def test( model ):
from Biskit import Pymoler
g = PatchGenerator( model )
r = g.randomPatches( 85, 50, max_overlap=25 )
profile = N.sum( N.array(r) )
pm = Pymoler()
pm.addPdb( model, 'o' )
ms = [ model.take( N.flatnonzero(mask) ) for mask in r ]
pm.addMovie( ms )
return pm
def test(model, center2center, nAtoms=10, exclude=None):
from Biskit import Pymoler, PDBModel
g = PatchGeneratorFromOrbit(model, center2center)
overlap = int(round(nAtoms / 4.0))
r = g.randomPatches(nAtoms, 500, max_overlap=overlap, exclude=exclude)
profile = N0.sum(N0.array(r))
pm = Pymoler()
pm.addPdb(model, 'all')
ms = [model.take(N0.nonzero(mask)) for mask in r]
pm.addMovie(ms)
return pm
def test( model, center2center, nAtoms=10, exclude=None ):
from Biskit import Pymoler, PDBModel
g = PatchGeneratorFromOrbit( model, center2center )
overlap = int( round( nAtoms / 4.0 ) )
r = g.randomPatches( nAtoms, 500, max_overlap=overlap, exclude=exclude )
profile = N0.sum( N0.array(r) )
pm = Pymoler()
pm.addPdb( model, 'all' )
ms = [ model.take( N0.nonzero(mask) ) for mask in r ]
pm.addMovie( ms )
return pm
def test_Benchmark(self):
"""Mod.Benchmark test"""
from Biskit import Pymoler
self.b = Benchmark(self.outfolder)
self.b.go()
pdb = T.load(self.outfolder + "/modeller/PDBModels.list")[0]
reference = PDBModel(self.outfolder + "/reference.pdb")
tmp_model = pdb.clone()
reference = reference.compress(reference.maskCA())
pdb = pdb.compress(pdb.maskCA())
tmp_model = tmp_model.compress(tmp_model.maskCA())
tm = tmp_model.transformation(reference,
n_it=0,
profname="rms_outliers")
pdb = pdb.transform(tm)
if self.local:
pm = Pymoler()
pm.addPdb(pdb, "m")
pm.addPdb(reference, "r")
pm.colorAtoms("m", tmp_model.profile("rms_outliers"))
pm.add('set ribbon_trace,1')
pm.add('show ribbon')
pm.show()
if self.DEBUG:
self.log.add(
'The result from the benchmarking is in %s/benchmark'%\
self.outfolder)
globals().update(locals())
def test_Benchmark(self):
"""Mod.Benchmark test"""
from Biskit import Pymoler
self.b = Benchmark( self.outfolder )
self.b.go()
pdb = T.load( self.outfolder + "/modeller/PDBModels.list" )[0]
reference = PDBModel(self.outfolder + "/reference.pdb" )
tmp_model = pdb.clone()
reference = reference.compress( reference.maskCA() )
pdb = pdb.compress( pdb.maskCA() )
tmp_model = tmp_model.compress(tmp_model.maskCA())
tm = tmp_model.transformation( reference, n_it=0,
profname="rms_outliers")
pdb = pdb.transform( tm )
if self.local:
pm = Pymoler()
pm.addPdb( pdb, "m" )
pm.addPdb( reference, "r" )
pm.colorAtoms( "m", tmp_model.profile("rms_outliers") )
pm.add('set ribbon_trace,1')
pm.add('show ribbon')
pm.show()
if self.DEBUG:
self.log.add(
'The result from the benchmarking is in %s/benchmark'%\
self.outfolder)
globals().update( locals() )
else:
folders = d
T.flushPrint("Starting job...\n")
for f in folders:
a = A(outFolder=f)
a.go()
T.flushPrint("Done.\n")
## show result in PyMol
if options.has_key('s'):
p=Pymoler()
p.addPdb( folders[0] + a.F_FINAL_PDB )
p.add('color_b')
p.add('select na, b<0')
p.add('color grey, na')
p.add('hide all')
p.add('show cartoon')
p.add('show stick')
p.add('hide stick, name o+c+n')
p.add('select ca, /////ca')
p.add('label ca,"%s-%s"%(resn, resi)')
p.add('select none')
p.show()
def main(options):
## ## get extra options from external file
## if options.has_key('x'):
## options.update( _parseExternalOptions( options['x'] ) )
fname = options['i'] # input pdb file
outPath = options['o']
chainMask = options.get('cmask', None)
if chainMask: chainMask = toIntList(chainMask)
try:
if options.has_key('h'):
fheader = options['h']
else:
fheader = options['t'] + '/head.inp'
if options.has_key('s'):
fsegment = options['s']
else:
fsegment = options['t'] + '/segment.inp'
if options.has_key('e'):
ftail = options['e']
else:
ftail = options['t'] + '/end.inp'
except:
errWriteln(
"You have to specify either all three template files or\n" +
"(option -t) a folder that contains head.inp, segment.inp, end.inp.\n"
+
"If both -t and -h, -s, or -e are present, files specified with\n"
+ "-h, -s, -e are preferred.")
## check that input pdb file name (stripped of its path and extension)
## is at least 5 characters long and starts with a number
## Prompt user for renaming of the file.
name = stripFilename(fname)
## the filename is OK, but it has the same name as used for the
## XPLOR output therefore we append _original to the input file
if toInt(name[0]) == None or len(name) == 4:
print "##### NOTE: ######"
print "The pdb file name you gave is OK, but exactly"
print "the same name will be used for the output from"
print "the XPLOR script. Therefore '_original' will be"
print "appended to the input pdb file you gave."
base, ext = absfile(fname).split('.')
new_fname = base + '_original.' + ext
os.rename(fname, new_fname)
fname = new_fname
if toInt(name[0]) == None or len(name) < 4:
print "##### WARNING: ######"
print "The pdb file name you gave is either shorter "
print "than 4 characters or it doesn't start with a number."
print "This will cause the X-PLOR job to fail"
msg = "Do you want to rename the file (Y/N)?"
if upper(raw_input(msg)) == 'Y':
new_name = upper(raw_input("Give a new filname:"))
## check that the new name is OK
if toInt(new_name[0]) == None or len(new_name) < 4:
raise StandardError, \
'You gave an incorrect new filename. Exiting'
## create link
else:
new_file = '%s/%s.%s' % (os.path.dirname(
absfile(fname)), new_name, fname.split('.')[-1])
os.link(fname, new_file)
print 'Link from %s to %s created sucessfully'\
%(absfile(fname), new_file)
fname = new_file
## switch on Amber specialities ?
amber = options.has_key('a')
## cap N- and C-term of chain breaks?
capBreaks = options.has_key('cap')
cleaner = ChainCleaner(
ChainSeparator(fname,
outPath,
int(options['c']),
capBreaks=capBreaks,
chainMask=chainMask))
# initialize with output path and base file name for generate.inp file
xplorer = Xplor(outPath,
cleaner,
fheader,
fsegment,
ftail,
amber,
extras=options)
xplorer.generateInp()
## run X-Plor
if options.has_key('exe'):
out, error, returncode = Executor(
'xplor',
strict=0,
f_in=xplorer.cleaner.pdbname + "_generate.inp",
f_out=xplorer.cleaner.pdbname + '_generate.log').run()
## Show structure in pymol
if options.has_key('view'):
pm = Pymoler()
mname = pm.addPdb(xplorer.outname + '.pdb')
pm.add('select xray-wat, segi 1XWW')
pm.add('select added-wat, segi 1WWW')
pm.add('select hydrogens, elem H')
pm.add('hide everything, xray-wat OR added-wat OR hydrogens')
pm.add('select none')
colors = [hex2rgb(c, str) for c in hexColors(len(xplorer.chains))]
i = 0
for c in xplorer.chains:
print colors[i], c.segment_id
pm.add('set_color col_%i, %s' % (i, colors[i]))
pm.add('color col_%i, segi %s and elem c' % (i, c.segment_id))
i += 1
pm.add('zoom all')
pm.show()
## get filenames of all models
models = glob.glob('%s/modeller/%s*.pdb' %
(outFolder, tools.stripFilename(f_target)))
## create a Trajectory object with the models
traj = Trajectory(pdbs=models)
## fit the models against the average structure iteratively
traj.blockFit2ref()
## calculate and print rmsd matrix
rmsHeavy = traj.pairwiseRmsd()
print '\nHEAVY ATOM RMSD BETWEEN MODELS::'
__printMatrix(rmsHeavy)
## same thing for backbone atoms
BBMask = traj[0].maskBB()
traj.blockFit2ref(mask=BBMask)
rmsBB = traj.pairwiseRmsd(aMask=BBMask)
print '\nBACKBONE RMSD BETWEEN MODELS:'
__printMatrix(rmsBB)
if options.has_key('view'):
## show backbone superimposed structures in pymol
pm = Pymoler()
for t in traj:
pm.addPdb(t)
pm.show()
## get filenames of all models
models = glob.glob( '%s/modeller/%s*.pdb'%(outFolder,
tools.stripFilename(f_target)) )
## create a Trajectory object with the models
traj = Trajectory( pdbs=models )
## fit the models against the average structure iteratively
traj.blockFit2ref()
## calculate and print rmsd matrix
rmsHeavy = traj.pairwiseRmsd()
print '\nHEAVY ATOM RMSD BETWEEN MODELS::'
__printMatrix( rmsHeavy )
## same thing for backbone atoms
BBMask = traj[0].maskBB()
traj.blockFit2ref( mask = BBMask )
rmsBB = traj.pairwiseRmsd( aMask = BBMask )
print '\nBACKBONE RMSD BETWEEN MODELS:'
__printMatrix( rmsBB )
if options.has_key('view'):
## show backbone superimposed structures in pymol
pm = Pymoler( )
for t in traj:
pm.addPdb( t )
pm.show()
def visualize(self, profile='so_min', wat=None, xwat=None):
"""
Create a receptor / ligand / water view with a profile color-coded
on it.
@param profile: name of the profile to color-project ['so_min']
@type profile: str
@param wat: chain ids of water molecules (default: None)
These will end up as spheres in group 'water'
@type wat: [ int ]
@param xwat: chain ids of crystal water molecules (default: None)
These will end up as spheres in group 'xwater'
@type xwat: [ int ]
@return: Pymoler instance with receptor and ligand colored by shelling
order (use pm.run() to make it show up)
@rtype: Pymoler
"""
import Biskit.Pymoler as Pymoler
model = self.model.clone()
## replace all 0 values by -1 to distinguish them better by color
model[profile] += (model[profile] == 0) * -1
rec = model.takeChains(self.chains_rec, breaks=self.breaks)
lig = model.takeChains(self.chains_lig, breaks=self.breaks)
water = xwater = None
if wat:
water = model.takeChains(wat, breaks=self.breaks)
water = water.compress(N.greater(water['n_facets'], 0))
if xwat:
xwater = model.takeChains(
xwat, breaks=self.breaks) ## X-ray determined water
## kick out waters that do not belong to the interface
xwater = xwater.compress(N.greater(xwater['n_facets'], 0))
pm = Pymoler()
pm.addPdb(model, 'com')
pm.addPdb(rec, 'rec')
pm.addPdb(lig, 'lig')
pm.colorAtoms('rec', rec[profile])
pm.colorAtoms('lig', lig[profile])
if xwater:
pm.addPdb(xwater, 'x-water')
pm.colorAtoms('x-water', xwater[profile])
if water:
pm.addPdb(water, 'water')
pm.colorAtoms('water', water[profile])
pm.add('hide')
pm.add('show surface, rec')
pm.add('show mesh, lig')
pm.add('show spheres, x-water')
pm.add('show spheres, water')
pm.add('zoom')
return pm
d = [f]
if options.has_key('d'):
folders = T.toList(options['d'])
else:
folders = d
T.flushPrint("Starting job...\n")
for f in folders:
a = A(outFolder=f)
a.go()
T.flushPrint("Done.\n")
## show result in PyMol
if options.has_key('s'):
p = Pymoler()
p.addPdb(folders[0] + a.F_FINAL_PDB)
p.add('color_b')
p.add('select na, b<0')
p.add('color grey, na')
p.add('hide all')
p.add('show cartoon')
p.add('show stick')
p.add('hide stick, name o+c+n')
p.add('select ca, /////ca')
p.add('label ca,"%s-%s"%(resn, resi)')
p.add('select none')
p.show()
class Test(BT.BiskitTest):
"""Test case"""
def test_Complex(self):
"""Dock.Complex test"""
lig = PCRModel( t.testRoot() + "/com/1BGS.psf",
t.testRoot() + "/com/lig.model")
rec = PCRModel( t.testRoot() + "/com/1BGS.psf",
t.testRoot() + "/com/rec.model")
rec = rec.compress( rec.maskHeavy() )
lig = lig.compress( lig.maskHeavy() )
c = Complex(rec, lig)
c.info['soln'] = 1
cont = c.atomContacts( 6.0 )
contProfile_lig = N.sum( cont )
contProfile_rec = N.sum( cont, 1 )
try:
dope = PDBDope( c.rec_model )
dope.addSurfaceRacer( probe=1.4 )
rec_surf = c.rec_model.profile2mask( 'MS', 0.0000001, 1000 )
dope = PDBDope( c.lig_model )
dope.addSurfaceRacer( probe=1.4 )
lig_surf = c.lig_model.profile2mask( 'MS', 0.0000001, 1000 )
except:
pass
if self.local:
from Biskit import Pymoler
self.pm = Pymoler()
self.pm.addPdb( c.rec(), 'rec' )
self.pm.addPdb( c.lig(), 'lig' )
self.pm.colorAtoms( 'rec', contProfile_rec )
self.pm.colorAtoms( 'lig', contProfile_lig )
rec_sphere = c.rec().clone()
rec_sphere.xyz = mathUtils.projectOnSphere( rec_sphere.xyz )
lig_sphere = c.lig().clone()
lig_sphere.xyz = mathUtils.projectOnSphere( lig_sphere.xyz )
self.pm.addPdb( rec_sphere, 'rec_sphere' )
self.pm.addPdb( lig_sphere, 'lig_sphere' )
self.pm.colorAtoms( 'rec_sphere', contProfile_rec )
self.pm.colorAtoms( 'lig_sphere', contProfile_lig )
self.pm.add( 'hide all')
self.pm.add( 'color grey, (b=0)' )
self.pm.add( 'show stick, (rec or lig)' )
self.pm.add( 'show surf, rec_sphere')
self.pm.add( 'zoom all' )
self.pm.show()
globals().update( locals() )
self.assertEqual( N.sum(contProfile_lig) + N.sum(contProfile_rec),
2462 )
def main(options):
## ## get extra options from external file
## if options.has_key('x'):
## options.update( _parseExternalOptions( options['x'] ) )
fname = options['i'] # input pdb file
outPath = options['o']
chainMask = options.get('cmask', None)
if chainMask: chainMask = toIntList(chainMask)
try:
if options.has_key('h'):
fheader = options['h']
else:
fheader = options['t'] + '/head.inp'
if options.has_key('s'):
fsegment = options['s']
else:
fsegment = options['t'] + '/segment.inp'
if options.has_key('e'):
ftail = options['e']
else:
ftail = options['t'] + '/end.inp'
except:
errWriteln("You have to specify either all three template files or\n"+
"(option -t) a folder that contains head.inp, segment.inp, end.inp.\n" +
"If both -t and -h, -s, or -e are present, files specified with\n" +
"-h, -s, -e are preferred.")
## check that input pdb file name (stripped of its path and extension)
## is at least 5 characters long and starts with a number
## Prompt user for renaming of the file.
name = stripFilename(fname)
## the filename is OK, but it has the same name as used for the
## XPLOR output therefore we append _original to the input file
if toInt( name[0] )== None or len(name)==4 :
print "##### NOTE: ######"
print "The pdb file name you gave is OK, but exactly"
print "the same name will be used for the output from"
print "the XPLOR script. Therefore '_original' will be"
print "appended to the input pdb file you gave."
base, ext = absfile(fname).split('.')
new_fname = base +'_original.' + ext
os.rename( fname, new_fname )
fname = new_fname
if toInt( name[0] )== None or len(name)<4 :
print "##### WARNING: ######"
print "The pdb file name you gave is either shorter "
print "than 4 characters or it doesn't start with a number."
print "This will cause the X-PLOR job to fail"
msg = "Do you want to rename the file (Y/N)?"
if upper( raw_input( msg ) ) == 'Y':
new_name = upper( raw_input( "Give a new filname:" ) )
## check that the new name is OK
if toInt( new_name[0] )== None or len(new_name)<4 :
raise StandardError, \
'You gave an incorrect new filename. Exiting'
## create link
else:
new_file = '%s/%s.%s'%(os.path.dirname(absfile(fname)),
new_name,
fname.split('.')[-1])
os.link(fname, new_file)
print 'Link from %s to %s created sucessfully'\
%(absfile(fname), new_file)
fname = new_file
## switch on Amber specialities ?
amber = options.has_key('a')
## cap N- and C-term of chain breaks?
capBreaks = options.has_key('cap')
cleaner = ChainCleaner(
ChainSeparator(fname, outPath,
int(options['c']),
capBreaks=capBreaks,
chainMask=chainMask) )
# initialize with output path and base file name for generate.inp file
xplorer = Xplor(outPath, cleaner, fheader, fsegment, ftail, amber, extras=options )
xplorer.generateInp()
## run X-Plor
if options.has_key('exe'):
out, error, returncode = Executor( 'xplor' , strict=0,
f_in=xplorer.cleaner.pdbname + "_generate.inp",
f_out=xplorer.cleaner.pdbname + '_generate.log').run()
## Show structure in pymol
if options.has_key('view'):
pm = Pymoler( )
mname = pm.addPdb( xplorer.outname + '.pdb' )
pm.add('select xray-wat, segi 1XWW')
pm.add('select added-wat, segi 1WWW')
pm.add('select hydrogens, elem H')
pm.add('hide everything, xray-wat OR added-wat OR hydrogens')
pm.add('select none')
colors = [ hex2rgb(c, str) for c in hexColors( len(xplorer.chains) )]
i=0
for c in xplorer.chains:
print colors[i], c.segment_id
pm.add( 'set_color col_%i, %s'%( i, colors[i] ) )
pm.add('color col_%i, segi %s and elem c'%( i, c.segment_id ) )
i += 1
pm.add('zoom all')
pm.show()
def visualize( self, profile='so_min', wat=None, xwat=None ):
"""
Create a receptor / ligand / water view with a profile color-coded
on it.
@param profile: name of the profile to color-project ['so_min']
@type profile: str
@param wat: chain ids of water molecules (default: None)
These will end up as spheres in group 'water'
@type wat: [ int ]
@param xwat: chain ids of crystal water molecules (default: None)
These will end up as spheres in group 'xwater'
@type xwat: [ int ]
@return: Pymoler instance with receptor and ligand colored by shelling
order (use pm.run() to make it show up)
@rtype: Pymoler
"""
import Biskit.Pymoler as Pymoler
model = self.model.clone()
## replace all 0 values by -1 to distinguish them better by color
model[profile] += (model[profile] == 0) * -1
rec = model.takeChains( self.chains_rec, breaks=self.breaks )
lig = model.takeChains( self.chains_lig, breaks=self.breaks )
water = xwater = None
if wat:
water = model.takeChains(wat, breaks=self.breaks)
water = water.compress( N.greater( water['n_facets'], 0) )
if xwat:
xwater = model.takeChains( xwat, breaks=self.breaks ) ## X-ray determined water
## kick out waters that do not belong to the interface
xwater = xwater.compress( N.greater( xwater['n_facets'], 0) )
pm = Pymoler()
pm.addPdb( model, 'com' )
pm.addPdb( rec, 'rec' )
pm.addPdb( lig, 'lig' )
pm.colorAtoms( 'rec', rec[profile])
pm.colorAtoms( 'lig', lig[profile])
if xwater:
pm.addPdb( xwater, 'x-water' )
pm.colorAtoms( 'x-water', xwater[profile] )
if water:
pm.addPdb( water, 'water' )
pm.colorAtoms( 'water', water[profile] )
pm.add( 'hide' )
pm.add( 'show surface, rec' )
pm.add( 'show mesh, lig' )
pm.add( 'show spheres, x-water' )
pm.add( 'show spheres, water' )
pm.add( 'zoom' )
return pm
