Mercurial > repos > chemteam > bio3d_dccm
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dccm.R Wed Mar 27 15:16:19 2019 -0400 @@ -0,0 +1,46 @@ +#!/usr/bin/env Rscript + +options(stringAsfactors = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +library(bio3d) +require(lattice) + +dcdfile <- args[1] +pdbfile <- args[2] + +dcd <- read.dcd(dcdfile) +pdb <- read.pdb(pdbfile) + +selection <- args[3] +domain <- args[4] + +output <- args[5] +dccm_plot <- args[6] + +dcd <- read.dcd(dcdfile) +pdb <- read.pdb(pdbfile) + +if (selection == "string") { + inds <- atom.select(pdb, string = domain) +} +if (selection == "elety") { + inds <- atom.select(pdb, elety = domain) +} +if (selection == "resid") { + inds <- atom.select(pdb, resid = domain) +} +if (selection == "segid") { + inds <- atom.select(pdb, segid = domain) +} + +xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz) +cij<-dccm(xyz[,inds$xyz]) + +write.table(cij, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t") + +png(dccm_plot) +plot(cij) +dev.off() + +