def plotAngle(l_p_filin, debug=1):
"""Excecute commande for draw angle plot
in: distance MAX and log file
out: Execute CMD -> draw plot
"""
for p_filin in l_p_filin:
# # # # substruct = p_filin.split ("_")[-1]
# do not need with the new criterion
# # if substruct == "Imidazole" or substruct == "Pyridine" or substruct == "Secondary" :
# # cmd_3d = pathManage.scriptR() + "angle3D_Secondary.R " + p_filin
# # elif substruct == "Tertiary" :
# # cmd_3d = pathManage.scriptR() + "angle3D_Tertiary.R " + p_filin
# every structure
cmd_density = pathManage.scriptR() + "angle_density.R " + p_filin + "&"
cmd_distribution = pathManage.scriptR() + "angle_distribution.R " + p_filin + "&"
cmdBarplot = pathManage.scriptR() + "angle_barplot.R " + p_filin + " 5"
cmd_densityandhist = pathManage.scriptR() + "angleVSDistance.R " + p_filin
if debug == 1:
print cmd_density
print cmdBarplot
print cmd_distribution
print cmd_densityandhist
system(cmdBarplot)
system(cmd_density)
system(cmd_distribution)
system(cmd_densityandhist)
def InteractionProportion(p_filin):
cmd_by_sub = pathManage.scriptR() + "proportionBySub.R " + p_filin
print cmd_by_sub
system(cmd_by_sub)
cmd_all = pathManage.scriptR() + "proportionAllSubs.R " + p_filin
print cmd_all
system(cmd_all)
def AFCBarplot(p_filin, logFile, verbose=1):
cmd = pathManage.scriptR() + "AFCNeighbor.R " + p_filin
system(cmd)
if verbose == 1:
print cmd
logFile.write(cmd)
def proportionAtomClassNeighbor(p_filin, logFile, verbose=1):
cmd = pathManage.scriptR() + "AnalysisNeighbor.R " + p_filin + " " + p_filin.split("/")[-1].split("_")[-1]
system(cmd)
if verbose == 1:
print cmd
logFile.write(cmd + "\n")
def histProportionTypeNeighbors(distance, dir_out, logFile):
"""Draw proportion type neighbor
in: Distance Max study, log file_data
out: excecute CMD -> draw plot"""
listStruct = structure.ListSub()
listStruct.append("GlobalAmine")
listStruct.append("Global")
for type in listStruct:
file_data = dir_out + "globalProportionType/" + "proportionType" + type + str("%.2f" % distance)
if tool.checkFileEmpty(file_data) == 1:
continue
cmd = (
pathManage.scriptR()
+ "barplotTypeNumberOfneighbors.R "
+ file_data
+ " "
+ type
+ " "
+ str("%.2f" % distance)
)
print cmd
logFile.write(cmd + "\n")
system(cmd)
def histNeigbor(dir_in, logFile):
l_study = structure.ListSub()
l_study.append("global")
for substruct in l_study:
cmd = (
pathManage.scriptR()
+ "AnalysisNeighbor.R "
+ dir_in
+ "neigbhor/"
+ "neighbor_"
+ substruct
+ " "
+ dir_in
+ "neigbhor/"
+ "distance_"
+ substruct
+ " "
+ substruct
)
cmd_hist = pathManage.scriptR() + "histAngle.R " + dir_in + "neigbhor/" + "angle_neighbor_" + substruct
if substruct == "Primary":
nb = 5
if substruct == "Secondary" or substruct == "Imidazole":
nb = 4
if substruct == "Tertiary":
nb = 3
else:
nb = 7
cmd_barplot = (
pathManage.scriptR() + "barplotNeighbor.R " + dir_in + "neigbhor/" + "barplot_" + substruct + " " + str(nb)
)
print cmd
print cmd_hist
print cmd_barplot
system(cmd_barplot)
system(cmd)
system(cmd_hist)
for i in range(1, 8):
AFC(dir_in + "neigbhor/", str(i))
def plot3D(p_file_coord, option="local"):
cmd = pathManage.scriptR() + "scatter3D.R " + p_file_coord + " " + option
print cmd
system(cmd)
# remove png temp
system("rm " + path.dirname(p_file_coord) + "/*.png")
def barplotResDist(p_filin, logFile):
"""Draw barplot proportion residue
in: log file_side
out: execute CMD"""
cmd = pathManage.scriptR() + "barplotResidueDistance.R " + p_filin + " all"
logFile.write(cmd + "\n")
system(cmd)
print cmd
def histDistance(p_filin, type_distance):
"""Draw CN length histogram and coplar histogram
in: nameFile data, option for execute R script
out: execute R script -> draw histogram distance"""
if tool.checkFileEmpty(p_filin) == 1:
return
cmd = pathManage.scriptR() + "distance.R " + str(p_filin) + " " + str(type_distance)
print cmd
system(cmd)
def barplotCombination(p_filin, logFile, debug=1):
repScript = pathManage.scriptR()
if tool.checkFileEmpty(p_filin) == 1:
return
cmd = repScript + "barplotCombination.R " + p_filin
if debug:
print cmd
logFile.write(cmd + "\n")
system(cmd)
def plotDistanceDensity(p_filin, logFile, debug=1):
"""Plot density"""
repScript = pathManage.scriptR()
if tool.checkFileEmpty(p_filin) == 1:
return
cmd = repScript + "densityDistance.R " + p_filin
if debug:
print cmd
logFile.write(cmd + "\n")
system(cmd)
def histProportionType(distanceMax, dir_out, logFile):
"""Draw proportion type graphe
in: Distance Max study, log file
out: excecute CMD -> draw plot"""
repScript = pathManage.scriptR()
cmd = repScript + "barplotPercentClasse.R " + dir_out
print cmd
logFile.write(cmd + "\n")
system(cmd)
def barplotQuantity(distance, type_study, p_filin, logFile, debug=1):
"""Plot count statistic
in: distance for legend plot, type histogram (coplar or length), p_filin with data, type of study, logFile
out: CMD in terminal -> plot """
if tool.checkFileEmpty(p_filin) == 1:
return
rep = pathManage.scriptR()
cmd = rep + "barplotQuantity.R " + p_filin + " " + str("%.2f" % distance) + " " + type_study
if debug:
print cmd
logFile.write(cmd + "\n")
system(cmd)
def CorInteractionVSNbNeighbours(p_file_interact, p_file_nb_neighbor, pr_result):
cmd_run = (
pathManage.scriptR()
+ "CorInteractVSneighbour.R "
+ p_file_interact
+ " "
+ p_file_nb_neighbor
+ " "
+ pr_result
)
print cmd_run
system(cmd_run)
def plotNbNeighbor(p_filin, logFile, debug=1):
"""Plot number neighbor
in: distance for legend plot, type histogram (coplar or length), file with data, type of study, logFile
out: CMD in terminal -> plot """
repScript = pathManage.scriptR()
if tool.checkFileEmpty(p_filin) == 1:
return
cmd = repScript + "plotNumberNeighbor.R " + p_filin
if debug:
print cmd
logFile.write(cmd + "\n")
system(cmd)
def histGlobalProportion(dir_out, logFile):
"""Proportion for each atom
in: log file
out: execute -> CMD
"""
repScript = pathManage.scriptR()
file = dir_out + "GlobalproportionCounterIonGlobal"
if tool.checkFileEmpty(file) == 1:
return
cmd = repScript + "barplotProportionGlobalRef.R " + file
logFile.write(cmd + "\n")
print cmd
system(cmd)
def MergeProportionAndDataset(p_atleast1, p_notatleast1, p_atleast2, p_notatleast2, pr_out):
cmd_R = (
pathManage.scriptR()
+ "mergeBarplotAndDataset.R "
+ str(p_atleast1)
+ " "
+ str(p_notatleast1)
+ " "
+ str(p_atleast2)
+ " "
+ str(p_notatleast2)
+ " "
+ str(pr_out)
)
print cmd_R
system(cmd_R)
def histProportion(distance, dir_in, logFile):
"""Draw proportion type neighbor
in: Distance Max study, log path_file
out: excecute CMD -> draw plot"""
repScript = pathManage.scriptR()
listType = structure.ListSub()
listType.append("Global")
listType.append("GlobalAmine")
for type in listType:
path_file = dir_in + "globalProportionAtom/" + "proportionAtom" + type + str("%.2f" % distance)
if tool.checkFileEmpty(path_file) == 1:
continue
cmd = repScript + "barplotQuantityGlobalAnalysis.R " + type + " " + path_file + " " + str(distance)
print cmd
system(cmd)
logFile.write(cmd + "\n")
def barplotQuantityByAA(distance, aminoAcid, path_file, logFile):
"""to do"""
if tool.checkFileEmpty(path_file) == 1:
return
rep = pathManage.scriptR()
cmd = (
rep
+ "barplotQuantityByAA.R "
+ path_file
+ " "
+ str("%.2f" % distance)
+ " "
+ aminoAcid
+ " "
+ str("%.2f" % distance)
)
print cmd
logFile.write(cmd + "\n")
system(cmd)
def CorpKaVSNb(p_file_pka):
cmd_run = pathManage.scriptR() + "corNbVSPKA.R " + p_file_pka
print cmd_run
system(cmd_run)
def MeansNumberNeighbors(p_filout):
cmd_run = pathManage.scriptR() + "barplotMeans.R " + str(p_filout)
print cmd_run
system(cmd_run)
def HistAngle(p_filin):
cmd_hist = pathManage.scriptR() + "plotAngleCriteria.R " + p_filin
print cmd_hist
system(cmd_hist)
def plotAngleVs(path_filin):
cmd = pathManage.scriptR() + "plotAngleVS.R " + path_filin
print cmd
system(cmd)
def MergeProportionInteractAtLeasNotAtLeast(p_atleast, p_notatleast, pr_out):
cmd_R = pathManage.scriptR() + "mergeBarplot.R " + str(p_atleast) + " " + str(p_notatleast) + " " + pr_out
print cmd_R
system(cmd_R)
def WaterMediated(p_filin):
cmd = pathManage.scriptR() + "barplotWaterMediated.R " + p_filin
print cmd
system(cmd)
def multiHist(pr_filin):
cmd = pathManage.scriptR() + "multihist.R " + pr_filin
print cmd
system(cmd)
def waterType(path_file, verbose=1):
cmd = pathManage.scriptR() + "plotWaterQuantity.R " + path_file
if verbose == 1:
print cmd
system(cmd)
def DistVSAngleNeighbor(p_filin):
cmd_area = pathManage.scriptR() + "plotAngleVSDistCombi.R " + p_filin
print cmd_area
system(cmd_area)
def AFC(pr_neighbors, number_neighbor):
cmd = pathManage.scriptR() + "AFCNeighbor.R " + pr_neighbors + " " + str(number_neighbor)
print cmd
system(cmd)
def barplotLenBond(path_filin):
cmd = pathManage.scriptR() + "boxplotBond.R " + path_filin
print cmd
system(cmd)