# -*- 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_HA",
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("ResidueFeatures", "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';
CREATE UNIQUE INDEX IF NOT EXISTS
residue_type_atom_residue_type_set_name_residue_type_name_atom_name ON
residue_type_atom ( residue_type_set_name, residue_type_name, atom_name );
CREATE TEMPORARY TABLE O_HA_atom_coords AS
SELECT
res.struct_id AS struct_id, res.resNum AS resNum,
O.x AS Ox, O.y AS Oy, O.z AS Oz,
HA.x AS HAx, HA.y AS HAy, HA.z AS HAz
FROM
residues AS res,
residue_type_atom AS O_type, residue_type_atom AS HA_type,
residue_atom_coords AS O, residue_atom_coords AS HA
WHERE
O_type.residue_type_set_name = 'fa_standard' AND
O_type.residue_type_name = res.res_type AND O_type.atom_name = ' O ' AND
HA_type.residue_type_set_name = 'fa_standard' AND
HA_type.residue_type_name = res.res_type AND HA_type.atom_name = ' HA ' AND
O.struct_id = res.struct_id AND O.seqpos = res.resNum AND
O.atomno = O_type.atom_index AND
HA.struct_id = res.struct_id AND HA.seqpos = res.resNum AND
HA.atomno = HA_type.atom_index;
CREATE UNIQUE INDEX O_HA_atom_coords_struct_id_resNum ON
O_HA_atom_coords (struct_id, resNum);
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_HA_O AS
SELECT (O.Ox-HA.HAx)*(O.Ox-HA.HAx) +
(O.Oy-HA.HAy)*(O.Oy-HA.HAy) +
(O.Oz-HA.HAz)*(O.Oz-HA.HAz) AS dist_sq,
'antiparallel' AS strand_orientation
FROM O_HA_atom_coords AS O, O_HA_atom_coords AS HA,
antiparallel_close_contact_residue_pairs AS atpairs
WHERE HA.struct_id = atpairs.struct_id AND HA.resNum = atpairs.resNum_i - 1 AND
O.struct_id = atpairs.struct_id AND O.resNum = atpairs.resNum_j;
CREATE TEMPORARY TABLE antiparallel_O_HA AS
SELECT (O.Ox-HA.HAx)*(O.Ox-HA.HAx) +
(O.Oy-HA.HAy)*(O.Oy-HA.HAy) +
(O.Oz-HA.HAz)*(O.Oz-HA.HAz) AS dist_sq,
'antiparallel' AS strand_orientation
FROM O_HA_atom_coords AS O, O_HA_atom_coords AS HA,
antiparallel_close_contact_residue_pairs AS atpairs
WHERE O.struct_id = atpairs.struct_id AND O.resNum = atpairs.resNum_i AND
HA.struct_id = atpairs.struct_id AND HA.resNum = atpairs.resNum_j - 1;
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_HA AS
SELECT
(O.Ox-HA.HAx)*(O.Ox-HA.HAx) +
(O.Oy-HA.HAy)*(O.Oy-HA.HAy) +
(O.Oz-HA.HAz)*(O.Oz-HA.HAz) AS dist_sq,
'parallel' AS strand_orientation
FROM
O_HA_atom_coords AS O, O_HA_atom_coords AS HA,
parallel_close_contact_residue_pairs AS apairs
WHERE
O.struct_id = apairs.struct_id AND O.resNum = apairs.resNum_i AND
HA.struct_id = apairs.struct_id AND HA.resNum = apairs.resNum_j;
SELECT * FROM antiparallel_HA_O UNION
SELECT * FROM antiparallel_O_HA UNION
SELECT * FROM parallel_O_HA;"
f <- query_sample_sources(sample_sources, sele)
sele <- "
DROP TABLE ee_bb_bb_hbonds;
DROP TABLE O_HA_atom_coords;
DROP TABLE antiparallel_close_contact_residue_pairs;
DROP TABLE antiparallel_HA_O;
DROP TABLE antiparallel_O_HA;
DROP TABLE parallel_close_contact_residue_pairs;
DROP TABLE parallel_O_HA;"
query_sample_sources(sample_sources, sele, warn_zero_rows=F)
f$dist <- sqrt(f$dist_sq)
dens <- estimate_density_1d(
f, c("sample_source", "strand_orientation"),
"dist", weight_fun = radial_3d_normalization, n_pts=1000)
dp <- dens[dens$strand_orientation == "parallel",]
dap <- dens[dens$strand_orientation == "antiparallel",]
plot_id <- "SSDists_Sheet_O_HA_parallel_anti_parallel"
p <- ggplot() + theme_bw() +
geom_line(data=dp, aes(x=x, y=y, colour=sample_source)) +
geom_indicator(data=dp, aes(indicator=counts, colour=sample_source, group=sample_source)) +
geom_line(data=dap, aes(x=x, y=y, colour=sample_source)) +
geom_indicator(data=dap, aes(indicator=counts, colour=sample_source, group=sample_source, xpos="left")) +
ggtitle("O--HA atom atom distances involving beta-sheet residues\nnormalized for equal weight per unit distance\n(antiparallel-counts left, parallel-counts right)") +
scale_y_continuous("Feature Density") +
scale_x_continuous(expression(paste('O--HA Distances (', ring(A), ')')),
limit=c(1.9, 6), breaks=c(2, 3, 4, 5, 6))
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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