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Commit message:
planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty |
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modified:
apoc.xml smina.xml |
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added:
lisica.xml psovina.xml test-data/lisica/database.mol2 test-data/lisica/output.txt test-data/lisica/reference.mol2 test-data/psovina/ligand.pdbqt test-data/psovina/protein.pdbqt tools/lisica/lisica tools/psovina/psovina |
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removed:
acpc.xml |
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| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 apoc.xml --- a/apoc.xml Mon Sep 12 06:00:34 2016 -0400 +++ b/apoc.xml Wed Sep 14 09:47:48 2016 -0400 |
| b |
| b'@@ -23,21 +23,22 @@\n -fa $fa\n -pvol $pvol\n -plen $plen\n- #if $sod=="true"\n+ #if $alignment_option.sod=="true"\n -sod\n #end if\n- -v $v\n- -m $m\n- #if $L\n- -L $L\n+ -v $alignment_option.v\n+\n+ -m $scoring_option.m\n+ #if $scoring_option.L\n+ -L $scoring_option.L\n #end if\n- #if $a=="true"\n+ #if $scoring_option.a=="true"\n -a\n #end if\n- #if $b=="true"\n+ #if $scoring_option.b=="true"\n -b\n #end if\n- #if $c=="true"\n+ #if $scoring_option.c=="true"\n -c\n #end if\n \n@@ -64,8 +65,8 @@\n <inputs>\n <conditional name="templates_source">\n <param name="template_source_select" type="select" label="Chose template source: pdb file or file with list of templates">\n- <option value="pdbfile">pdb file</option>\n- <option value="list">file with list of templates</option>\n+ <option value="pdbfile">pdb file</option>\n+ <option value="list">file with list of templates</option>\n </param>\n <when value="pdbfile">\n <param name="pdbfile1" type="data" format="pdb" label="First (template) structure for comparison" help="(pdbfile1)" />\n@@ -74,7 +75,7 @@\n <when value="list">\n <param name="lt" type="data" format="data" label="List of templates to compare in a file" help="(-lt)" />\n <repeat name="template" title="pdb file from list of templates">\n- <param name="input" type="data" format="pdb" label="pdbfile" />\n+ <param name="input" type="data" format="pdb" label="pdbfile" help="load all pdb files in the same order as in the list of templates" />\n </repeat>\n </when>\n </conditional>\n@@ -90,7 +91,7 @@\n <when value="list">\n <param name="lq" type="data" format="data" label="List of queries (targets) to compare in a file." help="(-lq)" />\n <repeat name="query" title="pdb file from list of queries">\n- <param name="input" type="data" format="pdb" label="pdbfile" />\n+ <param name="input" type="data" format="pdb" label="pdbfile" help="load all pdb files in the same order as in the list of queries" />\n </repeat>\n </when>\n </conditional>\n@@ -100,35 +101,39 @@\n </param>\n <param name="pvol" type="text" value="1000" label="Minimal pocket volume in grid points" help="(-pvol)" />\n <param name="plen" type="text" value="10" label="Minimal number of pocket residues" help="(-plen)" />\n- <param name="sod" type="select" label="Restrict to sequence-order-dependent alignment" help="(-sod)">\n- <option value="false" selected="true">Do not use this option</option>\n- <option value="true">Use this option</option>\n- '..b'ption value="ps" selected="true">PS-score</option>\n- </param>\n- <param name="L" type="text" label="Normalize the score with a fixed length specified by num" optional="true" help="(-L)" />\n- <param name="a" type="select" label="Normalize the score by the average size of two structures" help="(-a)">\n- <option value="false" selected="true">Do not use this option</option>\n- <option value="true">Use this option</option>\n- </param>\n- <param name="b" type="select" label="Normalize the score by the minimum size of two structures" help="(-b)">\n- <option value="false" selected="true">Do not use this option</option>\n- <option value="true">Use this option</option>\n- </param>\n- <param name="c" type="select" label="Normalize the score by the maximum size of two structures" help="(-c)">\n- <option value="false" selected="true">Do not use this option</option>\n- <option value="true">Use this option</option>\n- </param>\n+ <section name="alignment_option" title="Alignment option">\n+ <param name="sod" type="select" label="Restrict to sequence-order-dependent alignment" help="(-sod)">\n+ <option value="false" selected="true">Do not use this option</option>\n+ <option value="true">Use this option</option>\n+ </param>\n+ <param name="v" type="select" label="Restrict to sequence-order-dependent alignment" help="(-v)">\n+ <option value="0">none</option>\n+ <option value="1">concise</option>\n+ <option value="2" selected="true">detailed</option>\n+ </param> \n+ </section>\n+ <section name="scoring_option" title="Scoring option">\n+ <param name="m" type="select" label="Similarity scoring metric" help="(-m)">\n+ <option value="tm">TM-score</option>\n+ <option value="ps" selected="true">PS-score</option>\n+ </param>\n+ <param name="L" type="text" label="Normalize the score with a fixed length specified by num" optional="true" help="(-L)" />\n+ <param name="a" type="select" label="Normalize the score by the average size of two structures" help="(-a)">\n+ <option value="false" selected="true">Do not use this option</option>\n+ <option value="true">Use this option</option>\n+ </param>\n+ <param name="b" type="select" label="Normalize the score by the minimum size of two structures" help="(-b)">\n+ <option value="false" selected="true">Do not use this option</option>\n+ <option value="true">Use this option</option>\n+ </param>\n+ <param name="c" type="select" label="Normalize the score by the maximum size of two structures" help="(-c)">\n+ <option value="false" selected="true">Do not use this option</option>\n+ <option value="true">Use this option</option>\n+ </param>\n+ </section>\n </inputs>\n <outputs>\n- <data name="output_apoc" format="data" />\n+ <data name="output_apoc" format="txt" />\n </outputs>\n <tests>\n <test>\n@@ -253,6 +258,20 @@\n ]]>\n </help>\n <citations>\n- <citation type="doi">doi:10.1093/bioinformatics/btt024</citation>\n+ <citation type="bibtex">\n+ @article{Gao2013,\n+ doi = {10.1093/bioinformatics/btt024},\n+ url = {http://dx.doi.org/10.1093/bioinformatics/btt024},\n+ year = {2013},\n+ month = {jan},\n+ publisher = {Oxford University Press ({OUP})},\n+ volume = {29},\n+ number = {5},\n+ pages = {597--604},\n+ author = {M. Gao and J. Skolnick},\n+ title = {{APoc}: large-scale identification of similar protein pockets},\n+ journal = {Bioinformatics}\n+ }\n+ </citation>\n </citations>\n </tool>\n' |
| b |
| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 lisica.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lisica.xml Wed Sep 14 09:47:48 2016 -0400 |
| [ |
| @@ -0,0 +1,99 @@ +<tool id="lisica" name="LiSiCA" version="1.0"> + <description>A Software for Ligand-Based Virtual Screening</description> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + $__tool_directory__/tools/lisica/lisica + -R $R + -T $T + #if $n + -n $n + #end if + -d $graph_dimension.d + #if $graph_dimension.d=="2" + -s $graph_dimension.s + #end if + #if $graph_dimension.d=="3" + -m $graph_dimension.m + #end if + #if $h=="true" + -h + #end if + > $output; + + ]]> + </command> + <inputs> + <param name="R" type="data" format="mol2" label="reference molecule" help="(-R)" /> + <param name="T" type="data" format="mol2" label="target molecules" help="(-T)" /> + <param name="n" type="integer" label="the number of CPUs to use" help="(-n)" optional="true" /> + <conditional name="graph_dimension"> + <param name="d" type="select" label="product graph dimension" help="(-d)" > + <option value="2" selected="true">2</option> + <option value="3">3</option> + </param> + <when value="2"> + <param name="s" type="float" value="1" label="maximum allowed shortest path size for 2D product graph" help="(-s)" /> + </when> + <when value="3"> + <param name="m" type="float" value="1" label="maximum allowed atom spatial distance for 3D product graph" help="(-m)" /> + </when> + </conditional> + <!-- <param name="w" type="integer" label="number of highest ranked molecules to write to output" optional="true" help="(-w)" /> --> + <param name="h" type="select" label="consider hydrogens" help="(-h)" > + <option value="true" > + Use this option + </option> + <option value="false" selected="true" > + Do not use this option + </option> + </param> + </inputs> + <outputs> + <data name="output" format="txt" /> + </outputs> + <tests> + <test> + <param name="R" value="lisica/reference.mol2" /> + <param name="T" value="lisica/database.mol2" /> + <output name="output" file="lisica/output.txt" /> + </test> + </tests> + <help> + <![CDATA[ +*********** +Description +*********** +LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format. The similarities are expressed using the Tanimoto coefficients and the target compounds are ranked accordingly. + +****** +Help +****** + Use: ./lisica -R <path to reference molecule> -T <path to target molecules> [parameters] + + **Parameters** + + -n the number of CPUs to use + -d product graph dimension, possible input: 2, 3 + -m maximum allowed atom spatial distance for 3D product graph + -s maximum allowed shortest path size for 2D product graph + -h consider hydrogens + ]]> + </help> + <citations> + <citation type="bibtex"> + @article{lešnik2015lisica, + title={LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors}, + author={Lešnik, Samo and Štular, Tanja and Brus, Boris and Knez, Damijan and Gobec, Stanislav and Janežič, Dušanka and Konc, Janez}, + journal={Journal of chemical information and modeling}, + volume={55}, + number={8}, + pages={1521--1528}, + year={2015}, + publisher={ACS Publications} + } + </citation> + </citations> +</tool> |
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| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 psovina.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/psovina.xml Wed Sep 14 09:47:48 2016 -0400 |
| [ |
| b'@@ -0,0 +1,234 @@\n+<tool id="psovina" name="PSOVina" version="1.0">\n+ <description>Fast Protein-Ligand Docking Tool based on PSO and AutoDock Vina</description>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+ <![CDATA[ \n+ $__tool_directory__/tools/psovina/psovina \n+ --receptor $input.receptor\n+ --ligand $input.ligand \n+\n+ #if $input.flex\n+ --flex $input.flex\n+ #end if\n+\n+ --center_x $search_space.center_x \n+ --center_y $search_space.center_y\n+ --center_z $search_space.center_z \n+ --size_x $search_space.size_x\n+ --size_y $search_space.size_y\n+ --size_z $search_space.size_z\n+\n+ --num_particles $pso_parameters.num_particles\n+ --w $pso_parameters.w\n+ --c1 $pso_parameters.c1\n+ --c2 $pso_parameters.c2\n+\n+ --out ligand_out.pdbqt\n+ #if $output_sect.log=="true"\n+ --log output.log\n+ #end if \n+\n+ #if $advanced_options.score_only=="true"\n+ --score_only\n+ #end if\n+ #if $advanced_options.local_only=="true"\n+ --local_only\n+ #end if\n+ #if $advanced_options.randomize_only=="true"\n+ --randomize_only\n+ #end if\n+ --weight_gauss1 $advanced_options.weight_gauss1\n+ --weight_gauss2 $advanced_options.weight_gauss2\n+ --weight_repulsion $advanced_options.weight_repulsion\n+ --weight_hydrophobic $advanced_options.weight_hydrophobic\n+ --weight_hydrogen $advanced_options.weight_hydrogen\n+ --weight_rot $advanced_options.weight_rot\n+\n+ #if $misc.cpu\n+ --cpu $misc.cpu\n+ #end if\n+ #if $misc.seed\n+ --seed $misc.seed\n+ #end if\n+ --exhaustiveness $misc.exhaustiveness\n+ --num_modes $misc.num_modes\n+ --energy_range $misc.energy_range\n+ ;\n+ #if $output_sect.log=="true" #\n+ cat output.log > $output_log;\n+ #end if #\n+ cat ligand_out.pdbqt > $output\n+\n+ ]]>\n+ </command>\n+ <input'..b't_contents>\n+ <has_text_matching expression="Using random seed:" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+*************\n+Description\n+*************\n+\n+A fast docking tool based on the efficient optimization algorithm of Particle Swarm Intelligence and the framework of AutoDock Vina. In our rigorous docking tests using the PDBBind data set and the virtual screening experiments using the DUD data set, PSOVina achieves a 51-60% time reduction in execution without compromising the prediction accuracies of Vina. This improvement in time efficiency makes PSOVina a better choice of a docking tool in large-scale protein-ligand docking applications.\n+\n+***********\n+Help\n+***********\n+\n+ **Input:**\n+ --receptor arg rigid part of the receptor (PDBQT)\n+ --flex arg flexible side chains, if any (PDBQT)\n+ --ligand arg ligand (PDBQT)\n+ \n+ **Search space (required):**\n+ --center_x arg X coordinate of the center\n+ --center_y arg Y coordinate of the center\n+ --center_z arg Z coordinate of the center\n+ --size_x arg size in the X dimension (Angstroms)\n+ --size_y arg size in the Y dimension (Angstroms)\n+ --size_z arg size in the Z dimension (Angstroms)\n+ \n+ **PSO parameters (optional):**\n+ --num_particles arg Number of particles of each thread\n+ --w arg Inertia weight\n+ --c1 arg Cognitive weight\n+ --c2 arg Social weight\n+ \n+ **Output (optional):**\n+ --log optionally, write log file\n+ \n+ **Advanced options (see the manual):**\n+ --score_only score only - search space can be \n+ omitted\n+ --local_only do local search only\n+ --randomize_only randomize input, attempting to avoid \n+ clashes\n+ --weight_gauss1 arg gauss_1 weight\n+ --weight_gauss2 arg gauss_2 weight\n+ --weight_repulsion arg repulsion weight\n+ --weight_hydrophobic arg hydrophobic weight\n+ --weight_hydrogen arg Hydrogen bond weight\n+ --weight_rot arg N_rot weight\n+ \n+ **Misc (optional):**\n+ --cpu arg the number of CPUs to use (the default is to try to\n+ detect the number of CPUs or, failing that, use 1)\n+ --seed arg explicit random seed\n+ --exhaustiveness arg exhaustiveness of the global search (roughly \n+ proportional to time): 1+\n+ --num_modes arg maximum number of binding modes to generate\n+ --energy_range arg maximum energy difference between the best binding \n+ mode and the worst one displayed (kcal/mol)\n+\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="bibtex">\n+ @article{doi:10.1142/S0219720015410073,\n+ author = {Ng, Marcus C. K. and Fong, Simon and Siu, Shirley W. I.},\n+ title = {PSOVina: The hybrid particle swarm optimization algorithm for protein\xe2\x80\x93ligand docking},\n+ journal = {Journal of Bioinformatics and Computational Biology},\n+ volume = {13},\n+ number = {03},\n+ pages = {1541007},\n+ year = {2015},\n+ doi = {10.1142/S0219720015410073},\n+ note ={PMID: 25800162},\n+\n+ URL = {http://www.worldscientific.com/doi/abs/10.1142/S0219720015410073},\n+ eprint = {http://www.worldscientific.com/doi/pdf/10.1142/S0219720015410073}\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 smina.xml --- a/smina.xml Mon Sep 12 06:00:34 2016 -0400 +++ b/smina.xml Wed Sep 14 09:47:48 2016 -0400 |
| [ |
| b'@@ -5,237 +5,254 @@\n </stdio>\n <command>\n <![CDATA[ \n- cat $receptor > receptor.pdbqt;\n- cat $ligand > ligand.pdbqt;\n+ cat $input.receptor > receptor.pdbqt;\n+ cat $input.ligand > ligand.pdbqt;\n $__tool_directory__/tools/smina/smina.static \n --receptor receptor.pdbqt \n --ligand ligand.pdbqt \n \n- #if $flex\n- --flex $flex\n+ #if $input.flex\n+ --flex $input.flex\n #end if\n- #if $flexres\n- --flexres $flexres\n+ #if $input.flexres\n+ --flexres $input.flexres\n #end if\n- #if $flexdist_ligand\n- --flexdist_ligand $flexdist_ligand\n+ #if $input.flexdist_ligand\n+ --flexdist_ligand $input.flexdist_ligand\n #end if\n- #if $flexdist\n- --flexdist $flexdist\n+ #if $input.flexdist\n+ --flexdist $input.flexdist\n #end if\n \n- --center_x $center_x \n- --center_y $center_y\n- --center_z $center_z \n- --size_x $size_x\n- --size_y $size_y\n- --size_z $size_z\n+ --center_x $search_space.center_x \n+ --center_y $search_space.center_y\n+ --center_z $search_space.center_z \n+ --size_x $search_space.size_x\n+ --size_y $search_space.size_y\n+ --size_z $search_space.size_z\n \n- #if $autobox_ligand\n- --autobox_ligand $autobox_ligand \n+ #if $search_space.autobox_ligand\n+ --autobox_ligand $search_space.autobox_ligand \n #end if \n- #if $autobox_add \n- --autobox_add $autobox_add\n+ #if $search_space.autobox_add \n+ --autobox_add $search_space.autobox_add\n #end if\n- #if $no_lig=="true"\n+ #if $search_space.no_lig=="true"\n --no_lig\n #end if \n \n- --scoring $scoring \n- '..b'value="false" selected="true">Do not use this option</option>\n+ <option value="true">Use this option</option>\n+ </param>\n+ <param name="print_atom_types" type="select" label="Print all available atom types" help="(--print_atom_types)">\n+ <option value="false" selected="true">Do not use this option</option>\n+ <option value="true">Use this option</option>\n+ </param>\n+ </section>\n+ <section name="misc" title="Misc" >\n+ <param name="cpu" type="integer" label="the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)" optional="true" help="(--cpu)"/>\n+ <param name="seed" type="float" label="explicit random seed" optional="true" help="(--seed)"/>\n+ <param name="exhaustiveness" type="integer" value="8" label="exhaustiveness of the global search (roughly proportional to time)" help="(--exhaustiveness)"/>\n+ <param name="num_modes" type="integer" value="9" label="exhaustiveness of the global search (roughly proportional to time)" help="(--num_modes)">\n+ <validator type="in_range" min="1"/>\n+ </param>\n+ <param name="energy_range" type="float" value="3" label="maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" help="(--energy_range)"/>\n+ <param name="min_rmsd_filter" type="float" value="1" label="rmsd value used to filter final poses to remove redundancy" help="(--min_rmsd_filter)"/>\n+ <param name="addH" type="select" label="automatically add hydrogens in ligands (on by default)" help="(--addH)">\n+ <option value="false" >Do not use this option</option>\n+ <option value="true" selected="true">Use this option</option>\n+ </param>\n+ </section>\n </inputs>\n <outputs>\n- <data name="stand_output" format="data" />\n- <data name="out_output" format="data" />\n- <data name="out_flex_output" format="data" />\n- <data name="atom_terms_output" format="data" />\n+ <data name="output" format="txt" />\n+ <data name="out_flex_output" format="txt" label="smina: flexible receptor residues">\n+ <filter>output_sect[\'out_flex\']=="true"</filter>\n+ </data>\n+ <data name="output_log" format="txt" label="smina: log file">\n+ <filter>output_sect[\'log\']=="true"</filter>\n+ </data>\n+ <data name="atom_terms_output" format="txt" label="smima: per-atom interaction term values">\n+ <filter>output_sect[\'atom_terms\']=="true"</filter>\n+ </data>\n </outputs>\n <tests>\n <test>\n@@ -249,7 +266,7 @@\n <param name="size_z" value="28" />\n <output name="stand_output" >\n <assert_contents>\n- <has_text_matching expression="Using random seed" />\n+ <has_text_matching expression="END" />\n </assert_contents>\n </output>\n </test>\n@@ -335,7 +352,20 @@\n </help>\n <citations>\n <citation type="bibtex">\n- @misc{url = {https://sourceforge.net/projects/smina/}, }\n+ @article{Koes2013,\n+ doi = {10.1021/ci300604z},\n+ url = {http://dx.doi.org/10.1021/ci300604z},\n+ year = {2013},\n+ month = {aug},\n+ publisher = {American Chemical Society ({ACS})},\n+ volume = {53},\n+ number = {8},\n+ pages = {1893--1904},\n+ author = {David Ryan Koes and Matthew P. Baumgartner and Carlos J. Camacho},\n+ title = {Lessons Learned in Empirical Scoring with smina from the {CSAR} 2011 Benchmarking Exercise},\n+ journal = {Journal of Chemical Information and Modeling}\n+ }\n+ @misc{url = {https://sourceforge.net/projects/smina/}}\n </citation>\n </citations>\n </tool>\n' |
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| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 test-data/lisica/database.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lisica/database.mol2 Wed Sep 14 09:47:48 2016 -0400 |
| b |
| b'@@ -0,0 +1,9992 @@\n+@<TRIPOS>MOLECULE\n+ZINC00205726\n+ 37 38 0 0 0\n+SMALL\n+NO_CHARGES\n+\n+@<TRIPOS>ATOM\n+ 1 C1 -2.0033 3.8281 1.0379 C.2 1 <0> 0.0000\n+ 2 C2 -1.8312 4.9188 1.9383 C.2 1 <0> 0.0000\n+ 3 C3 -0.8238 3.4766 0.4192 C.2 1 <0> 0.0000\n+ 4 C4 -0.5263 5.3594 1.9737 C.2 1 <0> 0.0000\n+ 5 C5 -0.2854 1.1756 -0.2368 C.2 1 <0> 0.0000\n+ 6 C6 -0.0518 0.1220 -1.2587 C.2 1 <0> 0.0000\n+ 7 C7 0.1990 -0.7678 0.8558 C.2 1 <0> 0.0000\n+ 8 C8 -0.5926 2.4376 -0.5422 C.2 1 <0> 0.0000\n+ 9 C9 -1.6968 1.3354 2.7771 C.2 1 <0> 0.0000\n+ 10 C10 0.8427 5.9535 3.9885 C.3 1 <0> 0.0000\n+ 11 C11 0.5287 -2.2990 -1.1570 C.3 1 <0> 0.0000\n+ 12 C12 -3.9074 0.5782 2.4090 C.3 1 <0> 0.0000\n+ 13 C13 0.0529 6.4577 2.7774 C.3 1 <0> 0.0000\n+ 14 C14 -0.2813 1.3463 2.2497 C.3 1 <0> 0.0000\n+ 15 N1 -0.1260 0.6029 1.0075 N.pl3 1 <0> 0.0000\n+ 16 N2 0.2342 -1.0190 -0.5272 N.am 1 <0> 0.0000\n+ 17 O1 -0.1110 0.2789 -2.4658 O.2 1 <0> 0.0000\n+ 18 O2 -2.0103 1.9047 3.8174 O.2 1 <0> 0.0000\n+ 19 O3 -2.5447 0.6352 1.9744 O.3 1 <0> 0.0000\n+ 20 S1 0.4864 -1.8774 2.0749 S.2 1 <0> 0.0000\n+ 21 S2 0.4843 4.4597 0.9242 S.3 1 <0> 0.0000\n+ 22 H1 -2.9489 3.3314 0.8593 H 1 <0> 0.0000\n+ 23 H2 -2.6268 5.3546 2.5294 H 1 <0> 0.0000\n+ 24 H3 -0.7014 2.6897 -1.5971 H 1 <0> 0.0000\n+ 25 H4 0.2156 5.3211 4.6260 H 1 <0> 0.0000\n+ 26 H5 1.2108 6.7869 4.5949 H 1 <0> 0.0000\n+ 27 H6 1.7055 5.3587 3.6699 H 1 <0> 0.0000\n+ 28 H7 1.6029 -2.3905 -1.3376 H 1 <0> 0.0000\n+ 29 H8 0.0031 -2.3800 -2.1124 H 1 <0> 0.0000\n+ 30 H9 0.2092 -3.1208 -0.5105 H 1 <0> 0.0000\n+ 31 H10 -4.4943 -0.0047 1.6948 H 1 <0> 0.0000\n+ 32 H11 -4.3091 1.5917 2.4857 H 1 <0> 0.0000\n+ 33 H12 -3.9481 0.0970 3.3890 H 1 <0> 0.0000\n+ 34 H13 0.7201 7.0900 2.1620 H 1 <0> 0.0000\n+ 35 H14 -0.7359 7.1461 3.1348 H 1 <0> 0.0000\n+ 36 H15 0.3775 0.8885 2.9922 H 1 <0> 0.0000\n+ 37 H16 0.0199 2.3785 2.0539 H 1 <0> 0.0000\n+@<TRIPOS>BOND\n+ 1 1 2 1\n+ 2 1 3 2\n+ 3 2 4 2\n+ 4 3 8 1\n+ 5 3 21 1\n+ 6 4 13 1\n+ 7 4 21 1\n+ 8 5 6 1\n+ 9 5 8 2\n+ 10 5 15 1\n+ 11 6 16 am\n+ 12 6 17 2\n+ 13 7 15 1\n+ 14 7 16 1\n+ 15 7 20 2\n+ 16 9 14 1\n+ 17 9 18 2\n+ 18 9 19 1\n+ 19 10 13 1\n+ 20 11 16 1\n+ 21 12 19 1\n+ 22 14 15 1\n+ 23 1 22 1\n+ 24 2 23 1\n+ 25 8 24 1\n+ 26 10 25 1\n+ 27 10 26 1\n+ 28 10 27 1\n+ 29 11 28 1\n+ 30 11 29 1\n+ 31 11 30 1\n+ 32 12 31 1\n+ 33 12 32 1\n+ 34 12 33 1\n+ 35 13 34 1\n+ 36 13 35 1\n+ 37 14 36 1\n+ 38 14 37 1\n+@<TRIPOS>MOLECULE\n+ZINC69323649\n+ 39 41 0 0 0\n+SMALL\n+NO_CHARGES\n+\n+@<TRIPOS>ATOM\n+ 1 C1 3.1080 -0.4560 -0.5881 C.ar 1 <0> 0.0000\n+ '..b' 6 C6 1.8799 -0.6639 -3.8275 C.ar 1 <0> 0.0000\n+ 7 C7 -1.5658 -1.4541 -2.5474 C.2 1 <0> 0.0000\n+ 8 C8 -0.6686 1.7649 -0.6163 C.2 1 <0> 0.0000\n+ 9 C9 -3.2893 0.2091 0.0784 C.3 1 <0> 0.0000\n+ 10 C10 -3.1116 1.6957 -0.2347 C.3 1 <0> 0.0000\n+ 11 C11 -3.4524 -0.6051 -1.1985 C.3 1 <0> 0.0000\n+ 12 C12 -2.1240 1.0339 -2.4916 C.3 1 <0> 0.0000\n+ 13 C13 -2.0257 1.9540 -1.2768 C.3 1 <0> 0.0000\n+ 14 C14 2.8039 -0.4080 -6.1399 C.3 1 <0> 0.0000\n+ 15 C15 -0.2093 0.2634 -7.6676 C.3 1 <0> 0.0000\n+ 16 C16 3.2399 -0.4069 -1.8935 C.3 1 <0> 0.0000\n+ 17 N1 -2.3325 -0.3711 -2.1085 N.am 1 <0> 0.0000\n+ 18 N2 0.3105 2.5917 -1.1142 N.am 1 <0> 0.0000\n+ 19 O1 -1.7415 -2.6310 -2.2359 O.2 1 <0> 0.0000\n+ 20 O2 -0.4907 0.9539 0.2892 O.2 1 <0> 0.0000\n+ 21 O3 0.1722 -0.9678 -7.0575 O.3 1 <0> 0.0000\n+ 22 O4 3.1148 -0.4025 -3.3140 O.3 1 <0> 0.0000\n+ 23 H1 -1.6513 -1.4122 -5.2431 H 1 <0> 0.0000\n+ 24 H2 0.9904 -0.9046 -1.8822 H 1 <0> 0.0000\n+ 25 H3 -2.4160 -0.1533 0.6342 H 1 <0> 0.0000\n+ 26 H4 -4.1627 0.0687 0.7249 H 1 <0> 0.0000\n+ 27 H5 -4.0638 2.0861 -0.6167 H 1 <0> 0.0000\n+ 28 H6 -2.8978 2.2387 0.6938 H 1 <0> 0.0000\n+ 29 H7 -3.5328 -1.6687 -0.9515 H 1 <0> 0.0000\n+ 30 H8 -4.3706 -0.3200 -1.7252 H 1 <0> 0.0000\n+ 31 H9 -2.9904 1.3193 -3.1011 H 1 <0> 0.0000\n+ 32 H10 -1.2381 1.1445 -3.1231 H 1 <0> 0.0000\n+ 33 H11 -2.0581 2.9882 -1.5927 H 1 <0> 0.0000\n+ 34 H12 2.8696 0.6645 -6.3539 H 1 <0> 0.0000\n+ 35 H13 3.7566 -0.7389 -5.7098 H 1 <0> 0.0000\n+ 36 H14 2.6748 -0.9473 -7.0859 H 1 <0> 0.0000\n+ 37 H15 -0.3576 0.1093 -8.7393 H 1 <0> 0.0000\n+ 38 H16 0.5705 1.0108 -7.5007 H 1 <0> 0.0000\n+ 39 H17 -1.1438 0.6081 -7.2186 H 1 <0> 0.0000\n+ 40 H18 4.2735 -0.1847 -1.6173 H 1 <0> 0.0000\n+ 41 H19 2.9499 -1.3862 -1.5043 H 1 <0> 0.0000\n+ 42 H20 2.5811 0.3584 -1.4763 H 1 <0> 0.0000\n+ 43 H21 0.0688 3.2415 -1.8552 H 1 <0> 0.0000\n+ 44 H22 1.2653 2.5783 -0.7704 H 1 <0> 0.0000\n+@<TRIPOS>BOND\n+ 1 1 3 ar\n+ 2 1 5 ar\n+ 3 2 3 ar\n+ 4 2 6 ar\n+ 5 3 7 1\n+ 6 4 5 ar\n+ 7 4 6 ar\n+ 8 4 14 1\n+ 9 5 21 1\n+ 10 6 22 1\n+ 11 7 17 am\n+ 12 7 19 2\n+ 13 8 13 1\n+ 14 8 18 am\n+ 15 8 20 2\n+ 16 9 10 1\n+ 17 9 11 1\n+ 18 10 13 1\n+ 19 11 17 1\n+ 20 12 13 1\n+ 21 12 17 1\n+ 22 15 21 1\n+ 23 16 22 1\n+ 24 1 23 1\n+ 25 2 24 1\n+ 26 9 25 1\n+ 27 9 26 1\n+ 28 10 27 1\n+ 29 10 28 1\n+ 30 11 29 1\n+ 31 11 30 1\n+ 32 12 31 1\n+ 33 12 32 1\n+ 34 13 33 1\n+ 35 14 34 1\n+ 36 14 35 1\n+ 37 14 36 1\n+ 38 15 37 1\n+ 39 15 38 1\n+ 40 15 39 1\n+ 41 16 40 1\n+ 42 16 41 1\n+ 43 16 42 1\n+ 44 18 43 1\n+ 45 18 44 1\n' |
| b |
| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 test-data/lisica/output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lisica/output.txt Wed Sep 14 09:47:48 2016 -0400 |
| b |
| @@ -0,0 +1,103 @@ +0.545455 ZINC57271411 +0.53125 ZINC03481363 +0.485714 ZINC72060510 +0.484848 ZINC65292537 +0.472222 ZINC72441611 +0.470588 ZINC65375610 +0.46875 ZINC69419311 +0.454545 ZINC69323649 +0.444444 ZINC06606875 +0.441176 ZINC72346693 +0.441176 ZINC71281140 +0.441176 ZINC08087469 +0.428571 ZINC67842136 +0.424242 ZINC79370047 +0.4 ZINC77322510 +0.4 ZINC72002643 +0.394737 ZINC06394508 +0.388889 ZINC77454550 +0.387097 ZINC72147362 +0.378378 ZINC19293202 +0.375 ZINC02796227 +0.371429 ZINC69367382 +0.363636 ZINC47581862 +0.352941 ZINC48088125 +0.352941 ZINC08274681 +0.35 ZINC72453362 +0.344828 ZINC72190422 +0.342857 ZINC71498716 +0.333333 ZINC77488577 +0.333333 ZINC72367876 +0.333333 ZINC71549640 +0.333333 ZINC65513427 +0.333333 ZINC16957259 +0.333333 ZINC06742088 +0.333333 ZINC03339242 +0.333333 ZINC02779238 +0.324324 ZINC72234467 +0.324324 ZINC07054345 +0.323529 ZINC71979376 +0.322581 ZINC83319646 +0.321429 ZINC72201502 +0.314286 ZINC72172717 +0.314286 ZINC48343076 +0.311111 ZINC71963183 +0.305556 ZINC83173705 +0.30303 ZINC07522413 +0.302326 ZINC72392868 +0.3 ZINC77914743 +0.3 ZINC65534036 +0.3 ZINC65395084 +0.297297 ZINC72755164 +0.297297 ZINC72472882 +0.297297 ZINC52643824 +0.297297 ZINC06678583 +0.295455 ZINC72092480 +0.294118 ZINC03426686 +0.285714 ZINC72370511 +0.285714 ZINC70948092 +0.285714 ZINC19328158 +0.282051 ZINC71858523 +0.277778 ZINC74558893 +0.277778 ZINC48567140 +0.272727 ZINC00110318 +0.27027 ZINC67834297 +0.268293 ZINC06807237 +0.264706 ZINC77107611 +0.264706 ZINC71996452 +0.264706 ZINC07800766 +0.263158 ZINC77952398 +0.263158 ZINC72135181 +0.261905 ZINC71919013 +0.257143 ZINC71790351 +0.257143 ZINC04667239 +0.25641 ZINC31820077 +0.25 ZINC78773859 +0.25 ZINC77407482 +0.25 ZINC76086892 +0.25 ZINC72324671 +0.25 ZINC06719422 +0.243902 ZINC73668070 +0.243902 ZINC72421623 +0.243243 ZINC72290346 +0.236842 ZINC75125399 +0.230769 ZINC71479656 +0.230769 ZINC67674610 +0.205128 ZINC67909110 +0.195122 ZINC72404066 +0.195122 ZINC72168650 +0.194444 ZINC75156350 +0.191489 ZINC04010293 +0.184211 ZINC02782238 +0.181818 ZINC69699688 +0.175 ZINC72426115 +0.171429 ZINC72308968 +0.170732 ZINC23792296 +0.166667 ZINC67514210 +0.151515 ZINC75162573 +0.146341 ZINC72435482 +0.128205 ZINC67640948 +0.125 ZINC75765461 +0.125 ZINC69970250 +0.125 ZINC00205726 +0.09375 ZINC00801655 |
| b |
| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 test-data/lisica/reference.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lisica/reference.mol2 Wed Sep 14 09:47:48 2016 -0400 |
| b |
| @@ -0,0 +1,96 @@ +@<TRIPOS>MOLECULE +ZINC89846137 + 43 45 0 0 0 +SMALL +NO_CHARGES + +@<TRIPOS>ATOM + 1 C1 -4.8686 -0.2979 4.3193 C.ar 1 <0> 0.0000 + 2 C2 -5.2281 0.2613 3.0931 C.ar 1 <0> 0.0000 + 3 C3 -3.6819 -1.0219 4.4345 C.ar 1 <0> 0.0000 + 4 C4 -5.2017 -4.5260 -1.7818 C.ar 1 <0> 0.0000 + 5 C5 -3.1564 -3.7787 -2.8283 C.ar 1 <0> 0.0000 + 6 C6 -5.6738 -4.9658 -3.0184 C.ar 1 <0> 0.0000 + 7 C7 -3.6284 -4.2186 -4.0650 C.ar 1 <0> 0.0000 + 8 C8 -4.4009 0.0965 1.9821 C.ar 1 <0> 0.0000 + 9 C9 -2.8548 -1.1868 3.3235 C.ar 1 <0> 0.0000 + 10 C10 -6.5167 -6.0765 -6.9908 C.2 1 <0> 0.0000 + 11 C11 -6.5512 -5.8457 -5.6385 C.2 1 <0> 0.0000 + 12 C12 -3.9430 -3.9324 -1.6867 C.ar 1 <0> 0.0000 + 13 C13 -4.8872 -4.8122 -4.1600 C.ar 1 <0> 0.0000 + 14 C14 -3.2142 -0.6275 2.0973 C.ar 1 <0> 0.0000 + 15 C15 -3.4397 -3.4641 -0.3697 C.2 1 <0> 0.0000 + 16 C16 -0.2485 -1.0636 -0.1144 C.3 1 <0> 0.0000 + 17 C17 -1.4205 -3.0307 1.0054 C.3 1 <0> 0.0000 + 18 C18 -1.1456 -1.5255 1.0297 C.3 1 <0> 0.0000 + 19 N1 -5.3325 -5.6249 -7.5039 N.2 1 <0> 0.0000 + 20 N2 -4.6217 -5.1162 -6.5033 N.2 1 <0> 0.0000 + 21 N3 -5.3541 -5.2497 -5.3858 N.pl3 1 <0> 0.0000 + 22 N4 -2.3938 -0.7910 0.9960 N.pl3 1 <0> 0.0000 + 23 N5 -2.0618 -3.4382 -0.2239 N.am 1 <0> 0.0000 + 24 O1 -4.2448 -3.1526 0.5040 O.2 1 <0> 0.0000 + 25 H1 -5.5129 -0.1697 5.1843 H 1 <0> 0.0000 + 26 H2 -6.1519 0.8248 3.0035 H 1 <0> 0.0000 + 27 H3 -3.4022 -1.4574 5.3895 H 1 <0> 0.0000 + 28 H4 -5.8229 -4.6510 -0.8986 H 1 <0> 0.0000 + 29 H5 -2.1744 -3.3170 -2.7657 H 1 <0> 0.0000 + 30 H6 -6.6570 -5.4265 -3.0786 H 1 <0> 0.0000 + 31 H7 -3.0047 -4.0930 -4.9467 H 1 <0> 0.0000 + 32 H8 -4.6901 0.5362 1.0310 H 1 <0> 0.0000 + 33 H9 -1.9323 -1.7528 3.4254 H 1 <0> 0.0000 + 34 H10 -7.2704 -6.5362 -7.6119 H 1 <0> 0.0000 + 35 H11 -7.2912 -6.0471 -4.8763 H 1 <0> 0.0000 + 36 H12 -0.6942 -1.2711 -1.0934 H 1 <0> 0.0000 + 37 H13 -0.0807 0.0178 -0.0585 H 1 <0> 0.0000 + 38 H14 0.7269 -1.5590 -0.0693 H 1 <0> 0.0000 + 39 H15 -2.0672 -3.3081 1.8454 H 1 <0> 0.0000 + 40 H16 -0.4828 -3.5856 1.1188 H 1 <0> 0.0000 + 41 H17 -0.6408 -1.2882 1.9736 H 1 <0> 0.0000 + 42 H18 -2.6746 -0.3766 0.1169 H 1 <0> 0.0000 + 43 H19 -1.4600 -3.7706 -0.9704 H 1 <0> 0.0000 +@<TRIPOS>BOND + 1 1 2 ar + 2 1 3 ar + 3 2 8 ar + 4 3 9 ar + 5 4 6 ar + 6 4 12 ar + 7 5 7 ar + 8 5 12 ar + 9 6 13 ar + 10 7 13 ar + 11 8 14 ar + 12 9 14 ar + 13 10 11 2 + 14 10 19 1 + 15 11 21 1 + 16 12 15 1 + 17 13 21 1 + 18 14 22 1 + 19 15 23 am + 20 15 24 2 + 21 16 18 1 + 22 17 18 1 + 23 17 23 1 + 24 18 22 1 + 25 19 20 2 + 26 20 21 1 + 27 1 25 1 + 28 2 26 1 + 29 3 27 1 + 30 4 28 1 + 31 5 29 1 + 32 6 30 1 + 33 7 31 1 + 34 8 32 1 + 35 9 33 1 + 36 10 34 1 + 37 11 35 1 + 38 16 36 1 + 39 16 37 1 + 40 16 38 1 + 41 17 39 1 + 42 17 40 1 + 43 18 41 1 + 44 22 42 1 + 45 23 43 1 |
| b |
| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 test-data/psovina/ligand.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psovina/ligand.pdbqt Wed Sep 14 09:47:48 2016 -0400 |
| b |
| @@ -0,0 +1,66 @@ +REMARK 7 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C5_5 and C7_7 +REMARK 2 A between atoms: C9_9 and N13_13 +REMARK 3 A between atoms: N13_13 and C14_14 +REMARK 4 A between atoms: C16_16 and N21_21 +REMARK I between atoms: N21_21 and C22_22 +REMARK 5 A between atoms: C22_22 and C23_23 +REMARK 6 A between atoms: C27_26 and C46_30 +REMARK 7 A between atoms: C46_30 and N48_31 +ROOT +HETATM 1 C1 STI 202 15.290 78.984 63.105 1.00 0.00 -0.001 A +HETATM 2 C2 STI 202 14.162 78.322 62.514 1.00 0.00 0.095 A +HETATM 3 N3 STI 202 14.348 77.405 61.475 1.00 0.00 -0.243 NA +HETATM 4 C4 STI 202 15.604 77.088 60.967 1.00 0.00 0.097 A +HETATM 5 C5 STI 202 16.790 77.718 61.516 1.00 0.00 0.020 A +HETATM 6 C6 STI 202 16.610 78.678 62.599 1.00 0.00 0.057 A +ENDROOT +BRANCH 5 7 +HETATM 7 C7 STI 202 18.135 77.365 60.950 1.00 0.00 0.099 A +HETATM 8 N8 STI 202 18.991 76.649 61.763 1.00 0.00 -0.061 NA +HETATM 9 C9 STI 202 20.233 76.272 61.350 1.00 0.00 0.728 A +HETATM 10 N10 STI 202 20.667 76.608 60.078 1.00 0.00 -0.059 NA +HETATM 11 C11 STI 202 19.854 77.325 59.216 1.00 0.00 0.119 A +HETATM 12 C12 STI 202 18.556 77.729 59.622 1.00 0.00 0.041 A +BRANCH 9 13 +HETATM 13 N13 STI 202 21.026 75.546 62.243 1.00 0.00 -0.190 N +HETATM 14 H STI 202 20.822 74.493 62.382 1.00 0.00 0.184 HD +BRANCH 13 15 +HETATM 15 C14 STI 202 22.078 76.132 62.968 1.00 0.00 0.052 A +HETATM 16 C15 STI 202 21.784 76.754 64.221 1.00 0.00 0.087 A +HETATM 17 C16 STI 202 22.842 77.373 65.022 1.00 0.00 0.042 A +HETATM 18 C17 STI 202 24.173 77.343 64.522 1.00 0.00 0.013 A +HETATM 19 C18 STI 202 24.483 76.718 63.261 1.00 0.00 -0.002 A +HETATM 20 C19 STI 202 23.455 76.105 62.465 1.00 0.00 -0.009 A +HETATM 21 C20 STI 202 23.868 75.449 61.126 1.00 0.00 0.032 C +BRANCH 17 22 +HETATM 22 N21 STI 202 22.625 78.015 66.297 1.00 0.00 -0.325 N +HETATM 23 C22 STI 202 21.459 78.556 66.802 1.00 0.00 0.253 C +HETATM 24 O29 STI 202 20.459 78.777 66.146 1.00 0.00 -0.268 OA +HETATM 25 H STI 202 23.491 78.080 66.943 1.00 0.00 0.169 HD +BRANCH 23 26 +HETATM 26 C23 STI 202 21.395 78.922 68.248 1.00 0.00 0.034 A +HETATM 27 C25 STI 202 22.608 78.977 69.064 1.00 0.00 0.036 A +HETATM 28 C26 STI 202 22.516 79.314 70.461 1.00 0.00 0.029 A +HETATM 29 C27 STI 202 21.216 79.597 71.045 1.00 0.00 -0.011 A +HETATM 30 C28 STI 202 20.031 79.541 70.215 1.00 0.00 -0.007 A +HETATM 31 C29 STI 202 20.112 79.211 68.845 1.00 0.00 -0.000 A +BRANCH 29 32 +HETATM 32 C46 STI 202 21.035 79.941 72.527 1.00 0.00 0.273 C +BRANCH 32 33 +HETATM 33 N48 STI 202 21.864 81.048 73.091 1.00 0.00 0.145 N +HETATM 34 C49 STI 202 23.277 80.579 73.421 1.00 0.00 0.286 C +HETATM 35 C50 STI 202 24.142 81.743 73.995 1.00 0.00 0.286 C +HETATM 36 N51 STI 202 23.461 82.314 75.230 1.00 0.00 0.143 N +HETATM 37 C52 STI 202 22.054 82.791 74.907 1.00 0.00 0.286 C +HETATM 38 C54 STI 202 24.311 83.368 75.810 1.00 0.00 0.285 C +HETATM 39 C53 STI 202 21.211 81.634 74.310 1.00 0.00 0.286 C +ENDBRANCH 32 33 +ENDBRANCH 29 32 +ENDBRANCH 23 26 +ENDBRANCH 17 22 +ENDBRANCH 13 15 +ENDBRANCH 9 13 +ENDBRANCH 5 7 +TORSDOF 7 |
| b |
| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 test-data/psovina/protein.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psovina/protein.pdbqt Wed Sep 14 09:47:48 2016 -0400 |
| b |
| b'@@ -0,0 +1,2704 @@\n+REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.0\n+ATOM 1 N MET B 225 8.895 115.777 72.069 1.00 66.21 -0.058 N \n+ATOM 2 HN1 MET B 225 9.110 116.757 71.885 1.00 0.00 0.276 HD\n+ATOM 3 HN2 MET B 225 8.532 115.302 71.243 1.00 0.00 0.276 HD\n+ATOM 4 HN3 MET B 225 9.737 115.217 72.203 1.00 0.00 0.276 HD\n+ATOM 5 CA MET B 225 7.964 115.677 73.229 1.00 67.57 0.256 C \n+ATOM 6 C MET B 225 8.577 116.332 74.473 1.00 67.86 0.259 C \n+ATOM 7 O MET B 225 9.799 116.348 74.640 1.00 65.18 -0.271 OA\n+ATOM 8 CB MET B 225 7.641 114.206 73.505 1.00 69.59 0.051 C \n+ATOM 9 CG MET B 225 6.364 113.982 74.294 1.00 74.31 0.060 C \n+ATOM 10 SD MET B 225 5.924 112.234 74.408 1.00 78.96 -0.139 SA\n+ATOM 11 CE MET B 225 5.398 111.927 72.771 1.00 75.85 0.069 C \n+ATOM 12 N ASP B 226 7.720 116.875 75.335 1.00 67.79 -0.337 N \n+ATOM 13 HN ASP B 226 6.722 116.819 75.133 1.00 0.00 0.164 HD\n+ATOM 14 CA ASP B 226 8.152 117.550 76.561 1.00 65.70 0.170 C \n+ATOM 15 C ASP B 226 8.642 116.583 77.638 1.00 60.19 0.255 C \n+ATOM 16 O ASP B 226 7.934 115.651 78.012 1.00 58.11 -0.270 OA\n+ATOM 17 CB ASP B 226 7.001 118.404 77.109 1.00 72.35 0.129 C \n+ATOM 18 CG ASP B 226 7.265 118.916 78.515 1.00 77.69 0.188 C \n+ATOM 19 OD1 ASP B 226 8.325 119.540 78.739 1.00 80.27 -0.647 OA\n+ATOM 20 OD2 ASP B 226 6.406 118.698 79.397 1.00 80.93 -0.647 OA\n+ATOM 21 N PRO B 227 9.864 116.804 78.156 1.00 57.95 -0.312 N \n+ATOM 22 CA PRO B 227 10.484 115.970 79.194 1.00 56.85 0.163 C \n+ATOM 23 C PRO B 227 9.616 115.766 80.431 1.00 59.80 0.251 C \n+ATOM 24 O PRO B 227 9.603 114.682 81.013 1.00 60.52 -0.271 OA\n+ATOM 25 CB PRO B 227 11.767 116.724 79.522 1.00 56.20 0.034 C \n+ATOM 26 CG PRO B 227 12.113 117.376 78.233 1.00 58.49 0.027 C \n+ATOM 27 CD PRO B 227 10.774 117.891 77.754 1.00 57.18 0.105 C \n+ATOM 28 N SER B 228 8.899 116.812 80.833 1.00 61.30 -0.336 N \n+ATOM 29 HN SER B 228 8.956 117.684 80.308 1.00 0.00 0.164 HD\n+ATOM 30 CA SER B 228 8.032 116.744 82.007 1.00 64.43 0.189 C \n+ATOM 31 C SER B 228 6.834 115.817 81.792 1.00 66.62 0.254 C \n+ATOM 32 O SER B 228 6.408 115.119 82.714 1.00 66.74 -0.270 OA\n+ATOM 33 CB SER B 228 7.537 118.146 82.373 1.00 61.78 0.169 C \n+ATOM 34 OG SER B 228 8.629 119.010 82.648 1.00 60.05 -0.380 OA\n+ATOM 35 HG SER B 228 8.322 119.880 82.875 1.00 0.00 0.211 HD\n+ATOM 36 N SER B 229 6.299 115.818 80.574 1.00 68.62 -0.335 N \n+ATOM 37 HN SER B 229 6.705 116.422 79.859 1.00 0.00 0.164 HD\n+ATOM 38 CA SER B 229 5.151 114.985 80.225 1.00 71.77 0.189 C \n+ATOM 39 C SER B 229 5.192 113.597 80.847 1.00 72.94 0.257 C \n+ATOM 40 O SER B 229 6.250 112.971 80.936 1.00 73.97 -0.270 OA\n+ATOM 41 CB SER B 229 5.040 114.835 78.708 1.00 73.74 0.169 C \n+ATOM 42 OG SER B 229 4.090 113.836 78.376 1.00 73.66 -0.380 OA\n+ATOM 43 HG SER B 229 4.021 113.743 77.433 1.00 0.00 0.211 HD\n+ATOM 44 N PRO B 230 4.028 113.098 81.287 1.00 74.05 -0.312 N \n+ATOM 45 CA PRO B 230 3.893 111.777 81.908 1.00 73.39 0.163 C \n+ATOM 46 C PRO B 230 4.091 110.662 80.885 1.00 71.08 0.251 C \n+ATOM 47 O PRO B 230 4.531 109.563 81.220 1.00 72.24 -0.271 OA\n+ATOM 48 CB PRO B 230 2.462 111.792 82.449 1.00 73.99 0.034 C \n+ATOM 49 CG PRO B 230 2.173 113.250'..b'\n+ATOM 2654 C GLU B 494 36.358 83.980 62.758 1.00 74.90 0.251 C \n+ATOM 2655 O GLU B 494 37.407 84.611 62.661 1.00 75.94 -0.271 OA\n+ATOM 2656 CB GLU B 494 34.721 85.146 64.247 1.00 74.74 0.043 C \n+ATOM 2657 CG GLU B 494 35.660 86.227 64.764 1.00 82.17 0.100 C \n+ATOM 2658 CD GLU B 494 35.327 86.660 66.179 1.00 87.43 0.185 C \n+ATOM 2659 OE1 GLU B 494 34.384 86.089 66.769 1.00 90.63 -0.647 OA\n+ATOM 2660 OE2 GLU B 494 36.009 87.570 66.702 1.00 88.07 -0.647 OA\n+ATOM 2661 N THR B 495 36.317 82.653 62.817 1.00 77.31 -0.336 N \n+ATOM 2662 HN THR B 495 35.416 82.184 62.914 1.00 0.00 0.164 HD\n+ATOM 2663 CA THR B 495 37.536 81.853 62.746 1.00 80.18 0.186 C \n+ATOM 2664 C THR B 495 38.042 81.872 61.310 1.00 80.90 0.253 C \n+ATOM 2665 O THR B 495 39.239 82.018 61.066 1.00 81.34 -0.270 OA\n+ATOM 2666 CB THR B 495 37.285 80.396 63.173 1.00 80.26 0.140 C \n+ATOM 2667 CG2 THR B 495 38.523 79.548 62.921 1.00 80.29 0.034 C \n+ATOM 2668 OG1 THR B 495 36.961 80.356 64.568 1.00 80.67 -0.382 OA\n+ATOM 2669 HG1 THR B 495 36.188 80.885 64.725 1.00 0.00 0.210 HD\n+ATOM 2670 N MET B 496 37.121 81.723 60.362 1.00 82.31 -0.337 N \n+ATOM 2671 HN MET B 496 36.148 81.580 60.632 1.00 0.00 0.164 HD\n+ATOM 2672 CA MET B 496 37.468 81.759 58.946 1.00 84.62 0.160 C \n+ATOM 2673 C MET B 496 37.860 83.196 58.616 1.00 87.04 0.251 C \n+ATOM 2674 O MET B 496 37.836 83.618 57.460 1.00 86.75 -0.271 OA\n+ATOM 2675 CB MET B 496 36.269 81.338 58.096 1.00 81.82 0.043 C \n+ATOM 2676 CG MET B 496 35.860 79.888 58.278 1.00 80.74 0.060 C \n+ATOM 2677 SD MET B 496 34.320 79.500 57.429 1.00 75.91 -0.139 SA\n+ATOM 2678 CE MET B 496 33.187 79.402 58.804 1.00 78.90 0.069 C \n+ATOM 2679 N PHE B 497 38.211 83.936 59.663 1.00 90.42 -0.337 N \n+ATOM 2680 HN PHE B 497 38.193 83.501 60.585 1.00 0.00 0.164 HD\n+ATOM 2681 CA PHE B 497 38.620 85.332 59.572 1.00 93.05 0.164 C \n+ATOM 2682 C PHE B 497 39.740 85.555 60.585 1.00 94.67 0.251 C \n+ATOM 2683 O PHE B 497 40.909 85.261 60.324 1.00 92.26 -0.271 OA\n+ATOM 2684 CB PHE B 497 37.450 86.253 59.933 1.00 93.91 0.058 C \n+ATOM 2685 CG PHE B 497 36.866 86.994 58.768 1.00 93.96 -0.020 A \n+ATOM 2686 CD1 PHE B 497 35.755 86.498 58.095 1.00 94.24 -0.004 A \n+ATOM 2687 CD2 PHE B 497 37.420 88.200 58.351 1.00 93.85 -0.004 A \n+ATOM 2688 CE1 PHE B 497 35.202 87.197 57.023 1.00 94.81 -0.000 A \n+ATOM 2689 CE2 PHE B 497 36.877 88.904 57.282 1.00 94.40 -0.000 A \n+ATOM 2690 CZ PHE B 497 35.764 88.402 56.616 1.00 95.25 -0.000 A \n+ATOM 2691 N GLN B 498 39.346 86.074 61.747 1.00 97.48 -0.339 N \n+ATOM 2692 HN GLN B 498 38.354 86.278 61.866 1.00 0.00 0.164 HD\n+ATOM 2693 CA GLN B 498 40.241 86.370 62.861 1.00 99.26 0.146 C \n+ATOM 2694 C GLN B 498 41.016 87.663 62.621 1.00 99.49 0.229 C \n+ATOM 2695 O GLN B 498 42.257 87.648 62.759 1.00100.35 -0.286 OA\n+ATOM 2696 CB GLN B 498 41.211 85.205 63.093 1.00100.80 0.040 C \n+ATOM 2697 CG GLN B 498 41.391 84.831 64.556 1.00102.53 0.090 C \n+ATOM 2698 CD GLN B 498 40.090 84.391 65.210 1.00103.58 0.227 C \n+ATOM 2699 NE2 GLN B 498 40.041 83.136 65.647 1.00102.89 -0.369 N \n+ATOM 2700 1HE2 GLN B 498 39.169 82.841 66.086 1.00 0.00 0.159 HD\n+ATOM 2701 2HE2 GLN B 498 40.827 82.492 65.558 1.00 0.00 0.159 HD\n+ATOM 2702 OE1 GLN B 498 39.140 85.169 65.318 1.00103.62 -0.273 OA\n+TER 2703 GLN B 498 \n' |
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| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 tools/lisica/lisica |
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| diff -r dc6fb5c5d4c8 -r 958fa7ba4715 tools/psovina/psovina |
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| Binary file tools/psovina/psovina has changed |