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annotate dccm.R @ 3:ddef4de91df6 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
author chemteam
date Wed, 27 Mar 2019 15:15:54 -0400
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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1 #!/usr/bin/env Rscript
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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3 options(stringAsfactors = FALSE)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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4 args <- commandArgs(trailingOnly = TRUE)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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6 library(bio3d)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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7 require(lattice)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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9 dcdfile <- args[1]
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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10 pdbfile <- args[2]
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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12 dcd <- read.dcd(dcdfile)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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13 pdb <- read.pdb(pdbfile)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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15 selection <- args[3]
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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16 domain <- args[4]
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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18 output <- args[5]
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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19 dccm_plot <- args[6]
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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21 dcd <- read.dcd(dcdfile)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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22 pdb <- read.pdb(pdbfile)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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24 if (selection == "string") {
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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25 inds <- atom.select(pdb, string = domain)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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26 }
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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27 if (selection == "elety") {
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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28 inds <- atom.select(pdb, elety = domain)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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29 }
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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30 if (selection == "resid") {
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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31 inds <- atom.select(pdb, resid = domain)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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32 }
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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33 if (selection == "segid") {
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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34 inds <- atom.select(pdb, segid = domain)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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35 }
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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37 xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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38 cij<-dccm(xyz[,inds$xyz])
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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40 write.table(cij, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t")
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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42 png(dccm_plot)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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43 plot(cij)
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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44 dev.off()
ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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ddef4de91df6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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