inst/scripts/analysis/plots/hbonds/geo_dim_2d/chi_BAH_eq_polar_density_PBAtoPBA_low_resolution.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 = "chi_BAH_eq_polar_density_PBAtoPBA_low_resolution",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){



sele <-"
SELECT
	geom.AHdist,
	geom.cosBAH,
	geom.chi,
	acc_site.HBChemType AS acc_chem_type,
	don_site.HBChemType AS don_chem_type
FROM
	hbond_geom_coords AS geom,
	hbonds AS hbond,
	hbond_sites AS don_site,
	hbond_sites AS acc_site
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
	ABS(don_site.resNum - acc_site.resNum) > 5;";
f <- query_sample_sources(sample_sources, sele)

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

##orthographic projection
#f <- transform(f,
#	capx = sin(acos(cosBAH))*cos(chi),
#	capy = sin(acos(cosBAH))*sin(chi))

#capx_limits <- range(f$capx);
#capy_limits <- range(f$capy)
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits

f$weight <- radial_3d_normalization(f$AHdist)

plot_id = "chi_BAH_eq_polar_density_bb_to_bb"
l_ply(levels(f$sample_source), function(ss){
	ggplot(data=f) + theme_bw() +
		polar_equal_area_grids_bw() +
		geom_bin2d(aes(x=capx, y=capy, fill=log(..count..), weight=weight), binwidth=c(.06, .06)) +
		facet_grid(acc_chem_type ~ don_chem_type) +
		ggtitle(paste("Hydrogen Bonds chi vs BAH Angles with Sequence Separation > 5\nBackbone/Backbone Hydrogen Bonds\nEqual Coordinate Projection   Sample Source: ", ss, sep="")) +
		scale_x_continuous('2*sin(BAH/2) * cos(CHI)', limits=capx_limits, breaks=c(-1, 0, 1)) +
		scale_y_continuous('2*sin(BAH/2) * sin(CHI)', limits=capy_limits, breaks=c(-1, 0, 1)) +
		coord_fixed(ratio = 1) +
		scale_fill_viridis('log(Normalized\nDensity)') +
#        	theme(legend.position="bottom", legend.direction="horizontal")
	save_plots(self, plot_id, sample_sources[sample_sources$sample_source == ss,], output_dir, output_formats)
})


})) # end FeaturesAnalysis