| Next changeset 1:0692d9f9edd3 (2019-03-27) |
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Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4 |
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added:
macros.xml pca.R rmsd.R rmsf.R test-data/PCA_1.pdb test-data/PCA_plot.png test-data/PCA_raw_data.tabular test-data/RMSD_raw_data.tabular test-data/rmsf_plot.png test-data/rmsf_raw_data.tabular test-data/test.dcd test-data/test.pdb visualize_pc.R visualize_pc.xml |
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| diff -r 000000000000 -r 65bfd1b90b96 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Feb 26 08:29:24 2019 -0500 |
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| @@ -0,0 +1,26 @@ +<macros> + <token name="@VERSION@">2.3</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.3_3">r-bio3d</requirement> + <requirement type="package" version="1.16">r-ncdf4</requirement> + <requirement type="package" version="0.20_35">r-lattice</requirement> + <yield/> + </requirements> + </xml> + <xml name="analysis_inputs"> + <param format="dcd" name="dcdin" type="data" label="dcd trajectory input"/> + <param format="pdb" name="pdbin" type="data" label="pdb input"/> + <yield/> + </xml> + <xml name="tests_inputs"> + <param name="dcdin" value="test.dcd" ftype="dcd"/> + <param name="pdbin" value="test.pdb" ftype="pdb"/> + <yield/> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btl461</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 65bfd1b90b96 pca.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pca.R Tue Feb 26 08:29:24 2019 -0500 |
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| @@ -0,0 +1,61 @@ +#!/usr/bin/env Rscript + +options(stringAsfactors = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +library(bio3d) + +dcdfile <- args[1] +pdbfile <- args[2] + +dcd <- read.dcd(dcdfile) +pdb <- read.pdb(pdbfile) + +method <- args[3] +selection <- args[4] +domain <- args[5] + +output <- args[6] +pca_plot <- args[7] +pca_cluster <- args[8] +pc1_rmsf <- args[9] + + +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$xyz) + +if (method == "FALSE") { + pc <- pca.xyz(xyz[,inds$xyz], use.svd=FALSE) +} +if (method == "TRUE") { + pc <- pca.xyz(xyz[,inds$xyz], use.svd=TRUE) +} + +write.table(pc$au[,1:2:3], file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t") + +png(pca_plot) +plot(pc, col=bwr.colors(nrow(xyz)) ) +dev.off() + +png(pca_cluster) +hc <- hclust(dist(pc$z[,1:2])) +grps <- cutree(hc, k=2) +plot(pc, col=grps) +dev.off() + +png(pc1_rmsf) +plot.bio3d(pc$au[,1], ylab="PC1 (A)", xlab="Residue Position", typ="l") +points(pc$au[,2], typ="l", col="blue") +dev.off() + |
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| diff -r 000000000000 -r 65bfd1b90b96 rmsd.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmsd.R Tue Feb 26 08:29:24 2019 -0500 |
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| @@ -0,0 +1,67 @@ +#!/usr/bin/env Rscript + +options(stringAsfactors = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +library(bio3d) + +dcdfile <- args[1] +pdbfile <- args[2] +selection <- args[3] + +dcd <- read.dcd(dcdfile) +pdb <- read.pdb(pdbfile) + + +if (selection == "string") { + domain <- args[4] + output <- args[5] + rmsd_plot <- args[6] + rmsd_hist <- args[7] + inds <- atom.select(pdb, string = domain) +} +if (selection == "resno") { + res1 <- args[4] + res2 <- args[5] + output <- args[6] + rmsd_plot <- args[7] + rmsd_hist <- args[8] + inds <- atom.select(pdb, resno=res1:res2) +} +if (selection == "elety") { + domain <- args[4] + output <- args[5] + rmsd_plot <- args[6] + rmsd_hist <- args[7] + inds <- atom.select(pdb, elety = domain) +} +if (selection == "resid") { + domain <- args[4] + output <- args[5] + rmsd_plot <- args[6] + rmsd_hist <- args[7] + inds <- atom.select(pdb, resid = domain) +} +if (selection == "segid") { + domain <- args[4] + output <- args[5] + rmsd_plot <- args[6] + rmsd_hist <- args[7] + inds <- atom.select(pdb, segid = domain) +} + +xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz) + +rd <- rmsd(xyz[1,inds$xyz], xyz[,inds$xyz]) + +write.table(rd, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t") + +png(rmsd_plot) +plot(rd, typ="l", ylab="RMSD (Å)", xlab="Frame No.") +points(lowess(rd), typ="l", col="red", lty=2, lwd=2) +dev.off() + +png(rmsd_hist) +hist(rd, breaks=40, freq=FALSE, main="RMSD Histogram", xlab="RMSD") +lines(density(rd), typ="l", col="red", lty=2, lwd=2) +dev.off() |
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| diff -r 000000000000 -r 65bfd1b90b96 rmsf.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmsf.R Tue Feb 26 08:29:24 2019 -0500 |
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| @@ -0,0 +1,57 @@ +#!/usr/bin/env Rscript + +options(stringAsfactors = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +library(bio3d) + +dcdfile <- args[1] +pdbfile <- args[2] +selection <- args[3] + +dcd <- read.dcd(dcdfile) +pdb <- read.pdb(pdbfile) + + +if (selection == "string") { + domain <- args[4] + output <- args[5] + rmsf_plot <- args[6] + inds <- atom.select(pdb, string = domain) +} +if (selection == "resno") { + res1 <- args[4] + res2 <- args[5] + output <- args[6] + rmsf_plot <- args[7] + inds <- atom.select(pdb, resno=res1:res2) +} +if (selection == "elety") { + domain <- args[4] + output <- args[5] + rmsf_plot <- args[6] + inds <- atom.select(pdb, elety = domain) +} +if (selection == "resid") { + domain <- args[4] + output <- args[5] + rmsf_plot <- args[6] + inds <- atom.select(pdb, resid = domain) +} +if (selection == "segid") { + domain <- args[4] + output <- args[5] + rmsf_plot <- args[6] + inds <- atom.select(pdb, segid = domain) +} + +xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz) + +rf <- rmsf(xyz[,inds$xyz]) + +write.table(rf, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t") + +png(rmsf_plot) +plot(rf, ylab="RMSF", xlab="Residue Position", typ="l") +dev.off() + |
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| diff -r 000000000000 -r 65bfd1b90b96 test-data/PCA_1.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PCA_1.pdb Tue Feb 26 08:29:24 2019 -0500 |
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| b'@@ -0,0 +1,14791 @@\n+MODEL 1\n+ATOM 1 CA ALA 1 24.197 5.292 5.774 1.00 0.05 \n+ATOM 2 CA ALA 2 23.445 7.891 3.028 1.00 0.04 \n+ATOM 3 CA ALA 3 24.995 9.213 -0.229 1.00 0.04 \n+ATOM 4 CA ALA 4 24.439 12.164 -2.595 1.00 0.05 \n+ATOM 5 CA ALA 5 25.954 11.194 -5.963 1.00 0.08 \n+ATOM 6 CA ALA 6 22.514 11.125 -7.630 1.00 0.05 \n+ATOM 7 CA ALA 7 20.153 14.073 -7.862 1.00 0.08 \n+ATOM 8 CA ALA 8 17.482 13.463 -5.205 1.00 0.04 \n+ATOM 9 CA ALA 9 14.490 15.817 -5.576 1.00 0.02 \n+ATOM 10 CA ALA 10 11.052 14.708 -4.396 1.00 0.07 \n+ATOM 11 CA ALA 11 8.198 15.513 -6.896 1.00 0.02 \n+ATOM 12 CA ALA 12 5.822 18.263 -5.514 1.00 0.04 \n+ATOM 13 CA ALA 13 2.245 17.206 -4.720 1.00 0.05 \n+ATOM 14 CA ALA 14 -0.383 19.619 -3.321 1.00 0.04 \n+ATOM 15 CA ALA 15 -3.326 18.616 -1.169 1.00 0.03 \n+ATOM 16 CA ALA 16 -6.175 20.200 0.820 1.00 0.02 \n+ATOM 17 CA ALA 17 -6.648 20.354 4.596 1.00 0.01 \n+ATOM 18 CA ALA 18 -10.198 21.285 5.623 1.00 0.04 \n+ATOM 19 CA ALA 19 -11.428 22.994 8.812 1.00 0.05 \n+ATOM 20 CA ALA 20 -14.240 22.210 11.307 1.00 0.04 \n+ATOM 21 CA ALA 21 -15.968 25.339 9.926 1.00 0.04 \n+ATOM 22 CA ALA 22 -16.143 23.831 6.418 1.00 0.03 \n+ATOM 23 CA ALA 23 -13.303 25.671 4.682 1.00 0.02 \n+ATOM 24 CA ALA 24 -10.421 23.993 2.844 1.00 0.01 \n+ATOM 25 CA ALA 25 -6.811 25.245 2.494 1.00 0.01 \n+ATOM 26 CA ALA 26 -4.007 24.119 0.146 1.00 0.03 \n+ATOM 27 CA ALA 27 -1.040 22.400 1.855 1.00 0.02 \n+ATOM 28 CA ALA 28 2.156 21.854 -0.155 1.00 0.06 \n+ATOM 29 CA ALA 29 4.028 18.533 0.065 1.00 0.06 \n+ATOM 30 CA ALA 30 6.117 16.163 -2.035 1.00 0.04 \n+ATOM 31 CA ALA 31 6.368 12.391 -2.616 1.00 0.03 \n+ATOM 32 CA ALA 32 9.409 10.160 -1.944 1.00 0.01 \n+ATOM 33 CA ALA 33 10.183 6.647 -3.273 1.00 0.01 \n+ATOM 34 CA ALA 34 10.995 3.651 -1.004 1.00 0.01 \n+ATOM 35 CA ALA 35 14.535 2.434 -0.203 1.00 0.03 \n+ATOM 36 CA ALA 36 13.984 -0.881 -2.019 1.00 0.05 \n+ATOM 37 CA ALA 37 13.549 0.773 -5.456 1.00 0.03 \n+ATOM 38 CA ALA 38 16.787 2.795 -4.941 1.00 0.04 \n+ATOM 39 CA ALA 39 20.345 1.757 -5.847 1.00 0.07 \n+ATOM 40 CA ALA 40 22.321 0.268 -2.894 1.00 0.05 \n+ATOM 41 CA ALA 41 26.077 0.879 -3.164 1.00 0.03 \n+ATOM 42 CA ALA 42 29.273 1.550 -1.211 1.00 0.03 \n+ATOM 43 CA ALA 43 29.818 4.986 0.448 1.00 0.04 \n+ATOM 44 CA ALA 44 33.171 5.621 -1.259 1.00 0.02 \n+ATOM 45 CA ALA 45 32.479 4.215 -4.713 1.00 0.06 \n+ATOM 46 CA ALA 46 29.962 3.090 -7.378 1.00 0.04 \n+ATOM 47 CA ALA 47 30.361 -0.512 -6.123 1.00 0.03 \n+ATOM 48 CA ALA 48 27.092 -2.453 -5.754 1.00 0.05 \n+ATOM 49 CA ALA 49'..b'.271 -23.421 -6.056 1.00 0.05 \n+ATOM 386 CA ALA 386 -18.831 -20.648 -6.522 1.00 0.07 \n+ATOM 387 CA ALA 387 -20.917 -22.335 -3.781 1.00 0.07 \n+ATOM 388 CA ALA 388 -18.422 -21.355 -1.011 1.00 0.09 \n+ATOM 389 CA ALA 389 -19.049 -17.938 0.678 1.00 0.11 \n+ATOM 390 CA ALA 390 -16.213 -15.339 0.421 1.00 0.09 \n+ATOM 391 CA ALA 391 -14.237 -17.392 -2.120 1.00 0.05 \n+ATOM 392 CA ALA 392 -15.125 -15.344 -5.236 1.00 0.04 \n+ATOM 393 CA ALA 393 -13.819 -11.735 -5.068 1.00 0.04 \n+ATOM 394 CA ALA 394 -14.186 -10.779 -8.753 1.00 0.04 \n+ATOM 395 CA ALA 395 -14.563 -11.904 -12.357 1.00 0.03 \n+ATOM 396 CA ALA 396 -10.865 -12.326 -13.334 1.00 0.02 \n+ATOM 397 CA ALA 397 -9.716 -15.776 -14.545 1.00 0.02 \n+ATOM 398 CA ALA 398 -7.731 -18.105 -12.223 1.00 0.03 \n+ATOM 399 CA ALA 399 -5.424 -18.609 -15.234 1.00 0.04 \n+ATOM 400 CA ALA 400 -4.283 -14.973 -14.844 1.00 0.02 \n+ATOM 401 CA ALA 401 -2.147 -13.312 -12.122 1.00 0.04 \n+ATOM 402 CA ALA 402 1.155 -13.783 -13.925 1.00 0.02 \n+ATOM 403 CA ALA 403 3.548 -10.722 -13.835 1.00 0.02 \n+ATOM 404 CA ALA 404 5.405 -11.613 -17.064 1.00 0.04 \n+ATOM 405 CA ALA 405 2.104 -11.975 -18.956 1.00 0.04 \n+ATOM 406 CA ALA 406 0.828 -8.568 -17.766 1.00 0.02 \n+ATOM 407 CA ALA 407 4.203 -6.980 -18.675 1.00 0.08 \n+ATOM 408 CA ALA 408 3.835 -8.287 -22.218 1.00 0.11 \n+ATOM 409 CA ALA 409 0.169 -7.322 -22.591 1.00 0.07 \n+ATOM 410 CA ALA 410 -0.257 -4.001 -20.729 1.00 0.04 \n+ATOM 411 CA ALA 411 3.174 -2.365 -19.968 1.00 0.03 \n+ATOM 412 CA ALA 412 2.097 1.289 -20.212 1.00 0.03 \n+ATOM 413 CA ALA 413 -0.758 0.762 -17.730 1.00 0.01 \n+ATOM 414 CA ALA 414 -0.921 3.400 -15.002 1.00 0.02 \n+ATOM 415 CA ALA 415 -2.788 4.441 -11.864 1.00 0.01 \n+ATOM 416 CA ALA 416 -3.627 8.153 -11.551 1.00 0.02 \n+ATOM 417 CA ALA 417 -4.688 9.952 -8.356 1.00 0.04 \n+ATOM 418 CA ALA 418 -5.878 13.552 -7.876 1.00 0.03 \n+ATOM 419 CA ALA 419 -7.870 15.831 -5.583 1.00 0.03 \n+ATOM 420 CA ALA 420 -6.649 14.822 -2.057 1.00 0.02 \n+ATOM 421 CA ALA 421 -8.791 16.537 0.622 1.00 0.02 \n+ATOM 422 CA ALA 422 -8.475 15.737 4.352 1.00 0.02 \n+ATOM 423 CA ALA 423 -10.483 17.155 7.299 1.00 0.03 \n+ATOM 424 CA ALA 424 -13.106 16.563 10.015 1.00 0.05 \n+ATOM 425 CA ALA 425 -16.080 14.342 8.995 1.00 0.05 \n+ATOM 426 CA ALA 426 -18.451 16.404 6.797 1.00 0.03 \n+ATOM 427 CA ALA 427 -15.858 18.916 5.559 1.00 0.01 \n+ATOM 428 CA ALA 428 -14.438 17.551 2.262 1.00 0.01 \n+ATOM 429 CA ALA 429 -17.527 18.224 0.113 1.00 0.03 \n+ATOM 430 CA ALA 430 -16.755 21.948 0.408 1.00 0.01 \n+ATOM 431 CA ALA 431 -14.705 23.937 -2.210 1.00 0.07 \n+ATOM 432 CA ALA 432 -10.871 23.713 -2.349 1.00 0.04 \n+ATOM 433 CA ALA 433 -8.634 26.639 -1.246 1.00 0.00 \n+ENDMDL\n+END \n' |
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| diff -r 000000000000 -r 65bfd1b90b96 test-data/PCA_plot.png |
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| Binary file test-data/PCA_plot.png has changed |
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| diff -r 000000000000 -r 65bfd1b90b96 test-data/PCA_raw_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PCA_raw_data.tabular Tue Feb 26 08:29:24 2019 -0500 |
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| b'@@ -0,0 +1,433 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| b |
| diff -r 000000000000 -r 65bfd1b90b96 test-data/RMSD_raw_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RMSD_raw_data.tabular Tue Feb 26 08:29:24 2019 -0500 |
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| @@ -0,0 +1,15 @@ +1 0 +2 0.211 +3 0.292 +4 0.347 +5 0.384 +6 0.405 +7 0.419 +8 0.421 +9 0.424 +10 0.427 +11 0.553 +12 0.589 +13 0.634 +14 0.646 +15 0.658 |
| b |
| diff -r 000000000000 -r 65bfd1b90b96 test-data/rmsf_plot.png |
| b |
| Binary file test-data/rmsf_plot.png has changed |
| b |
| diff -r 000000000000 -r 65bfd1b90b96 test-data/rmsf_raw_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rmsf_raw_data.tabular Tue Feb 26 08:29:24 2019 -0500 |
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|
| b |
| diff -r 000000000000 -r 65bfd1b90b96 test-data/test.dcd |
| b |
| Binary file test-data/test.dcd has changed |
| b |
| diff -r 000000000000 -r 65bfd1b90b96 test-data/test.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.pdb Tue Feb 26 08:29:24 2019 -0500 |
| b |
| b'@@ -0,0 +1,61655 @@\n+REMARK FILENAME: MINIMIZE.INP \n+REMARK PURPOSE: SETUP PERIODIC BOUNDARY CONDITIONS AND ENERGY MINIMIZATION \n+REMARK AUTHOR: THARINDU SENAPATHI \n+REMARK DATE: 9/25/18 11:16:58 CREATED BY USER: galaxy \n+ATOM 1 N SER 2 23.711 4.396 5.292 1.00 0.00 PRO \n+ATOM 2 HT1 SER 2 22.774 4.012 5.048 1.00 0.00 PRO \n+ATOM 3 HT2 SER 2 23.993 4.056 6.233 1.00 0.00 PRO \n+ATOM 4 HT3 SER 2 24.412 4.016 4.606 1.00 0.00 PRO \n+ATOM 5 CA SER 2 23.692 5.909 5.232 1.00 0.00 PRO \n+ATOM 6 HA SER 2 23.045 6.255 6.026 1.00 0.00 PRO \n+ATOM 7 CB SER 2 25.129 6.479 5.468 1.00 0.00 PRO \n+ATOM 8 HB1 SER 2 25.502 6.112 6.451 1.00 0.00 PRO \n+ATOM 9 HB2 SER 2 25.108 7.590 5.522 1.00 0.00 PRO \n+ATOM 10 OG SER 2 26.032 6.062 4.445 1.00 0.00 PRO \n+ATOM 11 HG1 SER 2 26.928 6.382 4.649 1.00 0.00 PRO \n+ATOM 12 C SER 2 23.087 6.445 3.945 1.00 0.00 PRO \n+ATOM 13 O SER 2 22.287 5.741 3.315 1.00 0.00 PRO \n+ATOM 14 N ALA 3 23.417 7.674 3.515 1.00 0.00 PRO \n+ATOM 15 HN ALA 3 24.112 8.236 3.961 1.00 0.00 PRO \n+ATOM 16 CA ALA 3 22.937 8.280 2.293 1.00 0.00 PRO \n+ATOM 17 HA ALA 3 22.421 7.554 1.681 1.00 0.00 PRO \n+ATOM 18 CB ALA 3 22.012 9.476 2.583 1.00 0.00 PRO \n+ATOM 19 HB1 ALA 3 22.509 10.220 3.241 1.00 0.00 PRO \n+ATOM 20 HB2 ALA 3 21.086 9.125 3.082 1.00 0.00 PRO \n+ATOM 21 HB3 ALA 3 21.718 9.984 1.638 1.00 0.00 PRO \n+ATOM 22 C ALA 3 24.147 8.753 1.509 1.00 0.00 PRO \n+ATOM 23 O ALA 3 25.174 9.077 2.073 1.00 0.00 PRO \n+ATOM 24 N CYS 4 24.005 8.749 0.169 1.00 0.00 PRO \n+ATOM 25 HN CYS 4 23.142 8.478 -0.258 1.00 0.00 PRO \n+ATOM 26 CA CYS 4 25.025 9.149 -0.766 1.00 0.00 PRO \n+ATOM 27 HA CYS 4 25.769 9.761 -0.272 1.00 0.00 PRO \n+ATOM 28 CB CYS 4 25.700 7.948 -1.484 1.00 0.00 PRO \n+ATOM 29 HB1 CYS 4 26.256 8.290 -2.382 1.00 0.00 PRO \n+ATOM 30 HB2 CYS 4 24.907 7.257 -1.851 1.00 0.00 PRO \n+ATOM 31 SG CYS 4 26.887 7.076 -0.411 1.00 0.00 PRO \n+ATOM 32 C CYS 4 24.341 10.034 -1.774 1.00 0.00 PRO \n+ATOM 33 O CYS 4 23.104 10.106 -1.853 1.00 0.00 PRO \n+ATOM 34 N THR 5 25.135 10.817 -2.507 1.00 0.00 PRO \n+ATOM 35 HN THR 5 26.125 10.731 -2.426 1.00 0.00 PRO \n+ATOM 36 CA THR 5 24.625 11.886 -3.343 1.00 0.00 PRO \n+ATOM 37 HA THR 5 23.595 11.683 -3.608 1.00 0.00 PRO \n+ATOM 38 CB THR 5 24.715 13.266 -2.674 1.00 0.00 PRO \n+ATOM 39 HB THR 5 24.358 14.060 -3.371 1.00 0.00 PRO \n+ATOM 40 OG1 THR 5 26.051 13.580 -2.272 1.00 0.00 PRO \n+ATOM 41 HG1 THR 5 26.535 13.523 -3.104 1.00 0.00 PRO \n+ATOM 42 CG2 THR 5 23.787 13.298 -1.447 1.00 0.00 PRO \n+ATOM 43 HG21 THR 5 24.126 12.589 -0.663 1.00 0.00 PRO \n+ATOM 44 HG22 THR 5 22.759 13.003 -1.749 1.00 0.00 PRO \n+ATOM 45 HG23 THR 5 23.752 14.313 -1.003 1.00 0.00 PRO \n+ATOM 46 C THR 5 25.385 11.902 -4.645 1.00 0.00 PRO \n+ATOM 47 O THR 5 25.810'..b' CLA CLA 2 5.975 -34.097 -14.115 1.00 0.00 CLA \n+ATOM 61600 CLA CLA 3 3.049 -40.330 0.268 1.00 0.00 CLA \n+ATOM 61601 CLA CLA 4 -29.182 -19.908 -21.287 1.00 0.00 CLA \n+ATOM 61602 CLA CLA 5 32.119 26.809 -14.613 1.00 0.00 CLA \n+ATOM 61603 CLA CLA 6 -12.762 38.902 39.703 1.00 0.00 CLA \n+ATOM 61604 CLA CLA 7 -41.352 -6.310 -21.092 1.00 0.00 CLA \n+ATOM 61605 CLA CLA 8 -40.105 19.915 21.883 1.00 0.00 CLA \n+ATOM 61606 CLA CLA 9 -37.875 -10.640 -26.651 1.00 0.00 CLA \n+ATOM 61607 CLA CLA 10 -22.511 41.548 12.784 1.00 0.00 CLA \n+ATOM 61608 CLA CLA 11 35.216 33.731 -35.093 1.00 0.00 CLA \n+ATOM 61609 CLA CLA 12 -40.102 5.647 -2.397 1.00 0.00 CLA \n+ATOM 61610 CLA CLA 13 39.024 -12.398 -40.371 1.00 0.00 CLA \n+ATOM 61611 CLA CLA 14 18.261 -39.450 23.742 1.00 0.00 CLA \n+ATOM 61612 CLA CLA 15 6.178 41.435 -35.101 1.00 0.00 CLA \n+ATOM 61613 CLA CLA 16 24.358 15.109 39.388 1.00 0.00 CLA \n+ATOM 61614 CLA CLA 17 6.888 21.632 -18.643 1.00 0.00 CLA \n+ATOM 61615 CLA CLA 18 21.744 6.136 36.952 1.00 0.00 CLA \n+ATOM 61616 CLA CLA 19 37.313 -8.363 36.386 1.00 0.00 CLA \n+ATOM 61617 CLA CLA 20 -2.999 -20.832 23.104 1.00 0.00 CLA \n+ATOM 61618 CLA CLA 21 2.857 18.626 -27.815 1.00 0.00 CLA \n+ATOM 61619 CLA CLA 22 4.436 -15.917 42.798 1.00 0.00 CLA \n+ATOM 61620 CLA CLA 23 -36.824 -9.651 27.515 1.00 0.00 CLA \n+ATOM 61621 CLA CLA 24 30.595 -26.534 -13.854 1.00 0.00 CLA \n+ATOM 61622 CLA CLA 25 2.683 14.798 30.965 1.00 0.00 CLA \n+ATOM 61623 CLA CLA 26 29.848 -11.446 -12.895 1.00 0.00 CLA \n+ATOM 61624 CLA CLA 27 42.574 -16.385 39.148 1.00 0.00 CLA \n+ATOM 61625 CLA CLA 28 21.090 22.680 27.072 1.00 0.00 CLA \n+ATOM 61626 CLA CLA 29 31.477 21.841 -9.460 1.00 0.00 CLA \n+ATOM 61627 CLA CLA 30 -42.789 33.106 -42.003 1.00 0.00 CLA \n+ATOM 61628 CLA CLA 31 41.212 26.460 28.038 1.00 0.00 CLA \n+ATOM 61629 CLA CLA 32 31.330 -23.211 30.873 1.00 0.00 CLA \n+ATOM 61630 CLA CLA 33 -11.882 24.746 17.676 1.00 0.00 CLA \n+ATOM 61631 CLA CLA 34 42.509 41.966 29.673 1.00 0.00 CLA \n+ATOM 61632 CLA CLA 35 -21.155 -25.909 40.988 1.00 0.00 CLA \n+ATOM 61633 CLA CLA 36 -16.645 33.397 -20.493 1.00 0.00 CLA \n+ATOM 61634 CLA CLA 37 24.008 16.848 3.761 1.00 0.00 CLA \n+ATOM 61635 CLA CLA 38 -3.042 -26.229 -6.954 1.00 0.00 CLA \n+ATOM 61636 CLA CLA 39 -25.242 -29.525 -14.531 1.00 0.00 CLA \n+ATOM 61637 CLA CLA 40 34.942 -28.883 -36.691 1.00 0.00 CLA \n+ATOM 61638 CLA CLA 41 -35.913 -6.707 3.266 1.00 0.00 CLA \n+ATOM 61639 CLA CLA 42 -30.968 4.607 -32.953 1.00 0.00 CLA \n+ATOM 61640 CLA CLA 43 -5.809 15.242 42.418 1.00 0.00 CLA \n+ATOM 61641 CLA CLA 44 39.399 18.809 -13.827 1.00 0.00 CLA \n+ATOM 61642 CLA CLA 45 -15.805 29.210 -37.376 1.00 0.00 CLA \n+ATOM 61643 CLA CLA 46 0.091 -36.491 -34.859 1.00 0.00 CLA \n+ATOM 61644 CLA CLA 47 -12.875 -40.099 38.366 1.00 0.00 CLA \n+ATOM 61645 CLA CLA 48 -24.191 19.188 36.959 1.00 0.00 CLA \n+ATOM 61646 CLA CLA 49 16.215 -18.186 -29.406 1.00 0.00 CLA \n+ATOM 61647 CLA CLA 50 34.647 -7.708 -32.869 1.00 0.00 CLA \n+ATOM 61648 CLA CLA 51 -20.320 -38.996 6.847 1.00 0.00 CLA \n+ATOM 61649 CLA CLA 52 -28.453 0.614 -25.838 1.00 0.00 CLA \n+TER 61650 CLA 52\n+END\n' |
| b |
| diff -r 000000000000 -r 65bfd1b90b96 visualize_pc.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/visualize_pc.R Tue Feb 26 08:29:24 2019 -0500 |
| [ |
| @@ -0,0 +1,45 @@ +#!/usr/bin/env Rscript + +options(stringAsfactors = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +library(bio3d) + +dcdfile <- args[1] +pdbfile <- args[2] + +dcd <- read.dcd(dcdfile) +pdb <- read.pdb(pdbfile) + +method <- args[3] +selection <- args[4] +domain <- args[5] +id <- args[6] +pcid <- as.integer(id) + +pdbout <- args[7] + + +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$xyz) + +if (method == "FALSE") { + pc <- pca.xyz(xyz[,inds$xyz], use.svd=FALSE) +} +if (method == "TRUE") { + pc <- pca.xyz(xyz[,inds$xyz], use.svd=TRUE) +} + +mktrj.pca(pc, pc=pcid, b=pc$au[,pcid], file=pdbout) + |
| b |
| diff -r 000000000000 -r 65bfd1b90b96 visualize_pc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/visualize_pc.xml Tue Feb 26 08:29:24 2019 -0500 |
| [ |
| @@ -0,0 +1,134 @@ +<tool id="bio3d_pca_visualize" name="PCA visualization" version="@VERSION@"> + <description>Generate trajectories of principle components of motions</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> +<![CDATA[ + Rscript '$__tool_directory__/visualize_pc.R' + '$dcdin' + '$pdbin' + '$method' + #if $pca.sele == 'calpha': + "string" + "calpha" + #end if + #if $pca.sele == 'cbeta': + "string" + '$pca.cbeta' + #end if + #if $pca.sele == 'backbone': + "string" + "backbone" + #end if + #if $pca.sele == 'sidechain': + "string" + "sidechain" + #end if + #if $pca.sele == 'protein': + "string" + "protein" + #end if + #if $pca.sele == 'ligand': + "string" + "ligand" + #end if + #if $pca.sele == 'nucleic': + "string" + "nucleic" + #end if + #if $pca.sele == 'elety': + "elety" + '$pca.elety' + #end if + #if $pca.sele == 'resid': + "resid" + '$pca.resid' + #end if + #if $pca.sele == 'segid': + "segid" + '$pca.segid' + #end if + '$pc_id' + '$pdbout' + 2>&1 +]]></command> + <inputs> + <expand macro="analysis_inputs"/> + <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" + label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" /> + <conditional name="pca"> + <param name="sele" type="select" label="Select domains"> + <option value="calpha">Calpha</option> + <option value="cbeta">Cbeta</option> + <option value="backbone">Backbone</option> + <option value="sidechain">Sidechain</option> + <option value="protein">Protein</option> + <option value="ligand">Ligand</option> + <option value="nucleic">Nucleic Acids</option> + <option value="elety">Atom Names</option> + <option value="resid">Resid</option> + <option value="segid">Segid</option> + </param> + <when value="calpha"/> + <when value="cbeta"/> + <when value="backbone"/> + <when value="sidechain"/> + <when value="protein"/> + <when value="ligand"/> + <when value="nucleic"/> + <when value="elety"> + <param name="elety" type="text" value="CA" label="Atom Name"/> + </when> + <when value="resid"> + <param name="resid" type="text" value="BGLC" label="Resid"/> + </when> + <when value="segid"> + <param name="segid" type="text" value="SUBS" label="Segid"/> + </when> + </conditional> + <param name="pc_id" type="integer" value="1" label="Principle component id"/> + </inputs> + <outputs> + <data format="pdb" name="pdbout" label="PCA_${pc_id}.pdb"/> + </outputs> + <tests> + <test> + <expand macro="tests_inputs"/> + <param name="method" value="false"/> + <param name="sele" value="calpha"/> + <param name="pc_id" value="1"/> + <output name="pdbout" file="PCA_1.pdb" /> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +This tool can generate small trajectories of a given principle component. + +_____ + + +.. class:: infomark + +**Input** + + - Input file in PDB format + - Input file in dcd format + +_____ + + +.. class:: infomark + +**Output** + + - A short trajectory (as PDB) of the given priciple component id. + + + ]]></help> + <expand macro="citations" /> +</tool> |
