inst/scripts/analysis/plots/orbitals/eqpoldens/cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH.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 = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH",
author = "Matthew O'Meara, Steven Combs",
brief_description = "",
feature_reporter_dependencies = c("OrbitalFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
#################################################################################
###########################All cat-pi at 2.0A#############################
#################################################################################
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAOH,
OrbHdist,
chiBAOH,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'LYS' OR resName2 = 'ARG' ) AND (resName1 = 'PHE' OR resName1 = 'TRP' OR resName1 = 'TYR'))) AND
OrbHdist < 2.0 AND
OrbName1 = 'C.pi.sp2' AND
htype2 = 'Hpol' AND
ABS(resNum1 - resNum2) > 5;"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH_all_2A"
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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
"LYS+ARG to PHE+TYR+TRP at 2.0A", sep="")) +
scale_x_continuous(
'2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AOH/2) * sin(chiBAOH)', 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-Lys cat-pi at 2.0A#############################
#################################################################################
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAOH,
OrbHdist,
chiBAOH,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'LYS' ) AND (resName1 = 'PHE' ))) AND
OrbHdist < 2.0 AND
OrbName1 = 'C.pi.sp2' AND
htype2 = 'Hpol' AND
ABS(resNum1 - resNum2) > 5;"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH_lys_phe_2A"
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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
"LYS to PHE at 2.0", sep="")) +
scale_x_continuous(
'2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AOH/2) * sin(chiBAOH)', 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-ARG cat-pi at 2.0A#############################
#################################################################################
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAOH,
OrbHdist,
chiBAOH,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'ARG' ) AND (resName1 = 'PHE' ))) AND
OrbHdist < 2.0 AND
OrbName1 = 'C.pi.sp2' AND
htype2 = 'Hpol' AND
ABS(resNum1 - resNum2) > 5;"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH_arg_phe_2A"
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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
"ARG to PHE at 2.0", sep="")) +
scale_x_continuous(
'2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AOH/2) * sin(chiBAOH)', 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-Lys 3.5
# sele <- "
# SELECT
# resNum1,
# resName1,
# resNum2,
# resName2,
# OrbName1,
# cosAOH,
# OrbHdist,
# chiBAOH,
# htype2
# FROM
# Hpol_orbital
# WHERE
# (((resName2 = 'LYS' ) AND (resName1 = 'PHE' ))) AND
# OrbHdist < 3.5 AND
# OrbName1 = 'C.pi.sp2' AND
# htype2 = 'Hpol' AND
# ABS(resNum1 - resNum2) > 5;"
#
# f <- query_sample_sources(sample_sources, sele)
#
# f <- transform(f,
# capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
# capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
#
# capx_limits <- c(-1.5,1.5)
# capy_limits <- capx_limits
#
#
# plot_id = "chiBAOH_cosAOH_eqpoldens_cation_pi_cpisp2_lys_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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
# "Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
# "LYS to PHE at 3.5", sep="")) +
# scale_x_continuous(
# '2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
# scale_y_continuous(
# '2*sin(AOH/2) * sin(chiBAOH)', 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 - arg 3.5
# sele <- "
# SELECT
# resNum1,
# resName1,
# resNum2,
# resName2,
# OrbName1,
# cosAOH,
# OrbHdist,
# chiBAOH,
# htype2
# FROM
# Hpol_orbital
# WHERE
# (((resName2 = 'ARG' ) AND (resName1 = 'PHE' ))) AND
# OrbHdist < 3.5 AND
# OrbName1 = 'C.pi.sp2' AND
# htype2 = 'Hpol' AND
# ABS(resNum1 - resNum2) > 5;"
#
# f <- query_sample_sources(sample_sources, sele)
#
# f <- transform(f,
# capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
# capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
#
# capx_limits <- c(-1.5,1.5)
# capy_limits <- capx_limits
#
#
# plot_id = "chiBAOH_cosAOH_eqpoldens_cation_pi_cpisp2_arg_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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
# "Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
# "ARG to PHE at 3.5", sep="")) +
# scale_x_continuous(
# '2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
# scale_y_continuous(
# '2*sin(AOH/2) * sin(chiBAOH)', 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
momeara/RosettaFeatures documentation built on May 23, 2019, 6:07 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# -*- 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 = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH",
author = "Matthew O'Meara, Steven Combs",
brief_description = "",
feature_reporter_dependencies = c("OrbitalFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
#################################################################################
###########################All cat-pi at 2.0A#############################
#################################################################################
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAOH,
OrbHdist,
chiBAOH,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'LYS' OR resName2 = 'ARG' ) AND (resName1 = 'PHE' OR resName1 = 'TRP' OR resName1 = 'TYR'))) AND
OrbHdist < 2.0 AND
OrbName1 = 'C.pi.sp2' AND
htype2 = 'Hpol' AND
ABS(resNum1 - resNum2) > 5;"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH_all_2A"
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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
"LYS+ARG to PHE+TYR+TRP at 2.0A", sep="")) +
scale_x_continuous(
'2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AOH/2) * sin(chiBAOH)', 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-Lys cat-pi at 2.0A#############################
#################################################################################
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAOH,
OrbHdist,
chiBAOH,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'LYS' ) AND (resName1 = 'PHE' ))) AND
OrbHdist < 2.0 AND
OrbName1 = 'C.pi.sp2' AND
htype2 = 'Hpol' AND
ABS(resNum1 - resNum2) > 5;"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH_lys_phe_2A"
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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
"LYS to PHE at 2.0", sep="")) +
scale_x_continuous(
'2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AOH/2) * sin(chiBAOH)', 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-ARG cat-pi at 2.0A#############################
#################################################################################
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAOH,
OrbHdist,
chiBAOH,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'ARG' ) AND (resName1 = 'PHE' ))) AND
OrbHdist < 2.0 AND
OrbName1 = 'C.pi.sp2' AND
htype2 = 'Hpol' AND
ABS(resNum1 - resNum2) > 5;"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAOH_cosAOH_arg_phe_2A"
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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
"ARG to PHE at 2.0", sep="")) +
scale_x_continuous(
'2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AOH/2) * sin(chiBAOH)', 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-Lys 3.5
# sele <- "
# SELECT
# resNum1,
# resName1,
# resNum2,
# resName2,
# OrbName1,
# cosAOH,
# OrbHdist,
# chiBAOH,
# htype2
# FROM
# Hpol_orbital
# WHERE
# (((resName2 = 'LYS' ) AND (resName1 = 'PHE' ))) AND
# OrbHdist < 3.5 AND
# OrbName1 = 'C.pi.sp2' AND
# htype2 = 'Hpol' AND
# ABS(resNum1 - resNum2) > 5;"
#
# f <- query_sample_sources(sample_sources, sele)
#
# f <- transform(f,
# capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
# capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
#
# capx_limits <- c(-1.5,1.5)
# capy_limits <- capx_limits
#
#
# plot_id = "chiBAOH_cosAOH_eqpoldens_cation_pi_cpisp2_lys_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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
# "Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
# "LYS to PHE at 3.5", sep="")) +
# scale_x_continuous(
# '2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
# scale_y_continuous(
# '2*sin(AOH/2) * sin(chiBAOH)', 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 - arg 3.5
# sele <- "
# SELECT
# resNum1,
# resName1,
# resNum2,
# resName2,
# OrbName1,
# cosAOH,
# OrbHdist,
# chiBAOH,
# htype2
# FROM
# Hpol_orbital
# WHERE
# (((resName2 = 'ARG' ) AND (resName1 = 'PHE' ))) AND
# OrbHdist < 3.5 AND
# OrbName1 = 'C.pi.sp2' AND
# htype2 = 'Hpol' AND
# ABS(resNum1 - resNum2) > 5;"
#
# f <- query_sample_sources(sample_sources, sele)
#
# f <- transform(f,
# capx = 2*sin(acos(cosAOH)/2)*cos(chiBAOH),
# capy = 2*sin(acos(cosAOH)/2)*sin(chiBAOH))
#
# capx_limits <- c(-1.5,1.5)
# capy_limits <- capx_limits
#
#
# plot_id = "chiBAOH_cosAOH_eqpoldens_cation_pi_cpisp2_arg_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("Cation pi chiBAOH vs AOH Angles with Sequence Separation > 5\n",
# "Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
# "ARG to PHE at 3.5", sep="")) +
# scale_x_continuous(
# '2*sin(AOH/2) * cos(chiBAOH)', limits=capx_limits, breaks=c(-1, 0, 1)) +
# scale_y_continuous(
# '2*sin(AOH/2) * sin(chiBAOH)', 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
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