inst/scripts/analysis/plots/secondary_structure/SSDists_Sheet_O_HA.R

In momeara/RosettaFeatures: Tools for analyzing macromolecular feature distributions with Rosetta

# -*- tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
# vi: set ts=2 noet:
#
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
# (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

library(ggplot2)


feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "SSDists_Sheet_O_HA",
author = "Matthew O'Meara",
brief_description = "",
long_description = "
Measure the distance distribution between the backbone carbonyl oxygen and the backbone h-alpha atom for
parallel and anti-parallel sheets.


           RESi
     ---ACC1-DON2 -----<
    /    |    |
   |    HB1  HB2             ANTI-PARALLEL HBonding
    \    |    |
     ---DON1-ACC2------>
          RESj


            ||              ||
            ||      Bres1   Ares1
    ------- Ri+1 -- Ri ---- Ri-1 -------<
   /               /||    /               CLOSE Carbon HBond
  |            O_Ca || Ca_O               Geometry in anti-parallel sheets
   \           /    || /
    ------- Rj-1 -- Rj ---- Rj+1 -------->
            Bres2   Ares2   ||
            ||              ||


           |               |
           |      RESi     |
  ----Ca---|---DON1--ACC2--|--Ca-------->
       \      /      /  \      \
        \   HB1     /   HB2     \         PARALLEL HBonding
         \  /      /      \      \
  --DON--ACC1--|--Ca---|---DON2--ACC---->
     RESj-1    |  RESj |     RESj+1
               |       |
",

feature_reporter_dependencies = c("ResidueSecondaryStructureFeatures", "HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){


sele <-"
CREATE TEMPORARY TABLE ee_bb_bb_hbonds AS
SELECT
  hb.struct_id,
  acc_site.resNum AS acc_resNum,
  don_site.resNum AS don_resNum
FROM
  hbonds AS hb,
  hbond_sites AS acc_site,
  hbond_sites AS don_site,
  residue_secondary_structure AS r1ss,
  residue_secondary_structure AS r2ss
WHERE
  acc_site.HBChemType = 'hbacc_PBA' AND
  acc_site.struct_id = hb.struct_id AND
  acc_site.site_id   = hb.acc_id AND
  don_site.site_id   = hb.don_id AND
  don_site.HBChemType = 'hbdon_PBA' AND
  don_site.struct_id = acc_site.struct_id AND
  r1ss.struct_id     = acc_site.struct_id AND
  r1ss.resNum        = acc_site.resNum AND
  r1ss.dssp          = 'E' AND
  r2ss.struct_id     = don_site.struct_id AND
  r2ss.resNum        = don_site.resNum AND
  r2ss.dssp          = 'E';

CREATE TEMPORARY TABLE antiparallel_close_contact_residue_pairs AS
SELECT
  hb1.struct_id,
  hb1.acc_resNum AS resNum_i,
  hb1.don_resNum AS resNum_j
FROM
	ee_bb_bb_hbonds AS hb1,
  ee_bb_bb_hbonds AS hb2
WHERE
  hb1.struct_id  = hb2.struct_id AND
  hb1.acc_resNum = hb2.don_resNum AND
  hb1.don_resNum = hb2.acc_resNum AND
  hb1.acc_resNum < hb1.don_resNum;

CREATE TEMPORARY TABLE antiparallel_Ha_O AS
SELECT dist.Ha_O_dist AS dist, 'antiparallel' AS strand_orientation
FROM   protein_backbone_atom_atom_pairs AS dist,
       antiparallel_close_contact_residue_pairs AS atpairs
WHERE  dist.struct_id =  atpairs.struct_id AND
       dist.resNum1 = atpairs.resNum_i - 1 AND dist.resNum2 = atpairs.resNum_j;

CREATE TEMPORARY TABLE antiparallel_O_Ha AS
SELECT dist.O_Ha_dist AS dist, 'antiparallel' AS strand_orientation
FROM   protein_backbone_atom_atom_pairs AS dist,
       antiparallel_close_contact_residue_pairs AS atpairs
WHERE  dist.struct_id =  atpairs.struct_id AND
       dist.resNum1 = atpairs.resNum_i AND dist.resNum2 = atpairs.resNum_j - 1;

CREATE TEMPORARY TABLE parallel_close_contact_residue_pairs AS
SELECT
  hb1.struct_id,
  hb1.acc_resNum AS resNum_i,
  hb1.don_resNum AS resNum_j
FROM
  ee_bb_bb_hbonds AS hb1,
  ee_bb_bb_hbonds AS hb2
WHERE
  hb1.struct_id   = hb2.struct_id AND
  hb1.don_resNum  = hb2.acc_resNum AND
  hb1.acc_resNum +2 = hb2.don_resNum;

CREATE TEMPORARY TABLE parallel_O_Ha AS
SELECT dist.O_Ha_dist AS dist, 'parallel' AS strand_orientation
FROM   protein_backbone_atom_atom_pairs AS dist,
       parallel_close_contact_residue_pairs AS apairs
WHERE  dist.struct_id =  apairs.struct_id AND
       apairs.resNum_i < apairs.resNum_j AND
       dist.resNum1 = apairs.resNum_i AND dist.resNum2 = apairs.resNum_j;

CREATE TEMPORARY TABLE parallel_Ha_O AS
SELECT dist.Ha_O_dist AS dist, 'parallel' AS strand_orientation
FROM   protein_backbone_atom_atom_pairs AS dist,
       parallel_close_contact_residue_pairs AS apairs
WHERE  dist.struct_id =  apairs.struct_id AND
       apairs.resNum_j < apairs.resNum_i AND
       dist.resNum1 = apairs.resNum_i AND dist.resNum2 = apairs.resNum_j;

SELECT * FROM antiparallel_Ha_O UNION
SELECT * FROM antiparallel_O_Ha UNION
SELECT * FROM parallel_Ha_O     UNION
SELECT * FROM parallel_O_Ha;"

f <- query_sample_sources(sample_sources, sele)

sele <- "
DROP TABLE ee_bb_bb_hbonds;
DROP TABLE antiparallel_close_contact_residue_pairs;
DROP TABLE antiparallel_Ha_O;
DROP TABLE antiparallel_O_Ha;
DROP TABLE parallel_close_contact_residue_pairs;
DROP TABLE parallel_Ha_O;
DROP TABLE parallel_O_Ha;"
query_sample_sources(sample_sources, sele, warn_zero_rows=F)


dens <- estimate_density_1d(
  f, c("sample_source", "strand_orientation"),
	"dist", weight_fun = radial_3d_normalization)

dp <- dens[dens$strand_orientation == "parallel",]
dap <- dens[dens$strand_orientation == "antiparallel",]

ylims <- c(10^-3,5)
plot_id <- "SSDists_Sheet_O_HA_parallel_anti_parallel"
p <- ggplot() + theme_bw() +
  geom_line(data=dp, aes(x=x, y=y, colour=sample_source)) +
  geom_indicator(data=dp, aes(indicator=counts, colour=sample_source, group=sample_source)) +
  geom_line(data=dap, aes(x=x, y=y, colour=sample_source)) +
  geom_indicator(data=dap, aes(indicator=counts, colour=sample_source, group=sample_source, xpos="left")) +
  ggtitle("O--Ha atom atom distances involving beta-sheet residues\nnormalized for equal weight per unit distance\n(antiparallel-counts left, parallel-counts right)") +
  scale_y_log10("FeatureDensity", ylims) +
  scale_x_continuous(expression(paste('Atom Atom Distances (', ring(A), ')')),
		limits=c(1.75,3.75), breaks=c(1.75, 2, 2.25, 2.5, 2.75, 3, 3.25, 3.5, 3.75))

if(nrow(sample_sources) <= 3){
  p <- p + theme(legend.position="bottom", legend.direction="horizontal")
}
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


ylims <- c(.1,5)
plot_id <- "SSDists_Sheet_O_HA_parallel_anti_parallel_zoom_2_3"
p <- ggplot(data=dens) + theme_bw() +
	geom_line(data=dap, aes(x=x, y=y, colour=sample_source)) +
  geom_indicator(data=dap, aes(indicator=counts, colour=sample_source, group=sample_source)) +
  ggtitle("O--Ha atom atom distances involving beta-sheet residues (seq. sep. > 1)\nnormalized for equal weight per unit distance") +
  scale_y_continuous("FeatureDensity") +
  scale_x_continuous(expression(paste('Atom Atom Distances (', ring(A), ')')), limits=c(2,3.5), breaks=c(2, 2.25, 2.5, 2.75, 3, 3.25, 3.5) )
#	coord_trans(ytrans="log10", xtrans="identity", limx=c(2.1, 3.25), limy=c(.1, 5))

if(nrow(sample_sources) <= 3){
  p <- p + theme(legend.position="bottom", legend.direction="horizontal")
}

save_plots(self, plot_id, sample_sources, output_dir, output_formats)




gradual_reveal <- function(ss_ids) {
	dens_ref <- dens[
		as.character(dens$sample_source) %in% ss_ids &
		dens$strand_orientation == "antiparallel",]

	ylims <- c(.1,5)

	plot_id <- paste("SSDists_Sheet_O_HA_parallel_anti_parallel_zoom_2_3_", paste(ss_ids, collapse="", sep="_"), sep="")
	p <- ggplot(data=dens_ref) + theme_bw() +
	  geom_line(aes(x=x, y=y, colour=sample_source)) +
		geom_line(aes(x=x, y=y, colour=sample_source), size=2.8) +
	  ggtitle("O--Ha Distance: Close Contact Anti-parallel Beta-Sheets") +
	  scale_y_log10("FeatureDensity", limits=ylims, breaks=c(.1, .5, 1, 5, 10)) +
		theme(legend.position=c(.8,.8)) +
	  scale_x_continuous(expression(paste('Atom Atom Distance (', ring(A), ')')), limits=c(2,3.5), breaks=c(2, 2.25, 2.5, 2.75, 3, 3.25, 3.5) )
	save_plots(self, plot_id, sample_sources, output_dir, output_formats)
}

gradual_reveal(sample_sources[c(1), "sample_source"])
gradual_reveal(sample_sources[c(1,2), "sample_source"])
gradual_reveal(sample_sources[c(1,2,4), "sample_source"])
#gradual_reveal(sample_sources[c(1,2,4,5), "sample_source"])



})) # end FeaturesAnalysis