Mercurial > repos > chemteam > bio3d_pca_visualize
comparison visualize_pc.R @ 0:65bfd1b90b96 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
| author | chemteam |
|---|---|
| date | Tue, 26 Feb 2019 08:29:24 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:65bfd1b90b96 |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 options(stringAsfactors = FALSE) | |
| 4 args <- commandArgs(trailingOnly = TRUE) | |
| 5 | |
| 6 library(bio3d) | |
| 7 | |
| 8 dcdfile <- args[1] | |
| 9 pdbfile <- args[2] | |
| 10 | |
| 11 dcd <- read.dcd(dcdfile) | |
| 12 pdb <- read.pdb(pdbfile) | |
| 13 | |
| 14 method <- args[3] | |
| 15 selection <- args[4] | |
| 16 domain <- args[5] | |
| 17 id <- args[6] | |
| 18 pcid <- as.integer(id) | |
| 19 | |
| 20 pdbout <- args[7] | |
| 21 | |
| 22 | |
| 23 if (selection == "string") { | |
| 24 inds <- atom.select(pdb, string = domain) | |
| 25 } | |
| 26 if (selection == "elety") { | |
| 27 inds <- atom.select(pdb, elety = domain) | |
| 28 } | |
| 29 if (selection == "resid") { | |
| 30 inds <- atom.select(pdb, resid = domain) | |
| 31 } | |
| 32 if (selection == "segid") { | |
| 33 inds <- atom.select(pdb, segid = domain) | |
| 34 } | |
| 35 xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz) | |
| 36 | |
| 37 if (method == "FALSE") { | |
| 38 pc <- pca.xyz(xyz[,inds$xyz], use.svd=FALSE) | |
| 39 } | |
| 40 if (method == "TRUE") { | |
| 41 pc <- pca.xyz(xyz[,inds$xyz], use.svd=TRUE) | |
| 42 } | |
| 43 | |
| 44 mktrj.pca(pc, pc=pcid, b=pc$au[,pcid], file=pdbout) | |
| 45 |