inst/scripts/analysis/plots/hbonds/summary/num_hbonds_normalized.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(reshape2)
library(viridis)
source("../hbond_geo_dim_scales.R")
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "num_hbonds_normalized",
author = "Matthew O'Meara",
brief_description = "Count the number of hydrogen bonds formed conditional on the donor and acceptor chemical types.",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
do_analysis <- function(group_sele, bond_sele, id, title){
group_counts <- query_sample_sources(sample_sources, group_sele)
summary(group_counts)
group_counts[as.character(group_counts$chem_type) == "hbdon_AMO","count"] <-
group_counts[as.character(group_counts$chem_type) == "hbdon_AMO","count"] / 3
group_counts[as.character(group_counts$chem_type) == "hbdon_GDH","count"] <-
group_counts[as.character(group_counts$chem_type) == "hbdon_GDH","count"] / 2
group_counts[as.character(group_counts$chem_type) == "hbdon_CXA","count"] <-
group_counts[as.character(group_counts$chem_type) == "hbdon_CXA","count"] / 2
table_id <- paste(id, "group_counts", sep="_")
table_title <- paste(title, "Group Counts", sep="\n")
wide_group_counts <- dcast(group_counts, sample_source ~ chem_type, value="count")
save_tables( self,
wide_group_counts, table_id,
sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
bond_counts <- query_sample_sources(sample_sources, bond_sele)
#hacky filter for non-protein hbonds
bond_counts <- bond_counts[bond_counts$count > 30,]
table_id <- paste(id, "bond_counts", sep="_")
table_title <- paste(title, "Bond Counts", sep="\n")
wide_bond_counts <- dcast(
bond_counts, sample_source + don_chem_type ~ acc_chem_type, value="count")
save_tables( self,
wide_bond_counts, table_id,
sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
total_don <- sum(group_counts[group_counts$is_donor,"count"])
total_acc <- sum(group_counts[!group_counts$is_donor,"count"])
total_bonds <- sum(bond_counts$count)
p_score <- ddply(bond_counts, .(sample_source, acc_chem_type, don_chem_type), function(df){
sample_source <- as.character(df$sample_source)
don_chem_type <- as.character(df$don_chem_type[1])
acc_chem_type <- as.character(df$acc_chem_type[1])
p_bond <- df$count / total_bonds
p_don <- group_counts[
as.character(group_counts$sample_source) == sample_source &
as.character(group_counts$chem_type) == don_chem_type, "count"] / total_don
p_acc <- group_counts[
as.character(group_counts$sample_source) == sample_source &
as.character(group_counts$chem_type) == acc_chem_type, "count"] / total_acc
data.frame(
p_score = -log( p_bond / (p_don * p_acc) ) )
})
p_score$don_chem_type <- don_chem_type_name_linear(p_score$don_chem_type)
p_score$acc_chem_type <- acc_chem_type_name_linear(p_score$acc_chem_type)
p_score <- na.omit(p_score, method="r")
table_id <- paste(id, "narrow", sep="_")
save_tables( self,
p_score, table_id,
sample_sources, output_dir, output_formats,
caption=title, caption.placement="top")
wide_p_score <- dcast(p_score, sample_source + don_chem_type ~ acc_chem_type, value="p_score")
table_id <- id
save_tables( self,
wide_p_score, table_id,
sample_sources, output_dir, output_formats,
caption=title, caption.placement="top")
d_ply(p_score, .(sample_source), function(df){
new_sample_source <- df$sample_source[1]
plot_id <- paste(
id, new_sample_source, sep="_")
p <- ggplot(data=df) + theme_bw() +
ggtitle(
paste(title,"\nSample Source: ", new_sample_source, sep="")) +
geom_tile(aes(x=don_chem_type, y=acc_chem_type, fill=p_score)) +
scale_fill_viridis('P(Score)')
save_plots(self, plot_id, sample_sources, output_dir, output_formats)
})
}
#buried
# all hbond sites that have good B-Factor, are buried, and do not have
# any exposed partners with good B-Factor
#roup_sele <-"
#REATE TEMPORARY TABLE exposed_neighbor_count (
# struct_id BLOB,
# site_id INTEGER,
# PRIMARY KEY ( struct_id, site_id ));
#
#REATE INDEX IF NOT EXISTS hbonds_struct_id_acc_id ON hbonds ( struct_id, acc_id );
#REATE INDEX IF NOT EXISTS hbonds_struct_id_don_id ON hbonds ( struct_id, don_id );
#
#NSERT INTO exposed_neighbor_count
#ELECT DISTINCT
# site.struct_id,
# site.site_id
#ROM
# hbond_sites AS site,
# hbond_sites_pdb AS pdb,
# hbond_site_environment AS site_env,
# hbond_sites AS alt_site,
# hbond_sites_pdb AS alt_pdb,
# hbond_site_environment AS alt_site_env,
# hbonds AS hbond
#HERE
# site.struct_id = hbond.struct_id AND
# alt_site.struct_id = hbond.struct_id AND
# site.is_donor == 1 AND alt_site.is_donor == 0 AND
# hbond.don_id == site.site_id AND alt_site.site_id = hbond.acc_id AND
# pdb.struct_id = site.struct_id AND
# pdb.site_id = site.site_id AND
# pdb.heavy_atom_temperature < 30 AND
# site_env.struct_id = site.struct_id AND
# site_env.site_id = site.site_id AND
# site_env.sasa_r140 == 0 AND
# alt_pdb.struct_id = alt_site.struct_id AND
# alt_pdb.site_id = alt_site.site_id AND
# alt_pdb.heavy_atom_temperature < 30 AND
# alt_site_env.struct_id = alt_site.struct_id AND
# alt_site_env.site_id = alt_site.site_id AND
# alt_site_env.sasa_r140 > 0
#ROUP BY
# site.struct_id, site.site_id;
#
#
#NSERT INTO exposed_neighbor_count
#ELECT DISTINCT
# site.struct_id,
# site.site_id
#ROM
# hbond_sites AS site,
# hbond_sites_pdb AS pdb,
# hbond_site_environment AS site_env,
# hbond_sites AS alt_site,
# hbond_sites_pdb AS alt_pdb,
# hbond_site_environment AS alt_site_env,
# hbonds AS hbond
#HERE
# site.struct_id = hbond.struct_id AND
# alt_site.struct_id = hbond.struct_id AND
# site.is_donor == 0 AND alt_site.is_donor == 1 AND
# hbond.acc_id == site.site_id AND alt_site.site_id = hbond.don_id AND
# pdb.struct_id = site.struct_id AND
# pdb.site_id = site.site_id AND
# pdb.heavy_atom_temperature < 30 AND
# site_env.struct_id = site.struct_id AND
# site_env.site_id = site.site_id AND
# site_env.sasa_r140 == 0 AND
# alt_pdb.struct_id = alt_site.struct_id AND
# alt_pdb.site_id = alt_site.site_id AND
# alt_pdb.heavy_atom_temperature < 30 AND
# alt_site_env.struct_id = alt_site.struct_id AND
# alt_site_env.site_id = alt_site.site_id AND
# alt_site_env.sasa_r140 > 0
#ROUP BY
# site.struct_id, site.site_id;
#
#ELECT
# site.HBChemType AS chem_type,
# site.is_donor,
# count( * ) AS count
#ROM
# hbond_sites AS site,
# hbond_sites_pdb AS site_pdb,
# hbond_site_environment AS site_env
# LEFT JOIN
# exposed_neighbor_count
# ON
# exposed_neighbor_count.struct_id == site.struct_id AND
# exposed_neighbor_count.site_id == site.site_id
#HERE
# site_env.struct_id = site.struct_id AND
# site_env.site_id = site.site_id AND
# site_env.sasa_r140 == 0 AND
# site_pdb.struct_id = site.struct_id AND
# site_pdb.site_id = site.site_id AND
# site_pdb.heavy_atom_temperature < 30 AND
# exposed_neighbor_count.struct_id IS NULL
#ROUP BY
# chem_type;"
#
#ond_sele <-"
#ELECT
# acc_site.HBChemType AS acc_chem_type,
# don_site.HBChemType AS don_chem_type,
# count(*) AS count
#ROM
# hbonds AS hbond,
# hbond_sites AS acc_site,
# hbond_sites AS don_site,
# hbond_sites_pdb AS don_pdb,
# hbond_sites_pdb AS acc_pdb,
# hbond_site_environment AS don_env,
# hbond_site_environment AS acc_env
#HERE
# don_site.is_donor == 1 AND acc_site.is_donor == 0 AND
# hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
# hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
# don_pdb.struct_id = don_site.struct_id AND don_pdb.site_id = don_site.site_id AND
# acc_pdb.struct_id = acc_site.struct_id AND acc_pdb.site_id = acc_site.site_id AND
# don_pdb.heavy_atom_temperature < 30 AND
# acc_pdb.heavy_atom_temperature < 30 AND
# don_env.struct_id = don_site.struct_id AND don_env.site_id = don_site.site_id AND
# acc_env.struct_id = acc_site.struct_id AND acc_env.site_id = acc_site.site_id AND
# don_env.sasa_r140 == 0 AND acc_env.sasa_r140 == 0
#ROUP BY
# acc_site.HBChemType, don_site.HBChemType;"
#o_analysis(
# group_sele, bond_sele,
# "hbond_interaction_score_buried", "H-Bond (Buried) Interaction Score; B-Factor < 30")
#
#buried
group_sele <-"
SELECT
site.HBChemType AS chem_type,
site.is_donor AS is_donor,
count(site.HBChemType) AS count
FROM
hbond_sites AS site,
hbond_sites_pdb AS site_pdb,
hbond_site_environment AS site_env
WHERE
site_pdb.struct_id = site.struct_id AND
site_pdb.site_id = site.site_id AND
-- site_pdb.heavy_atom_temperature < 30 AND
site_env.struct_id = site.struct_id AND
site_env.site_id = site.site_id AND
site_env.sasa_r140 == 0
GROUP BY
site.HBChemType;"
bond_sele <-"
SELECT
acc_site.HBChemType AS acc_chem_type,
don_site.HBChemType AS don_chem_type,
count(*) AS count
FROM
hbonds AS hbond,
hbond_sites AS acc_site,
hbond_sites AS don_site,
hbond_sites_pdb AS don_pdb,
hbond_sites_pdb AS acc_pdb,
hbond_site_environment AS don_env,
hbond_site_environment AS acc_env
WHERE
hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
don_pdb.struct_id = don_site.struct_id AND don_pdb.site_id = don_site.site_id AND
acc_pdb.struct_id = acc_site.struct_id AND acc_pdb.site_id = acc_site.site_id AND
-- don_pdb.heavy_atom_temperature < 30 AND
-- acc_pdb.heavy_atom_temperature < 30 AND
don_env.struct_id = don_site.struct_id AND don_env.site_id = don_site.site_id AND
acc_env.struct_id = acc_site.struct_id AND acc_env.site_id = acc_site.site_id AND
don_env.sasa_r140 == 0 AND acc_env.sasa_r140 == 0
GROUP BY
acc_site.HBChemType, don_site.HBChemType;"
do_analysis(
group_sele, bond_sele,
"hbond_interaction_score_buried", "H-Bond (Buried) Interaction Score; B-Factor < 30")
#
##exposed
#group_sele <-"
#SELECT
# site.HBChemType AS chem_type,
# site.is_donor AS is_donor,
# count(site.HBChemType) AS count
#FROM
# hbond_sites AS site,
# hbond_sites_pdb AS site_pdb,
# hbond_site_environment AS site_env
#WHERE
# site_pdb.struct_id = site.struct_id AND
# site_pdb.site_id = site.site_id AND
# site_pdb.heavy_atom_temperature < 30 AND
# site_env.struct_id = site.struct_id AND
# site_env.site_id = site.site_id AND
# site_env.sasa_r100 > 0
#GROUP BY
# site.HBChemType;"
#
#bond_sele <-"
#SELECT
# acc_site.HBChemType AS acc_chem_type,
# don_site.HBChemType AS don_chem_type,
# count(*) AS count
#FROM
# hbonds AS hbond,
# hbond_sites AS acc_site,
# hbond_sites AS don_site,
# hbond_sites_pdb AS don_pdb,
# hbond_sites_pdb AS acc_pdb,
# hbond_site_environment AS don_env,
# hbond_site_environment AS acc_env
#WHERE
# hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
# hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
# don_pdb.struct_id = don_site.struct_id AND don_pdb.site_id = don_site.site_id AND
# acc_pdb.struct_id = acc_site.struct_id AND acc_pdb.site_id = acc_site.site_id AND
# don_pdb.heavy_atom_temperature < 30 AND
# acc_pdb.heavy_atom_temperature < 30 AND
# don_env.struct_id = don_site.struct_id AND don_env.site_id = don_site.site_id AND
# acc_env.struct_id = acc_site.struct_id AND acc_env.site_id = acc_site.site_id AND
# don_env.sasa_r100 > 0 AND acc_env.sasa_r100 > 0
#GROUP BY
# acc_site.HBChemType, don_site.HBChemType;"
#do_analysis(
# group_sele, bond_sele,
# "hbond_interaction_score_exposed", "H-Bond (Exposed) Interaction Score; B-Factor < 30")
#
})) # 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(reshape2)
library(viridis)
source("../hbond_geo_dim_scales.R")
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "num_hbonds_normalized",
author = "Matthew O'Meara",
brief_description = "Count the number of hydrogen bonds formed conditional on the donor and acceptor chemical types.",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
do_analysis <- function(group_sele, bond_sele, id, title){
group_counts <- query_sample_sources(sample_sources, group_sele)
summary(group_counts)
group_counts[as.character(group_counts$chem_type) == "hbdon_AMO","count"] <-
group_counts[as.character(group_counts$chem_type) == "hbdon_AMO","count"] / 3
group_counts[as.character(group_counts$chem_type) == "hbdon_GDH","count"] <-
group_counts[as.character(group_counts$chem_type) == "hbdon_GDH","count"] / 2
group_counts[as.character(group_counts$chem_type) == "hbdon_CXA","count"] <-
group_counts[as.character(group_counts$chem_type) == "hbdon_CXA","count"] / 2
table_id <- paste(id, "group_counts", sep="_")
table_title <- paste(title, "Group Counts", sep="\n")
wide_group_counts <- dcast(group_counts, sample_source ~ chem_type, value="count")
save_tables( self,
wide_group_counts, table_id,
sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
bond_counts <- query_sample_sources(sample_sources, bond_sele)
#hacky filter for non-protein hbonds
bond_counts <- bond_counts[bond_counts$count > 30,]
table_id <- paste(id, "bond_counts", sep="_")
table_title <- paste(title, "Bond Counts", sep="\n")
wide_bond_counts <- dcast(
bond_counts, sample_source + don_chem_type ~ acc_chem_type, value="count")
save_tables( self,
wide_bond_counts, table_id,
sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
total_don <- sum(group_counts[group_counts$is_donor,"count"])
total_acc <- sum(group_counts[!group_counts$is_donor,"count"])
total_bonds <- sum(bond_counts$count)
p_score <- ddply(bond_counts, .(sample_source, acc_chem_type, don_chem_type), function(df){
sample_source <- as.character(df$sample_source)
don_chem_type <- as.character(df$don_chem_type[1])
acc_chem_type <- as.character(df$acc_chem_type[1])
p_bond <- df$count / total_bonds
p_don <- group_counts[
as.character(group_counts$sample_source) == sample_source &
as.character(group_counts$chem_type) == don_chem_type, "count"] / total_don
p_acc <- group_counts[
as.character(group_counts$sample_source) == sample_source &
as.character(group_counts$chem_type) == acc_chem_type, "count"] / total_acc
data.frame(
p_score = -log( p_bond / (p_don * p_acc) ) )
})
p_score$don_chem_type <- don_chem_type_name_linear(p_score$don_chem_type)
p_score$acc_chem_type <- acc_chem_type_name_linear(p_score$acc_chem_type)
p_score <- na.omit(p_score, method="r")
table_id <- paste(id, "narrow", sep="_")
save_tables( self,
p_score, table_id,
sample_sources, output_dir, output_formats,
caption=title, caption.placement="top")
wide_p_score <- dcast(p_score, sample_source + don_chem_type ~ acc_chem_type, value="p_score")
table_id <- id
save_tables( self,
wide_p_score, table_id,
sample_sources, output_dir, output_formats,
caption=title, caption.placement="top")
d_ply(p_score, .(sample_source), function(df){
new_sample_source <- df$sample_source[1]
plot_id <- paste(
id, new_sample_source, sep="_")
p <- ggplot(data=df) + theme_bw() +
ggtitle(
paste(title,"\nSample Source: ", new_sample_source, sep="")) +
geom_tile(aes(x=don_chem_type, y=acc_chem_type, fill=p_score)) +
scale_fill_viridis('P(Score)')
save_plots(self, plot_id, sample_sources, output_dir, output_formats)
})
}
#buried
# all hbond sites that have good B-Factor, are buried, and do not have
# any exposed partners with good B-Factor
#roup_sele <-"
#REATE TEMPORARY TABLE exposed_neighbor_count (
# struct_id BLOB,
# site_id INTEGER,
# PRIMARY KEY ( struct_id, site_id ));
#
#REATE INDEX IF NOT EXISTS hbonds_struct_id_acc_id ON hbonds ( struct_id, acc_id );
#REATE INDEX IF NOT EXISTS hbonds_struct_id_don_id ON hbonds ( struct_id, don_id );
#
#NSERT INTO exposed_neighbor_count
#ELECT DISTINCT
# site.struct_id,
# site.site_id
#ROM
# hbond_sites AS site,
# hbond_sites_pdb AS pdb,
# hbond_site_environment AS site_env,
# hbond_sites AS alt_site,
# hbond_sites_pdb AS alt_pdb,
# hbond_site_environment AS alt_site_env,
# hbonds AS hbond
#HERE
# site.struct_id = hbond.struct_id AND
# alt_site.struct_id = hbond.struct_id AND
# site.is_donor == 1 AND alt_site.is_donor == 0 AND
# hbond.don_id == site.site_id AND alt_site.site_id = hbond.acc_id AND
# pdb.struct_id = site.struct_id AND
# pdb.site_id = site.site_id AND
# pdb.heavy_atom_temperature < 30 AND
# site_env.struct_id = site.struct_id AND
# site_env.site_id = site.site_id AND
# site_env.sasa_r140 == 0 AND
# alt_pdb.struct_id = alt_site.struct_id AND
# alt_pdb.site_id = alt_site.site_id AND
# alt_pdb.heavy_atom_temperature < 30 AND
# alt_site_env.struct_id = alt_site.struct_id AND
# alt_site_env.site_id = alt_site.site_id AND
# alt_site_env.sasa_r140 > 0
#ROUP BY
# site.struct_id, site.site_id;
#
#
#NSERT INTO exposed_neighbor_count
#ELECT DISTINCT
# site.struct_id,
# site.site_id
#ROM
# hbond_sites AS site,
# hbond_sites_pdb AS pdb,
# hbond_site_environment AS site_env,
# hbond_sites AS alt_site,
# hbond_sites_pdb AS alt_pdb,
# hbond_site_environment AS alt_site_env,
# hbonds AS hbond
#HERE
# site.struct_id = hbond.struct_id AND
# alt_site.struct_id = hbond.struct_id AND
# site.is_donor == 0 AND alt_site.is_donor == 1 AND
# hbond.acc_id == site.site_id AND alt_site.site_id = hbond.don_id AND
# pdb.struct_id = site.struct_id AND
# pdb.site_id = site.site_id AND
# pdb.heavy_atom_temperature < 30 AND
# site_env.struct_id = site.struct_id AND
# site_env.site_id = site.site_id AND
# site_env.sasa_r140 == 0 AND
# alt_pdb.struct_id = alt_site.struct_id AND
# alt_pdb.site_id = alt_site.site_id AND
# alt_pdb.heavy_atom_temperature < 30 AND
# alt_site_env.struct_id = alt_site.struct_id AND
# alt_site_env.site_id = alt_site.site_id AND
# alt_site_env.sasa_r140 > 0
#ROUP BY
# site.struct_id, site.site_id;
#
#ELECT
# site.HBChemType AS chem_type,
# site.is_donor,
# count( * ) AS count
#ROM
# hbond_sites AS site,
# hbond_sites_pdb AS site_pdb,
# hbond_site_environment AS site_env
# LEFT JOIN
# exposed_neighbor_count
# ON
# exposed_neighbor_count.struct_id == site.struct_id AND
# exposed_neighbor_count.site_id == site.site_id
#HERE
# site_env.struct_id = site.struct_id AND
# site_env.site_id = site.site_id AND
# site_env.sasa_r140 == 0 AND
# site_pdb.struct_id = site.struct_id AND
# site_pdb.site_id = site.site_id AND
# site_pdb.heavy_atom_temperature < 30 AND
# exposed_neighbor_count.struct_id IS NULL
#ROUP BY
# chem_type;"
#
#ond_sele <-"
#ELECT
# acc_site.HBChemType AS acc_chem_type,
# don_site.HBChemType AS don_chem_type,
# count(*) AS count
#ROM
# hbonds AS hbond,
# hbond_sites AS acc_site,
# hbond_sites AS don_site,
# hbond_sites_pdb AS don_pdb,
# hbond_sites_pdb AS acc_pdb,
# hbond_site_environment AS don_env,
# hbond_site_environment AS acc_env
#HERE
# don_site.is_donor == 1 AND acc_site.is_donor == 0 AND
# hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
# hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
# don_pdb.struct_id = don_site.struct_id AND don_pdb.site_id = don_site.site_id AND
# acc_pdb.struct_id = acc_site.struct_id AND acc_pdb.site_id = acc_site.site_id AND
# don_pdb.heavy_atom_temperature < 30 AND
# acc_pdb.heavy_atom_temperature < 30 AND
# don_env.struct_id = don_site.struct_id AND don_env.site_id = don_site.site_id AND
# acc_env.struct_id = acc_site.struct_id AND acc_env.site_id = acc_site.site_id AND
# don_env.sasa_r140 == 0 AND acc_env.sasa_r140 == 0
#ROUP BY
# acc_site.HBChemType, don_site.HBChemType;"
#o_analysis(
# group_sele, bond_sele,
# "hbond_interaction_score_buried", "H-Bond (Buried) Interaction Score; B-Factor < 30")
#
#buried
group_sele <-"
SELECT
site.HBChemType AS chem_type,
site.is_donor AS is_donor,
count(site.HBChemType) AS count
FROM
hbond_sites AS site,
hbond_sites_pdb AS site_pdb,
hbond_site_environment AS site_env
WHERE
site_pdb.struct_id = site.struct_id AND
site_pdb.site_id = site.site_id AND
-- site_pdb.heavy_atom_temperature < 30 AND
site_env.struct_id = site.struct_id AND
site_env.site_id = site.site_id AND
site_env.sasa_r140 == 0
GROUP BY
site.HBChemType;"
bond_sele <-"
SELECT
acc_site.HBChemType AS acc_chem_type,
don_site.HBChemType AS don_chem_type,
count(*) AS count
FROM
hbonds AS hbond,
hbond_sites AS acc_site,
hbond_sites AS don_site,
hbond_sites_pdb AS don_pdb,
hbond_sites_pdb AS acc_pdb,
hbond_site_environment AS don_env,
hbond_site_environment AS acc_env
WHERE
hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
don_pdb.struct_id = don_site.struct_id AND don_pdb.site_id = don_site.site_id AND
acc_pdb.struct_id = acc_site.struct_id AND acc_pdb.site_id = acc_site.site_id AND
-- don_pdb.heavy_atom_temperature < 30 AND
-- acc_pdb.heavy_atom_temperature < 30 AND
don_env.struct_id = don_site.struct_id AND don_env.site_id = don_site.site_id AND
acc_env.struct_id = acc_site.struct_id AND acc_env.site_id = acc_site.site_id AND
don_env.sasa_r140 == 0 AND acc_env.sasa_r140 == 0
GROUP BY
acc_site.HBChemType, don_site.HBChemType;"
do_analysis(
group_sele, bond_sele,
"hbond_interaction_score_buried", "H-Bond (Buried) Interaction Score; B-Factor < 30")
#
##exposed
#group_sele <-"
#SELECT
# site.HBChemType AS chem_type,
# site.is_donor AS is_donor,
# count(site.HBChemType) AS count
#FROM
# hbond_sites AS site,
# hbond_sites_pdb AS site_pdb,
# hbond_site_environment AS site_env
#WHERE
# site_pdb.struct_id = site.struct_id AND
# site_pdb.site_id = site.site_id AND
# site_pdb.heavy_atom_temperature < 30 AND
# site_env.struct_id = site.struct_id AND
# site_env.site_id = site.site_id AND
# site_env.sasa_r100 > 0
#GROUP BY
# site.HBChemType;"
#
#bond_sele <-"
#SELECT
# acc_site.HBChemType AS acc_chem_type,
# don_site.HBChemType AS don_chem_type,
# count(*) AS count
#FROM
# hbonds AS hbond,
# hbond_sites AS acc_site,
# hbond_sites AS don_site,
# hbond_sites_pdb AS don_pdb,
# hbond_sites_pdb AS acc_pdb,
# hbond_site_environment AS don_env,
# hbond_site_environment AS acc_env
#WHERE
# hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id AND
# hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
# don_pdb.struct_id = don_site.struct_id AND don_pdb.site_id = don_site.site_id AND
# acc_pdb.struct_id = acc_site.struct_id AND acc_pdb.site_id = acc_site.site_id AND
# don_pdb.heavy_atom_temperature < 30 AND
# acc_pdb.heavy_atom_temperature < 30 AND
# don_env.struct_id = don_site.struct_id AND don_env.site_id = don_site.site_id AND
# acc_env.struct_id = acc_site.struct_id AND acc_env.site_id = acc_site.site_id AND
# don_env.sasa_r100 > 0 AND acc_env.sasa_r100 > 0
#GROUP BY
# acc_site.HBChemType, don_site.HBChemType;"
#do_analysis(
# group_sele, bond_sele,
# "hbond_interaction_score_exposed", "H-Bond (Exposed) Interaction Score; B-Factor < 30")
#
})) # end FeaturesAnalysis
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