inst/scripts/analysis/plots/orbitals/eqpoldens/pi_pi_eqpoldens_scOrbCpi_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 = "pi_pi_eqpoldens_scOrbCpi_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){


	#################################################################################
	###########################All pi-pi at 2.5A#############################
	#################################################################################

	sele <- "
			SELECT
			resNum1,
			resName1,
			resNum2,
			resName2,
			OrbName1,
			cosDHO,
			OrbHdist,
			chiBDHO,
			htype2
			FROM
			Haro_orbital
			WHERE
			(((resName1 = 'PHE' OR resName1 = 'TYR' OR resName1 = 'TRP' ) AND (resName2 = 'PHE' OR resName2 = 'TYR' OR resName2 = 'TRP')))  AND
			OrbHdist < 2.5 AND
			OrbName1 = 'C.pi.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 = "pi_pi_eqpoldens_scOrbCpi_Haro_chiBDHO_cosDHO_all_2.5A"

	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("Pi Stacking chiBDHO vs DHO Angles with Sequence Separation > 5\n",
									"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
									"PHE+TYR+TRP to PHE+TYR+TRP at 2.5A", 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)



	#################################################################################
	###########################Phe-Phe pi-pi at 2.5A#############################
	#################################################################################

	sele <- "
			SELECT
			resNum1,
			resName1,
			resNum2,
			resName2,
			OrbName1,
			cosDHO,
			OrbHdist,
			chiBDHO,
			htype2
			FROM
			Haro_orbital
			WHERE
			(((resName1 = 'PHE' ) AND (resName2 = 'PHE' )))  AND
			OrbHdist < 2.5 AND
			OrbName1 = 'C.pi.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 = "pi_pi_eqpoldens_scOrbCpi_Haro_chiBDHO_cosDHO_phe_phe_2.5A"

	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("Pi Stacking chiBDHO vs DHO Angles with Sequence Separation > 5\n",
									"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
									"PHE to PHE at 2.5A", 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)

	#####Pi Stacking interactions 3.5
#
#sele <- "
#SELECT
#  resNum1,
#  resName1,
#  resNum2,
#  resName2,
#  OrbName1,
#  cosDHO,
#  OrbHdist,
#  chiBDHO,
#  htype2
#FROM
#  Haro_orbital
#WHERE
#  (((resName1 = 'PHE' OR resName1 = 'TYR' OR resName1 = 'TRP' ) AND (resName2 = 'PHE' OR resName2 = 'TYR' OR resName2 = 'TRP')))  AND
#  OrbHdist < 3.5 AND
#  OrbName1 = 'C.pi.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 = "chiBDHO_cosDHO_eqpoldens_pi_stacking_cpisp2_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("Pi Stacking chiBDHO vs DHO Angles with Sequence Separation > 5\n",
#    "Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
#    "PHE+TYR+TRP 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)

	###Phe-Phe 2.0


	###Phe -Phe 3.5
#sele <- "
#SELECT
#  resNum1,
#  resName1,
#  resNum2,
#  resName2,
#  OrbName1,
#  cosDHO,
#  OrbHdist,
#  chiBDHO,
#  htype2
#FROM
#  Haro_orbital
#WHERE
#  (((resName1 = 'PHE' ) AND (resName2 = 'PHE' )))  AND
#  OrbHdist < 3.5 AND
#  OrbName1 = 'C.pi.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 = "chiBDHO_cosDHO_eqpoldens_pi_stacking_cpisp2_phe_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("Pi Stacking chiBDHO vs DHO Angles with Sequence Separation > 5\n",
#    "Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
#    "PHE 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