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CheckGens.py
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CheckGens.py
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#!/home/mlawrenz/Programs/epd-7.3-1-rh5-x86_64/bin/python
import pylab
from msmbuilder import Trajectory, Project, io
from msmbuilder import Project
import optparse
import numpy
import os
from numpy import linalg
def main(modeldir):
proj=Project.load_from('%s/ProjectInfo.yaml' % modeldir.split('Data')[0])
ass=io.loadh('%s/Assignments.Fixed.h5' % modeldir)
data=dict()
data['dist']=numpy.loadtxt('%s/prot_lig_distance.dat' % modeldir, usecols=(1,))
data['rmsd']=numpy.loadtxt('%s/Gens.rmsd.dat' % modeldir, usecols=(2,))
com=numpy.loadtxt('%s/Gens.vmd_com.dat' % modeldir, usecols=(1,))
refcom=com[0]
data['com']=com[1:]
data['com']=numpy.array(data['com'])
pops=numpy.loadtxt('%s/Populations.dat' % modeldir)
map=numpy.loadtxt('%s/Mapping.dat' % modeldir)
frames=numpy.where(map!=-1)[0]
pylab.scatter(data['com'][frames], data['rmsd'][frames])
pylab.scatter([refcom,], [0,], c='k', marker='x', s=100)
pylab.xlabel('P-L COM')
pylab.ylabel('P-L RMSD')
pylab.show()
def parse_commandline():
parser = optparse.OptionParser()
parser.add_option('-d', '--dir', dest='dir',
help='directory')
(options, args) = parser.parse_args()
return (options, args)
#run the function main if namespace is main
if __name__ == "__main__":
(options, args) = parse_commandline()
main(modeldir=options.dir)