inst/scripts/analysis/plots/hbonds/geo_dim_2d/AHchi_AHD_eq_polar_density_chem_type.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(dplyr)
library(viridis)
source("../hbond_geo_dim_scales.R")
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "AHchi_AHD_eq_polar_density_chem_type",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("StructureFeatures", "HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
SELECT
geom.cosAHD, geom.chi,
don_site.HBChemType AS don_chem_type,
acc_site.HBChemType AS acc_chem_type,
acc_atoms.base_x AS abx, acc_atoms.base_y AS aby, acc_atoms.base_z AS abz, -- acceptor base atom
acc_atoms.atm_x AS ax, acc_atoms.atm_y AS ay, acc_atoms.atm_z AS az, -- acceptor atom
don_atoms.atm_x AS hx, don_atoms.atm_y AS hy, don_atoms.atm_z AS hz, -- hydrogen atom
don_atoms.base_x AS dx, don_atoms.base_y AS dy, don_atoms.base_z AS dz, -- donor atom
hbond.accRank AS acc_rank, don_site.resNum - acc_site.resNum AS seq_sep,
struct.tag,
don_pdb.chain AS don_chain,
don_pdb.resNum AS don_resNum,
don_pdb.iCode AS don_iCode,
acc_pdb.chain AS acc_chain,
acc_pdb.resNum AS acc_resNum,
acc_pdb.iCode AS acc_iCode
FROM
structures AS struct,
hbond_geom_coords AS geom,
hbonds AS hbond,
hbond_sites AS don_site,
hbond_sites AS acc_site,
hbond_site_atoms AS don_atoms, hbond_site_atoms AS acc_atoms,
hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb
WHERE
struct.struct_id = hbond.struct_id AND
don_site.HBChemType != 'hbdon_PBA' AND acc_site.HBChemType != 'hbacc_PBA' AND
hbond.struct_id = geom.struct_id AND hbond.hbond_id = geom.hbond_id AND
hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
don_atoms.struct_id = hbond.struct_id AND don_atoms.site_id = hbond.don_id AND
acc_atoms.struct_id = hbond.struct_id AND acc_atoms.site_id = hbond.acc_id AND
don_pdb.struct_id = hbond.struct_id AND don_pdb.site_id = don_site.site_id AND
acc_pdb.struct_id = hbond.struct_id AND acc_pdb.site_id = acc_site.site_id AND
don_pdb.heavy_atom_temperature < 20 AND acc_pdb.heavy_atom_temperature < 20;"
f <- query_sample_sources(sample_sources, sele)
f <- f %>%
mutate(
don_chem_type_name = don_chem_type_name_wrap(don_chem_type),
acc_chem_type_name = acc_chem_type_name_wrap(acc_chem_type)) %>%
na.omit(method="r") %>%
mutate(
acc_rank = factor(acc_rank)) %>%
filter(
!is.na(don_chem_type_name),
!is.na(acc_chem_type_name)) %>%
mutate(
orbital = ifelse(chi < pi/2 & chi > -pi/2, "anti", "syn") %>% factor,
seq_sep = ifelse(abs(seq_sep) <= 5, seq_sep, factor("long_range")),
AHchi = vector_dihedral(
cbind(abx, aby, abz), cbind(ax, ay, az),
cbind(hx, hy, hz), cbind(dx, dy, dz)),
capx = 2*sin(acos(cosAHD)/2)*cos(AHchi),
capy = 2*sin(acos(cosAHD)/2)*sin(AHchi))
capx_limits <- capy_limits <- c(-1.5,1.5)
plot_parts <- list(
theme_bw(),
stat_density2d(
aes(x=capx,y=capy, fill=log(..density..+1)), geom="tile", contour=FALSE),
polar_equal_area_grids_bw(),
geom_indicator(aes(indicator=counts), color="white", group=1),
scale_x_continuous("", limits=capx_limits, breaks=c(-1, 0, 1)),
scale_y_continuous("", limits=capy_limits, breaks=c(-1, 0, 1)),
coord_fixed(ratio = 1),
scale_fill_viridis('log(Density+1)'))
narrow_output_formats <- transform(output_formats, width=height)
d_ply(f, .(sample_source), function(sub_f){
ss_id <- sub_f$sample_source[1]
ss <- sample_sources[sample_sources$sample_source == ss_id,]
##################
plot_id = paste("AHchi_AHD_eq_polar_density_by_don", ss_id, sep="_")
sub_f <- ddply(sub_f, .(don_chem_type), transform, counts=length(sample_source))
ggplot(data=sub_f) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles Sidechain-Sidechain\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ don_chem_type)
save_plots(self, plot_id, ss, output_dir, narrow_output_formats)
#################
plot_id = paste("AHchi_AHD_eq_polar_density_by_acc", ss_id, sep="_")
sub_f <- ddply(sub_f, .(acc_chem_type), transform, counts = length(sample_source))
ggplot(data=sub_f) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles Sidechain-Sidechain\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ acc_chem_type)
save_plots(self, plot_id, ss, output_dir, output_formats)
#################
plot_id = paste("AHchi_AHD_eq_polar_density", ss_id, sep="_")
sub_f$counts <- nrow(sub_f)
ggplot(data=sub_f) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles Sidechain-Sidechain\nLambert Azimuthal Projection Sample Source: ", ss_id, sep=""))
save_plots(self, plot_id, ss, output_dir, output_formats)
#################
sub_f <- ddply(sub_f, .(don_chem_type, acc_chem_type),
transform, counts = length(sample_source))
plot_id = paste("AHchi_AHD_eq_polar_density_dGDE", ss_id, sep="_")
ggplot(data=subset(sub_f, don_chem_type == "hbdon_GDE")) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles GDE Donor\nLambert Azimuthal Projection Sample Source: ", ss_id, sep=""))
facet_wrap( ~ acc_chem_type)
save_plots(self, plot_id, ss, output_dir, output_formats)
plot_id = paste("AHchi_AHD_eq_polar_density_dGDH", ss_id, sep="_")
ggplot(data=subset(sub_f, don_chem_type == "hbdon_GDH")) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles GDH Donor\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ acc_chem_type)
save_plots(self, plot_id, ss, output_dir, output_formats)
################
sub_f <- ddply(sub_f, .(don_chem_type, acc_chem_type, acc_rank),
transform, counts = length(sample_source))
plot_id = paste("AHchi_AHD_eq_polar_density_dGDE_aCXL_by_acc_rank", ss_id, sep="_")
ggplot(data=subset(
sub_f,
don_chem_type == "hbdon_GDE" & acc_chem_type == "hbacc_CXL")) +
plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDE by Acc Rank\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ acc_rank)
save_plots(self, plot_id, ss, output_dir, output_formats)
plot_id = paste("AHchi_AHD_eq_polar_density_dGDH_aCXL_by_acc_rank", ss_id, sep="_")
ggplot(data=subset(
sub_f,
don_chem_type == "hbdon_GDH" & acc_chem_type == "hbacc_CXL")) +
plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDH by Acc Rank\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ acc_rank)
save_plots(self, plot_id, ss, output_dir, output_formats)
################
sub_f <- ddply(sub_f, .(don_chem_type, orbital),
transform, counts = length(sample_source))
ggplot(data=subset(
sub_f,
don_chem_type == "hbdon_GDE" & acc_chem_type == "hbacc_CXL")) +
plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDE by Acc Orbital\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ orbital)
save_plots(self, plot_id, ss, output_dir, output_formats)
plot_id = paste("AHchi_AHD_eq_polar_density_dGDH_aCXL_by_acc_orbital", ss_id, sep="_")
ggplot(data=subset(
sub_f,
don_chem_type == "hbdon_GDH" & acc_chem_type == "hbacc_CXL")) +
plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDH by Acc Orbital\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ orbital)
save_plots(self, plot_id, ss, output_dir, output_formats)
################
sub_sub_f <- subset(
sub_f,
orbital == "anti" &
don_chem_type == "hbdon_GDH" & acc_chem_type == "hbacc_CXL")
sub_sub_f <- ddply(sub_sub_f, .(seq_sep), transform, counts = length(sample_source))
plot_id = paste("AHchi_AHD_eq_polar_density_dGDH_aCXL_acc_anti_orbital_by_seq_sep", ss_id, sep="_")
ggplot(data=sub_sub_f) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDH Acc Anti Orbital by don.resNum - acc.resNum\nEqArea Proj. Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ seq_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.
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(plyr)
library(dplyr)
library(viridis)
source("../hbond_geo_dim_scales.R")
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "AHchi_AHD_eq_polar_density_chem_type",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("StructureFeatures", "HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
SELECT
geom.cosAHD, geom.chi,
don_site.HBChemType AS don_chem_type,
acc_site.HBChemType AS acc_chem_type,
acc_atoms.base_x AS abx, acc_atoms.base_y AS aby, acc_atoms.base_z AS abz, -- acceptor base atom
acc_atoms.atm_x AS ax, acc_atoms.atm_y AS ay, acc_atoms.atm_z AS az, -- acceptor atom
don_atoms.atm_x AS hx, don_atoms.atm_y AS hy, don_atoms.atm_z AS hz, -- hydrogen atom
don_atoms.base_x AS dx, don_atoms.base_y AS dy, don_atoms.base_z AS dz, -- donor atom
hbond.accRank AS acc_rank, don_site.resNum - acc_site.resNum AS seq_sep,
struct.tag,
don_pdb.chain AS don_chain,
don_pdb.resNum AS don_resNum,
don_pdb.iCode AS don_iCode,
acc_pdb.chain AS acc_chain,
acc_pdb.resNum AS acc_resNum,
acc_pdb.iCode AS acc_iCode
FROM
structures AS struct,
hbond_geom_coords AS geom,
hbonds AS hbond,
hbond_sites AS don_site,
hbond_sites AS acc_site,
hbond_site_atoms AS don_atoms, hbond_site_atoms AS acc_atoms,
hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb
WHERE
struct.struct_id = hbond.struct_id AND
don_site.HBChemType != 'hbdon_PBA' AND acc_site.HBChemType != 'hbacc_PBA' AND
hbond.struct_id = geom.struct_id AND hbond.hbond_id = geom.hbond_id AND
hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
don_atoms.struct_id = hbond.struct_id AND don_atoms.site_id = hbond.don_id AND
acc_atoms.struct_id = hbond.struct_id AND acc_atoms.site_id = hbond.acc_id AND
don_pdb.struct_id = hbond.struct_id AND don_pdb.site_id = don_site.site_id AND
acc_pdb.struct_id = hbond.struct_id AND acc_pdb.site_id = acc_site.site_id AND
don_pdb.heavy_atom_temperature < 20 AND acc_pdb.heavy_atom_temperature < 20;"
f <- query_sample_sources(sample_sources, sele)
f <- f %>%
mutate(
don_chem_type_name = don_chem_type_name_wrap(don_chem_type),
acc_chem_type_name = acc_chem_type_name_wrap(acc_chem_type)) %>%
na.omit(method="r") %>%
mutate(
acc_rank = factor(acc_rank)) %>%
filter(
!is.na(don_chem_type_name),
!is.na(acc_chem_type_name)) %>%
mutate(
orbital = ifelse(chi < pi/2 & chi > -pi/2, "anti", "syn") %>% factor,
seq_sep = ifelse(abs(seq_sep) <= 5, seq_sep, factor("long_range")),
AHchi = vector_dihedral(
cbind(abx, aby, abz), cbind(ax, ay, az),
cbind(hx, hy, hz), cbind(dx, dy, dz)),
capx = 2*sin(acos(cosAHD)/2)*cos(AHchi),
capy = 2*sin(acos(cosAHD)/2)*sin(AHchi))
capx_limits <- capy_limits <- c(-1.5,1.5)
plot_parts <- list(
theme_bw(),
stat_density2d(
aes(x=capx,y=capy, fill=log(..density..+1)), geom="tile", contour=FALSE),
polar_equal_area_grids_bw(),
geom_indicator(aes(indicator=counts), color="white", group=1),
scale_x_continuous("", limits=capx_limits, breaks=c(-1, 0, 1)),
scale_y_continuous("", limits=capy_limits, breaks=c(-1, 0, 1)),
coord_fixed(ratio = 1),
scale_fill_viridis('log(Density+1)'))
narrow_output_formats <- transform(output_formats, width=height)
d_ply(f, .(sample_source), function(sub_f){
ss_id <- sub_f$sample_source[1]
ss <- sample_sources[sample_sources$sample_source == ss_id,]
##################
plot_id = paste("AHchi_AHD_eq_polar_density_by_don", ss_id, sep="_")
sub_f <- ddply(sub_f, .(don_chem_type), transform, counts=length(sample_source))
ggplot(data=sub_f) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles Sidechain-Sidechain\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ don_chem_type)
save_plots(self, plot_id, ss, output_dir, narrow_output_formats)
#################
plot_id = paste("AHchi_AHD_eq_polar_density_by_acc", ss_id, sep="_")
sub_f <- ddply(sub_f, .(acc_chem_type), transform, counts = length(sample_source))
ggplot(data=sub_f) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles Sidechain-Sidechain\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ acc_chem_type)
save_plots(self, plot_id, ss, output_dir, output_formats)
#################
plot_id = paste("AHchi_AHD_eq_polar_density", ss_id, sep="_")
sub_f$counts <- nrow(sub_f)
ggplot(data=sub_f) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles Sidechain-Sidechain\nLambert Azimuthal Projection Sample Source: ", ss_id, sep=""))
save_plots(self, plot_id, ss, output_dir, output_formats)
#################
sub_f <- ddply(sub_f, .(don_chem_type, acc_chem_type),
transform, counts = length(sample_source))
plot_id = paste("AHchi_AHD_eq_polar_density_dGDE", ss_id, sep="_")
ggplot(data=subset(sub_f, don_chem_type == "hbdon_GDE")) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles GDE Donor\nLambert Azimuthal Projection Sample Source: ", ss_id, sep=""))
facet_wrap( ~ acc_chem_type)
save_plots(self, plot_id, ss, output_dir, output_formats)
plot_id = paste("AHchi_AHD_eq_polar_density_dGDH", ss_id, sep="_")
ggplot(data=subset(sub_f, don_chem_type == "hbdon_GDH")) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles GDH Donor\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ acc_chem_type)
save_plots(self, plot_id, ss, output_dir, output_formats)
################
sub_f <- ddply(sub_f, .(don_chem_type, acc_chem_type, acc_rank),
transform, counts = length(sample_source))
plot_id = paste("AHchi_AHD_eq_polar_density_dGDE_aCXL_by_acc_rank", ss_id, sep="_")
ggplot(data=subset(
sub_f,
don_chem_type == "hbdon_GDE" & acc_chem_type == "hbacc_CXL")) +
plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDE by Acc Rank\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ acc_rank)
save_plots(self, plot_id, ss, output_dir, output_formats)
plot_id = paste("AHchi_AHD_eq_polar_density_dGDH_aCXL_by_acc_rank", ss_id, sep="_")
ggplot(data=subset(
sub_f,
don_chem_type == "hbdon_GDH" & acc_chem_type == "hbacc_CXL")) +
plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDH by Acc Rank\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ acc_rank)
save_plots(self, plot_id, ss, output_dir, output_formats)
################
sub_f <- ddply(sub_f, .(don_chem_type, orbital),
transform, counts = length(sample_source))
ggplot(data=subset(
sub_f,
don_chem_type == "hbdon_GDE" & acc_chem_type == "hbacc_CXL")) +
plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDE by Acc Orbital\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ orbital)
save_plots(self, plot_id, ss, output_dir, output_formats)
plot_id = paste("AHchi_AHD_eq_polar_density_dGDH_aCXL_by_acc_orbital", ss_id, sep="_")
ggplot(data=subset(
sub_f,
don_chem_type == "hbdon_GDH" & acc_chem_type == "hbacc_CXL")) +
plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDH by Acc Orbital\nLambert Azimuthal Projection Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ orbital)
save_plots(self, plot_id, ss, output_dir, output_formats)
################
sub_sub_f <- subset(
sub_f,
orbital == "anti" &
don_chem_type == "hbdon_GDH" & acc_chem_type == "hbacc_CXL")
sub_sub_f <- ddply(sub_sub_f, .(seq_sep), transform, counts = length(sample_source))
plot_id = paste("AHchi_AHD_eq_polar_density_dGDH_aCXL_acc_anti_orbital_by_seq_sep", ss_id, sep="_")
ggplot(data=sub_sub_f) + plot_parts +
ggtitle(paste("Hydrogen Bonds AHchi vs AHD Angles aCXL-dGDH Acc Anti Orbital by don.resNum - acc.resNum\nEqArea Proj. Sample Source: ", ss_id, sep="")) +
facet_wrap( ~ seq_sep)
save_plots(self, plot_id, ss, output_dir, output_formats)
})
})) # end FeaturesAnalysis
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