# HG changeset patch
# User marpiech
# Date 1473860868 14400
# Node ID 958fa7ba471520e533693cb20c8fce47ee082b88
# Parent dc6fb5c5d4c8fb1d2906535177252fdcb307f786
planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty
diff -r dc6fb5c5d4c8 -r 958fa7ba4715 acpc.xml
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
@@ -23,21 +23,22 @@
-fa $fa
-pvol $pvol
-plen $plen
- #if $sod=="true"
+ #if $alignment_option.sod=="true"
-sod
#end if
- -v $v
- -m $m
- #if $L
- -L $L
+ -v $alignment_option.v
+
+ -m $scoring_option.m
+ #if $scoring_option.L
+ -L $scoring_option.L
#end if
- #if $a=="true"
+ #if $scoring_option.a=="true"
-a
#end if
- #if $b=="true"
+ #if $scoring_option.b=="true"
-b
#end if
- #if $c=="true"
+ #if $scoring_option.c=="true"
-c
#end if
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]]>
- doi:10.1093/bioinformatics/btt024
+
+ @article{Gao2013,
+ doi = {10.1093/bioinformatics/btt024},
+ url = {http://dx.doi.org/10.1093/bioinformatics/btt024},
+ year = {2013},
+ month = {jan},
+ publisher = {Oxford University Press ({OUP})},
+ volume = {29},
+ number = {5},
+ pages = {597--604},
+ author = {M. Gao and J. Skolnick},
+ title = {{APoc}: large-scale identification of similar protein pockets},
+ journal = {Bioinformatics}
+ }
+
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 @@
+
+ A Software for Ligand-Based Virtual Screening
+
+
+
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+ $output;
+
+ ]]>
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+ -T [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
+ ]]>
+
+
+
+ @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}
+ }
+
+
+
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
@@ -0,0 +1,234 @@
+
+ Fast Protein-Ligand Docking Tool based on PSO and AutoDock Vina
+
+
+
+
+ $output_log;
+ #end if #
+ cat ligand_out.pdbqt > $output
+
+ ]]>
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+ output_sect['log']=="true"
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+ @article{doi:10.1142/S0219720015410073,
+ author = {Ng, Marcus C. K. and Fong, Simon and Siu, Shirley W. I.},
+ title = {PSOVina: The hybrid particle swarm optimization algorithm for protein–ligand docking},
+ journal = {Journal of Bioinformatics and Computational Biology},
+ volume = {13},
+ number = {03},
+ pages = {1541007},
+ year = {2015},
+ doi = {10.1142/S0219720015410073},
+ note ={PMID: 25800162},
+
+ URL = {http://www.worldscientific.com/doi/abs/10.1142/S0219720015410073},
+ eprint = {http://www.worldscientific.com/doi/pdf/10.1142/S0219720015410073}
+ }
+
+
+
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
@@ -5,237 +5,254 @@
receptor.pdbqt;
- cat $ligand > ligand.pdbqt;
+ cat $input.receptor > receptor.pdbqt;
+ cat $input.ligand > ligand.pdbqt;
$__tool_directory__/tools/smina/smina.static
--receptor receptor.pdbqt
--ligand ligand.pdbqt
- #if $flex
- --flex $flex
+ #if $input.flex
+ --flex $input.flex
#end if
- #if $flexres
- --flexres $flexres
+ #if $input.flexres
+ --flexres $input.flexres
#end if
- #if $flexdist_ligand
- --flexdist_ligand $flexdist_ligand
+ #if $input.flexdist_ligand
+ --flexdist_ligand $input.flexdist_ligand
#end if
- #if $flexdist
- --flexdist $flexdist
+ #if $input.flexdist
+ --flexdist $input.flexdist
#end if
- --center_x $center_x
- --center_y $center_y
- --center_z $center_z
- --size_x $size_x
- --size_y $size_y
- --size_z $size_z
+ --center_x $search_space.center_x
+ --center_y $search_space.center_y
+ --center_z $search_space.center_z
+ --size_x $search_space.size_x
+ --size_y $search_space.size_y
+ --size_z $search_space.size_z
- #if $autobox_ligand
- --autobox_ligand $autobox_ligand
+ #if $search_space.autobox_ligand
+ --autobox_ligand $search_space.autobox_ligand
#end if
- #if $autobox_add
- --autobox_add $autobox_add
+ #if $search_space.autobox_add
+ --autobox_add $search_space.autobox_add
#end if
- #if $no_lig=="true"
+ #if $search_space.no_lig=="true"
--no_lig
#end if
- --scoring $scoring
- #if $custom_scoring
- --custom_scoring $custom_scoring
- #end if
- #if $custom_atoms
- --custom_atoms $custom_atoms
- #end if
- #if $score_only=="true"
- --score_only
- #end if
- #if $local_only=="true"
- --local_only
- #end if
- #if $minimize=="true"
- --minimize
- #end if
- #if $randomize_only=="true"
- --randomize_only
- #end if
- #if $minimize_iters
- --minimize_iters $minimize_iters
- #end if
- #if $accurate_line=="true"
- --accurate_line
- #end if
- #if $minimize_early_term=="true"
- --minimize_early_term
+ --out ligand_out.pdbqt
+ #if $output_sect.out_flex=="true"
+ --out_flex output_flex
+ #end if
+ #if $output_sect.log=="true"
+ --log output_log
#end if
- #if $approximation
- --approximation $approximation
- #end if
- #if $factor
- --factor $factor
- #end if
- #if $force_cap
- --force_cap $force_cap
- #end if
- #if $user_grid
- --user_grid $user_grid
- #end if
- #if $user_grid_lambda
- --user_grid_lambda $user_grid_lambda
+ #if $output_sect.atom_terms=="true"
+ --atom_terms output_atom_terms
#end if
- #if $print_terms=="true"
- --print_terms
- #end if
- #if $print_atom_types=="true"
- --print_atom_types
- #end if
-
- #if $out
- --out $out
- #end if
- #if $out_flex
- --out_flex $out_flex
- #end if
- #if $atom_terms
- --atom_terms $atom_terms
- #end if
- #if $atom_term_data=="true"
+ #if $output_sect.atom_term_data=="true"
--atom_term_data
#end if
- #if $seed
- --seed $seed
+ --scoring $scoring_and_minimization.scoring
+ #if $scoring_and_minimization.custom_scoring
+ --custom_scoring $scoring_and_minimization.custom_scoring
+ #end if
+ #if $scoring_and_minimization.custom_atoms
+ --custom_atoms $scoring_and_minimization.custom_atoms
+ #end if
+ #if $scoring_and_minimization.score_only=="true"
+ --score_only
+ #end if
+ #if $scoring_and_minimization.local_only=="true"
+ --local_only
#end if
- #if $exhaustiveness
- --exhaustiveness $exhaustiveness
+ #if $scoring_and_minimization.minimize=="true"
+ --minimize
+ #end if
+ #if $scoring_and_minimization.randomize_only=="true"
+ --randomize_only
+ #end if
+ --minimize_iters $scoring_and_minimization.minimize_iters
+ #if $scoring_and_minimization.accurate_line=="true"
+ --accurate_line
+ #end if
+ #if $scoring_and_minimization.minimize_early_term=="true"
+ --minimize_early_term
+ #end if
+ #if $scoring_and_minimization.approximation
+ --approximation $scoring_and_minimization.approximation
#end if
- #if $num_modes
- --num_modes $num_modes
+ #if $scoring_and_minimization.factor
+ --factor $scoring_and_minimization.factor
+ #end if
+ #if $scoring_and_minimization.force_cap
+ --force_cap $scoring_and_minimization.force_cap
+ #end if
+ #if $scoring_and_minimization.user_grid
+ --user_grid $scoring_and_minimization.user_grid
+ #end if
+ --user_grid_lambda $scoring_and_minimization.user_grid_lambda
+ #if $scoring_and_minimization.print_terms=="true"
+ --print_terms
#end if
- #if $energy_range
- --energy_range $energy_range
+ #if $scoring_and_minimization.print_atom_types=="true"
+ --print_atom_types
+ #end if
+
+ #if $misc.cpu
+ --cpu $misc.cpu
#end if
- #if $min_rmsd_filter
- --min_rmsd_filter $min_rmsd_filter
+ #if $misc.seed
+ --seed $misc.seed
#end if
- #if $addH=="false"
+ --exhaustiveness $misc.exhaustiveness
+ --num_modes $misc.num_modes
+ --energy_range $misc.energy_range
+ --min_rmsd_filter $misc.min_rmsd_filter
+ #if $misc.addH=="false"
--addH false
#end if
+ ;
+ #if $output_sect.out_flex=="true" #
+ cat output_flex > $out_flex_output;
+ #end if #
+ #if $output_sect.log=="true" #
+ cat output_log > $output_log;
+ #end if #
+ #if $output_sect.atom_terms=="true" #
+ cat output_atom_terms > $atom_terms_output;
+ #end if #
- > $stand_output;
- #if $out # cat $out > $out_output; #end if #
- #if $out_flex # cat $out_flex > $out_flex_output; #end if #
- #if $atom_terms # cat $atom_terms > $atom_terms_output; #end if #
-
- cat $stand_output > /tmp/ouput
+ cat ligand_out.pdbqt > $output
]]>
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+
@@ -249,7 +266,7 @@
@@ -335,7 +352,20 @@
- @misc{url = {https://sourceforge.net/projects/smina/}, }
+ @article{Koes2013,
+ doi = {10.1021/ci300604z},
+ url = {http://dx.doi.org/10.1021/ci300604z},
+ year = {2013},
+ month = {aug},
+ publisher = {American Chemical Society ({ACS})},
+ volume = {53},
+ number = {8},
+ pages = {1893--1904},
+ author = {David Ryan Koes and Matthew P. Baumgartner and Carlos J. Camacho},
+ title = {Lessons Learned in Empirical Scoring with smina from the {CSAR} 2011 Benchmarking Exercise},
+ journal = {Journal of Chemical Information and Modeling}
+ }
+ @misc{url = {https://sourceforge.net/projects/smina/}}
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
@@ -0,0 +1,9992 @@
+@MOLECULE
+ZINC00205726
+ 37 38 0 0 0
+SMALL
+NO_CHARGES
+
+@ATOM
+ 1 C1 -2.0033 3.8281 1.0379 C.2 1 <0> 0.0000
+ 2 C2 -1.8312 4.9188 1.9383 C.2 1 <0> 0.0000
+ 3 C3 -0.8238 3.4766 0.4192 C.2 1 <0> 0.0000
+ 4 C4 -0.5263 5.3594 1.9737 C.2 1 <0> 0.0000
+ 5 C5 -0.2854 1.1756 -0.2368 C.2 1 <0> 0.0000
+ 6 C6 -0.0518 0.1220 -1.2587 C.2 1 <0> 0.0000
+ 7 C7 0.1990 -0.7678 0.8558 C.2 1 <0> 0.0000
+ 8 C8 -0.5926 2.4376 -0.5422 C.2 1 <0> 0.0000
+ 9 C9 -1.6968 1.3354 2.7771 C.2 1 <0> 0.0000
+ 10 C10 0.8427 5.9535 3.9885 C.3 1 <0> 0.0000
+ 11 C11 0.5287 -2.2990 -1.1570 C.3 1 <0> 0.0000
+ 12 C12 -3.9074 0.5782 2.4090 C.3 1 <0> 0.0000
+ 13 C13 0.0529 6.4577 2.7774 C.3 1 <0> 0.0000
+ 14 C14 -0.2813 1.3463 2.2497 C.3 1 <0> 0.0000
+ 15 N1 -0.1260 0.6029 1.0075 N.pl3 1 <0> 0.0000
+ 16 N2 0.2342 -1.0190 -0.5272 N.am 1 <0> 0.0000
+ 17 O1 -0.1110 0.2789 -2.4658 O.2 1 <0> 0.0000
+ 18 O2 -2.0103 1.9047 3.8174 O.2 1 <0> 0.0000
+ 19 O3 -2.5447 0.6352 1.9744 O.3 1 <0> 0.0000
+ 20 S1 0.4864 -1.8774 2.0749 S.2 1 <0> 0.0000
+ 21 S2 0.4843 4.4597 0.9242 S.3 1 <0> 0.0000
+ 22 H1 -2.9489 3.3314 0.8593 H 1 <0> 0.0000
+ 23 H2 -2.6268 5.3546 2.5294 H 1 <0> 0.0000
+ 24 H3 -0.7014 2.6897 -1.5971 H 1 <0> 0.0000
+ 25 H4 0.2156 5.3211 4.6260 H 1 <0> 0.0000
+ 26 H5 1.2108 6.7869 4.5949 H 1 <0> 0.0000
+ 27 H6 1.7055 5.3587 3.6699 H 1 <0> 0.0000
+ 28 H7 1.6029 -2.3905 -1.3376 H 1 <0> 0.0000
+ 29 H8 0.0031 -2.3800 -2.1124 H 1 <0> 0.0000
+ 30 H9 0.2092 -3.1208 -0.5105 H 1 <0> 0.0000
+ 31 H10 -4.4943 -0.0047 1.6948 H 1 <0> 0.0000
+ 32 H11 -4.3091 1.5917 2.4857 H 1 <0> 0.0000
+ 33 H12 -3.9481 0.0970 3.3890 H 1 <0> 0.0000
+ 34 H13 0.7201 7.0900 2.1620 H 1 <0> 0.0000
+ 35 H14 -0.7359 7.1461 3.1348 H 1 <0> 0.0000
+ 36 H15 0.3775 0.8885 2.9922 H 1 <0> 0.0000
+ 37 H16 0.0199 2.3785 2.0539 H 1 <0> 0.0000
+@BOND
+ 1 1 2 1
+ 2 1 3 2
+ 3 2 4 2
+ 4 3 8 1
+ 5 3 21 1
+ 6 4 13 1
+ 7 4 21 1
+ 8 5 6 1
+ 9 5 8 2
+ 10 5 15 1
+ 11 6 16 am
+ 12 6 17 2
+ 13 7 15 1
+ 14 7 16 1
+ 15 7 20 2
+ 16 9 14 1
+ 17 9 18 2
+ 18 9 19 1
+ 19 10 13 1
+ 20 11 16 1
+ 21 12 19 1
+ 22 14 15 1
+ 23 1 22 1
+ 24 2 23 1
+ 25 8 24 1
+ 26 10 25 1
+ 27 10 26 1
+ 28 10 27 1
+ 29 11 28 1
+ 30 11 29 1
+ 31 11 30 1
+ 32 12 31 1
+ 33 12 32 1
+ 34 12 33 1
+ 35 13 34 1
+ 36 13 35 1
+ 37 14 36 1
+ 38 14 37 1
+@MOLECULE
+ZINC69323649
+ 39 41 0 0 0
+SMALL
+NO_CHARGES
+
+@ATOM
+ 1 C1 3.1080 -0.4560 -0.5881 C.ar 1 <0> 0.0000
+ 2 C2 3.1415 -0.1560 -1.9504 C.ar 1 <0> 0.0000
+ 3 C3 4.4829 -3.6876 4.3666 C.ar 1 <0> 0.0000
+ 4 C4 4.0394 -2.7517 6.5494 C.ar 1 <0> 0.0000
+ 5 C5 4.9192 -4.8708 4.9626 C.ar 1 <0> 0.0000
+ 6 C6 4.4756 -3.9349 7.1454 C.ar 1 <0> 0.0000
+ 7 C7 0.7908 -1.1179 -0.7840 C.ar 1 <0> 0.0000
+ 8 C8 0.8241 -0.8058 -2.1444 C.ar 1 <0> 0.0000
+ 9 C9 1.9342 -0.9357 -0.0057 C.ar 1 <0> 0.0000
+ 10 C10 1.9945 -0.3224 -2.7270 C.ar 1 <0> 0.0000
+ 11 C11 4.0431 -2.6279 5.1600 C.ar 1 <0> 0.0000
+ 12 C12 4.9155 -4.9945 6.3520 C.ar 1 <0> 0.0000
+ 13 C13 -0.3443 -0.6504 -4.2598 C.2 1 <0> 0.0000
+ 14 C14 2.9440 -1.1228 2.2932 C.2 1 <0> 0.0000
+ 15 C15 0.8588 0.1610 -4.7089 C.3 1 <0> 0.0000
+ 16 C16 1.3688 -0.7016 4.2171 C.3 1 <0> 0.0000
+ 17 C17 2.5090 -1.5599 3.6897 C.3 1 <0> 0.0000
+ 18 N1 -0.3094 -1.0204 -2.9352 N.am 1 <0> 0.0000
+ 19 N2 1.9062 -1.2397 1.3558 N.am 1 <0> 0.0000
+ 20 O1 -1.2909 -0.8788 -5.0100 O.2 1 <0> 0.0000
+ 21 O2 4.0808 -0.7108 2.0804 O.2 1 <0> 0.0000
+ 22 O3 2.0985 -0.0578 -4.0636 O.3 1 <0> 0.0000
+ 23 O4 3.6145 -1.4642 4.5738 O.3 1 <0> 0.0000
+ 24 Br1 5.5045 -6.5985 7.1597 Br 1 <0> 0.0000
+ 25 H1 4.0057 -0.3177 0.0095 H 1 <0> 0.0000
+ 26 H2 4.0631 0.2062 -2.3979 H 1 <0> 0.0000
+ 27 H3 4.4887 -3.5971 3.2838 H 1 <0> 0.0000
+ 28 H4 3.6987 -1.9292 7.1726 H 1 <0> 0.0000
+ 29 H5 5.2591 -5.6869 4.3301 H 1 <0> 0.0000
+ 30 H6 4.4661 -4.0149 8.2293 H 1 <0> 0.0000
+ 31 H7 -0.1211 -1.5017 -0.3319 H 1 <0> 0.0000
+ 32 H8 1.0127 -0.0436 -5.7742 H 1 <0> 0.0000
+ 33 H9 0.6001 1.2229 -4.6143 H 1 <0> 0.0000
+ 34 H10 1.6605 0.3541 4.2558 H 1 <0> 0.0000
+ 35 H11 1.0634 -1.0037 5.2233 H 1 <0> 0.0000
+ 36 H12 0.5002 -0.7680 3.5534 H 1 <0> 0.0000
+ 37 H13 2.2061 -2.6121 3.6556 H 1 <0> 0.0000
+ 38 H14 -1.1176 -1.4755 -2.5212 H 1 <0> 0.0000
+ 39 H15 1.0138 -1.5883 1.7243 H 1 <0> 0.0000
+@BOND
+ 1 1 2 ar
+ 2 1 9 ar
+ 3 2 10 ar
+ 4 3 5 ar
+ 5 3 11 ar
+ 6 4 6 ar
+ 7 4 11 ar
+ 8 5 12 ar
+ 9 6 12 ar
+ 10 7 8 ar
+ 11 7 9 ar
+ 12 8 10 ar
+ 13 8 18 1
+ 14 9 19 1
+ 15 10 22 1
+ 16 11 23 1
+ 17 12 24 1
+ 18 13 15 1
+ 19 13 18 am
+ 20 13 20 2
+ 21 14 17 1
+ 22 14 19 am
+ 23 14 21 2
+ 24 15 22 1
+ 25 16 17 1
+ 26 17 23 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 15 32 1
+ 35 15 33 1
+ 36 16 34 1
+ 37 16 35 1
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+ 21 H10 0.1856 -1.1786 1.7698 H 1 <0> 0.0000
+ 22 H11 -0.3709 -2.6879 -0.1660 H 1 <0> 0.0000
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+ 46 H22 -2.1283 -2.6153 -3.2041 H 1 <0> 0.0000
+ 47 H23 -0.4370 -2.7170 -1.4272 H 1 <0> 0.0000
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