Mercurial > repos > chemteam > bio3d_dccm
comparison 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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-1:000000000000 | 0:386b4f4b6a85 |
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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 |