inst/scripts/analysis/plots/hbonds/geo_dim_2d/AHchi_AHD_eq_polar_density_PBAtoPBA.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)
library(plyr)
library(viridis)

feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "AHchi_AHD_eq_polar_density_PBAtoPBA",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){

sele <-"
SELECT
	geom.cosAHD,
	don_site.HBChemType AS don_chem_type,
	acc_site.HBChemType  acc_chem_type,
  don_ss.dssp AS don_dssp,
 	acc_atoms.base_x AS abx, acc_atoms.base_y AS aby, acc_atoms.base_z AS abz, -- acceptor base atom
	acc_atoms.atm_x  AS ax,  acc_atoms.atm_y  AS ay,  acc_atoms.atm_z  AS az,  -- acceptor atom
	don_atoms.atm_x  AS hx,  don_atoms.atm_y  AS hy,  don_atoms.atm_z  AS hz,  -- hydrogen atom
	don_atoms.base_x AS dx,  don_atoms.base_y AS dy,  don_atoms.base_z AS dz   -- donor atom
FROM
	hbond_geom_coords AS geom,
	hbonds AS hbond,
	hbond_sites AS don_site,
	hbond_sites AS acc_site,
	residue_secondary_structure AS don_ss,
	hbond_site_atoms AS don_atoms, hbond_site_atoms AS acc_atoms
WHERE
	don_site.HBChemType == 'hbdon_PBA' AND acc_site.HBChemType == 'hbacc_PBA' AND
	hbond.struct_id = geom.struct_id AND hbond.hbond_id = geom.hbond_id AND
	hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
	hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
	don_atoms.struct_id = hbond.struct_id AND don_atoms.site_id = hbond.don_id AND
	acc_atoms.struct_id = hbond.struct_id AND acc_atoms.site_id = hbond.acc_id AND
  don_ss.struct_id = hbond.struct_id AND don_ss.resNum = don_site.resNum;";

f <- query_sample_sources(sample_sources, sele)

f <- ddply(f, .(sample_source, don_dssp), transform, counts = length(sample_source))

# reorder factors for better layout
f$don_dssp <- factor(f$don_dssp,
	levels = c(
		"H", "E", "T",
		"G", "B", "S",
		"I", " "),
	labels = c(
		'H: a-Helix',    'E: b-Sheet',  'T: HB Turn',
		'G: 3/10 Helix', 'B: b-Bridge', 'S: Bend',
		'I: pi-Helix',   'Irregular'))

# remove non-canonical amino acids
f <- na.omit(f, method="r")

f <- transform(f,
  AHchi = vector_dihedral(
    cbind(abx, aby, abz), cbind(ax, ay, az),
    cbind(hx, hy, hz), cbind(dx, dy, dz)))

#equal area projection
f <- transform(f,
	capx = 2*sin(acos(cosAHD)/2)*cos(AHchi),
	capy = 2*sin(acos(cosAHD)/2)*sin(AHchi))

capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits

narrow_output_formats <- transform(output_formats, width=height*.8)

plot_parts <- list(
	theme_bw(),
	theme(panel.background=element_rect(fill="#00007F", colour="#00007F")),
	geom_raster(aes(x=x, y=y, fill=z)),
	geom_indicator(aes(indicator=counts), color="white", group=1),
	polar_equal_area_grids_bw(scale=.4, label_scale=.6),
	coord_equal(ratio=1),
	scale_fill_viridis("Density"),
	scale_x_continuous('', limits=capx_limits, breaks=c()),
	scale_y_continuous('', limits=capy_limits, breaks=c()),
	theme(
		axis.text.x = element_blank(),
		axis.text.y = element_blank(),
		axis.title.x = element_blank(),
		axis.title.y = element_blank(),
		axis.ticks.x = element_blank(),
		axis.ticks.y = element_blank()))

d_ply(f, .(sample_source), function(sub_f){
	ss_id <- sub_f$sample_source[1]
	plot_id = paste("AHchi_AHD_eq_polar_density_bbbb_by_sec_struct", ss_id, sep="_")

	dens <- estimate_density_2d(
		sub_f, c("don_dssp"), "capx", "capy", n_pts=500, scaled=T)

	ggplot(data=dens) + plot_parts +
		facet_wrap(~don_dssp) +
		ggtitle(
			paste("Backbone Backbone Hydrogen Bonds AHchi vs AHD Angles\n",
			"Equal Coordinate Projection   Sample Source: ", ss_id, sep=""))
	save_plots(self, plot_id, sample_sources[sample_sources$sample_source == ss_id,],
		output_dir, narrow_output_formats)
})

})) # end FeaturesAnalysis