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moldyn/xvg2csv/xvg2csv.py
arcan1s 7f328e7746 fix #1 
some edit of python files
2014-12-06 01:07:15 +03:00

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#!/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("istance") > -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] = rawData[system] + getRmsdOutput(file, first)
elif (type == "dist"):
rawData[system] = rawData[system] + getDistanceOutput(file, first)
elif (type == "angl"):
rawData[system] = rawData[system] + 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")
iter = 0
suffix = ""
while (os.path.exists(file + suffix)):
suffix = ".%i" % (iter)
iter = iter + 1
if (suffix != ""):
os.rename(file, file + suffix)
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")
iter = 0
suffix = ""
while (os.path.exists(file + suffix)):
suffix = ".%i" % (iter)
iter = iter + 1
if (suffix != ""):
os.rename(file, file + suffix)
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', type = int,
help = 'Averaging time', action = 'store', default = 1)
parser.add_argument('-s', '--step', dest = 'step', type = float,
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)
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