def test_AmberCrdParser(self):
"""AmberCrdParser test"""
self.p = AmberCrdParser(self.finp,
self.fref,
box=True,
rnAmber=True,
log=self.log,
verbose=self.local)
self.t = self.p.crd2traj()
self.t.removeAtoms(
lambda a: a['residue_name'] in ['WAT', 'Na+', 'Cl-'])
self.t.removeAtoms(lambda a: a['element'] == 'H')
if self.local:
print("Dumping result to ", self.fout)
T.dump(self.t, T.absfile(self.fout))
if self.local:
print("Dumped Trajectory with %i frames and %i atoms." % \
(len(self.t), self.t.lenAtoms() ))
self.assertEqual(len(self.t), 10)
self.assertEqual(self.t.lenAtoms(), 440)
def dump( self, o ):
"""
Try to pickle an object to the currently valid path.
:return: the absolute path to which o was pickled
:rtype: str
"""
try:
f = self.local()
T.dump( f, o )
return f
except:
T.errWriteln("Couldn't dump to %s (constructed from %s)" %\
self.formatted(), self.local() )
raise
def dump(self, o):
"""
Try to pickle an object to the currently valid path.
:return: the absolute path to which o was pickled
:rtype: str
"""
try:
f = self.local()
T.dump(f, o)
return f
except:
T.errWriteln("Couldn't dump to %s (constructed from %s)" %\
self.formatted(), self.local() )
raise
def test_AmberCrdParser(self):
"""AmberCrdParser test"""
self.p = AmberCrdParser( self.finp, self.fref, box=True, rnAmber=True,
log=self.log, verbose=self.local )
self.t = self.p.crd2traj()
self.t.removeAtoms(lambda a: a['residue_name'] in ['WAT','Na+','Cl-'] )
self.t.removeAtoms(lambda a: a['element'] == 'H' )
if self.local:
print("Dumping result to ", self.fout)
T.dump( self.t, T.absfile(self.fout) )
if self.local:
print("Dumped Trajectory with %i frames and %i atoms." % \
(len(self.t), self.t.lenAtoms() ))
self.assertEqual( len(self.t), 10 )
self.assertEqual( self.t.lenAtoms(), 440 )
#!/usr/bin/env python
## re-generate binary test data in this folder
import biskit as B
import biskit.tools as T
from biskit.md import AmberCrdParser, EnsembleTraj, traj2ensemble
p = AmberCrdParser('raw/traj.crd', 'raw/traj_ref.pdb' )
## create standard trajectory object
t = p.crd2traj()
t.frameNames = T.load('raw/traj_framenames.list')
te = traj2ensemble(t, members=10)
te.fit(fit=0) ## re-calculate profile 'rms' (all-atom fit to average structure)
T.dump(te, 'traj.dat')
import biskit.tools as T
t = T.load('com_fake.etraj')
x = t.takeFrames(range(0, t.n_members * 5))
x.ref.disconnect()
T.dump(x, 'extract.etraj')
import biskit as B
import biskit.tools as T
import biskit.dock.hexparser as H
rec = B.XplorModel(source='rec/1A2P_clean.pdb',
fPsf='1A2P.psf',
pdbCode='1A2P')
rec.saveAs('rec/1A2P.model')
rec_dic = {1: rec}
T.dump(rec_dic, 'rec/1A2P_model.dic')
lig = B.XplorModel(source='lig/1A19_clean.pdb',
fPsf='1A19.psf',
pdbCode='1A19')
lig.saveAs('lig/1A19.model')
lig_dic = {1: lig}
T.dump(lig_dic, 'lig/1A19_model.dic')
## generate complex list from Hex docking result for this rec and lig
h = H.HexParser('hex/1A2P-1A19_hex5.out', rec_dic, lig_dic)
c_lst = h.parseHex()
T.dump(c_lst, 'hex/complexes.cl')
p = AmberCrdParser('rpa_com.crd', '0_com.pdb', box=1)
## create standard trajectory object
com = p.crd2traj()
##com = T.load( 'com.traj' )
# re-order frames into 4 parallel trajectories
frames = N.zeros(len(com), int)
for i in range(11):
N.put(frames, range(i * 4, i * 4 + 4), N.arange(i, 44, 11))
etraj = EnsembleTraj(n_members=4)
etraj.frames = com.takeFrames(frames).frames
etraj.ref = com.ref
etraj.resetFrameNames()
etraj.ref.disconnect()
# separate protein and DNA into two chains
etraj.ref.chainIndex(breaks=True, force=True, cache=True)
etraj.ref.addChainId()
## extract only some residues for speed
t1 = etraj.takeAtoms(etraj.ref.res2atomIndices(range(10)))
t2 = etraj.takeChains([1])
etraj = t1.concatAtoms(t2)
T.dump(etraj, 'com_fake.etraj')
## MAIN ##
use()
o = T.cmdDict( {'n':10} )
f_in = T.absfile( o['i'] )
f_out = T.absfile( o.get('o', f_in) )
n = int( o['n'] )
T.flushPrint("Loading...")
t = T.load( f_in )
T.flushPrint("Converting %i frames..." % len(t) )
if isinstance(t, EnsembleTraj ):
T.flushPrint( "Nothing to be done!\n")
sys.exit(0)
t = traj2ensemble( t, n )
if 'pdb' in o:
t.ref.pdbCode = o['pdb']
if f_in == f_out:
os.rename( f_in, f_in + '_backup')
T.flushPrint("Saving...")
T.dump( t, f_out )
T.flushPrint("Done.\n")
#!/usr/bin/env python
## re-generate binary test data in this folder
import biskit as B
import biskit.tools as T
from biskit.md import AmberCrdParser, EnsembleTraj, traj2ensemble
p = AmberCrdParser('raw/traj.crd', 'raw/traj_ref.pdb')
## create standard trajectory object
t = p.crd2traj()
t.frameNames = T.load('raw/traj_framenames.list')
te = traj2ensemble(t, members=10)
te.fit(
fit=0) ## re-calculate profile 'rms' (all-atom fit to average structure)
T.dump(te, 'traj.dat')
#!/usr/bin/env python
## re-generate binary test data in this folder
import biskit as B
import biskit.tools as T
m1 = B.PDBModel('raw/rec.pdb')
m1.saveAs('rec.model')
m2 = B.PDBModel('raw/lig.pdb')
m2.saveAs('lig.model')
## not tested
import biskit.dock as D
com = D.Complex(m1, m2)
T.dump(com, 'ref.complex')
p = AmberCrdParser('rpa_com.crd', '0_com.pdb', box=1 )
## create standard trajectory object
com = p.crd2traj()
##com = T.load( 'com.traj' )
# re-order frames into 4 parallel trajectories
frames = N.zeros( len(com), int )
for i in range( 11 ):
N.put( frames, range(i*4,i*4+4), N.arange(i,44,11) )
etraj = EnsembleTraj( n_members=4 )
etraj.frames = com.takeFrames( frames ).frames
etraj.ref = com.ref
etraj.resetFrameNames()
etraj.ref.disconnect()
# separate protein and DNA into two chains
etraj.ref.chainIndex(breaks=True, force=True, cache=True)
etraj.ref.addChainId()
## extract only some residues for speed
t1 = etraj.takeAtoms( etraj.ref.res2atomIndices(range(10)) )
t2 = etraj.takeChains( [1] )
etraj = t1.concatAtoms( t2 )
T.dump( etraj, 'com_fake.etraj' )
import biskit.tools as T t = T.load( 'com_fake.etraj' ) x = t.takeFrames( range(0, t.n_members * 5) ) x.ref.disconnect() T.dump( x, 'extract.etraj' )