# -*- 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)
source("../hbond_geo_dim_scales.R")
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "chi_BAH_eq_polar_density",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
SELECT
geom.chi,
acc_atoms.base_x AS bx, acc_atoms.base_y AS by, acc_atoms.base_z AS bz,
acc_atoms.base2_x AS b2x, acc_atoms.base2_y AS b2y, acc_atoms.base2_z AS b2z,
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,
acc_site.HBChemType AS acc_chem_type,
don_site.HBChemType AS don_chem_type,
CASE acc_site.HBChemType
WHEN 'hbacc_IMD' THEN 'ring' WHEN 'hbacc_IME' THEN 'ring'
WHEN 'hbacc_AHX' THEN 'sp3' WHEN 'hbacc_HXL' THEN 'sp3'
WHEN 'hbacc_CXA' THEN 'sp2' WHEN 'hbacc_CXL' THEN 'sp2'
WHEN 'hbacc_PBA' THEN 'bb_sp2' END AS hybrid
FROM
hbond_geom_coords AS geom,
hbonds AS hb,
hbond_sites AS don_site,
hbond_sites AS acc_site,
hbond_site_atoms AS don_atoms,
hbond_site_atoms AS acc_atoms
WHERE
hb.struct_id = geom.struct_id AND hb.hbond_id = geom.hbond_id AND
hb.struct_id = don_site.struct_id AND hb.don_id = don_site.site_id AND
hb.struct_id = acc_site.struct_id AND hb.acc_id = acc_site.site_id 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
ABS(don_site.resNum - acc_site.resNum) > 5;"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
don_chem_type_name = don_chem_type_name_linear(don_chem_type),
acc_chem_type_name = acc_chem_type_name_linear(acc_chem_type),
cosBAH = ifelse(hybrid %in% c("sp3", "ring"),
vector_dotprod(
vector_normalize(cbind(ax-(bx+b2x)/2, ay-(by+b2y)/2, az-(bz+b2z)/2)),
vector_normalize(cbind(hx-ax, hy-ay, hz-az))),
vector_dotprod(
vector_normalize(cbind(ax-bx, ay-by, az-bz)),
vector_normalize(cbind(hx-ax, hy-ay, hz-az)))),
chi = ifelse(hybrid %in% c("sp3", "ring"),
vector_dihedral(
cbind(b2x, b2y, b2z),
cbind((bx+b2x)/2, (by+b2y)/2, (bz+b2z)/2),
cbind(ax, ay, az),
cbind(hx, hy, hz)),
vector_dihedral(
cbind(b2x, b2y, b2z),
cbind(bx, by, bz),
cbind(ax, ay, az),
cbind(hx, hy, hz))),
hybrid = factor(
hybrid,
levels=c("ring", "sp3", "sp2", "bb_sp2"),
labels=c("ring", "Sp3", "Sp2", "BB Sp2")))
f <- na.omit(f, method="r")
#equal area projection
f <- transform(f,
capx = 2*sin(acos(cosBAH)/2)*cos(chi),
capy = 2*sin(acos(cosBAH)/2)*sin(chi))
capx_limits <- c(-1.5,1.5)
capy_limits <- c(-1.5,1.5)
max_BAH_angle = 110 # in degrees
capx_limits <- c(-1.5, 1.5)
capy_limits <- c(-1.5, 1.5)
narrow_output_formats <- transform(output_formats, width=height)
plot_parts <- 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(scale=.4, label_scale=.6),
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()))
dens <- estimate_density_2d(
f, c("sample_source", "hybrid"), "capx", "capy", n_pts=500, scaled=T)
plot_id <- "hbond_chi_BAH_eq_polar_density"
d_ply(dens, .(sample_source), function(sub_dens){
ss_id <- sub_dens$sample_source[1]
hybrid <- sub_dens$hybrid[1]
sub_plot_id <- paste(plot_id, ss_id, sep="_")
ggplot(data=sub_dens) + plot_parts +
facet_wrap(~hybrid, nrow=2) +
polar_equal_area_grids_bw() +
ggtitle(paste(hybrid, " Acceptor H-Bonds SeqSep > 5: chi vs BAH; ss_id: ", ss_id, sep="")) +
save_plots(self, sub_plot_id, sample_sources, output_dir, narrow_output_formats)
})
plot_id <- "hbond_chi_BAH_eq_polar_density"
d_ply(dens, .(sample_source, hybrid), function(sub_dens){
ss_id <- sub_dens$sample_source[1]
hybrid <- sub_dens$hybrid[1]
sub_plot_id <- paste(plot_id, ss_id, hybrid, sep="_")
ggplot(data=sub_dens) + plot_parts +
polar_equal_area_grids_bw() +
ggtitle(paste(hybrid, " Acceptor H-Bonds SeqSep > 5: chi vs BAH; ss_id: ", ss_id, sep="")) +
save_plots(self, sub_plot_id, sample_sources, output_dir, narrow_output_formats)
})
dens <- estimate_density_2d(
f, c("sample_source", "acc_chem_type_name", "don_chem_type_name"), "capx", "capy")
plot_id = "hbond_chi_BAH_eq_polar_density_by_chem_type"
ddply(dens, c("sample_source"), function(sub_dens){
ss_id <- sub_dens$sample_source[1]
sub_plot_id <- paste(plot_id, ss_id, sep="_")
ggplot(data=sub_dens) + plot_parts +
polar_equal_area_grids_bw(scale=.3, label_scale=.5) +
facet_grid(acc_chem_type_name ~ don_chem_type_name) +
ggtitle(paste("H-Bonds SeqSep > 5: chi vs BAH by Chemical Type; ss_id: ", ss_id, sep="")) +
save_plots(self, sub_plot_id, sample_sources, output_dir, output_formats)
})
cat("dens:\n")
print(str(dens))
plot_id = "hbond_chi_BAH_eq_polar_density"
d_ply(dens, c("sample_source", "don_chem_type_name", "acc_chem_type_name"), function(sub_dens){
ss_id <- sub_dens$sample_source[1]
sub_plot_id <- paste(
plot_id, ss_id, sub_dens$don_chem_type_name[1], sub_dens$acc_chem_type_name[1], sep="_")
ggplot(data=sub_dens) + plot_parts +
polar_equal_area_grids_bw() +
ggtitle(paste(
"H-Bonds: chi vs BAH SeqSep > 5 ",
"Don:", sub_dens$don_chem_type_name[1], " ",
"Acc:", sub_dens$acc_chem_type_name[1], "\n",
"ss_id: ", ss_id, sep=""))
save_plots(self, sub_plot_id, sample_sources, output_dir, output_formats)
})
})) # end FeaturesAnalysis
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