def prepareSource(inFile,
outFile,
wat=1,
sort=1,
foldx=1,
surf=1,
dens=1,
cons=1,
dssp=1,
delphi=0):
"""
Strip waters, add profiles and save as doped source model.
"""
source = PDBModel(inFile)
if wat:
source.remove(lambda a: a['residue_name'] in ['HOH', 'WAT', 'TIP3'])
if sort:
source = source.sort()
doper = PDBDope(source)
if surf:
## doper.addASA()
## doper.addSurfaceMask()
doper.addSurfaceRacer(probe=1.4)
if foldx:
doper.addFoldX()
if dens:
doper.addDensity()
if dssp:
doper.addSecondaryStructure()
if delphi:
doper.addDelphi()
try:
if cons:
doper.addConservation()
except:
errWriteln('\n ERROR: Conservation profile could not be added to '\
+ str(sourceOut) + '\n' )
source.saveAs(outFile)
return source
def changeModel(inFile, prefix, sourceModel):
print '\nget ' + os.path.basename(inFile) + '..',
model = PDBModel(inFile)
model.update()
model = model.sort()
eq = model.equals(sourceModel)
if not eq[0] and eq[1]:
raise ConvertError('source and other models are not equal: ' + str(eq))
# model.validSource()
model.setSource(sourceModel.validSource())
#model.atomsChanged = 0
for k in model.atoms:
model.atoms[k, 'changed'] = N0.all(model[k] == sourceModel[k])
model.xyzChanged = (0 != N0.sum(N0.ravel(model.xyz - sourceModel.xyz)))
model.update(updateMissing=1)
if model.xyzChanged:
doper = PDBDope(model)
if 'MS' in sourceModel.atoms.keys():
doper.addSurfaceRacer(probe=1.4)
if 'density' in sourceModel.atoms.keys():
doper.addDensity()
if 'foldX' in sourceModel.info.keys():
doper.addFoldX()
if 'delphi' in sourceModel.info.keys():
doper.addDelphi()
outFile = os.path.dirname( inFile ) + '/' + prefix +\
T.stripFilename( inFile ) + '.model'
T.dump(model, outFile)
print '-> ' + os.path.basename(outFile)
def changeModel( inFile, prefix, sourceModel ):
print '\nget ' + os.path.basename( inFile ) + '..',
model = PDBModel( inFile )
model.update()
model = model.sort()
eq = model.equals( sourceModel )
if not eq[0] and eq[1]:
raise ConvertError('source and other models are not equal: ' + str(eq))
# model.validSource()
model.setSource( sourceModel.validSource() )
#model.atomsChanged = 0
for k in model.atoms:
model.atoms[k,'changed'] = N0.all( model[k] == sourceModel[k] )
model.xyzChanged = ( 0 != N0.sum( N0.ravel( model.xyz - sourceModel.xyz)) )
model.update( updateMissing=1 )
if model.xyzChanged:
doper = PDBDope( model )
if 'MS' in sourceModel.atoms.keys():
doper.addSurfaceRacer( probe=1.4 )
if 'density' in sourceModel.atoms.keys():
doper.addDensity()
## if 'foldX' in sourceModel.info.keys():
## doper.addFoldX()
if 'delphi' in sourceModel.info.keys():
doper.addDelphi()
outFile = os.path.dirname( inFile ) + '/' + prefix +\
T.stripFilename( inFile ) + '.model'
T.dump( model, outFile )
print '-> ' + os.path.basename( outFile )
def prepareSource( inFile, outFile, wat=1, sort=1,
surf=1, dens=1, cons=1, dssp=1, delphi=0 ):
"""
Strip waters, add profiles and save as doped source model.
"""
source = PDBModel( inFile )
if wat:
source.remove( lambda a: a['residue_name'] in ['HOH','WAT','TIP3'] )
if sort:
source = source.sort()
doper = PDBDope( source )
if surf:
## doper.addASA()
## doper.addSurfaceMask()
doper.addSurfaceRacer( probe=1.4 )
## if foldx:
## doper.addFoldX()
if dens:
doper.addDensity()
if dssp:
doper.addSecondaryStructure()
if delphi:
doper.addDelphi()
try:
if cons:
doper.addConservation( )
except:
errWriteln('\n ERROR: Conservation profile could not be added to '\
+ str(sourceOut) + '\n' )
source.saveAs( outFile )
return source
