Mercurial > repos > chemteam > bio3d_rmsf
comparison dccm.R @ 3:d8004331b257 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
| author | chemteam |
|---|---|
| date | Wed, 27 Mar 2019 15:17:17 -0400 |
| parents | |
| children |
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| 2:50a2b87784b5 | 3:d8004331b257 |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 options(stringAsfactors = FALSE) | |
| 4 args <- commandArgs(trailingOnly = TRUE) | |
| 5 | |
| 6 library(bio3d) | |
| 7 require(lattice) | |
| 8 | |
| 9 dcdfile <- args[1] | |
| 10 pdbfile <- args[2] | |
| 11 | |
| 12 dcd <- read.dcd(dcdfile) | |
| 13 pdb <- read.pdb(pdbfile) | |
| 14 | |
| 15 selection <- args[3] | |
| 16 domain <- args[4] | |
| 17 | |
| 18 output <- args[5] | |
| 19 dccm_plot <- args[6] | |
| 20 | |
| 21 dcd <- read.dcd(dcdfile) | |
| 22 pdb <- read.pdb(pdbfile) | |
| 23 | |
| 24 if (selection == "string") { | |
| 25 inds <- atom.select(pdb, string = domain) | |
| 26 } | |
| 27 if (selection == "elety") { | |
| 28 inds <- atom.select(pdb, elety = domain) | |
| 29 } | |
| 30 if (selection == "resid") { | |
| 31 inds <- atom.select(pdb, resid = domain) | |
| 32 } | |
| 33 if (selection == "segid") { | |
| 34 inds <- atom.select(pdb, segid = domain) | |
| 35 } | |
| 36 | |
| 37 xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz) | |
| 38 cij<-dccm(xyz[,inds$xyz]) | |
| 39 | |
| 40 write.table(cij, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t") | |
| 41 | |
| 42 png(dccm_plot) | |
| 43 plot(cij) | |
| 44 dev.off() | |
| 45 | |
| 46 |