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coarse_ass.py
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coarse_ass.py
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from msmbuilder import io, Trajectory, Project
import sys
import os
import optparse
import numpy
def make_map(index, all, new, map):
return map
def main(coarse_val, orig_val, rcut):
data=dict()
data['coarse']=dict()
data['orig']=dict()
dirs=dict()
dirs['coarse']='./d%s' % coarse_val
dirs['orig']='./d%s' % orig_val
proj=Project.load_from('ProjectInfo.yaml')
types=['ass', 'rmsd', 'dist', 'gens']
for key in ['coarse', 'orig']:
for type in types:
if 'ass' in type:
ass=io.loadh('%s/Data/Assignments.h5' % dirs[key])
data[key][type]=ass['arr_0']
elif 'dist' in type:
ass=io.loadh('%s/Data/Assignments.h5.distances' % dirs[key])
data[key][type]=ass['arr_0']
elif 'rmsd' in type:
rmsd=numpy.loadtxt('%s/Gens.rmsd.dat' % dirs[key])
data[key][type]=rmsd
elif 'gens' in type:
gens=Trajectory.load_from_lhdf('%s/Gens.lh5' % dirs[key])
data[key][type]=gens
unboundmap=dict()
boundmap=dict()
#unboundstates=dict()
#unboundrmsd=dict()
# build map dict for orig to coarse unbound states, bound will stay same
newass=-1*numpy.ones(( data['orig']['ass'].shape[0], data['orig']['ass'].shape[1]), dtype=int)
for j in range(0, data['orig']['ass'].shape[0]):
for (n,i) in enumerate(data['orig']['ass'][j]):
# if unbound
if i != -1:
if data['orig']['rmsd'][i] > float(rcut):
state=data['coarse']['ass'][j][n]
newass[j][n]=state+10000
else:
newass[j][n]=i
count=0
unique=set(newass.flatten())
boundmap=dict()
unboundmap=dict()
for x in unique:
locations=numpy.where(newass==x)
newass[locations]=count
if x >= 10000:
unboundmap[count]=(x-10000)
else:
boundmap[count]=x
count+=1
io.saveh('%s/Coarsed_r%s_Assignments.h5' % (dirs['orig'], rcut), newass)
subdir='%s/Coarsed_r%s_gen/' % (dirs['orig'], rcut)
if not os.path.exists(subdir):
os.mkdir(subdir)
ohandle=open('%s/Coarsed%s_r%s_Gens.rmsd.dat' % (subdir, coarse_val, rcut), 'w')
b=data['orig']['gens']['XYZList'].shape[1]
c=data['orig']['gens']['XYZList'].shape[2]
dicts=[boundmap, unboundmap]
names=['bound', 'unbound']
labels=['orig', 'coarse']
total=len(boundmap.keys()) + len(unboundmap.keys())
structure=proj.empty_traj()
structure['XYZList']=numpy.zeros((total, b, c), dtype='float32')
count=0
for (name, label, mapdata) in zip( names, labels, dicts):
print "writing coarse gen %s out of %s pdbs" % (count, len(mapdata.keys()))
for i in sorted(mapdata.keys()):
macro=mapdata[i]
structure['XYZList'][count]=data[label]['gens']['XYZList'][macro]
ohandle.write('%s\t%s\t%s\n' % (name, count, data[label]['rmsd'][macro]))
print name, count
count+=1
structure.save_to_xtc('%s/Coarsed%s_r%s_Gens.xtc' % (subdir, coarse_val, rcut))
#return data
def parse_commandline():
parser = optparse.OptionParser()
parser.add_option('-r', '--rcut', dest='rcut',
help='unbound state distance cutoff')
parser.add_option('-c', '--coarse', dest='coarse_val',
help='coarse clustering cutoff')
parser.add_option('-o', '--orig', dest='orig_val',
help='original clustering cutoff')
(options, args) = parser.parse_args()
return (options, args)
if __name__ == "__main__":
(options, args) = parse_commandline()
main(coarse_val=options.coarse_val, orig_val=options.orig_val, rcut=options.rcut)