inst/scripts/analysis/statistics/hbonds/ADdist_chem_type_comparison.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.

source("../../plots/hbonds/hbond_geo_dim_scales.R")

feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "ADdist_chem_type_comparison",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){


sele <- "
SELECT
	don_atoms.base_x AS dx, don_atoms.base_y AS dy, don_atoms.base_z AS dz,
	acc_atoms.atm_x  AS ax, acc_atoms.atm_y  AS ay, acc_atoms.atm_z  AS az,
	don.HBChemType AS don_chem_type, acc.HBChemType AS acc_chem_type,
	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
	hbonds AS hb,
	hbond_sites AS don, hbond_sites AS acc,
	hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb,
	hbond_site_atoms AS don_atoms, hbond_site_atoms AS acc_atoms
WHERE
	don.struct_id = hb.struct_id AND don.site_id =hb.don_id AND
	acc.struct_id = hb.struct_id AND acc.site_id =hb.acc_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_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;"


# Execute the SQL query on each sample source.
f <- query_sample_sources(sample_sources, sele)

# A-D distance is not stored directly in the features database,
# however it can be computed from the coordinates of the hydrogen
# bonding atoms.
f <- transform(f,
	ADdist = vector_distance(cbind(dx, dy, dz), cbind(ax, ay, az)))

# This shouldn't happend, but if it does get rid of them
f <- f[f$ADdist < 5,]

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", "primary_modes_radial_3d_norm_diff")

comp_stats <- comparison_statistics(
	sample_sources, f, c(), "ADdist", tests)
table_id <- "ADdist_chem_type_comparison"
table_title <- "H-Bond A-D Distance Distribution Comparison, B-Factor < 30"
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, f, c("don_chem_type_name"), "ADdist", tests)
table_id <- paste("ADdist_chem_type_comparison", "by_don_chem_type", sep="_")
table_title <- "H-Bond A-D Distance by Donor Chemical Type\nDistribution Comparison, B-Factor < 30"
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, f, c("acc_hybrid"), "ADdist", tests)
table_id <- paste("ADdist_chem_type_comparison", "by_acc_hybrid", sep="_")
table_title <- "H-Bond A-D Distance by Acceptor Hybrid\nDistribution Comparison, B-Factor < 30"
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, f, c("acc_chem_type_name"), "ADdist", tests)
table_id <- paste("ADdist_chem_type_comparison", "by_acc_chem_type", sep="_")
table_title <- "H-Bond A-D Distance by Acceptor Chemical Type\nDistribution Comparison, B-Factor < 30"
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, f, c("don_chem_type_name", "acc_chem_type_name"), "ADdist", tests)
table_id <- paste("ADdist_chem_type_comparison", "by_don_chem_type_acc_chem_type", sep="_")
table_title <- "H-Bond A-D Distance by Donor and Acceptor Chemical Types\nDistribution Comparison, B-Factor < 30"
save_tables(self,
	comp_stats, table_id, sample_sources, output_dir, output_formats,
	caption=table_title, caption.placement="top")

})) # end FeaturesAnalysis