1032 1.040 12.760 -3.150 1.00 0.00 \n+ATOM 704 O HOH 1033 3.430 19.850 7.600 1.00 0.00 \n+ATOM 705 O HOH 1034 -14.760 20.660 8.330 1.00 0.00 \n+ATOM 706 O HOH 1035 0.570 21.250 -6.830 1.00 0.00 \n+ATOM 707 O HOH 1036 -0.530 14.950 -3.540 1.00 0.00 \n+ATOM 708 O HOH 1037 -7.610 17.050 -4.660 1.00 0.00 \n+ATOM 709 O HOH 1038 -8.990 24.640 -3.150 1.00 0.00 \n+ATOM 710 O HOH 1039 -21.420 24.470 7.460 1.00 0.00 \n+ATOM 711 O HOH 1040 -18.170 9.210 3.860 1.00 0.00 \n+ATOM 712 O HOH 1041 -9.690 32.210 6.290 1.00 0.00 \n+ATOM 713 O HOH 1042 -11.100 20.710 7.990 1.00 0.00 \n+ATOM 714 O HOH 1043 -5.900 5.760 7.690 1.00 0.00 \n+ATOM 715 O HOH 1044 -16.030 19.580 -6.120 1.00 0.00 \n+ATOM 716 O HOH 1045 -19.870 18.200 -1.490 1.00 0.00 \n+ATOM 717 O HOH 1046 -5.490 21.040 -4.590 1.00 0.00 \n+ATOM 718 O HOH 1047 -20.200 13.310 -2.710 1.00 0.00 \n+ATOM 719 O HOH 1048 -9.450 20.710 -5.550 1.00 0.00 \n+ATOM 720 O HOH 1049 -16.750 29.010 9.480 1.00 0.00 \n+ATOM 721 O HOH 1050 -1.380 29.660 9.480 1.00 0.00 \n+ATOM 722 O HOH 1051 -21.250 18.270 8.360 1.00 0.00 \n+ATOM 723 O HOH 1052 -18.840 16.740 -6.800 1.00 0.00 \n+ATOM 724 O HOH 1053 -11.020 34.250 1.990 1.00 0.00 \n+ATOM 725 O HOH 1054 -11.450 25.190 -5.160 1.00 0.00 \n+ATOM 726 O HOH 1055 -18.540 14.850 -4.260 1.00 0.00 \n+ATOM 727 O HOH 1056 -14.140 34.780 8.210 1.00 0.00 \n+ATOM 728 O HOH 1057 -5.490 31.340 6.880 1.00 0.00 \n+ATOM 729 O HOH 1058 -8.690 30.140 9.980 1.00 0.00 \n+ATOM 730 O HOH 1059 -1.860 22.590 -6.800 1.00 0.00 \n+ATOM 731 O HOH 1060 -13.000 33.170 0.000 1.00 0.00 \n+TER\n+ENDMDL\n' |
| b |
| diff -r 000000000000 -r acce5039ece7 test-data/traj.dcd |
| b |
| Binary file test-data/traj.dcd has changed |
| b |
| diff -r 000000000000 -r acce5039ece7 test-data/traj.trr |
| b |
| Binary file test-data/traj.trr has changed |
| b |
| diff -r 000000000000 -r acce5039ece7 test-data/traj.xtc |
| b |
| Binary file test-data/traj.xtc has changed |