# -*- 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)
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "SSDists_Sheet_O_O",
author = "Matthew O'Meara",
brief_description = "",
long_description = "
RESi
---ACC1-DON2 -----<
/ | |
| HB1 HB2 ANTI-PARALLEL HBonding
\ | |
---DON1-ACC2------>
RESj
|| ||
|| Bres1 Ares1
------- Ri+1 -- Ri ---- Ri-1 -------<
/ /|| / CLOSE Carbon HBond
| O_Ca || Ca_O Geometry in anti-parallel sheets
\ / || /
------- Rj-1 -- Rj ---- Rj+1 -------->
Bres2 Ares2 ||
|| ||
| |
| RESi |
----Ca---|---DON1--ACC2--|--Ca-------->
\ / / \ \
\ HB1 / HB2 \ PARALLEL HBonding
\ / / \ \
--DON--ACC1--|--Ca---|---DON2--ACC---->
RESj-1 | RESj | RESj+1
| |
",
feature_reporter_dependencies = c("ResidueSecondaryStructureFeatures", "HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
CREATE TEMPORARY TABLE ee_bb_bb_hbonds AS
SELECT
hb.struct_id,
acc_site.resNum AS acc_resNum,
don_site.resNum AS don_resNum
FROM
hbonds AS hb,
hbond_sites AS acc_site,
hbond_sites AS don_site,
residue_secondary_structure AS r1ss,
residue_secondary_structure AS r2ss
WHERE
acc_site.HBChemType = 'hbacc_PBA' AND
acc_site.struct_id = hb.struct_id AND
acc_site.site_id = hb.acc_id AND
don_site.site_id = hb.don_id AND
don_site.HBChemType = 'hbdon_PBA' AND
don_site.struct_id = acc_site.struct_id AND
r1ss.struct_id = acc_site.struct_id AND
r1ss.resNum = acc_site.resNum AND
r1ss.dssp = 'E' AND
r2ss.struct_id = don_site.struct_id AND
r2ss.resNum = don_site.resNum AND
r2ss.dssp = 'E'
ORDER BY RANDOM()
LIMIT 100000;
CREATE TEMPORARY TABLE antiparallel_close_contact_residue_pairs AS
SELECT
hb1.struct_id,
hb1.acc_resNum AS resNum_i,
hb1.don_resNum AS resNum_j
FROM
ee_bb_bb_hbonds AS hb1,
ee_bb_bb_hbonds AS hb2
WHERE
hb1.struct_id = hb2.struct_id AND
hb1.acc_resNum = hb2.don_resNum AND
hb1.don_resNum = hb2.acc_resNum AND
hb1.acc_resNum < hb1.don_resNum;
CREATE TEMPORARY TABLE antiparallel_O_O AS
SELECT dist.O_O_dist AS dist, 'antiparallel' AS strand_orientation
FROM protein_backbone_atom_atom_pairs AS dist,
antiparallel_close_contact_residue_pairs AS atpairs
WHERE dist.struct_id = atpairs.struct_id AND
dist.resNum1 = atpairs.resNum_i AND dist.resNum2 = atpairs.resNum_j;
CREATE TEMPORARY TABLE parallel_close_contact_residue_pairs AS
SELECT
hb1.struct_id,
hb1.acc_resNum AS resNum_i,
hb1.don_resNum AS resNum_j
FROM
ee_bb_bb_hbonds AS hb1,
ee_bb_bb_hbonds AS hb2
WHERE
hb1.struct_id = hb2.struct_id AND
hb1.don_resNum = hb2.acc_resNum AND
hb1.acc_resNum +2 = hb2.don_resNum;
CREATE TEMPORARY TABLE parallel_O_O_minus AS
SELECT dist.O_O_dist AS dist, 'parallel_minus' AS strand_orientation
FROM protein_backbone_atom_atom_pairs AS dist,
parallel_close_contact_residue_pairs AS apairs
WHERE dist.struct_id = apairs.struct_id AND
apairs.resNum_i < apairs.resNum_j AND
dist.resNum1 = apairs.resNum_i AND dist.resNum2 = apairs.resNum_j - 1;
CREATE TEMPORARY TABLE parallel_O_O_plus AS
SELECT dist.O_O_dist AS dist, 'parallel_plus' AS strand_orientation
FROM protein_backbone_atom_atom_pairs AS dist,
parallel_close_contact_residue_pairs AS apairs
WHERE dist.struct_id = apairs.struct_id AND
apairs.resNum_i < apairs.resNum_j AND
dist.resNum1 = apairs.resNum_i AND dist.resNum2 = apairs.resNum_j + 1;
SELECT * FROM antiparallel_O_O UNION
SELECT * FROM parallel_O_O_minus UNION
SELECT * FROM parallel_O_O_plus;"
f <- query_sample_sources(sample_sources, sele)
sele <- "
DROP TABLE ee_bb_bb_hbonds;
DROP TABLE antiparallel_close_contact_residue_pairs;
DROP TABLE antiparallel_O_O;
DROP TABLE parallel_close_contact_residue_pairs;
DROP TABLE parallel_O_O_minus;
DROP TABLE parallel_O_O_plus;"
query_sample_sources(sample_sources, sele, warn_zero_rows=F)
dens <- estimate_density_1d(
f, c("sample_source", "strand_orientation"),
"dist", weight_fun = radial_3d_normalization)
dpM <- dens[dens$strand_orientation == "parallel_minus",]
dpP <- dens[dens$strand_orientation == "parallel_plus",]
dap <- dens[dens$strand_orientation == "antiparallel",]
plot_id <- "SSDists_Sheet_O_O_parallel_anti_parallel"
p <- ggplot() + theme_bw() +
geom_line(data=dpP, aes(x=x, y=y, colour=sample_source)) +
geom_line(data=dpM, aes(x=x, y=y, colour=sample_source)) +
geom_line(data=dap, aes(x=x, y=y, colour=sample_source)) +
geom_indicator(data=dpP, aes(indicator=counts, colour=sample_source, group=sample_source, xpos="right")) +
geom_indicator(data=dpM, aes(indicator=counts, colour=sample_source, group=sample_source, xpos="center")) +
geom_indicator(data=dap, aes(indicator=counts, colour=sample_source, group=sample_source, xpos="left")) +
ggtitle("O--O atom atom distances involving beta-sheet residues\nnormalized for equal weight per unit distance\n(antiparallel parallel-minus parallel-plus)") +
scale_y_log10("FeatureDensity", limits=c(1e-2,5))+
scale_x_continuous(expression(paste('Atom Atom Distances (', ring(A), ')')), limits=c(2.5,9), breaks=c(3, 4, 5, 6, 7, 8, 9))
if(nrow(sample_sources) <= 3){
p <- p + theme(legend.position="bottom", legend.direction="horizontal")
}
save_plots(self, plot_id, sample_sources, output_dir, output_formats)
# zooom in on the anti_parallel peak
lims <- c(.1, 3)
plot_id <- "SSDists_Sheet_O_O_anti_parallel_zoom"
p <- ggplot(data=dap) + theme_bw() +
geom_line(aes(x=x, y=y, colour=sample_source)) +
geom_indicator(aes(indicator=counts, colour=sample_source, group=sample_source)) +
ggtitle("O--O atom atom distances involving antiparallel beta-sheet residues\nnormalized for equal weight per unit distance") +
scale_y_log10("FeatureDensity", limits=lims) +
scale_x_continuous(expression(paste('Atom Atom Distances (', ring(A), ')')), limits=c(3,4), breaks=c(3, 3.25, 3.5, 3.75, 4) )
if(nrow(sample_sources) <= 3){
p <- p + theme(legend.position="bottom", legend.direction="horizontal")
}
save_plots(self, plot_id, sample_sources, output_dir, output_formats)
# zooom in on the parallel-minus peak
lims <- c(.1, 5)
plot_id <- "SSDists_Sheet_O_O_parallel_minus_zoom"
p <- ggplot(data=dpM) + theme_bw() +
geom_line(aes(x=x, y=y, colour=sample_source)) +
geom_indicator(aes(indicator=counts, colour=sample_source, group=sample_source)) +
ggtitle("O--O atom atom distances involving parallel beta-sheet residues i to j-1\nnormalized for equal weight per unit distance") +
scale_y_log10("FeatureDensity", limits=lims) +
scale_x_continuous(expression(paste('Atom Atom Distances (', ring(A), ')')), limits=c(4.5,5.5), breaks=c(4.5, 4.75, 5, 5.25, 5.5) )
if(nrow(sample_sources) <= 3){
p <- p + theme(legend.position="bottom", legend.direction="horizontal")
}
save_plots(self, plot_id, sample_sources, output_dir, output_formats)
# zooom in on the parallel-plus peak
lims <- c(.1, 1.5)
plot_id <- "SSDists_Sheet_O_O_parallel_plus_zoom"
p <- ggplot(data=dpP) + theme_bw() +
geom_line(aes(x=x, y=y, colour=sample_source)) +
geom_indicator(aes(indicator=counts, colour=sample_source, group=sample_source)) +
ggtitle("O--O atom atom distances involving parallel beta-sheet residues i to j+1\nnormalized for equal weight per unit distance") +
scale_y_log10("FeatureDensity", limits=lims) +
scale_x_continuous(expression(paste('Atom Atom Distances (', ring(A), ')')), limits=c(7.5,8.5), breaks=c(7.5, 7.75, 8, 8.25, 8.5) )
if(nrow(sample_sources) <= 3){
p <- p + theme(legend.position="bottom", legend.direction="horizontal")
}
save_plots(self, plot_id, sample_sources, output_dir, output_formats)
})) # end FeaturesAnalysis
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