# -*- 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.
# Commend out plot because the secondary structure feature APSA is not integrated into the FeaturesReporter framework.
##
#sele <- "
#CREATE TEMPORARY TABLE IF NOT EXISTS hbond_cosBAH AS SELECT
# hbond.struct_id AS struct_id,
# don_site.resNum AS don_resNum,
# acc_site.resNum AS acc_resNum,
# geom.cosBAH AS cosBAH
#FROM
# hbonds AS hbond,
# hbond_geom_coords AS geom,
# hbond_sites AS don_site,
# hbond_sites AS acc_site
#WHERE
# 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_site.HBChemType = 'hbdon_PBA' AND
# acc_site.HBChemType = 'hbacc_PBA';
#
#CREATE INDEX hbond_cosBAH_don_site on
# hbond_cosBAH ( struct_id, don_resNum );
#
#CREATE INDEX hbond_cosBAH_acc_site on
# hbond_cosBAH ( struct_id, acc_resNum );
#
#ANALYZE;
#
#SELECT
# don_apsa.secondary_struct AS don_ss,
# acc_apsa.secondary_struct AS acc_ss,
# hb.cosBAH AS cosBAH
#FROM
# hbond_cosBAH AS hb,
# apsa AS don_apsa,
# apsa AS acc_apsa
#WHERE
# don_apsa.struct_id = hb.struct_id AND
# acc_apsa.struct_id = don_apsa.struct_id AND
# don_apsa.resNum = hb.don_resNum AND
# acc_apsa.resNum = hb.acc_resNum;"
#
#
#all <- query_sample_sources(
# sample_sources,
# sele)
#
#all$don_ss <- factor(all$don_ss)
#all$acc_ss <- factor(all$acc_ss)
#
#dens <- estimate_density_1d(
# data = all,
# ids = c("sample_source", "acc_ss", "don_ss"),
# variable = "cosBAH")
#
#plot_id <- "backbone_backbone_hbond_cosBAH_trellis"
#p <- ggplot(data=dens, aes(x=x, y=log(y+1), colour=sample_source, group=sample_source, indicator=counts))
#p <- p + geom_line()
#p <- p + geom_indicator()
#p <- p + facet_grid( don_ss ~ acc_ss)
#p <- p + ggtitle("Backbone Backbone Hydrogen Bond A-H Distance by Secondary Structure (APSA Method)\nnormalized for equal weight per unit distance")
#p <- p + labs(x=expression(paste('Acceptor -- Proton Distance (', ring(A), ')')),
# y="log(FeatureDensity + 1)")
#p <- p + theme_bw()
#p <- p + theme(axis.text.y=element_blank())
#p <- p + scale_y_continuous(limits=c(0,2.9), breaks=0:2)
#p <- p + scale_x_continuous(limits=c(1.4,2.7), breaks=c(1.6, 1.9, 2.2, 2.6))
#
#save_plots(self, plot_id, sample_sources, output_dir, output_formats)
#
#
#dens <- estimate_density_1d(
# data = all,
# ids = c("sample_source", "acc_ss"),
# variable = "cosBAH")
#
#plot_id <- "backbone_backbone_hbond_cosBAH_diversity_acceptor"
#p <- ggplot(data=dens, aes(x=x, y=log(y+1), colour=acc_ss))
#p <- p + geom_line()
#p <- p + facet_wrap( ~ sample_source )
#p <- p + ggtitle("Backbone Backbone Hydrogen Bond A-H Distance by Acceptor Secondary Structure (APSA Method)\nnormalized for equal weight per unit distance")
#p <- p + labs(x=expression(paste('Acceptor -- Proton Distance (', ring(A), ')')),
# y="log(FeatureDensity + 1)")
#p <- p + theme_bw()
#p <- p + theme(axis.text.y=element_blank())
#p <- p + scale_y_continuous(limits=c(0,2.9), breaks=0:2)
#p <- p + scale_x_continuous(limits=c(1.4,2.7), breaks=c(1.6, 1.9, 2.2, 2.6))
#
#save_plots(self, plot_id, sample_sources, output_dir, output_formats)
#
#dens <- estimate_density_1d(
# data = all,
# ids = c("sample_source", "don_ss"),
# variable = "cosBAH")
#
#
#plot_id <- "backbone_backbone_hbond_cosBAH_diversity_donor"
#p <- ggplot(data=dens, aes(x=x, y=log(y+1), colour=don_ss))
#p <- p + geom_line()
#p <- p + facet_wrap( ~ sample_source )
#p <- p + ggtitle("Backbone Backbone Hydrogen Bond A-H Distance by Donor Secondary Structure (APSA Method)\nnormalized for equal weight per unit distance")
#p <- p + labs(x=expression(paste('Acceptor -- Proton Distance (', ring(A), ')')),
# y="log(FeatureDensity + 1)")
#p <- p + theme_bw()
#p <- p + theme(axis.text.y=element_blank())
#p <- p + scale_y_continuous(limits=c(0,2.9), breaks=0:2)
#p <- p + scale_x_continuous(limits=c(1.4,2.7), breaks=c(1.6, 1.9, 2.2, 2.6))
#
#save_plots(self, plot_id, sample_sources, output_dir, output_formats)
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