Merge pull request #36 from HubLot/Fig_stereo

Organize stereospecific Figure

Fig/Makefile

@@ -4,6 +4,7 @@
 # For each figure, a serie of variables can be set (mainly for the location of the script
 # and for the path of the data files). The rule to generate the figure is below those.
 # The idea is to only re-generate the output when the dependencies (script or data) are changed.
+# BE AWARE, all variables must have different names otherwise Makefile will fail.
 #
 # At the beginning of the Makefile, the output filename can be also changed.
 #
@@ -13,7 +14,7 @@
 ## Figure filenames ##
 ######################
 dehydrationPN = dehydrationPN.pdf
-
+stereospecific = stereospecificOPs.pdf
 
 
 # Generate TARGETs from all filenames
@@ -29,26 +30,51 @@ all: $(TARGETS)
 
 # Variables 
 # =========
-SCRIPT = scripts/plotDehydrationPNvector.gpl
-DATA_BERGER = ../DATAreportediINblog/POPC/dehydration/PN-vector/Berger-298K.dat
-DATA_BERGER_DLPC = ../DATAreportediINblog/DLPC/dehydration/PN-vector/Berger-300K.dat
-DATA_MACROG = ../DATAreportediINblog/POPC/dehydration/PN-vector/MacRog-310K.dat
-DATA_CHARMM36 = ../DATAreportediINblog/POPC/dehydration/PN-vector/CHARMM36-303K.dat
-DATA_GAFF = ../DATAreportediINblog/POPC/dehydration/PN-vector/GAFF-303K.dat
+SCRIPT_DEHY = scripts/plotDehydrationPNvector.gpl
+DEHY_BERGER = ../DATAreportediINblog/POPC/dehydration/PN-vector/Berger-298K.dat
+DEHY_BERGER_DLPC = ../DATAreportediINblog/DLPC/dehydration/PN-vector/Berger-300K.dat
+DEHY_MACROG = ../DATAreportediINblog/POPC/dehydration/PN-vector/MacRog-310K.dat
+DEHY_CHARMM36 = ../DATAreportediINblog/POPC/dehydration/PN-vector/CHARMM36-303K.dat
+DEHY_GAFF = ../DATAreportediINblog/POPC/dehydration/PN-vector/GAFF-303K.dat
 
 # Rule
 # ====
-$(dehydrationPN): $(SCRIPT) $(DATA_BERGER) $(DATA_MACROG) $(DATA_CHARMM36) $(DATA_GAFF)
-	gnuplot -e "OUTPUTFILE='$@'" -e "DATA_BERGER='$(DATA_BERGER)'" -e "DATA_BERGER_DLPC='$(DATA_BERGER_DLPC)'" \
-	        -e "DATA_MACROG='$(DATA_MACROG)'" -e "DATA_CHARMM36='$(DATA_CHARMM36)'" \
-	        -e "DATA_GAFF='$(DATA_GAFF)'" \
-	        $(SCRIPT)
+$(dehydrationPN): $(SCRIPT_DEHY) $(DEHY_BERGER) $(DEHY_BERGER_DLPC) $(DEHY_MACROG) $(DEHY_CHARMM36) $(DEHY_GAFF)
+	gnuplot -e "OUTPUTFILE='$@'" -e "DATA_BERGER='$(DEHY_BERGER)'" -e "DATA_BERGER_DLPC='$(DEHY_BERGER_DLPC)'" \
+	        -e "DATA_MACROG='$(DEHY_MACROG)'" -e "DATA_CHARMM36='$(DEHY_CHARMM36)'" \
+	        -e "DATA_GAFF='$(DEHY_GAFF)'" \
+	        $(SCRIPT_DEHY)
 
 #------------#
 # end Figure #
 #------------#
 
 
+#----------------------------------------------#
+# Figure regarding the sterero specificity     #
+#----------------------------------------------#
+
+# Variables 
+# =========
+SCRIPT_STER = scripts/plotWithStereospecificity.gpl
+STER_EXP = ../DATAreportediINblog/POPC-for-stereospecific/EXP-Ferreira2013.dat
+STER_BERGER = ../DATAreportediINblog/POPC-for-stereospecific/BERGER-298K_recalculated-22-04-15.dat
+STER_MACROG = ../DATAreportediINblog/POPC-for-stereospecific/MACROG-310K_recalculated-29-04-15.dat
+STER_CHARMM36 = ../DATAreportediINblog/POPC-for-stereospecific/CHARMM36-303K_blogged-01-12-14.dat
+STER_GAFF = ../DATAreportediINblog/POPC-for-stereospecific/GAFF-303K_blogged-12-11-14.dat
+
+# Rule
+# ====
+$(stereospecific): $(SCRIPT_STER) $(STER_EXP) $(STER_BERGER) $(STER_MACROG) $(STER_CHARMM36) $(STER_GAFF)
+	gnuplot -e "OUTPUTFILE='$@'" -e "DATA_EXP='$(STER_EXP)'" -e "DATA_BERGER='$(STER_BERGER)'" \
+	        -e "DATA_MACROG='$(STER_MACROG)'" -e "DATA_CHARMM36='$(STER_CHARMM36)'" \
+	        -e "DATA_GAFF='$(STER_GAFF)'" \
+	        $(SCRIPT_STER)
+
+#------------#
+# end Figure #
+#------------#
+
 
 
 clean:

DATAreportediINblog/plotWithStereospecificity.gpl → Fig/scripts/plotWithStereospecificity.gpl

@@ -1,5 +1,5 @@
 set term pdfcairo enhanced rounded color dashed dashlength 1 size 10cm, 21cm #16.2cm
-set out "stereospecificOPs.pdf"
+set out OUTPUTFILE
 
 # write name of the blog on the plot:
 # set label 1 right at screen 0.982,0.995 "nmrlipids.blogspot.fi" font ",9" tc rgb "gray"
@@ -49,17 +49,12 @@ set linetype 24  lt 1 lw w lc rgb "#FFD300" # for GAFF
 set linetype 30  lt 1 lw w lc rgb "#00A368" # for MacRog
 
 plot [0.5:7.5][0.152659:-0.26] \
-  "./POPC-for-stereospecific/BERGER-298K_recalculated-22-04-15.dat" u ($1-0.4):($2):($3) w ye lt 21 pt 7 ps r \
-  t "{298K}  Berger", \
-  "./POPC-for-stereospecific/MACROG-310K_recalculated-29-04-15.dat" u ($1-0.2):($2):($3) w ye lt 30 pt 7 ps r \
-  t "{310K}  MacRog", \
-  "./POPC-for-stereospecific/EXP-Ferreira2013.dat" u ($1):($2):($3) w ye lt 101 pt 7 ps 1.5*r \
-  t "300K  ^{_{^{13}}}C-NMR", \
+  DATA_BERGER u ($1-0.4):($2):($3) w ye lt 21 pt 7 ps r t "{298K}  Berger", \
+  DATA_MACROG u ($1-0.2):($2):($3) w ye lt 30 pt 7 ps r t "{310K}  MacRog", \
+  DATA_EXP u ($1):($2):($3) w ye lt 101 pt 7 ps 1.5*r t "300K  ^{_{^{13}}}C-NMR", \
   x w p ls 1 ps 0 t " ", \
-  "./POPC-for-stereospecific/GAFF-303K_blogged-12-11-14.dat" u ($1+0.2):($2):($3) w ye lt 24 pt 7 ps r \
-  t "{303K}  GAFFlipid", \
-  "./POPC-for-stereospecific/CHARMM36-303K_blogged-01-12-14.dat" u ($1+0.4):($2):($3) w ye lt 23 pt 7 ps r \
-  t "@{\\ \\  \"}&{303K}  CHARMM36"
+  DATA_GAFF u ($1+0.2):($2):($3) w ye lt 24 pt 7 ps r t "{303K}  GAFFlipid", \
+  DATA_CHARMM36 u ($1+0.4):($2):($3) w ye lt 23 pt 7 ps r t "@{\\ \\  \"}&{303K}  CHARMM36"
 
 
 

HGmodelMANUSCRIPT/HGmodel_ACStemplate.tex

@@ -596,7 +596,7 @@ \subsection{Full hydration: Experimental order parameters for the glycerol backb
 and the stereospecific labeling from~\cite{gally81}, and shown in Fig.~\ref{HGorderparameters2}.
 \begin{figure*}[]
   \centering
-  \includegraphics[width=8.6cm]{../DATAreportediINblog/stereospecificOPs.pdf} \\
+  \includegraphics[width=8.6cm]{../Fig/stereospecificOPs.pdf} \\
   \caption{\label{HGorderparameters2}
   Order parameteres for POPC glycerol and choline groups
   from simulations with Berger-POPC-07, MacRog, GAFFlipid, and CHARMM36 force fields