Whitespace cleanups in the rest of the figures/*/*.asy files.

Used sed to replace tabs with spaces and strip trailing spaces.

diff --git a/src/figures/asy/wtk_graph.asy b/src/figures/asy/wtk_graph.asy
index e35a62e56a41a71d3e77e426ae106c59e07f631b..64f420168ffe89b0b0b716a07943554946dcc15a 100644 (file)
--- a/src/figures/asy/wtk_graph.asy
+++ b/src/figures/asy/wtk_graph.asy
@@ -17,8 +17,8 @@ Label sLabel(string s, align align=NoAlign, int extra_spaces=0) {
 void graphData(picture pic=currentpicture, real[] x, real[] y,
                real xscale=1, real yscale=1, real dx=0, real dy=0, pen p=red,
                path mpath=scale(0.8mm)*unitcircle,
-              markroutine markroutine=marknodes,
-              string t="Title",
+               markroutine markroutine=marknodes,
+               string t="Title",
                bool dots=false) {
   pen pline=p;
   marker mk = nomarker;
@@ -28,18 +28,18 @@ void graphData(picture pic=currentpicture, real[] x, real[] y,
   }
   if (t != "Title") {
     draw(pic=pic, graph(pic,xscale*(x+dx),yscale*(y+dy)), p=pline,
-        legend=sLabel(t,extra_spaces=1), marker=mk);
+         legend=sLabel(t,extra_spaces=1), marker=mk);
   } else {
     draw(pic=pic, graph(pic,xscale*(x+dx),yscale*(y+dy)), p=pline, marker=mk);
   }
 }
 
 void graphFile(picture pic=currentpicture, string file="datafile",
-              int xcol=0, int ycol=1,
+               int xcol=0, int ycol=1,
                real xscale=1, real yscale=1, real dx=0, real dy=0, pen p=red,
                path mpath=scale(0.8mm)*unitcircle,
-              markroutine markroutine=marknodes,
-              string t="Title",
+               markroutine markroutine=marknodes,
+               string t="Title",
                bool dots=false) {
   file fin = input(file).line();
   real[][] a = fin.dimension(0,0);
@@ -51,14 +51,14 @@ void graphFile(picture pic=currentpicture, string file="datafile",
   else
     x = sequence(y.length);
   graphData(pic=pic, x=x, y=y, xscale=xscale, yscale=yscale, dx=dx, dy=dy, p=p,
-           mpath=mpath, markroutine=markroutine, t=t, dots=dots);
+            mpath=mpath, markroutine=markroutine, t=t, dots=dots);
 }
 
 void fitFile(picture pic=currentpicture, string file="fitparamfile",
-            int pcol=0, real f(real x, real[] params),
-            real xmin=realMin, real xmax=realMax,
-            real xscale=1, real yscale=1, pen p=red,
-            string t="Title") {
+             int pcol=0, real f(real x, real[] params),
+             real xmin=realMin, real xmax=realMax,
+             real xscale=1, real yscale=1, pen p=red,
+             string t="Title") {
   file fin=input(file).line();
   real[][] a=fin.dimension(0,0);
   a=transpose(a);
@@ -74,17 +74,17 @@ void fitFile(picture pic=currentpicture, string file="fitparamfile",
   */
   if (t != "Title") {
     draw(pic=pic, graph(pic, fn, a=xmin*xscale, b=xmax*xscale), p=p,
-        legend=sLabel(t,extra_spaces=1));
+         legend=sLabel(t,extra_spaces=1));
   } else {
     draw(pic=pic, graph(pic, fn, a=xmin*xscale, b=xmax*xscale), p=p);
   }
 }
 
 void histFile(picture pic=currentpicture, string file="datafile",
-             int bin_col=0, int count_col=1,
+              int bin_col=0, int count_col=1,
               real bin_scale=1, real count_scale=1, real low=-infinity,
-             pen fillpen=red, pen drawpen=nullpen, bool bars=false,
-             string t="Title") {
+              pen fillpen=red, pen drawpen=nullpen, bool bars=false,
+              string t="Title") {
   file fin = input(file).line();
   real[][] a = fin.dimension(0,0);
   a = transpose(a);
@@ -99,11 +99,11 @@ void histFile(picture pic=currentpicture, string file="datafile",
   count = count / total;
   if (t != "Title") {
     histogram(pic=pic, bins=bins, count=count, low=low,
-             fillpen=fillpen, drawpen=drawpen, bars=bars,
-             legend=sLabel(t,extra_spaces=1));
+              fillpen=fillpen, drawpen=drawpen, bars=bars,
+              legend=sLabel(t,extra_spaces=1));
   } else {
     histogram(pic=pic, bins=bins, count=count, low=low,
-             fillpen=fillpen, drawpen=drawpen, bars=bars);
+              fillpen=fillpen, drawpen=drawpen, bars=bars);
   }
 }
 
@@ -135,10 +135,10 @@ real[][] extract_matrix(real[] xs, real[] ys, real[] zs) {
   for (i=0; i<x_set.length; ++i) {
     for (j=0; j<y_set.length; ++j) {
       for (k=0; k<x_set.length*y_set.length; ++k) {
-       if (xs[k] == x_set[i] && ys[k] == y_set[j]) {
-         z_matrix[i][j] = zs[k];
-         break;
-       }
+        if (xs[k] == x_set[i] && ys[k] == y_set[j]) {
+          z_matrix[i][j] = zs[k];
+          break;
+        }
       }
     }
   }
@@ -146,12 +146,12 @@ real[][] extract_matrix(real[] xs, real[] ys, real[] zs) {
 }
 
 void graphMatrixFile(picture pic=currentpicture, string file="datafile",
-                    int xcol=0, int ycol=1, int zcol=2,
+                     int xcol=0, int ycol=1, int zcol=2,
                      real xscale=1, real yscale=1,
-                    real[] zfn(real[] z)=identity_zfn,
-                    pen[] p=BWRainbow(), Label x_label=null,
-                    Label y_label=null, Label palette_label=null,
-                    real palette_offset=6pt, real palette_width=12pt) {
+                     real[] zfn(real[] z)=identity_zfn,
+                     pen[] p=BWRainbow(), Label x_label=null,
+                     Label y_label=null, Label palette_label=null,
+                     real palette_offset=6pt, real palette_width=12pt) {
   file fin = input(file).line();
   real[][] a = fin.dimension(0,0);
   /* drop blank lines used to separate Gnuplot blocks. */
@@ -178,13 +178,13 @@ void graphMatrixFile(picture pic=currentpicture, string file="datafile",
   pair p_initial_graph = pic_to_graph * (p_SE_pic + palette_offset*E);
   pair p_NE_pic = graph_to_pic * (xscale*max(xs), yscale*max(ys));
   pair p_final_graph = pic_to_graph * (p_NE_pic
-                                      + (palette_offset+palette_width)*E);
+                                       + (palette_offset+palette_width)*E);
   if (palette_label == null)
     palette(pic, bounds=range, initial=p_initial_graph, final=p_final_graph,
-           axis=Right, palette=p);
+            axis=Right, palette=p);
   else
     palette(pic, L=palette_label, bounds=range, initial=p_initial_graph,
-           final=p_final_graph, axis=Right, palette=p);
+            final=p_final_graph, axis=Right, palette=p);
 }
 
 string math(string contents) {

diff --git a/src/figures/cantilever-data/loading-rate.asy b/src/figures/cantilever-data/loading-rate.asy
index e655b935076f5b47bdeabddcb8f31c666c8f1eb5..75ae3585050b9554b40c5b43bb611a76b29ab476 100644 (file)
--- a/src/figures/cantilever-data/loading-rate.asy
+++ b/src/figures/cantilever-data/loading-rate.asy
@@ -7,9 +7,9 @@ real xscale=1;
 real yscale=1;
 
 graphFile("loading-rate.d/loading_rate_131.98.dat", xscale, yscale, phard, m8,
-         t=math(units("131.98","pN/nm")), dots=true);
+          t=math(units("131.98","pN/nm")), dots=true);
 graphFile("loading-rate.d/loading_rate_24.33.dat", xscale, yscale, red, m8,
-         t=math(units("24.33","pN/nm")), dots=true);
+          t=math(units("24.33","pN/nm")), dots=true);
 
 xlimits(1,3e3);
 ylimits(90,620);

diff --git a/src/figures/cantilever-sim/i-dep.asy b/src/figures/cantilever-sim/i-dep.asy
index 167743b9786f42dd0ef40259dfd574ad9bb7e5cc..2fa7d8056c6dddd21561e780392e3465fc3ba60d 100644 (file)
--- a/src/figures/cantilever-sim/i-dep.asy
+++ b/src/figures/cantilever-sim/i-dep.asy
@@ -6,17 +6,17 @@ real xscale=1;
 real yscale=1e12;
 
 graphFile("i-dep.d/i_dep_127_8_1e-6", xscale, yscale, phard, m8,
-         t=math(units("127","pN/nm"))+", 8 domains");
+          t=math(units("127","pN/nm"))+", 8 domains");
 graphFile("i-dep.d/i_dep_27_8_1e-6", xscale, yscale, pmed, m8,
-         t=math(units("27","pN/nm"))+", 8 domains");
+          t=math(units("27","pN/nm"))+", 8 domains");
 graphFile("i-dep.d/i_dep_127_30_1e-6", xscale, yscale, phard, m30,
-         t=math(units("127","pN/nm"))+", 30 domains");
+          t=math(units("127","pN/nm"))+", 30 domains");
 graphFile("i-dep.d/i_dep_27_30_1e-6", xscale, yscale, pmed, m30,
-         t=math(units("27","pN/nm"))+", 30 domains");
+          t=math(units("27","pN/nm"))+", 30 domains");
 graphFile("i-dep.d/i_dep_0.1_1_1e-6", xscale, yscale, psoft, m1,
-         t=math(units("0.1","pN/nm"))+", 1 domain");
+          t=math(units("0.1","pN/nm"))+", 1 domain");
 graphFile("i-dep.d/i_dep_0.1_30_1e-6", xscale, yscale, psoft, m30,
-         t=math(units("0.1","pN/nm"))+", 30 domains");
+          t=math(units("0.1","pN/nm"))+", 30 domains");
 
 ylimits(140, 320);
 

diff --git a/src/figures/cantilever-sim/loading-rate.asy b/src/figures/cantilever-sim/loading-rate.asy
index c59bbdd6caca471886da824f842e4893e026b3be..14cc1db341e75180ae195f8cc5fe57ff6749c554 100644 (file)
--- a/src/figures/cantilever-sim/loading-rate.asy
+++ b/src/figures/cantilever-sim/loading-rate.asy
@@ -7,11 +7,11 @@ real xscale=1e12;
 real yscale=1e12;
 
 graphFile(file="loading-rate.d/loading_rate_dep_127_8",
-         xscale=xscale, yscale=yscale, p=phard, mpath=mdot,
-         t=math(units("127","pN/nm")), dots=true);
+          xscale=xscale, yscale=yscale, p=phard, mpath=mdot,
+          t=math(units("127","pN/nm")), dots=true);
 graphFile(file="loading-rate.d/loading_rate_dep_27_8",
-         xscale=xscale, yscale=yscale, p=red, mpath=mdot,
-         t=math(units("27","pN/nm")), dots=true);
+          xscale=xscale, yscale=yscale, p=red, mpath=mdot,
+          t=math(units("27","pN/nm")), dots=true);
 
 xlimits(20,7e5);
 ylimits(40,400);

diff --git a/src/figures/cantilever-sim/v-dep.asy b/src/figures/cantilever-sim/v-dep.asy
index 8f1efe5cbeb5bd14c9dd3f2969dd755697e3b46e..f36be76e058f9653479e07200887f9cbfc005eac 100644 (file)
--- a/src/figures/cantilever-sim/v-dep.asy
+++ b/src/figures/cantilever-sim/v-dep.asy
@@ -15,29 +15,29 @@ real fn_logxliny(real x, real[] params) {
 }
 
 graphFile("v-dep.d/v_dep_127_8", vscale, fscale, p=phard, mpath=m8,
-         t=math(units("127","pN/nm"))+", 8 domains", dots=true);
+          t=math(units("127","pN/nm"))+", 8 domains", dots=true);
 graphFile("v-dep.d/v_dep_27_8", vscale, fscale, p=pmed, mpath=m8,
-         t=math(units("27","pN/nm"))+", 8 domains", dots=true);
+          t=math(units("27","pN/nm"))+", 8 domains", dots=true);
 graphFile("v-dep.d/v_dep_127_30", vscale, fscale, p=phard, mpath=m30,
-         t=math(units("127","pN/nm"))+", 30 domains", dots=true);
+          t=math(units("127","pN/nm"))+", 30 domains", dots=true);
 graphFile("v-dep.d/v_dep_27_30", vscale, fscale, p=pmed, mpath=m30,
-         t=math(units("27","pN/nm"))+", 30 domains", dots=true);
+          t=math(units("27","pN/nm"))+", 30 domains", dots=true);
 graphFile("v-dep.d/v_dep_0.1_1", vscale, fscale, p=psoft, mpath=m1,
-         t=math(units("0.1","pN/nm"))+", 1 domain", dots=true);
+          t=math(units("0.1","pN/nm"))+", 1 domain", dots=true);
 graphFile("v-dep.d/v_dep_0.1_30", vscale, fscale, p=psoft, mpath=m30,
-         t=math(units("0.1","pN/nm"))+", 30 domains", dots=true);
+          t=math(units("0.1","pN/nm"))+", 30 domains", dots=true);
 fitFile("v-dep.d/v_dep_127_8.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=phard);
+        xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=phard);
 fitFile("v-dep.d/v_dep_27_8.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=pmed);
+        xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=pmed);
 fitFile("v-dep.d/v_dep_127_30.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=phard);
+        xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=phard);
 fitFile("v-dep.d/v_dep_27_30.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=pmed);
+        xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=pmed);
 fitFile("v-dep.d/v_dep_0.1_1.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=psoft);
+        xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=psoft);
 fitFile("v-dep.d/v_dep_0.1_30.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=psoft);
+        xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=psoft);
 
 ylimits(150, 340, crop=true);
 

diff --git a/src/figures/fit-space/fit-valley.asy b/src/figures/fit-space/fit-valley.asy
index 854f79ca5db25c88727e300e0ec105d3603446d9..cc0e0e78558d424590172662b6e90b506ea640bb 100644 (file)
--- a/src/figures/fit-space/fit-valley.asy
+++ b/src/figures/fit-space/fit-valley.asy
@@ -7,7 +7,7 @@ real xscale=1;
 real yscale=1e9;
 
 graphMatrixFile("data", xscale=xscale, yscale=yscale,
-               x_label="$k_{uo}$ (s$^{-1}$)", y_label="$x_u$ (nm)",
-               palette_label="$D_\text{JS}$");
+                x_label="$k_{uo}$ (s$^{-1}$)", y_label="$x_u$ (nm)",
+                palette_label="$D_\text{JS}$");
 
 label(sLabel("Fit quality"), point(N),N);

diff --git a/src/figures/fit-space/king_vs_best.asy b/src/figures/fit-space/king_vs_best.asy
index bc5e64658d7e0dcb246ce49d5be6b49810bf4dca..2511541c463ece4969e6d250ea51a841741baa27 100644 (file)
--- a/src/figures/fit-space/king_vs_best.asy
+++ b/src/figures/fit-space/king_vs_best.asy
@@ -15,14 +15,14 @@ real xmin = 1.01457e-05;
 real xmax = 0.10364;
 
 graphFile("Best_2002_detailed_unfolding_pathway/fig3a.dat", xcol=1, ycol=0,
-         xscale=xscale, yscale=yscale, p=psoft, mpath=m30,
-         t="Best valley", dots=true);
+          xscale=xscale, yscale=yscale, p=psoft, mpath=m30,
+          t="Best valley", dots=true);
 graphFile("fit-valley.dat", xscale=xscale, yscale=yscale, p=phard, mpath=m30,
-         t="King valley", dots=true);
+          t="King valley", dots=true);
 fitFile("Best_2002_detailed_unfolding_pathway/fig3a.dat.fit.dat",f=fn_logxliny,
-       xmin=xmin, xmax=xmax, xscale=xscale, yscale=yscale, p=psoft);
+        xmin=xmin, xmax=xmax, xscale=xscale, yscale=yscale, p=psoft);
 fitFile("fit-valley.dat.fit.dat", f=fn_logxliny,
-       xmin=xmin, xmax=xmax, xscale=xscale, yscale=yscale, p=phard);
+        xmin=xmin, xmax=xmax, xscale=xscale, yscale=yscale, p=phard);
 
 label(sLabel(""), point(N), N);
 xaxis(sLabel("$k_{u0}$ ($1/$s)"), BottomTop, LeftTicks);

diff --git a/src/figures/kappa-sawteeth/kappa-sawteeth.asy b/src/figures/kappa-sawteeth/kappa-sawteeth.asy
index e994a17c360d9a689482c35bf464036cbc8e2df3..6ea0c4eddc966a292922f0e4f728d60168e9f719 100644 (file)
--- a/src/figures/kappa-sawteeth/kappa-sawteeth.asy
+++ b/src/figures/kappa-sawteeth/kappa-sawteeth.asy
@@ -7,9 +7,9 @@ real xscale=1e9;
 real fscale=1e12;
 
 void graphSawtooth(string file="datafile", real k,
-                  int xcol=0, int fcol=1,
-                  real xscale=1, real fscale=1, real dx=0, real df=0,
-                  pen p=red, string t="Title") {
+                   int xcol=0, int fcol=1,
+                   real xscale=1, real fscale=1, real dx=0, real df=0,
+                   pen p=red, string t="Title") {
   file fin=input(file).line();
   real[][] a=fin.dimension(0,0);
   a=transpose(a);
@@ -17,7 +17,7 @@ void graphSawtooth(string file="datafile", real k,
   real[] f=a[fcol];
   x = x - f/k; /* Remove cantilever extension */
   graphData(x=x, y=f, xscale=xscale, yscale=fscale,
-           dx=dx, dy=df, p=p, t=t, dots=false);
+            dx=dx, dy=df, p=p, t=t, dots=false);
 }
 
 real[] k = {0.001, 0.01, 0.05, 0.1, 0.5, 1, 10};
@@ -31,7 +31,7 @@ for (i=k.length-1; i>=0; --i) {/* count down so legend and plot orders match */
     label = math("k="+units(format("%f",k[i]),"nN/nm"));
   // TODO: rainbow pen(N, i)
   graphSawtooth(file=file, k=k[i], xscale=xscale, fscale=fscale,
-               df=300e-12*i, p=psoft, t=label);
+                df=300e-12*i, p=psoft, t=label);
 }
 
 xlimits(0, 300e-9*xscale, crop=true);

diff --git a/src/figures/order-dep/order-dep.asy b/src/figures/order-dep/order-dep.asy
index a4958ec9370f24572abb0d67ddcddf558f1911fe..6bf91f08c53512808b709f02b4e9ba32fc6dc4af 100644 (file)
--- a/src/figures/order-dep/order-dep.asy
+++ b/src/figures/order-dep/order-dep.asy
@@ -23,39 +23,39 @@ real kappa(real i, real Kc=Kc, real Kwlc=Kwlc) {
 }
 
 real theory(real i, int N, real Kc=Kc, real Kwlc=Kwlc, real ko=ko, real dx=dx,
-           real v=v, real T=T, real kB=kB, real g=g) {
+            real v=v, real T=T, real kB=kB, real g=g) {
   real f = kB*T/dx;
   return f*(log((kappa(i, Kc, Kwlc)*v)/((N-i)*ko*f)) - g);
 }
 
 // todo: colorpen(N,i)
 graphFile(pic, "data/order.avg-4", xcol=-1, ycol=0,
-         xscale=xscale, yscale=fscale, p=psoft, dots=true);
+          xscale=xscale, yscale=fscale, p=psoft, dots=true);
 graphFile(pic, "data/order.avg-8", xcol=-1, ycol=0,
-         xscale=xscale, yscale=fscale, p=pmed, dots=true);
+          xscale=xscale, yscale=fscale, p=pmed, dots=true);
 graphFile(pic, "data/order.avg-12", xcol=-1, ycol=0,
-         xscale=xscale, yscale=fscale, p=phard, dots=true);
+          xscale=xscale, yscale=fscale, p=phard, dots=true);
 graphFile(pic, "data/order.avg-16", xcol=-1, ycol=0,
-         xscale=xscale, yscale=fscale, p=black, dots=true);
+          xscale=xscale, yscale=fscale, p=black, dots=true);
 real fn(real x, real[] params) {return theory(i=x, N=4, Kwlc=params[0]);}
 fitFile(pic, "data/order.avg-4.fit.dat", f=fn, xmin=0, xmax=3,
-       xscale=xscale, yscale=fscale, p=psoft);
+        xscale=xscale, yscale=fscale, p=psoft);
 real fn(real x, real[] params) {return theory(i=x, N=8, Kwlc=params[0]);}
 fitFile(pic, "data/order.avg-8.fit.dat", f=fn, xmin=0, xmax=7,
-       xscale=xscale, yscale=fscale, p=pmed);
+        xscale=xscale, yscale=fscale, p=pmed);
 real fn(real x, real[] params) {return theory(i=x, N=12, Kwlc=params[0]);}
 fitFile(pic, "data/order.avg-12.fit.dat", f=fn, xmin=0, xmax=11,
-       xscale=xscale, yscale=fscale, p=phard);
+        xscale=xscale, yscale=fscale, p=phard);
 real fn(real x, real[] params) {return theory(i=x, N=16, Kwlc=params[0]);}
 fitFile(pic, "data/order.avg-16.fit.dat", f=fn, xmin=0, xmax=15,
-       xscale=xscale, yscale=fscale, p=black);
+        xscale=xscale, yscale=fscale, p=black);
 
 xaxis(pic, sLabel("Unfolding peak index $i=N_u$"), BottomTop, LeftTicks);
 yaxis(pic, sLabel("Force (pN)"), LeftRight, RightTicks);
 
 picture hist_picture(string datafile,
-                    real xmin=-infinity, real xmax=infinity,
-                    real ymin=-infinity, real ymax=infinity) {
+                     real xmin=-infinity, real xmax=infinity,
+                     real ymin=-infinity, real ymax=infinity) {
   picture pic;
   size(pic, 4cm, 3cm, IgnoreAspect);
   scale(pic, Linear, Log);

diff --git a/src/figures/sim-sawtooth/sim-sawtooth.asy b/src/figures/sim-sawtooth/sim-sawtooth.asy
index a75d84ea5e4188fcb5474546abef22c61d9dd1e1..c1063af732bd98383ff57999ed97c0c2af5ce991 100644 (file)
--- a/src/figures/sim-sawtooth/sim-sawtooth.asy
+++ b/src/figures/sim-sawtooth/sim-sawtooth.asy
@@ -8,9 +8,9 @@ real xscale=1e9;
 real fscale=1e12;
 
 void graphSawtooth(string file="datafile", real k,
-                  int xcol=0, int fcol=1,
-                  real xscale=1, real fscale=1, real dx=0, real df=0,
-                  pen p=red) {
+                   int xcol=0, int fcol=1,
+                   real xscale=1, real fscale=1, real dx=0, real df=0,
+                   pen p=red) {
   file fin=input(file).line();
   real[][] a=fin.dimension(0,0);
   a=transpose(a);
@@ -18,14 +18,14 @@ void graphSawtooth(string file="datafile", real k,
   real[] f=a[fcol];
   x = x - f/k; /* Remove cantilever extension */
   graphData(x=x, y=f, xscale=xscale, yscale=fscale,
-           dx=dx, dy=df, p=p, dots=false);
+            dx=dx, dy=df, p=p, dots=false);
 }
 
 graphSawtooth("fig1.dat", k=k, xscale=xscale, fscale=fscale, p=psoft);
 graphSawtooth("fig2.dat", k=k, xscale=xscale, fscale=fscale,
-             df=200e-12, p=pmed);
+              df=200e-12, p=pmed);
 graphSawtooth("fig3.dat", k=k, xscale=xscale, fscale=fscale,
-             df=400e-12, p=phard);
+              df=400e-12, p=phard);
 
 xaxis(sLabel("Distance (nm)"), BottomTop, LeftTicks);
 yaxis(sLabel("Force (pN)"), LeftRight, RightTicks);

diff --git a/src/figures/v-dep/v-dep-sd.asy b/src/figures/v-dep/v-dep-sd.asy
index 0a9851d4ee3ec34259e1eb94675d9867e926504e..5de276efb7150e2e8be765da323a885d920b58c5 100644 (file)
--- a/src/figures/v-dep/v-dep-sd.asy
+++ b/src/figures/v-dep/v-dep-sd.asy
@@ -21,20 +21,20 @@ string kx_title(string kval, string kexp, string xval) {
 }
 
 graphFile(pic, "v_dep-5e-5_0.1e-9/v_dep", ycol=2,
-         xscale=xscale, yscale=yscale, p=psoft,
-         t=kx_title(kval="5", kexp="-5", xval="0.100"), dots=true);
+          xscale=xscale, yscale=yscale, p=psoft,
+          t=kx_title(kval="5", kexp="-5", xval="0.100"), dots=true);
 graphFile(pic, "v_dep-1e-5_0.225e-9/v_dep", ycol=2,
-         xscale=xscale, yscale=yscale, p=pmed,
-         t=kx_title(kval="1", kexp="-5", xval="0.225"), dots=true);
+          xscale=xscale, yscale=yscale, p=pmed,
+          t=kx_title(kval="1", kexp="-5", xval="0.225"), dots=true);
 graphFile(pic, "v_dep-5e-5_0.225e-9/v_dep", ycol=2,
-         xscale=xscale, yscale=yscale, p=phard,
-         t=kx_title(kval="5", kexp="-5", xval="0.225"), dots=true);
+          xscale=xscale, yscale=yscale, p=phard,
+          t=kx_title(kval="5", kexp="-5", xval="0.225"), dots=true);
 fitFile(pic, "v_dep-5e-5_0.1e-9/v_dep-sd.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=psoft);
+        xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=psoft);
 fitFile(pic, "v_dep-1e-5_0.225e-9/v_dep-sd.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=pmed);
+        xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=pmed);
 fitFile(pic, "v_dep-5e-5_0.225e-9/v_dep-sd.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=phard);
+        xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=phard);
 xequals(pic, x=1e-6*xscale, p=dashed);
 
 xaxis(pic, sLabel("Pulling speed (nm/s)"), BottomTop, LeftTicks);
@@ -42,8 +42,8 @@ yaxis(pic, sLabel("Unfolding force (pN)"), LeftRight, RightTicks);
 add(pic, legend(pic), point(pic, E), 20E, UnFill);
 
 picture hist_picture(string datafile,
-                    real xmin=-infinity, real xmax=infinity,
-                    real ymin=-infinity, real ymax=infinity) {
+                     real xmin=-infinity, real xmax=infinity,
+                     real ymin=-infinity, real ymax=infinity) {
   picture pic;
   size(pic, 4cm, 3cm, IgnoreAspect);
   scale(pic, Linear, Log);

diff --git a/src/figures/v-dep/v-dep.asy b/src/figures/v-dep/v-dep.asy
index e5a2a4dd234d1b940fa91fd3bedaa4cd08abc6a5..a91fc1dbb557ba5e3e5d43d712365aa1765cf4df 100644 (file)
--- a/src/figures/v-dep/v-dep.asy
+++ b/src/figures/v-dep/v-dep.asy
@@ -18,17 +18,17 @@ string kx_title(string kval, string kexp, string xval) {
 
 
 graphFile("v_dep-5e-5_0.1e-9/v_dep", xscale=xscale, yscale=yscale, p=psoft,
-         t=kx_title(kval="5", kexp="-5", xval="0.100"), dots=true);
+          t=kx_title(kval="5", kexp="-5", xval="0.100"), dots=true);
 graphFile("v_dep-1e-5_0.225e-9/v_dep", xscale=xscale, yscale=yscale, p=pmed,
-         t=kx_title(kval="1", kexp="-5", xval="0.225"), dots=true);
+          t=kx_title(kval="1", kexp="-5", xval="0.225"), dots=true);
 graphFile("v_dep-5e-5_0.225e-9/v_dep", xscale=xscale, yscale=yscale, p=phard,
-         t=kx_title(kval="5", kexp="-5", xval="0.225"), dots=true);
+          t=kx_title(kval="5", kexp="-5", xval="0.225"), dots=true);
 fitFile("v_dep-5e-5_0.1e-9/v_dep.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=psoft);
+        xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=psoft);
 fitFile("v_dep-1e-5_0.225e-9/v_dep.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=pmed);
+        xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=pmed);
 fitFile("v_dep-5e-5_0.225e-9/v_dep.fit.dat", f=fn_logxliny,
-       xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=phard);
+        xmin=1e-9, xmax=1e-5, xscale=xscale, yscale=yscale, p=phard);
 xequals(x=1e-6*xscale, p=dashed);
 
 label(sLabel("Pulling speed dependence"), point(N), N);