inst/scripts/analysis/plots/orbitals/eqpoldens/cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_.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_chiBAHD_cosAHD",
author = "Matthew O'Meara, Steven Combs",
brief_description = "",
feature_reporter_dependencies = c("OrbitalFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
#####cation pi interactions
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAHD,
OrbHdist,
chiBAHD,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'LYS' OR resName2 = 'ARG' ) AND (resName1 = 'PHE' OR resName1 = 'TRP' OR resName1 = 'TYR'))) 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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_all_3.5"
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 chiBAHD vs AHD Angles with Sequence Separation > 5\n",
"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
"LYS+ARG to PHE+TYR+TRP", sep="")) +
scale_x_continuous(
'2*sin(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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,
cosAHD,
OrbHdist,
chiBAHD,
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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_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 chiBAHD vs AHD 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(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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 2.0
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAHD,
OrbHdist,
chiBAHD,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'LYS' ) AND (resName1 = 'PHE' ))) AND
OrbHdist < 2 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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_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 chiBAHD vs AHD 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(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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 2.0
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAHD,
OrbHdist,
chiBAHD,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'ARG' ) AND (resName1 = 'PHE' ))) AND
OrbHdist < 2 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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_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 chiBAHD vs AHD 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(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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,
cosAHD,
OrbHdist,
chiBAHD,
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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_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 chiBAHD vs AHD 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(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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.
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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_chiBAHD_cosAHD",
author = "Matthew O'Meara, Steven Combs",
brief_description = "",
feature_reporter_dependencies = c("OrbitalFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
#####cation pi interactions
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAHD,
OrbHdist,
chiBAHD,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'LYS' OR resName2 = 'ARG' ) AND (resName1 = 'PHE' OR resName1 = 'TRP' OR resName1 = 'TYR'))) 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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_all_3.5"
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 chiBAHD vs AHD Angles with Sequence Separation > 5\n",
"Sidechain Donors to Sidechain sp2 Acceptors, Equal Coordinate Projection\n",
"LYS+ARG to PHE+TYR+TRP", sep="")) +
scale_x_continuous(
'2*sin(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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,
cosAHD,
OrbHdist,
chiBAHD,
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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_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 chiBAHD vs AHD 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(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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 2.0
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAHD,
OrbHdist,
chiBAHD,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'LYS' ) AND (resName1 = 'PHE' ))) AND
OrbHdist < 2 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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_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 chiBAHD vs AHD 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(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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 2.0
sele <- "
SELECT
resNum1,
resName1,
resNum2,
resName2,
OrbName1,
cosAHD,
OrbHdist,
chiBAHD,
htype2
FROM
Hpol_orbital
WHERE
(((resName2 = 'ARG' ) AND (resName1 = 'PHE' ))) AND
OrbHdist < 2 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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_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 chiBAHD vs AHD 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(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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,
cosAHD,
OrbHdist,
chiBAHD,
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(cosAHD)/2)*cos(chiBAHD),
capy = 2*sin(acos(cosAHD)/2)*sin(chiBAHD))
capx_limits <- c(-1.5,1.5)
capy_limits <- capx_limits
plot_id = "cation_pi_eqpoldens_scOrbCpi_Hpol_chiBAHD_cosAHD_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 chiBAHD vs AHD 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(AHD/2) * cos(chiBAHD))', limits=capx_limits, breaks=c(-1, 0, 1)) +
scale_y_continuous(
'2*sin(AHD/2) * sin(chiBAHD)', 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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