def displayStructure(self, srecs):
"""Display a structure"""
app = self.preferences.get('molgraphApplication')
path = self.preferences.get('molgraphAppPath')
DBActions.DB = self.DB
if DBActions.yasara != None:
DBActions.yasara.Clear()
colors = ['green', 250, 270, 290, 310, 320, 340]
i = 0
for r in srecs:
color = colors[i]
i += 1
DBActions.displayStructure(r, 'Structure', app, path, color, False)
#try to align objects
Y = DBActions.yasara
if hasattr(Y, 'objects') and len(Y.objects) > 1:
Y.AlignMultiAll()
return
def displayStructure(self, srecs):
"""Display a structure"""
app = self.preferences.get('molgraphApplication')
path = self.preferences.get('molgraphAppPath')
DBActions.DB = self.DB
if DBActions.yasara != None:
DBActions.yasara.Clear()
colors = ['green',250,270,290,310,320,340]
i=0
for r in srecs:
color = colors[i]
i+=1
DBActions.displayStructure(r, 'Structure', app, path, color, False)
#try to align objects
Y = DBActions.yasara
if hasattr(Y, 'objects') and len(Y.objects)>1:
Y.AlignMultiAll()
return
def remodel():
#DB=PDatabase(local='hewlsample.fs')
DB=PDatabase(server='localhost',port=8080,
username='******',password='******',
project='novo')
print DB, 'curr ref:', DB.meta.refprotein
'''rec= DB['wt+D52N']
print rec.getDisplayAttribute('Structure')
rec['Structure'] = rec.Structure'''
r='6 c9'
rec= DB[r]
DBActions.checkModels(DB=DB, selected=[r])
print rec.Structure
#print rec.aaseq
'''for r in DB.getRecs():
print r, type(DB.get(r).Structure)
print DB.get(r).getDisplayAttribute('Structure')'''
#DB.commit(note='modelling')
return
def remodel():
#DB=PDatabase(local='hewlsample.fs')
DB = PDatabase(server='localhost',
port=8080,
username='******',
password='******',
project='novo')
print DB, 'curr ref:', DB.meta.refprotein
'''rec= DB['wt+D52N']
print rec.getDisplayAttribute('Structure')
rec['Structure'] = rec.Structure'''
r = '6 c9'
rec = DB[r]
DBActions.checkModels(DB=DB, selected=[r])
print rec.Structure
#print rec.aaseq
'''for r in DB.getRecs():
print r, type(DB.get(r).Structure)
print DB.get(r).getDisplayAttribute('Structure')'''
#DB.commit(note='modelling')
return
def modelontheFly(self, DB, operations):
"""Produce the PDBlines for the mutant file"""
self.MUT = DBActions.initProtool()
# Create temporary array holding models
if not getattr(DB, 'tmp_3Dmodels', None):
DB.tmp_3Dmodels = {}
# Get the structure from the parent
parent = operations['parent']
parentrec = DB.get(parent)
if parentrec.hasStructure() == 'available':
# Have we already modelled this one?
if DB.tmp_3Dmodels.has_key(str(operations)):
pdblines = DB.tmp_3Dmodels[str(operations)]
import Protool
X = Protool.structureIO()
X.parsepdb(pdblines)
return pdblines, X
# Read parent structure
pdblines = parentrec.Structure
import Protool
X = Protool.structureIO()
X.parsepdb(pdblines)
# Perform all the operations
# First do all the deletes
print operations['Rotamer_operations']
for operation, uniqueid, atom in operations['Rotamer_operations']:
#print operation,uniqueid,atom
if operation == 'delete':
X.remove_atom(uniqueid)
for operation, uniqueid, atom in operations['Rotamer_operations']:
if operation == 'add':
# Add atom
chainID = uniqueid.split(':')[0]
atomname = uniqueid.split(':')[-1]
residuenumber = uniqueid.split(':')[1]
resid = '%s:%s' % (chainID, residuenumber)
status = X.add_atom(uniqueid=uniqueid,
atomname=atomname,
residuenumber=residuenumber,
chainid=chainID,
residuename=atom['RESNAME'],
xcoord=atom['X'],
ycoord=atom['Y'],
zcoord=atom['Z'])
if not status:
self.parent.record_event(
'Modelling failed in model_on_the_fly for operations: %s'
% (str(operations)))
return []
# Update the arrays
X.Update()
# Rename the rest of the atoms
for this_atom in X.residues[resid]:
X.atoms[this_atom]['RESNAME'] = atom['RESNAME']
X.Update()
#put mutation stuff into a tuple and return it too
#mutantinfo = (chainID,residuenumber)
# Return the PDBlines and the instance
pdblines = X.writepdb('dummy', nowrite=1)
# Store for next use
DB.tmp_3Dmodels[str(operations)] = pdblines[:]
return pdblines, X
else:
print 'Parent does not have a structure'
return [], None
def modelontheFly(self, DB, operations):
"""Produce the PDBlines for the mutant file"""
self.MUT = DBActions.initProtool()
# Create temporary array holding models
if not getattr(DB,'tmp_3Dmodels',None):
DB.tmp_3Dmodels={}
# Get the structure from the parent
parent = operations['parent']
parentrec = DB.get(parent)
if parentrec.hasStructure() == 'available':
# Have we already modelled this one?
if DB.tmp_3Dmodels.has_key(str(operations)):
pdblines = DB.tmp_3Dmodels[str(operations)]
import Protool
X=Protool.structureIO()
X.parsepdb(pdblines)
return pdblines,X
# Read parent structure
pdblines = parentrec.Structure
import Protool
X=Protool.structureIO()
X.parsepdb(pdblines)
# Perform all the operations
# First do all the deletes
print operations['Rotamer_operations']
for operation,uniqueid,atom in operations['Rotamer_operations']:
#print operation,uniqueid,atom
if operation=='delete':
X.remove_atom(uniqueid)
for operation,uniqueid,atom in operations['Rotamer_operations']:
if operation=='add':
# Add atom
chainID=uniqueid.split(':')[0]
atomname=uniqueid.split(':')[-1]
residuenumber=uniqueid.split(':')[1]
resid='%s:%s' %(chainID,residuenumber)
status=X.add_atom(uniqueid=uniqueid,
atomname=atomname,
residuenumber=residuenumber,
chainid=chainID,
residuename=atom['RESNAME'],
xcoord=atom['X'],ycoord=atom['Y'],zcoord=atom['Z'])
if not status:
self.parent.record_event('Modelling failed in model_on_the_fly for operations: %s' %(str(operations)))
return []
# Update the arrays
X.Update()
# Rename the rest of the atoms
for this_atom in X.residues[resid]:
X.atoms[this_atom]['RESNAME']=atom['RESNAME']
X.Update()
#put mutation stuff into a tuple and return it too
#mutantinfo = (chainID,residuenumber)
# Return the PDBlines and the instance
pdblines=X.writepdb('dummy',nowrite=1)
# Store for next use
DB.tmp_3Dmodels[str(operations)]=pdblines[:]
return pdblines, X
else:
print 'Parent does not have a structure'
return [], None