mirror of
https://github.com/arcan1s/moldyn.git
synced 2025-06-28 06:41:42 +00:00
add xvg2csv
This commit is contained in:
arcan1s
236
xvg2csv/xvg2csv.py
Executable file
236
xvg2csv/xvg2csv.py
Executable file
@ -0,0 +1,236 @@
|
||||
#!/usr/bin/python2
|
||||
# xvg2csv
|
||||
# Copyright (C) 2014 Evgeniy Alekseev <esalexeev@gmail.com>
|
||||
#
|
||||
# This program is free software: you can redistribute it and/or modify
|
||||
# it under the terms of the GNU General Public License as published by
|
||||
# the Free Software Foundation, either version 3 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program is distributed in the hope that it will be useful,
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
# GNU General Public License for more details.
|
||||
#
|
||||
# You should have received a copy of the GNU General Public License
|
||||
# along with this program. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
|
||||
import argparse, datetime, os
|
||||
|
||||
|
||||
def defineType(file):
|
||||
"""function to define type of input file"""
|
||||
type = None
|
||||
with open(file, 'r') as input:
|
||||
for line in input:
|
||||
if (line[0] == '@') and (line.find("title") > -1):
|
||||
if (line.find("RMSD") > -1):
|
||||
type = "rmsd"
|
||||
elif (line.find("distance") > -1):
|
||||
type = "dist"
|
||||
elif (line.find("Angle") > -1):
|
||||
type = "angl"
|
||||
break
|
||||
return type
|
||||
|
||||
|
||||
def getAngleOutput(file, first=True):
|
||||
"""function to parse angle file"""
|
||||
data = []
|
||||
with open(file, 'r') as input:
|
||||
for line in input:
|
||||
if ((line[0] == '@') or (line[0] == '#')):
|
||||
continue
|
||||
try:
|
||||
if ((not first) and (float(line.split()[0]) == 0.0)):
|
||||
continue
|
||||
data.append(float(line.split()[2]))
|
||||
except:
|
||||
pass
|
||||
return data
|
||||
|
||||
|
||||
def getDistanceOutput(file, first=True):
|
||||
"""function to parse distance file"""
|
||||
data = []
|
||||
with open(file, 'r') as input:
|
||||
for line in input:
|
||||
if ((line[0] == '@') or (line[0] == '#')):
|
||||
continue
|
||||
try:
|
||||
if ((not first) and (float(line.split()[0]) == 0.0)):
|
||||
continue
|
||||
data.append(float(line.split()[1]) * 10.0)
|
||||
except:
|
||||
pass
|
||||
return data
|
||||
|
||||
|
||||
def getRmsdOutput(file, first=True):
|
||||
"""function to parse rmsd files"""
|
||||
data = []
|
||||
with open(file, 'r') as input:
|
||||
for line in input:
|
||||
if ((line[0] == '@') or (line[0] == '#')):
|
||||
continue
|
||||
try:
|
||||
if ((not first) and (float(line.split()[0]) == 0.0)):
|
||||
continue
|
||||
data.append(float(line.split()[1]) * 10.0)
|
||||
except:
|
||||
pass
|
||||
return data
|
||||
|
||||
|
||||
def getFullFileList(dirs):
|
||||
"""function to get full file list"""
|
||||
fileList = {}
|
||||
for dir in dirs:
|
||||
directory = os.path.abspath(dir)
|
||||
if (os.path.exists(directory)) and (os.path.isdir(directory)):
|
||||
newFileList = getFileList(directory)
|
||||
for label in newFileList.keys():
|
||||
if (not fileList.has_key(label)): fileList[label] = {}
|
||||
for system in newFileList[label].keys():
|
||||
if (not fileList[label].has_key(system)): fileList[label][system] = []
|
||||
fileList[label][system].append(newFileList[label][system])
|
||||
return fileList
|
||||
|
||||
|
||||
def getFileList(directory):
|
||||
"""function to get file list"""
|
||||
rawFileList = [file for file in os.listdir(directory) if (os.path.splitext(file)[1] == ".xvg")]
|
||||
rawFileList.sort()
|
||||
return parseFileList(directory, rawFileList)
|
||||
|
||||
|
||||
def parseFileList(directory, rawFileList):
|
||||
"""function to parse file list"""
|
||||
fileList = {}
|
||||
for file in rawFileList:
|
||||
fullFileName = os.path.join(directory, file)
|
||||
label = os.path.splitext(file)[0].split('_')[-2]
|
||||
system = '_'.join(os.path.splitext(file)[0].split('_')[:-2])
|
||||
if (not fileList.has_key(label)): fileList[label] = {}
|
||||
if (not fileList[label].has_key(system)): fileList[label][system] = []
|
||||
if (fileList[label][system].count(fullFileName) == 0):
|
||||
fileList[label][system].append(fullFileName)
|
||||
return fileList
|
||||
|
||||
|
||||
def getAveragingData(rawData, time):
|
||||
"""function to get averaging data"""
|
||||
data = {}
|
||||
for system in rawData.keys():
|
||||
if (not data.has_key(system)): data[system] = []
|
||||
count = len(rawData[system]) / time
|
||||
for i in range(count):
|
||||
value = sum(rawData[system][i*time:(i+1)*time]) / float(time)
|
||||
data[system].append(value)
|
||||
return data
|
||||
|
||||
|
||||
|
||||
def getData(fileList):
|
||||
"""function to get data from files"""
|
||||
rawData = {}
|
||||
for system in fileList.keys():
|
||||
first = True
|
||||
type = None
|
||||
if (not rawData.has_key(system)): rawData[system] = []
|
||||
for files in fileList[system]:
|
||||
for file in files:
|
||||
if (first):
|
||||
type = defineType(file)
|
||||
if (type == "rmsd"):
|
||||
rawData[system].append(getRmsdOutput(file, first))
|
||||
elif (type == "dist"):
|
||||
rawData[system] = rawData[system] + getDistanceOutput(file, first)
|
||||
elif (type == "angl"):
|
||||
rawData[system].append(getAngleOutput(file, first))
|
||||
if (first):
|
||||
first = False
|
||||
return rawData
|
||||
|
||||
|
||||
def createCsv(directory, label, data, timeStep):
|
||||
"""function to create *.csv file"""
|
||||
file = os.path.join(directory, label + ".csv")
|
||||
with open(file, "w") as output:
|
||||
output.write("t\t%s\n" % ('\t'.join(data.keys())))
|
||||
count = max([len(data[system]) for system in data.keys()])
|
||||
for i in range(count):
|
||||
line = "%.3f" % (i * timeStep + timeStep / 2.0)
|
||||
for system in data.keys():
|
||||
if (len(data[system]) > i):
|
||||
line = "%s\t%.5f" % (line, data[system][i])
|
||||
else:
|
||||
line = "%s\t" % (line)
|
||||
output.write(line + "\n")
|
||||
|
||||
|
||||
def createQti(directory, label, data, timeStep):
|
||||
"""function to create *.qti file"""
|
||||
file = os.path.join(directory, label + ".qti")
|
||||
with open(file, "w") as output:
|
||||
count = max([len(data[system]) for system in data.keys()])
|
||||
timestamp = datetime.datetime.now().strftime("%d.%m.%y %H:%M")
|
||||
output.write("QtiPlot 0.9.8 project file\n")
|
||||
output.write("<scripting-lang>\tPython\n")
|
||||
output.write("<windows>\t1\n")
|
||||
output.write("<table>\n")
|
||||
output.write("%s\t%i\t%i\t%s\n" % (label, count, len(data.keys()) + 1, timestamp))
|
||||
output.write("geometry\t0\t0\t445\t220\t\n")
|
||||
output.write("header\tt[X]\t%s[Y]\n" % ('[Y]\t'.join(data.keys())))
|
||||
output.write("ColWidth\t100")
|
||||
for system in data.keys(): output.write("\t100")
|
||||
output.write("\n<com>\n</com>\n")
|
||||
output.write("ColType\t0;0/13")
|
||||
for system in data.keys(): output.write("\t0;0/13")
|
||||
output.write("\nReadOnlyColumn\t0")
|
||||
for system in data.keys(): output.write("\t0")
|
||||
output.write("\nHiddenColumn\t0")
|
||||
for system in data.keys(): output.write("\t0")
|
||||
output.write("\nComments\t\t")
|
||||
for system in data.keys(): output.write("\t")
|
||||
output.write("\nWindowLabel\t\t2\n<data>\n")
|
||||
for i in range(count):
|
||||
line = "%i\t%.3f" % (i, i * timeStep + timeStep / 2.0)
|
||||
for system in data.keys():
|
||||
if (len(data[system]) > i):
|
||||
line = "%s\t%.8f" % (line, data[system][i])
|
||||
else:
|
||||
line = "%s\t" % (line)
|
||||
output.write(line + "\n")
|
||||
output.write("</data>\n</table>\n")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
parser = argparse.ArgumentParser(description = 'Convert GROMACS *.xvg files to *.csv and *.qti. Example filename is "system_label_number.xvg"')
|
||||
parser.add_argument('-d', '--directories', dest = 'dirs',
|
||||
help = 'Directories, comma separared', action = 'store', default = ".")
|
||||
parser.add_argument('-o', '--output', dest = 'output',
|
||||
help = 'Output directory', action = 'store', default = ".")
|
||||
parser.add_argument('-nc', '--nocsv', dest = 'nocsv',
|
||||
help = 'Do not create *.csv file', action = 'store_true', default = False)
|
||||
parser.add_argument('-nq', '--noqti', dest = 'noqti',
|
||||
help = 'Do not create *.qti file', action = 'store_true', default = False)
|
||||
parser.add_argument('-t', '--time', dest = 'time',
|
||||
help = 'Averaging time', action = 'store', default = 100)
|
||||
parser.add_argument('-s', '--step', dest = 'step',
|
||||
help = 'Time step', action = 'store', default = 1.0)
|
||||
args = parser.parse_args()
|
||||
|
||||
dirs = args.dirs.split(',')
|
||||
output = os.path.abspath(args.output)
|
||||
if not os.path.exists(output): os.makedirs(output)
|
||||
|
||||
fileList = getFullFileList(dirs)
|
||||
for label in fileList.keys():
|
||||
rawData = getData(fileList[label])
|
||||
data = getAveragingData(rawData, args.time)
|
||||
if (not args.nocsv):
|
||||
createCsv(output, label, data, args.step)
|
||||
if (not args.noqti):
|
||||
createQti(output, label, data, args.step)
|
||||
Reference in New Issue
Block a user