Mercurial > repos > chemteam > bio3d_dccm
annotate dccm.R @ 0:386b4f4b6a85 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
author | chemteam |
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date | Wed, 27 Mar 2019 15:16:19 -0400 |
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386b4f4b6a85
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 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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2 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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3 options(stringAsfactors = FALSE) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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4 args <- commandArgs(trailingOnly = TRUE) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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5 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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6 library(bio3d) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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7 require(lattice) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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8 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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9 dcdfile <- args[1] |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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10 pdbfile <- args[2] |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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11 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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12 dcd <- read.dcd(dcdfile) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
changeset
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13 pdb <- read.pdb(pdbfile) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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14 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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15 selection <- args[3] |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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16 domain <- args[4] |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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17 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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18 output <- args[5] |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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19 dccm_plot <- args[6] |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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20 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
changeset
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21 dcd <- read.dcd(dcdfile) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
changeset
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22 pdb <- read.pdb(pdbfile) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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23 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
changeset
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24 if (selection == "string") { |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
changeset
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25 inds <- atom.select(pdb, string = domain) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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26 } |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
changeset
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27 if (selection == "elety") { |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
changeset
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28 inds <- atom.select(pdb, elety = domain) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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29 } |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
changeset
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30 if (selection == "resid") { |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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31 inds <- atom.select(pdb, resid = domain) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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32 } |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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33 if (selection == "segid") { |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
diff
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34 inds <- atom.select(pdb, segid = domain) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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35 } |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
parents:
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36 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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37 xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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38 cij<-dccm(xyz[,inds$xyz]) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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39 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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40 write.table(cij, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t") |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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41 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
chemteam
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42 png(dccm_plot) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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43 plot(cij) |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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44 dev.off() |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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45 |
386b4f4b6a85
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
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46 |