inst/scripts/analysis/plots/orbitals/eqpoldens/anion_pi_eqpoldens_scOrbOp_Haro_chiBDHO_cosDHO.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(viridis)

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


#####Anion Pi interactions 2.0

sele <- "
SELECT
	resNum1,
	resName1,
	resNum2,
	resName2,
	OrbName1,
	cosDHO,
	OrbHdist,
	chiBDHO,
	htype2
FROM
	Haro_orbital
WHERE
	(((resName1 = 'GLU' OR resName1 = 'ASP') AND (resName2 = 'PHE' OR resName2 = 'TYR' OR resName2 = 'TRP')))  AND
	OrbHdist < 2 AND
	OrbName1 = 'O.p.sp2' AND
	ABS(resNum1 - resNum2) > 5;"

f <- query_sample_sources(sample_sources, sele)

f <- transform(f,
	capx = 2*sin(acos(cosDHO)/2)*cos(chiBDHO),
	capy = 2*sin(acos(cosDHO)/2)*sin(chiBDHO))

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


plot_id = "anion_pi_eqpoldens_scOrbOp_Haro_chiBDHO_cosDHO_all_2.0A"

f_first <- f[ f$sample_source == levels(sample_sources$sample_source), ]

ggplot(data=f_first) + theme_bw() +
	theme(panel.background=element_rect(fill="#00007F", colour="#00007F")) +
	stat_density2d(
		aes(x=capx, y=capy, fill=..density..), geom="tile", contour=FALSE ) +
	polar_equal_area_grids_bw() +
	ggtitle(
		paste("Anion Pi chiBDHO vs DHO Angles with Sequence Separation > 5\n",
		"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
		"GLU+ASP to PHE+TYR+TRP at 2.0A", sep="")) +
	scale_x_continuous(
		'2*sin(DHO/2) * cos(chiBDHO)', limits=capx_limits, breaks=c(-1, 0, 1)) +
	scale_y_continuous(
		'2*sin(DHO/2) * sin(chiBDHO)', limits=capy_limits, breaks=c(-1, 0, 1)) +
	coord_fixed(ratio = 1) +
	scale_fill_viridis("Density")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


#####Pi Stacking interactions 3.5

sele <- "
SELECT
	resNum1,
	resName1,
	resNum2,
	resName2,
	OrbName1,
	cosDHO,
	OrbHdist,
	chiBDHO,
	htype2
FROM
	Haro_orbital
WHERE
	(((resName1 = 'GLU' OR resName1 = 'ASP') AND (resName2 = 'PHE' OR resName2 = 'TYR' OR resName2 = 'TRP')))  AND
	OrbHdist < 3.5 AND
	OrbName1 = 'O.p.sp2' AND
	ABS(resNum1 - resNum2) > 5;"

f <- query_sample_sources(sample_sources, sele)

f <- transform(f,
	capx = 2*sin(acos(cosDHO)/2)*cos(chiBDHO),
	capy = 2*sin(acos(cosDHO)/2)*sin(chiBDHO))

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


plot_id = "anion_pi_eqpoldens_scOrbOp_Haro_chiBDHO_cosDHO_all_3.5A"

f_first <- f[ f$sample_source == levels(sample_sources$sample_source), ]

ggplot(data=f_first) + theme_bw() +
	theme(panel.background=element_rect(fill="#00007F", colour="#00007F")) +
	stat_density2d(
		aes(x=capx, y=capy, fill=..density..), geom="tile", contour=FALSE ) +
	polar_equal_area_grids_bw() +
	ggtitle(
		paste("Anion pi chiBDHO vs DHO Angles with Sequence Separation > 5\n",
		"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
		"GLU+ASP to PHE+TYR+TRP at 3.5A", sep="")) +
	scale_x_continuous(
		'2*sin(DHO/2) * cos(chiBDHO)', limits=capx_limits, breaks=c(-1, 0, 1)) +
	scale_y_continuous(
		'2*sin(DHO/2) * sin(chiBDHO)', limits=capy_limits, breaks=c(-1, 0, 1)) +
	coord_fixed(ratio = 1) +
	scale_fill_viridis("Density")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)

###GLU+ASP-Phe 2.0
sele <- "
SELECT
	resNum1,
	resName1,
	resNum2,
	resName2,
	OrbName1,
	cosDHO,
	OrbHdist,
	chiBDHO,
	htype2
FROM
	Haro_orbital
WHERE
	(((resName1 = 'GLU' OR resName1= 'ASP' ) AND (resName2 = 'PHE' )))  AND
	OrbHdist < 2 AND
	OrbName1 = 'O.p.sp2' AND
	ABS(resNum1 - resNum2) > 5;"

f <- query_sample_sources(sample_sources, sele)

f <- transform(f,
	capx = 2*sin(acos(cosDHO)/2)*cos(chiBDHO),
	capy = 2*sin(acos(cosDHO)/2)*sin(chiBDHO))

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


plot_id = "anion_pi_eqpoldens_scOrbOp_Haro_chiBDHO_cosDHO_glu_asp_phe_2.0A"

f_first <- f[ f$sample_source == levels(sample_sources$sample_source), ]

ggplot(data=f_first) + theme_bw() +
	theme(panel.background=element_rect(fill="#00007F", colour="#00007F")) +
	stat_density2d(
		aes(x=capx, y=capy, fill=..density..), geom="tile", contour=FALSE ) +
	polar_equal_area_grids_bw() +
	ggtitle(
		paste("Anion Pi chiBDHO vs DHO Angles with Sequence Separation > 5\n",
		"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
		"GLU+ASP to PHE at 2.0A", sep="")) +
	scale_x_continuous(
		'2*sin(DHO/2) * cos(chiBDHO)', limits=capx_limits, breaks=c(-1, 0, 1)) +
	scale_y_continuous(
		'2*sin(DHO/2) * sin(chiBDHO)', limits=capy_limits, breaks=c(-1, 0, 1)) +
	coord_fixed(ratio = 1) +
	scale_fill_viridis("Density")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)

###Phe -Phe 3.5
sele <- "
SELECT
	resNum1,
	resName1,
	resNum2,
	resName2,
	OrbName1,
	cosDHO,
	OrbHdist,
	chiBDHO,
	htype2
FROM
	Haro_orbital
WHERE
	(((resName1 = 'GLU' OR resName1 = 'ASP' ) AND (resName2 = 'PHE' )))  AND
	OrbHdist < 3.5 AND
	OrbName1 = 'O.p.sp2' AND
	ABS(resNum1 - resNum2) > 5;"

f <- query_sample_sources(sample_sources, sele)

f <- transform(f,
	capx = 2*sin(acos(cosDHO)/2)*cos(chiBDHO),
	capy = 2*sin(acos(cosDHO)/2)*sin(chiBDHO))

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


plot_id = "anion_pi_eqpoldens_scOrbOp_Haro_chiBDHO_cosDHO_glu_asp_phe_3.5A"

f_first <- f[ f$sample_source == levels(sample_sources$sample_source), ]

ggplot(data=f_first) + theme_bw() +
	theme(panel.background=element_rect(fill="#00007F", colour="#00007F")) +
	stat_density2d(
		aes(x=capx, y=capy, fill=..density..), geom="tile", contour=FALSE ) +
	polar_equal_area_grids_bw() +
	ggtitle(
		paste("Anion pi chiBDHO vs DHO Angles with Sequence Separation > 5\n",
		"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
		"GLU+ASP to PHE at 3.5A", sep="")) +
	scale_x_continuous(
		'2*sin(DHO/2) * cos(chiBDHO)', limits=capx_limits, breaks=c(-1, 0, 1)) +
	scale_y_continuous(
		'2*sin(DHO/2) * sin(chiBDHO)', limits=capy_limits, breaks=c(-1, 0, 1)) +
	coord_fixed(ratio = 1) +
	scale_fill_viridis("Density")
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


})) # end FeaturesAnalysis