inst/scripts/analysis/plots/hbonds/hydroxyl_sites/VBAH_VBchi_equal_area.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(plyr)
library(viridis)
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "VBAH_VBchi_equal_area",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
SELECT
acc_atoms.base_x AS abx, acc_atoms.base_y AS aby, acc_atoms.base_z AS abz,
acc_atoms.base2_x AS ab2x, acc_atoms.base2_y AS ab2y, acc_atoms.base2_z AS ab2z,
acc_atoms.atm_x AS ax, acc_atoms.atm_y AS ay, acc_atoms.atm_z AS az,
don_atoms.atm_x AS hx, don_atoms.atm_y AS hy, don_atoms.atm_z AS hz,
CASE don.resNum - don.resNum
WHEN -1 THEN '-1' WHEN -2 THEN '-2' WHEN -3 THEN '-3' WHEN -4 THEN '-4'
WHEN 1 THEN '1,2,3,4' WHEN 2 THEN '1,2,3,4' WHEN 3 THEN '1,2,3,4' WHEN 4 THEN '1,2,3,4'
ELSE 'long' END AS seq_sep,
acc.HBChemType AS acc_chem_type,
don.HBChemType AS don_chem_type,
don_ss_code.label AS don_dssp
FROM
hbonds AS hb cross join
hbond_sites AS don cross join
hbond_sites AS acc cross join
hbond_sites_pdb AS don_pdb cross join
hbond_sites_pdb AS acc_pdb cross join
hbond_site_atoms AS don_atoms cross join
hbond_site_atoms AS acc_atoms cross join
residue_secondary_structure AS don_ss cross join
dssp_codes AS don_ss_code
WHERE
acc.struct_id = hb.struct_id AND acc.site_id = hb.acc_id AND
don.struct_id = hb.struct_id AND don.site_id = hb.don_id AND
(acc.HBChemType = 'hbacc_HXL' OR acc.HBChemType = 'hbacc_AHX') AND
don.HBChemType = 'hbdon_PBA' AND
don_pdb.struct_id = hb.struct_id AND don_pdb.site_id = hb.don_id AND
don_pdb.heavy_atom_temperature < 30 AND
acc_pdb.struct_id = hb.struct_id AND acc_pdb.site_id = hb.acc_id AND
acc_pdb.heavy_atom_temperature < 30 AND
don_atoms.struct_id = hb.struct_id AND don_atoms.site_id = hb.don_id AND
acc_atoms.struct_id = hb.struct_id AND acc_atoms.site_id = hb.acc_id AND
don_ss.struct_id = don.struct_id AND don_ss.resNum = don.resNum AND
don_ss_code.code = don_ss.dssp;"
f <- query_sample_sources(sample_sources, sele)
f$acc_chem_type_name <- factor(f$acc_chem_type,
levels = c("hbacc_HXL", "hbacc_AHX"),
labels = c("aHXL: s,t", "aAHX: y"))
f <- transform(f,
vBAH = acos(vector_dotprod(
vector_normalize(cbind(ax-(abx+ab2x)/2, ay-(aby+ab2y)/2, az-(abz+ab2z)/2)),
vector_normalize(cbind(hx-ax, hy-ay, hz-az)))),
vBAchi = vector_dihedral(
cbind(ab2x, ab2y, ab2z), cbind((abx+ab2x)/2, (aby+ab2y)/2, (abz+ab2z)/2),
cbind(ax, ay, az), cbind(hx, hy, hz)))
#equal area projection
f <- transform(f,
x = 2*sin(vBAH/2)*cos(vBAchi),
y = 2*sin(vBAH/2)*sin(vBAchi))
capx_limits <- c(-1.5,1.5); capy_limits <- capx_limits;
narrow_output_formats <- transform(output_formats, width=height)
plot_parts <- function(){list(
theme_bw(),
theme(panel.background=element_rect(fill="#00007F", colour="#00007F")),
geom_raster(aes(x=x, y=y, fill=z)),
geom_indicator(aes(indicator=counts), color="white", group=1),
polar_equal_area_grids_bw(),
coord_equal(ratio=1),
scale_fill_viridis("Density"),
scale_x_continuous('', limits=capx_limits, breaks=c()),
scale_y_continuous('', limits=capy_limits, breaks=c()),
theme(
axis.text.x=element_blank(),
axis.text.y=element_blank(),
axis.title.x=element_blank(),
axis.title.y=element_blank(),
axis.ticks.x = element_blank(),
axis.ticks.y = element_blank()))
}
#plot_id = "hbond_VBAH_VBAchi_equal_area_log_scale_seq_sep"
#ggplot(data=f) + plot_parts() +
# facet_grid(seq_sep ~ sample_source) +
# ggtitle("Sp3 Acc H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection") +
#save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
#
d_ply(
.data=f[f$don_chem_type == "hbdon_PBA", ],
.variables=.(seq_sep),
.fun=function(df)
{
seq_sep <- as.character(df$seq_sep[1])
dens <- estimate_density_2d(
df, c("sample_source"), "x", "y")
print(summary(dens))
plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_seq_sep_", seq_sep, sep="")
ggplot(data=dens) + plot_parts() +
facet_wrap( ~ sample_source, nrow=ceiling(sqrt(nrow(sample_sources)))) +
ggtitle(paste("Sp3 Acc H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection Sequence Separation: ", seq_sep, sep="")) +
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
})
d_ply(
.data=f[f$don_chem_type == "hbdon_PBA", ],
.variables=.(seq_sep, acc_chem_type_name, sample_source),
.fun=function(df){
seq_sep <- as.character(df$seq_sep[1])
acc_chem_type_name <- as.character(df$acc_chem_type_name[1])
ss_id <- as.character(df$sample_source[1])
ss <- sample_sources[sample_sources$sample_source == ss_id, ]
dens <- estimate_density_2d(
df, c(), "x", "y")
plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_seq_sep_", seq_sep, "_", acc_chem_type_name, "_", ss_id, sep="")
ggplot(data=dens) + plot_parts() +
ggtitle(paste(acc_chem_type_name, " Acc BB Don H-Bonds Base Acceptor Hydrogen projection\nSeqSep: ", seq_sep, " SS: ", ss_id, sep="")) +
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
})
#
#
#d_ply(
# .data=f[f$don_chem_type == "hbdon_PBA", ],
# .variables=.(sample_source),
# .fun=function(df){
# ss_id <- as.character(df$sample_source[1])
# ss <- sample_sources[sample_sources$sample_source == ss_id, ]
# plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_seq_sep_ss_id_", ss_id, sep="")
# counts <- group_counts(df, c("seq_sep"))
# ggplot(data=df) + plot_parts() +
# facet_wrap( ~ seq_sep, ncol=3) +
# ggtitle(paste("Sp3 Acc H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection By Sequence Separation Sample Source: ", ss_id, sep="")) +
# save_plots(self, plot_id, ss, output_dir, output_formats)
#
#})
#
#plot_id = "hbond_VBAH_VBAchi_equal_area_log_scale_don_dssp"
#ggplot(data=f) + plot_parts() +
# facet_grid( don_dssp ~ sample_source ) +
# ggtitle("Sp3 Acc - BB Don H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection") +
#save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
#
#d_ply(
# .data=f[as.character(f$don_dssp) == "hbdon_PBA",],
# .variables=.(don_dssp),
# .fun=function(df){
# don_dssp <- as.character(df$don_dssp[1])
# plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_don_dssp_", don_dssp, sep="")
# ggplot(data=df) + plot_parts() +
# facet_wrap( ~ sample_source, nrow=ceiling(sqrt(nrow(sample_sources)))) +
# ggtitle(paste("Sp3 Acc - BB Don H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection Donor DSSP: ", don_dssp, sep="")) +
# save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
#})
#
#d_ply(
# .data=f[as.character(f$don_dssp) == "hbdon_PBA",],
# .variables=.(sample_source),
# .fun=function(df){
# ss_id <- as.character(df$sample_source[1])
# ss <- sample_sources[sample_sources$sample_source == ss_id, ]
# plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_don_dssp_ss_id_", ss_id, sep="")
# ggplot(data=df) + plot_parts() +
# facet_wrap( ~ don_dssp) +
# ggtitle(paste("Sp3 Acc - BB Don H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection by Donor DSSP Sample Source: ", ss_id, sep="")) +
# save_plots(self, plot_id, ss, output_dir, output_formats)
#})
})) # end FeaturesAnalysis
momeara/RosettaFeatures documentation built on May 23, 2019, 6:07 a.m.
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# -*- 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(plyr)
library(viridis)
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "VBAH_VBchi_equal_area",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
SELECT
acc_atoms.base_x AS abx, acc_atoms.base_y AS aby, acc_atoms.base_z AS abz,
acc_atoms.base2_x AS ab2x, acc_atoms.base2_y AS ab2y, acc_atoms.base2_z AS ab2z,
acc_atoms.atm_x AS ax, acc_atoms.atm_y AS ay, acc_atoms.atm_z AS az,
don_atoms.atm_x AS hx, don_atoms.atm_y AS hy, don_atoms.atm_z AS hz,
CASE don.resNum - don.resNum
WHEN -1 THEN '-1' WHEN -2 THEN '-2' WHEN -3 THEN '-3' WHEN -4 THEN '-4'
WHEN 1 THEN '1,2,3,4' WHEN 2 THEN '1,2,3,4' WHEN 3 THEN '1,2,3,4' WHEN 4 THEN '1,2,3,4'
ELSE 'long' END AS seq_sep,
acc.HBChemType AS acc_chem_type,
don.HBChemType AS don_chem_type,
don_ss_code.label AS don_dssp
FROM
hbonds AS hb cross join
hbond_sites AS don cross join
hbond_sites AS acc cross join
hbond_sites_pdb AS don_pdb cross join
hbond_sites_pdb AS acc_pdb cross join
hbond_site_atoms AS don_atoms cross join
hbond_site_atoms AS acc_atoms cross join
residue_secondary_structure AS don_ss cross join
dssp_codes AS don_ss_code
WHERE
acc.struct_id = hb.struct_id AND acc.site_id = hb.acc_id AND
don.struct_id = hb.struct_id AND don.site_id = hb.don_id AND
(acc.HBChemType = 'hbacc_HXL' OR acc.HBChemType = 'hbacc_AHX') AND
don.HBChemType = 'hbdon_PBA' AND
don_pdb.struct_id = hb.struct_id AND don_pdb.site_id = hb.don_id AND
don_pdb.heavy_atom_temperature < 30 AND
acc_pdb.struct_id = hb.struct_id AND acc_pdb.site_id = hb.acc_id AND
acc_pdb.heavy_atom_temperature < 30 AND
don_atoms.struct_id = hb.struct_id AND don_atoms.site_id = hb.don_id AND
acc_atoms.struct_id = hb.struct_id AND acc_atoms.site_id = hb.acc_id AND
don_ss.struct_id = don.struct_id AND don_ss.resNum = don.resNum AND
don_ss_code.code = don_ss.dssp;"
f <- query_sample_sources(sample_sources, sele)
f$acc_chem_type_name <- factor(f$acc_chem_type,
levels = c("hbacc_HXL", "hbacc_AHX"),
labels = c("aHXL: s,t", "aAHX: y"))
f <- transform(f,
vBAH = acos(vector_dotprod(
vector_normalize(cbind(ax-(abx+ab2x)/2, ay-(aby+ab2y)/2, az-(abz+ab2z)/2)),
vector_normalize(cbind(hx-ax, hy-ay, hz-az)))),
vBAchi = vector_dihedral(
cbind(ab2x, ab2y, ab2z), cbind((abx+ab2x)/2, (aby+ab2y)/2, (abz+ab2z)/2),
cbind(ax, ay, az), cbind(hx, hy, hz)))
#equal area projection
f <- transform(f,
x = 2*sin(vBAH/2)*cos(vBAchi),
y = 2*sin(vBAH/2)*sin(vBAchi))
capx_limits <- c(-1.5,1.5); capy_limits <- capx_limits;
narrow_output_formats <- transform(output_formats, width=height)
plot_parts <- function(){list(
theme_bw(),
theme(panel.background=element_rect(fill="#00007F", colour="#00007F")),
geom_raster(aes(x=x, y=y, fill=z)),
geom_indicator(aes(indicator=counts), color="white", group=1),
polar_equal_area_grids_bw(),
coord_equal(ratio=1),
scale_fill_viridis("Density"),
scale_x_continuous('', limits=capx_limits, breaks=c()),
scale_y_continuous('', limits=capy_limits, breaks=c()),
theme(
axis.text.x=element_blank(),
axis.text.y=element_blank(),
axis.title.x=element_blank(),
axis.title.y=element_blank(),
axis.ticks.x = element_blank(),
axis.ticks.y = element_blank()))
}
#plot_id = "hbond_VBAH_VBAchi_equal_area_log_scale_seq_sep"
#ggplot(data=f) + plot_parts() +
# facet_grid(seq_sep ~ sample_source) +
# ggtitle("Sp3 Acc H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection") +
#save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
#
d_ply(
.data=f[f$don_chem_type == "hbdon_PBA", ],
.variables=.(seq_sep),
.fun=function(df)
{
seq_sep <- as.character(df$seq_sep[1])
dens <- estimate_density_2d(
df, c("sample_source"), "x", "y")
print(summary(dens))
plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_seq_sep_", seq_sep, sep="")
ggplot(data=dens) + plot_parts() +
facet_wrap( ~ sample_source, nrow=ceiling(sqrt(nrow(sample_sources)))) +
ggtitle(paste("Sp3 Acc H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection Sequence Separation: ", seq_sep, sep="")) +
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
})
d_ply(
.data=f[f$don_chem_type == "hbdon_PBA", ],
.variables=.(seq_sep, acc_chem_type_name, sample_source),
.fun=function(df){
seq_sep <- as.character(df$seq_sep[1])
acc_chem_type_name <- as.character(df$acc_chem_type_name[1])
ss_id <- as.character(df$sample_source[1])
ss <- sample_sources[sample_sources$sample_source == ss_id, ]
dens <- estimate_density_2d(
df, c(), "x", "y")
plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_seq_sep_", seq_sep, "_", acc_chem_type_name, "_", ss_id, sep="")
ggplot(data=dens) + plot_parts() +
ggtitle(paste(acc_chem_type_name, " Acc BB Don H-Bonds Base Acceptor Hydrogen projection\nSeqSep: ", seq_sep, " SS: ", ss_id, sep="")) +
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
})
#
#
#d_ply(
# .data=f[f$don_chem_type == "hbdon_PBA", ],
# .variables=.(sample_source),
# .fun=function(df){
# ss_id <- as.character(df$sample_source[1])
# ss <- sample_sources[sample_sources$sample_source == ss_id, ]
# plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_seq_sep_ss_id_", ss_id, sep="")
# counts <- group_counts(df, c("seq_sep"))
# ggplot(data=df) + plot_parts() +
# facet_wrap( ~ seq_sep, ncol=3) +
# ggtitle(paste("Sp3 Acc H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection By Sequence Separation Sample Source: ", ss_id, sep="")) +
# save_plots(self, plot_id, ss, output_dir, output_formats)
#
#})
#
#plot_id = "hbond_VBAH_VBAchi_equal_area_log_scale_don_dssp"
#ggplot(data=f) + plot_parts() +
# facet_grid( don_dssp ~ sample_source ) +
# ggtitle("Sp3 Acc - BB Don H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection") +
#save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
#
#d_ply(
# .data=f[as.character(f$don_dssp) == "hbdon_PBA",],
# .variables=.(don_dssp),
# .fun=function(df){
# don_dssp <- as.character(df$don_dssp[1])
# plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_don_dssp_", don_dssp, sep="")
# ggplot(data=df) + plot_parts() +
# facet_wrap( ~ sample_source, nrow=ceiling(sqrt(nrow(sample_sources)))) +
# ggtitle(paste("Sp3 Acc - BB Don H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection Donor DSSP: ", don_dssp, sep="")) +
# save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
#})
#
#d_ply(
# .data=f[as.character(f$don_dssp) == "hbdon_PBA",],
# .variables=.(sample_source),
# .fun=function(df){
# ss_id <- as.character(df$sample_source[1])
# ss <- sample_sources[sample_sources$sample_source == ss_id, ]
# plot_id = paste("hbond_VBAH_VBAchi_equal_area_log_scale_don_dssp_ss_id_", ss_id, sep="")
# ggplot(data=df) + plot_parts() +
# facet_wrap( ~ don_dssp) +
# ggtitle(paste("Sp3 Acc - BB Don H-Bonds Virtual-Base Acceptor Hydrogen projection\nEqual Coordinate Projection by Donor DSSP Sample Source: ", ss_id, sep="")) +
# save_plots(self, plot_id, ss, output_dir, output_formats)
#})
})) # end FeaturesAnalysis
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