inst/scripts/analysis/plots/hbonds/hydroxyl_sites/OHdonor.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 = "OHdonor",
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.cosAHD,
  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
  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_site.HBChemType = 'hbdon_AHX' OR don_site.HBChemType = 'hbdon_HXL' );";

all_geom <- query_sample_sources(sample_sources, sele)

plot_id <- "OHdonor_AHdist_all_acceptor_types"
dens <- estimate_density_1d(
  data = all_geom,
  ids = c("sample_source"),
  variable = "AHdist",
  weight_fun = radial_3d_normalization)

p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(x=x, y=y, colour=sample_source), size=1.5) +
	geom_indicator(aes(indicator=counts, colour=sample_source, group=sample_source)) +
	ggtitle("Hydroxyl Donor Hydrogen Bonds A-H Distance\n(normalized for equal weight per unit distance)") +
	scale_y_continuous("Feature Density") +
	scale_x_continuous(
		expression(paste('Acceptor -- Hydrogen Distance (', ring(A), ')')),
		limits=c(1.4,2.3), breaks=c(1.6, 1.8, 2.0, 2.2))

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

plot_id <- "OHdonor_cosBAH_all_acceptor_types"
dens <- estimate_density_1d(
  data = all_geom,
  ids = c("sample_source"),
  variable = "cosBAH")
p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(x=acos(x)*180/pi, y=y, colour=sample_source)) +
	geom_indicator(aes(indicator=counts, colour=sample_source, group=sample_source)) +
	ggtitle("Hydroxyl Donor Hydrogen Bonds BAH Angle \n(normalized for equal weight per unit distance)") +
	labs(x=expression(paste('Base -- Acceptor -- Hydrogen (degrees)')),
	     y="Feature Density")


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

plot_id <- "OHdonor_cosAHD_all_acceptor_types"
dens <- estimate_density_1d(
  data = all_geom,
  ids = c("sample_source"),
  variable = "cosAHD")
p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(x=acos(x)*180/pi, y=y, colour=sample_source)) +
	geom_indicator(aes(indicator=counts, colour=sample_source, group=sample_source)) +
	ggtitle("Hydroxyl Donor Hydrogen Bonds BAH Angle \n(normalized for equal weight per unit distance)") +
	labs(x=expression(paste('Acceptor -- Hydrogen -- Donor (degrees)')),
              y="Feature Density")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)

plot_id <- "OHdonor_chi_all_acceptor_types"
dens <- estimate_density_1d_logspline(
  data = all_geom,
  ids = c("sample_source"),
  variable = "chi")
p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(x=acos(x)*360/pi, y=y, colour=sample_source)) +
	geom_indicator(aes(colour=sample_source, indicator=counts, group=sample_source)) +
	ggtitle("Hydroxyl Donor Hydrogen Bonds BAH Angle \n(normalized for equal weight per unit distance)") +
	labs(x=expression(paste('Acceptor Base -- Acceptor Torsion (degrees)')),
	     y="Feature Density")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)



sidechain_geom <- all_geom[all_geom$acc_chem_type != "hbacc_PBA",]

plot_id <- "OHdonor_AHdist_sidechain_acceptor_types"
dens <- estimate_density_1d(
  data = sidechain_geom,
  ids = c("sample_source"),
  variable = "AHdist",
  weight_fun = radial_3d_normalization)
p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(x=x, y=y, colour=sample_source), size=1.5) +
	geom_indicator(aes(indicator=counts, colour=sample_source, group=sample_source)) +
	ggtitle("Hydroxyl Donor Hydrogen Bonds A-H Distance to Sidechain Acceptors\n(normalized for equal weight per unit distance)") +
	scale_y_continuous("Feature Density") +
	scale_x_continuous(
		expression(paste('Acceptor -- Proton Distance (', ring(A), ')')),
		limits=c(1.4,2.4), breaks=c(1.6, 1.8, 2.0, 2.2))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)

plot_id <- "OHdonor_cosBAH_sidechain_acceptor_types"
dens <- estimate_density_1d(
  data = sidechain_geom,
  ids = c("sample_source"),
  variable = "cosBAH")
p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(x=acos(x)*360/pi, y=y, colour=sample_source)) +
	geom_indicator(aes(colour=sample_source, indicator=counts, group=sample_source)) +
	ggtitle("Hydroxyl Donor Hydrogen Bonds BAH Angle to Sidechain Acceptors\n(normalized for equal weight per unit distance)") +
	labs(x=expression(paste('Base -- Acceptor -- Hydrogen (degrees)')),
              y="Feature Density")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)

plot_id <- "OHdonor_cosAHD_sidechain_acceptor_types"
dens <- estimate_density_1d(
  data = sidechain_geom,
  ids = c("sample_source"),
  variable = "cosAHD")
p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(x=acos(x)*360/pi, y=y, colour=sample_source)) +
	geom_indicator(aes(colour=sample_source, indicator=counts, group=sample_source)) +
	ggtitle("Hydroxyl Donor Hydrogen Bonds AHD Angle to Sidechain Acceptors\n(normalized for equal weight per unit distance)") +
	labs(x=expression(paste('Acceptor -- Hydrogen -- Donor (degrees)')),
              y="Feature Density")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)

plot_id <- "OHdonor_chi_sidechain_acceptor_types"
dens <- estimate_density_1d_logspline(
  data = sidechain_geom,
  ids = c("sample_source"),
  variable = "chi")
p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(x=acos(x)*360/pi, y=y, colour=sample_source)) +
	geom_indicator(aes(colour=sample_source, indicator=counts, group=sample_source)) +
	ggtitle("Hydroxyl Donor Hydrogen Bonds chi Torsion Angle to Sidechain Acceptors\n(normalized for equal weight per unit distance)") +
	labs(x=expression(paste('Acceptor Base -- Acceptor Torsion (degrees)')),
	     y="log(FeatureDensity + 1)")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)

})) # end FeaturesAnalysis