From: W. Trevor King Date: Mon, 15 Mar 2010 11:18:13 +0000 (-0400) Subject: Brought in cantilever-data generation scripts. X-Git-Tag: v1.0~423 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=d455f7435d8f6e740bf3b783a2884b0b6387bd50;p=thesis.git Brought in cantilever-data generation scripts. --- diff --git a/tex/src/cantilever/simulations.tex b/tex/src/cantilever/simulations.tex index 7b14616..fd9ff15 100644 --- a/tex/src/cantilever/simulations.tex +++ b/tex/src/cantilever/simulations.tex @@ -9,19 +9,19 @@ following results (\cref{fig:cant:sim:v-dep,fig:cant:sim:load-dep,fig:cant:sim:i-dep}). \begin{figure} - \asyfig{figures/cantilever-data/v-dep} + \asyfig{figures/cantilever-sim/v-dep} \caption{Unfolding force velocity dependence for different cantilevers.\label{fig:cant:sim:v-dep}} \end{figure} \begin{figure} - \asyfig{figures/cantilever-data/loading-rate-sim} + \asyfig{figures/cantilever-sim/loading-rate} \caption{Unfolding force loading rate dependence simulations for different cantilevers.\label{fig:cant:sim:load-dep}} \end{figure} \begin{figure} - \asyfig{figures/cantilever-data/i-dep} + \asyfig{figures/cantilever-sim/i-dep} \caption{Unfolding force peak index dependence simulations for different cantilevers.\label{fig:cant:sim:i-dep}} \end{figure} diff --git a/tex/src/figures/Makefile b/tex/src/figures/Makefile index 742e0bf..96fdf01 100644 --- a/tex/src/figures/Makefile +++ b/tex/src/figures/Makefile @@ -1,5 +1,6 @@ -SUBDIRS = biotin-streptavidin cantilever-data contour expt-sawtooth fit-space i27 \ - kappa-sawteeth order-dep schematic sim-hist sim-sawtooth v-dep \ +SUBDIRS = biotin-streptavidin cantilever-data cantilever-sim contour \ + expt-sawtooth fit-space i27 kappa-sawteeth order-dep schematic \ + sim-hist sim-sawtooth v-dep \ # calibration-concept-map all : diff --git a/tex/src/figures/cantilever-data/Makefile b/tex/src/figures/cantilever-data/Makefile index 6f968f8..02e8e76 100644 --- a/tex/src/figures/cantilever-data/Makefile +++ b/tex/src/figures/cantilever-data/Makefile @@ -3,7 +3,7 @@ ASYPROCESS = ../asy/asyprocess \ --pretex='\documentclass{drexel-thesis} \input{packages}' \ -- -FIGS = loading-rate sim-loading-rate v-dep i-dep +FIGS = plot-splits loading-rate all : $(FIGS:%=%_.tex) diff --git a/tex/src/figures/cantilever-data/README b/tex/src/figures/cantilever-data/README new file mode 100644 index 0000000..5c49101 --- /dev/null +++ b/tex/src/figures/cantilever-data/README @@ -0,0 +1,5 @@ +./extract_f_v_k_data.sh > data +./avg_data.py +./make_plots.sh +./get_loading_rates +./makeplotsplits.sh diff --git a/tex/src/figures/cantilever-data/avg_data.py b/tex/src/figures/cantilever-data/avg_data.py new file mode 100755 index 0000000..b1bb276 --- /dev/null +++ b/tex/src/figures/cantilever-data/avg_data.py @@ -0,0 +1,66 @@ +#!/usr/bin/python + +import numpy, sys + +DATAFILE='./data' +KFILE='./spring_constants' +AVGFILE='./averaged_data' + +KCUTS=[45, 90] + +FofV = {} +Ks = [] +for i in range(len(KCUTS)+1): + Ks.append([]) + +for line in file(DATAFILE, 'r'): + if line[0] == '#': + continue # ignore comments + fields = line.strip().split('\t') + force = float(fields[0]) + rate = float(fields[1]) + spring = float(fields[2]) + + ispring = 0 + while ispring < len(KCUTS) and spring > KCUTS[ispring]: + ispring += 1 + Ks[ispring].append(spring) + if rate not in FofV.keys(): + FofV[rate]=[] + for i in range(len(Ks)): + FofV[rate].append([]) + FofV[rate][ispring].append(force) + +avgK = [0]*len(Ks) +stdK = [0]*len(Ks) +numK = [0]*len(Ks) +kf = file(KFILE, 'w') +for i in range(len(Ks)): + K = numpy.array(Ks[i]) + avgK[i] = K.mean() + stdK[i] = K.std() + numK[i] = len(K) + + if i == 1: + continue # poor calibration bumps for the older cantilevers + print >> kf, "K(%d) = %g +/- %g, (# %d)" % (i, avgK[i], stdK[i], numK[i]) +kf.close() + + +Vs = FofV.keys() +Vs.sort() +af = file(AVGFILE, 'w') +print >> af, '#'+'\t'.join(['Pulling speed (nm/s)','Spring constant (pN/nm)', + 'Mean force (pN)','Std. force (pN)','Events (#)']) +for V in Vs: + for i,k in enumerate(avgK): + if i == 1: + continue # poor calibration bumps for the older cantilevers + F = numpy.array(FofV[V][i]) + if len(F) == 0: + continue + outs= [V, k, F.mean(), F.std(), len(F)] + souts = ["%.2f" % (x) for x in outs] + souts[-1] = "%d" % outs[-1] # special treatment for the integer + print >> af, '\t'.join(souts) +af.close() diff --git a/tex/src/figures/cantilever-data/data b/tex/src/figures/cantilever-data/data new file mode 100644 index 0000000..6bc2313 --- /dev/null +++ b/tex/src/figures/cantilever-data/data @@ -0,0 +1,433 @@ +#Unfolding force (pN) Unfolding rate (nm/s) Spring constant (pN/nm) Datafile +231.2 1357.2088083 14.1236 34.7852617567 /home/wking/rsrch/data/scaled_unfold/20090114/20090114122724_unfold +232.8 1357.2088083 14.1236 28.9221197049 /home/wking/rsrch/data/scaled_unfold/20090114/20090114122724_unfold +249.9 1357.2088083 14.1236 31.2565188551 /home/wking/rsrch/data/scaled_unfold/20090114/20090114122724_unfold +271 3237.39401435 14.7206 139.466934138 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a/tex/src/figures/cantilever-data/extract_f_v_k_data.sh b/tex/src/figures/cantilever-data/extract_f_v_k_data.sh new file mode 100755 index 0000000..976d4b7 --- /dev/null +++ b/tex/src/figures/cantilever-data/extract_f_v_k_data.sh @@ -0,0 +1,92 @@ +#!/bin/bash +# +# Extract v,f,k data. Ignore index, temperature, etc. + +set -e # exit immediately on failed command +set -o pipefail # pipes fail if any stage fails + +BASE_DATA_DIR="$HOME/rsrch/data" +SCALED_DATA_DIR="scaled_unfold" +CALIBRATION_DATA_DIR="calibration" + +EXTRACT_UNFOLDS="$HOME/src/lab/analysis/sawmodel/extract_unfolds.py" +SCALE_UNFOLD="$HOME/src/lab/analysis/sawtooth_worming-0.1/scale_unfold.py" + +DATA_DAYS[8]=20090114 +#DATA_DAYS[9]=20090128 # No good sawteeth +DATA_DAYS[10]=20090203 +#DATA_DAYS[11]=20090211 # No good sawteeth +DATA_DAYS[12]=20090212 +DATA_DAYS[13]=20090214 +DATA_DAYS[14]=20090219 +DATA_DAYS[15]=20090222 + +echo -e "#Unfolding force (pN)\tUnfolding rate (nm/s)\tSpring constant (pN/nm)\tLoading rate (pN/s)\tDatafile" + +function NotEmpty () +{ + NAME=$1 + VALUE=$2 + if [ -z "$VALUE" ]; then + echo "Error parsing" + echo "$UNFOLD_LINE" + echo "$NAME not defined. File format must have changed." + exit 1 + fi +} + +FIELD_INDEX="" +function FieldIndex () +{ + LINE="$1" + TITLE_REGEXP="$2" + FIELD_INDEX=`echo "$LINE" | sed 's/\t/\n/g' | grep -n "$TITLE_REGEXP" | cut -d: -f1` +} + +for DAY in ${DATA_DAYS[*]} +do + echo "---Processing day $DAY---" >&2 + DATAFILE_FIELD="" + FORCE_FIELD="" + LAST_DATAFILE="" # Caching for efficiency + while read UNFOLD_LINE + do + echo "Parsing '$UNFOLD_LINE'" >&2 + if [ "${UNFOLD_LINE:0:1}" == "#" ] ; then + # reading the header line + FieldIndex "$UNFOLD_LINE" "Datafile" + DATAFILE_FIELD="$FIELD_INDEX" + FieldIndex "$UNFOLD_LINE" "Force (pN)" + FORCE_FIELD="$FIELD_INDEX" + FieldIndex "$UNFOLD_LINE" "Stiffness (pN/nm)" + STIFFNESS_FIELD="$FIELD_INDEX" + NotEmpty 'Datafile field' "$DATAFILE_FIELD" + NotEmpty 'Force field' "$FORCE_FIELD" + NotEmpty 'Stiffness field' "$STIFFNESS_FIELD" + continue + fi + NotEmpty "$DAY extraction header" "$DATAFILE_FIELD" + DATAFILE=`echo "$UNFOLD_LINE" | cut -f $DATAFILE_FIELD` + NotEmpty 'Datafile' "$DATAFILE" + DATAFILE="$BASE_DATA_DIR/$SCALED_DATA_DIR/$DATAFILE" + UNFOLDING_FORCE=`echo "$UNFOLD_LINE" | cut -f $FORCE_FIELD` + NotEmpty 'Unfolding force' "$UNFOLDING_FORCE" + STIFFNESS=`echo "$UNFOLD_LINE" | cut -f $STIFFNESS_FIELD` + NotEmpty 'Stiffness' "$STIFFNESS" + if [ "$DATAFILE" != "$LAST_DATAFILE" ]; then + UNFOLDING_RATE=`sed -n 's/^Unfold rate (nm\/s):\t//p' "${DATAFILE}_param"` + NotEmpty 'Unfolding rate' "$UNFOLDING_RATE" + SPRING_CONSTANT_STRING=`$SCALE_UNFOLD --print-k "$DATAFILE"` + NotEmpty 'Spring constant string' "$SPRING_CONSTANT_STRING" + SPRING_CONSTANT_N_PER_M=`echo "$SPRING_CONSTANT_STRING" | sed -n 's/ N\/m$//p'` + NotEmpty 'Spring constant (N/m)' "$SPRING_CONSTANT_N_PER_M" + SPRING_CONSTANT=`echo "print ($SPRING_CONSTANT_N_PER_M * 1e3)" | python` + NotEmpty 'Spring constant (pN/nm)' "$SPRING_CONSTANT" + fi + LOADING_RATE=`python -c "print $STIFFNESS * $UNFOLDING_RATE"` # pN/s + echo -e "$UNFOLDING_FORCE\t$UNFOLDING_RATE\t$SPRING_CONSTANT\t$LOADING_RATE\t$DATAFILE" + LAST_DATAFILE="$DATAFILE" + done < <(cd $BASE_DATA_DIR/$SCALED_DATA_DIR/ && $EXTRACT_UNFOLDS ${DAY}_select_fit.xml) +done + +exit 0 diff --git a/tex/src/figures/cantilever-data/fit_data.py b/tex/src/figures/cantilever-data/fit_data.py new file mode 100755 index 0000000..f87a6e0 --- /dev/null +++ b/tex/src/figures/cantilever-data/fit_data.py @@ -0,0 +1,45 @@ +#!/usr/bin/python + +import sys +from scipy.stats import linregress +from math import log10 + +fname = sys.argv[1] + +WEIGHTHACK=True +LOGX=True + +x = [] +y = [] +w = [] # weights + +print >> sys.stderr, "Fitting data from", fname +for line in file(fname, 'r'): + fields = [float(a) for a in line.strip().split()] + if WEIGHTHACK==True: + w = int(fields[3]) + x.extend([fields[0]]*w) + y.extend([fields[1]]*w) + else: + x.append(fields[0]) + y.append(fields[1]) + w.append(fields[3]) + +if LOGX == True: + slope,intercept,r,two_tailed_prob,stderr_of_the_estimate = linregress([log10(xi) for xi in x],y) +else: + slope,intercept,r,two_tailed_prob,stderr_of_the_estimate = linregress(x,y) +#print slope,intercept,r,two_tailed_prob,stderr_of_the_estimate + +def f(x): + if LOGX == True: + x = log10(x) + val = intercept+slope*x + return val + +x.sort() +xmin = x[0] +xmax = x[-1] +print '#fitted line' +print '%g\t%g' % (xmin, f(xmin)) +print '%g\t%g' % (xmax, f(xmax)) diff --git a/tex/src/figures/cantilever-data/get_loading_rates.py b/tex/src/figures/cantilever-data/get_loading_rates.py new file mode 100755 index 0000000..8010910 --- /dev/null +++ b/tex/src/figures/cantilever-data/get_loading_rates.py @@ -0,0 +1,40 @@ +#!/usr/bin/python + +DATA="./data" +UNFOLD_FORCE_COL=0 +UNFOLD_RATE_COL=1 +SPRING_CONST_COL=2 +LOAD_RATE_COL=3 + +from avg_data import KCUTS + +Ks = [24.33, None, 131.98] # HACK! +OFILEs = [None, None, None] + +for i,K in enumerate(Ks): + if K == None: + continue + OFILEs[i] = file('loading_rate_%.2f' % K, 'w') + +for line in file(DATA, 'r'): + if line[0] == '#': + continue + fields = line.strip().split() + F = float(fields[UNFOLD_FORCE_COL]) + V = float(fields[UNFOLD_RATE_COL]) + K = float(fields[SPRING_CONST_COL]) + L = float(fields[LOAD_RATE_COL]) + + ispring = 0 + while ispring < len(KCUTS) and K > KCUTS[ispring]: + ispring += 1 + if ispring == 1: + continue # drop middle spring constants + + print >> OFILEs[ispring], "%g\t%g" % (L, F) + +for i,K in enumerate(Ks): + if K == None: + continue + OFILEs[i].close() + OFILEs[i] = None diff --git a/tex/src/figures/cantilever-data/make_plots.sh b/tex/src/figures/cantilever-data/make_plots.sh new file mode 100755 index 0000000..43baa96 --- /dev/null +++ b/tex/src/figures/cantilever-data/make_plots.sh @@ -0,0 +1,41 @@ +#!/bin/bash + +KFILE='./spring_constants' +AVGFILE='./averaged_data' +GPSPLIT='./plot_splits.gp' + +PLOTS="" +while read LINE +do + Kprecise=`echo "$LINE" | sed 's/.*= \([0-9.]*\) +.*/\1/'` + K=`python -c "print '%.2f' % $Kprecise"` + FILE="v_dep_$K" + echo "clearing $FILE" + > "$FILE" + rm "$FILE.fit" + PLOTS="$PLOTS, '$FILE' using 1:2:(sqrt(\$4)) with points pt 6 pointsize variable t '$K (pN/nm)'" + PLOTS="$PLOTS, '$FILE.fit' using 1:2 with lines notitle" +done < <(tac "$KFILE") +PLOTS="${PLOTS:2}" # remove leading ' ,' + +while read DATA +do + V=`echo "$DATA" | awk '{print $1}'` + K=`echo "$DATA" | awk '{print $2}'` + F=`echo "$DATA" | awk '{print $3}'` + Fstd=`echo "$DATA" | awk '{print $4}'` + N=`echo "$DATA" | awk '{print $5}'` + FILE="v_dep_$K" + echo "adding $V, $F, $Fstd, $N to $FILE" + echo -e "$V\t$F\t$Fstd\t$N" >> "$FILE" +done < <(cat "$AVGFILE" | grep -v '^#') + +for FILE in v_dep_* +do + ./fit_data.py "$FILE" > "$FILE.fit" +done + +echo "set xlabel 'Pulling speed (nm/s)' +set ylabel 'Unfolding force (pN)' +set logscale x; +plot $PLOTS" > "$GPSPLIT" diff --git a/tex/src/figures/cantilever-data/makeplotsplits.sh b/tex/src/figures/cantilever-data/makeplotsplits.sh new file mode 100755 index 0000000..38d148e --- /dev/null +++ b/tex/src/figures/cantilever-data/makeplotsplits.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +gnuplot plot_splits.gp +epstopdf plot_splits.eps +pdftk plot_splits.pdf cat 1E output plot_splits_rotated.pdf +cp plot_splits_rotated.pdf ../../posters/2009_biophysical_society_poster/plot_splits.pdf diff --git a/tex/src/figures/cantilever-data/plot_avg.gp b/tex/src/figures/cantilever-data/plot_avg.gp new file mode 100644 index 0000000..f9ce6a6 --- /dev/null +++ b/tex/src/figures/cantilever-data/plot_avg.gp @@ -0,0 +1,10 @@ + +# see: show palette rgbformulae +set palette rgbformulae 3,13,-3 +set xlabel 'Pulling speed (nm/s)' +set ylabel 'Unfolding force (pN)' +set zlabel 'Spring constant (pN/nm)' +set view map +set logscale x +set style line 1 lt 1 lw 1 pt 2 ps 3 +splot 'averaged_data' using 1:3:2:(sqrt($5)) with points pt 6 pointsize variable lt palette z diff --git a/tex/src/figures/cantilever-data/plot_raw.gp b/tex/src/figures/cantilever-data/plot_raw.gp new file mode 100644 index 0000000..d8772ac --- /dev/null +++ b/tex/src/figures/cantilever-data/plot_raw.gp @@ -0,0 +1,8 @@ +# see: show palette rgbformulae +set palette rgbformulae 3,13,-3 +set xlabel 'Pulling speed (nm/s)' +set ylabel 'Unfolding force (pN)' +set zlabel 'Spring constant (pN/nm)' +set view map +set logscale x +splot 'data' using 2:1:3 with points palette z diff --git a/tex/src/figures/cantilever-data/plot_splits.pdf b/tex/src/figures/cantilever-data/plot_splits.pdf deleted file mode 100644 index a9702d0..0000000 Binary files a/tex/src/figures/cantilever-data/plot_splits.pdf and /dev/null differ diff --git a/tex/src/figures/cantilever-data/plot_splits_nolandscape.pdf b/tex/src/figures/cantilever-data/plot_splits_nolandscape.pdf deleted file mode 100644 index 0b1f403..0000000 Binary files a/tex/src/figures/cantilever-data/plot_splits_nolandscape.pdf and /dev/null differ diff --git a/tex/src/figures/cantilever-data/plot_splits_rotated.pdf b/tex/src/figures/cantilever-data/plot_splits_rotated.pdf deleted file mode 100644 index 28a2e30..0000000 Binary files a/tex/src/figures/cantilever-data/plot_splits_rotated.pdf and /dev/null differ diff --git a/tex/src/figures/cantilever-sim/Makefile b/tex/src/figures/cantilever-sim/Makefile new file mode 100644 index 0000000..7a28e49 --- /dev/null +++ b/tex/src/figures/cantilever-sim/Makefile @@ -0,0 +1,14 @@ +ASYPROCESS = ../asy/asyprocess \ + --texinputs=../.. \ + --pretex='\documentclass{drexel-thesis} \input{packages}' \ + -- + +FIGS = loading-rate v-dep i-dep + +all : $(FIGS:%=%_.tex) + +clean : + rm -f $(FIGS:%=%_*) $(FIGS:%=%-*) + +%_.tex : %.asy + $(ASYPROCESS) $(patsubst %.asy, %, $<) diff --git a/tex/src/figures/cantilever-data/i-dep.asy b/tex/src/figures/cantilever-sim/i-dep.asy similarity index 100% rename from tex/src/figures/cantilever-data/i-dep.asy rename to tex/src/figures/cantilever-sim/i-dep.asy diff --git 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--git a/tex/src/figures/cantilever-data/wtk_graph.asy b/tex/src/figures/cantilever-sim/wtk_graph.asy similarity index 100% rename from tex/src/figures/cantilever-data/wtk_graph.asy rename to tex/src/figures/cantilever-sim/wtk_graph.asy diff --git a/tex/src/root.bib b/tex/src/root.bib index 47583a2..f874527 100644 --- a/tex/src/root.bib +++ b/tex/src/root.bib @@ -42,6 +42,7 @@ % Listed in alphebetical order. @String{AIP = "AIP"} @String{APS = "American Physical Society"} +@String{SPRINGER = "Springer Science + Business Media, LLC"} % Define some journal name shortcuts (useful for consistency) % Listed in alphebetical order. @@ -228,6 +229,7 @@ @String{SNg = "Ng, Sean P."} @String{SNie = "Nie, S."} @String{RNome = "Nome, Rene A."} +@String{ANoy = "Noy, Aleksandr"} @String{AOberhauser = "Oberhauser, Andres F."} @String{FOesterhelt = "Oesterhelt, Filipp"} @String{TOhashi = "Ohashi, Tomoo"} @@ -2442,7 +2444,7 @@ doi = "10.1110/ps.0224602", URL = "http://www.proteinscience.org/cgi/content/abstract/11/12/2759", eprint = "http://www.proteinscience.org/cgi/reprint/11/12/2759.pdf", - note = "Introduces unfolding-order effects on average unfolding force.", + note = "Introduces unfolding-order \emph{scaffold effect} on average unfolding force.", project = "sawtooth simulation", } @@ -6002,6 +6004,7 @@ doi = {10.1063/1.439715} doi = "10.1038/nsb968", url = "http://www.nature.com/nsmb/journal/v10/n9/abs/nsb968.html", eprint = "http://www.nature.com/nsmb/journal/v10/n9/pdf/nsb968.pdf", + note = "Another scaffold effect paper. TODO: details", } @article{friddle08, @@ -7755,7 +7758,7 @@ doi = "DOI: 10.1016/j.ijbiomac.2009.12.001", url = "http://www.sciencedirect.com/science/article/B6T7J-4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e", } -@Article {metropolis87, +@Article{metropolis87, author = "Nicholas Metropolis", title = "The Beginning of the Monte Carlo Method", journal = "Los Alamos Science", @@ -7765,3 +7768,12 @@ url = "http://www.sciencedirect.com/science/article/B6T7J-4XWMND2-1/2/7ef768562b publisher = "Los Alamos National Laboratory", url = "http://library.lanl.gov/cgi-bin/getfile?15-12.pdf", } + +@Book{noy08, + editor = ANoy, + title = "Handbook of Molecular Force Spectroscopy", + publisher = SPRINGER, + year = 2008, + ISBN="978-0-387-49987-1", + note="The first book about force spectroscopy. Discusses the scaffold effect in section 8.4.1.", +}