# -*- 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(plyr)
source("../../plots/hbonds/hbond_geo_dim_scales.R")
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "AHD_chem_type_solvent_exposure_comparison",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
SELECT
geom.cosAHD,
acc.HBChemType AS acc_chem_type,
don.HBChemType AS don_chem_type,
CASE
WHEN don_env.sasa_r140 == 0 AND acc_env.sasa_r140 == 0 THEN 'Buried'
WHEN don_env.sasa_r140 > 0 AND acc_env.sasa_r140 > 0 THEN 'Exposed'
ELSE 'Partial' END AS sasa_burial,
CASE acc.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 'sp2' END AS acc_hybrid
FROM
hbond_geom_coords AS geom,
hbonds AS hb,
hbond_sites_pdb AS don_pdb,
hbond_sites_pdb AS acc_pdb,
hbond_sites AS don,
hbond_sites AS acc,
hbond_site_environment AS don_env,
hbond_site_environment AS acc_env
WHERE
hb.struct_id = geom.struct_id AND
hb.hbond_id = geom.hbond_id AND
hb.struct_id = don.struct_id AND
hb.don_id = don.site_id AND
hb.struct_id = acc.struct_id AND
hb.acc_id = acc.site_id 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_env.struct_id = hb.struct_id AND don_env.site_id = hb.don_id AND
acc_env.struct_id = hb.struct_id AND acc_env.site_id = hb.acc_id;";
f <- query_sample_sources(sample_sources, sele)
f$AHD <- acos(f$cosAHD)
f$don_chem_type_name <- don_chem_type_name_linear(f$don_chem_type)
f$acc_chem_type_name <- acc_chem_type_name_linear(f$acc_chem_type)
f <- na.omit(f, method="r")
tests <- c("kolmogorov_smirnov_test", "histogram_kl_divergence")
d_ply(f, .(sasa_burial), function(sub_f){
sasa_burial <- as.character(sub_f$sasa_burial[1])
comp_stats <- comparison_statistics(
sample_sources, sub_f, c(), "AHD", tests)
table_id <- paste("AHD_chem_type_solvent_exposure_comparison", sasa_burial, sep="_")
table_title <- paste("H-Bond AHD Angle Distribution Comparison ", sasa_burial, ", B-Factor < 30", sep="")
save_tables(self,
comp_stats, table_id,
sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
comp_stats <- comparison_statistics(
sample_sources, sub_f, c("don_chem_type_name"), "AHD", tests)
table_id <- paste("AHD_chem_type_solvent_exposure_comparison", sasa_burial, "by_don_chem_type", sep="_")
table_title <- paste("H-Bond AHD Angle by Donor Chemical Type\nDistribution Comparison ", sasa_burial, ", B-Factor < 30", sep="")
save_tables(self,
comp_stats, table_id, sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
comp_stats <- comparison_statistics(
sample_sources, sub_f, c("acc_chem_type_name"), "AHD", tests)
table_id <- paste("AHD_chem_type_solvent_exposure_comparison", sasa_burial, "by_acc_chem_type", sep="_")
table_title <- paste("H-Bond AHD Angle by Acceptor Chemical Type\nDistribution Comparison ", sasa_burial, ", B-Factor < 30", sep="")
save_tables(self,
comp_stats, table_id, sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
comp_stats <- comparison_statistics(
sample_sources, sub_f, c("acc_hybrid"), "AHD", tests)
table_id <- paste("AHD_chem_type_solvent_exposure_comparison", sasa_burial, "by_acc_hybrid", sep="_")
table_title <- paste("H-Bond AHD Angle by Acceptor Hybrid\nDistribution Comparison ", sasa_burial, ", B-Factor < 30", sep="")
save_tables(self,
comp_stats, table_id, sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
comp_stats <- comparison_statistics(
sample_sources, sub_f, c("don_chem_type_name", "acc_chem_type_name"), "AHD", tests)
table_id <- paste("AHD_chem_type_solvent_exposure_comparison", sasa_burial, "by_don_chem_type_acc_chem_type", sep="_")
table_title <- paste("H-Bond AHD Angle by Donor and Acceptor Chemical Types\nDistribution Comparison ", sasa_burial, ", B-Factor < 30", sep="")
save_tables(self,
comp_stats, table_id, sample_sources, output_dir, output_formats,
caption=table_title, caption.placement="top")
})
})) # end FeaturesAnalysis
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