Brought in cantilever-data generation scripts.

author W. Trevor King <wking@drexel.edu>

Mon, 15 Mar 2010 11:18:13 +0000 (07:18 -0400)

committer W. Trevor King <wking@drexel.edu>

Mon, 15 Mar 2010 11:18:13 +0000 (07:18 -0400)
author W. Trevor King <wking@drexel.edu>
Mon, 15 Mar 2010 11:18:13 +0000 (07:18 -0400)
committer W. Trevor King <wking@drexel.edu>
Mon, 15 Mar 2010 11:18:13 +0000 (07:18 -0400)
diff --git a/tex/src/cantilever/simulations.tex b/tex/src/cantilever/simulations.tex

index 7b14616dbce6b9530341e5c4577489ff2994cddc..fd9ff150e377e1eaef2a622e4028732f0bb77140 100644 (file)
--- 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 742e0bff645a513078872f6574717ee80009a4ca..96fdf01863b52b0771d75584c0181497440876fa 100644 (file)
--- 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 6f968f86e0c140b6c27b241c2c117e02f2ac4da8..02e8e7678596eda2ee2a34ac048be71f1f279d05 100644 (file)
--- 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 (file)

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 (executable)

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 (file)

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
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+225.7  211.474252688   35.1535 6.23003148419   /home/wking/rsrch/data/scaled_unfold/20090222/20090222213222_unfold
+298.8  211.474252688   35.1535 7.82243260693   /home/wking/rsrch/data/scaled_unfold/20090222/20090222213222_unfold
+324.5  211.474252688   35.1535 8.23480739967   /home/wking/rsrch/data/scaled_unfold/20090222/20090222213222_unfold
+201.5  945.741609003   35.1535 248.162598202   /home/wking/rsrch/data/scaled_unfold/20090222/20090222214527_unfold
+262.9  945.741609003   35.1535 134.579030961   /home/wking/rsrch/data/scaled_unfold/20090222/20090222214527_unfold
+237.2  945.741609003   35.1535 627.12126093    /home/wking/rsrch/data/scaled_unfold/20090222/20090222220126_unfold
+299.1  945.741609003   35.1535 259.133200867   /home/wking/rsrch/data/scaled_unfold/20090222/20090222220126_unfold
+319.5  447.2135955     132.727 248.650759098   /home/wking/rsrch/data/scaled_unfold/20090222/20090222224649_unfold
+378.4  447.2135955     132.727 110.103987212   /home/wking/rsrch/data/scaled_unfold/20090222/20090222224649_unfold
+258    945.741609003   132.727 82.5726998821   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230350_unfold
+276.8  945.741609003   132.727 55.7041807703   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230350_unfold
+366.8  945.741609003   132.727 69.1620838664   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230350_unfold
+338.7  945.741609003   132.727 46.1427331033   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230350_unfold
+316.9  2000.0  132.727 217.6   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230533_unfold
+386    2000.0  132.727 230.8   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230533_unfold
+284.8  2000.0  132.727 94.88   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230533_unfold
+326.7  945.741609003   132.727 61.9460753897   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230646_unfold
+347.7  945.741609003   132.727 49.263680413    /home/wking/rsrch/data/scaled_unfold/20090222/20090222230646_unfold
+247.4  945.741609003   132.727 30.8973783661   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230646_unfold
+444    945.741609003   132.727 65.1899691086   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230646_unfold
+247.8  447.2135955     132.727 32.897032085    /home/wking/rsrch/data/scaled_unfold/20090222/20090222230924_unfold
+388.7  447.2135955     132.727 45.9735576174   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230924_unfold
+505.5  447.2135955     132.727 59.6135722802   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230924_unfold
+355    447.2135955     132.727 13.6802638863   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230924_unfold
+342.6  447.2135955     132.727 10.9925101774   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230924_unfold
+336.5  447.2135955     132.727 10.0444173549   /home/wking/rsrch/data/scaled_unfold/20090222/20090222230924_unfold
+190.9  211.474252688   132.727 8.47165856268   /home/wking/rsrch/data/scaled_unfold/20090222/20090222231202_unfold
+315.9  211.474252688   132.727 11.2800366384   /home/wking/rsrch/data/scaled_unfold/20090222/20090222231202_unfold
+357.2  211.474252688   132.727 14.0736115164   /home/wking/rsrch/data/scaled_unfold/20090222/20090222231202_unfold
+500.8  211.474252688   132.727 20.5827890141   /home/wking/rsrch/data/scaled_unfold/20090222/20090222231202_unfold
+377.5  447.2135955     132.727 101.741092976   /home/wking/rsrch/data/scaled_unfold/20090222/20090222232706_unfold
+396    447.2135955     132.727 73.9691286957   /home/wking/rsrch/data/scaled_unfold/20090222/20090222232706_unfold
+259.9  211.474252688   132.727 9.31544083091   /home/wking/rsrch/data/scaled_unfold/20090222/20090222232816_unfold
+357.7  211.474252688   132.727 12.390276465    /home/wking/rsrch/data/scaled_unfold/20090222/20090222232816_unfold
+410.8  211.474252688   132.727 14.4225440333   /home/wking/rsrch/data/scaled_unfold/20090222/20090222232816_unfold
+410.4  211.474252688   132.727 11.5782153347   /home/wking/rsrch/data/scaled_unfold/20090222/20090222232816_unfold
+252.7  447.2135955     132.727 35.1062672468   /home/wking/rsrch/data/scaled_unfold/20090222/20090222232834_unfold
+282.3  447.2135955     132.727 25.7326702851   /home/wking/rsrch/data/scaled_unfold/20090222/20090222232834_unfold
+269.3  100.0   132.727 5.993   /home/wking/rsrch/data/scaled_unfold/20090222/20090222232921_unfold
+202.3  945.741609003   132.727 57.1227931838   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+314.4  945.741609003   132.727 70.0794532271   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+303.4  945.741609003   132.727 52.5926908767   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+339    945.741609003   132.727 55.5150324485   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+397.2  945.741609003   132.727 62.2297978724   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+402.9  945.741609003   132.727 57.7280678135   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+397.9  945.741609003   132.727 48.2990239718   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+380.4  945.741609003   132.727 36.2502758731   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+396.3  945.741609003   132.727 35.6355438272   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+374.6  945.741609003   132.727 29.8570625962   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+443.3  945.741609003   132.727 36.5718280201   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233019_unfold
+343.5  945.741609003   132.727 146.589949395   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233613_unfold
+400.8  945.741609003   132.727 146.211652752   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233613_unfold
+387.4  2000.0  132.727 294.6   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233757_unfold
+393.2  2000.0  132.727 255.6   /home/wking/rsrch/data/scaled_unfold/20090222/20090222233757_unfold
+304.9  2000.0  132.727 227.6   /home/wking/rsrch/data/scaled_unfold/20090222/20090222235356_unfold
+397.7  2000.0  132.727 224.4   /home/wking/rsrch/data/scaled_unfold/20090222/20090222235356_unfold
+248.1  447.2135955     132.727 45.9735576174   /home/wking/rsrch/data/scaled_unfold/20090222/20090223000513_unfold
+313.3  447.2135955     132.727 39.1669666939   /home/wking/rsrch/data/scaled_unfold/20090222/20090223000513_unfold
+373.6  945.741609003   132.727 76.6239851614   /home/wking/rsrch/data/scaled_unfold/20090222/20090223001009_unfold
+449.6  945.741609003   132.727 117.933978643   /home/wking/rsrch/data/scaled_unfold/20090222/20090223001009_unfold
+346.7  945.741609003   132.727 49.5190306474   /home/wking/rsrch/data/scaled_unfold/20090222/20090223001009_unfold
+332.2  945.741609003   132.727 40.439911201    /home/wking/rsrch/data/scaled_unfold/20090222/20090223001009_unfold
+396.2  945.741609003   132.727 43.8256661612   /home/wking/rsrch/data/scaled_unfold/20090222/20090223001009_unfold
diff --git 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 (executable)

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 (executable)

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 (executable)

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 (executable)

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 (executable)

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 (file)

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 (file)

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 (file)

index a9702d0..0000000

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index 0b1f403..0000000

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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 (file)

index 28a2e30..0000000

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diff --git a/tex/src/figures/cantilever-sim/Makefile b/tex/src/figures/cantilever-sim/Makefile

new file mode 100644 (file)

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, %, $<)
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diff --git a/tex/src/figures/cantilever-data/wtk_graph.asy b/tex/src/figures/cantilever-sim/wtk_graph.asy

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diff --git a/tex/src/root.bib b/tex/src/root.bib

index 47583a27ab4361b42765f817c96abd055cdedb48..f874527fc0842617219bda56ee5b67516a596b59 100644 (file)
--- 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.",
+}
author	W. Trevor King <wking@drexel.edu>
	Mon, 15 Mar 2010 11:18:13 +0000 (07:18 -0400)
committer	W. Trevor King <wking@drexel.edu>
	Mon, 15 Mar 2010 11:18:13 +0000 (07:18 -0400)
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