def __init__(self, hitfile, master=None):
Tkinter.Toplevel.__init__(self, master)
self.hitfile = hitfile
self.hitNodeList = HitNodeList(self.hitfile.hits)
self.maxScore = 0
self.models = []
basename = os.path.basename(hitfile.filename)
(pdbid, ext) = os.path.splitext(basename)
self.pdbid = pdbid
# Find MaxScore for slider
if self.hitfile.hits:
self.maxScore = max(self.hitfile.hits).score
# Open Molecule if it isn't already open
self.mol = None
if myvrml.getModelNo(pdbid.lower()) == None:
self.mol = myvrml.openMolecule(pdbid)
# highlight hetatms
Midas.represent("sphere", "#%d:.het" % self.mol.id)
Midas.represent("sphere", "#%d:ca" % self.mol.id)
self._buildGui()
def pdbSelect(self):
# Identify selected pbid
sels = self.pdbListBox.getcurselection()
if not sels:
return
pdbid = sels[0]
# Set pdbid
self.pdbid = pdbid
# clean up previous pdbid selection
self.cleanupPdbSelect()
# Open Molecule if it isn't already open
if myvrml.getModelNo(pdbid.lower()) == None:
self.mol = myvrml.openMolecule(pdbid)
# highlight hetatms
Midas.represent("sphere", "#%d:.het" % self.mol.id)
Midas.represent("sphere", "#%d:ca" % self.mol.id)
# Get sites for the pdbid
self.sites = self.sitefile.getByPdbid(pdbid)
# Update listbox
siteStrings = [PrettySiteString(s) for s in self.sites]
self.siteListBox.setlist(siteStrings)
# Select all sites
self.siteListBox._listbox.select_set(0,'end')
self.siteSelect()
def _clearModelColor(self):
# obtain modelNo
modelNo = myvrml.getModelNo(self.pdbid.lower())
if modelNo == None:
return
# Reset model color
Midas.uncolor(None, "#%d" % modelNo)
Midas.unrescolor(None, "#%d" % modelNo)
def __init__(self, pdbid, motifs, master=None):
Tkinter.Toplevel.__init__(self, master)
self.pdbid = pdbid
self.motifs = motifs
self.models = []
self.motifs.sort()
# Open Molecule if it isn't already open
self.mol = None
if myvrml.getModelNo(pdbid.lower()) == None:
self.mol = myvrml.openMolecule(pdbid)
# highlight hetatms
Midas.represent("sphere", "#%d:.het" % self.mol.id)
Midas.represent("sphere", "#%d:ca" % self.mol.id)
self._displayGui()
def _displayMotif(self, motif):
# obtain modelNo
modelNo = myvrml.getModelNo(motif.pdbid.lower())
if modelNo == None:
print "No Model"
return
group = myvrml.GroupNode()
# obtain chain residue numbers
chainRes = []
mol = chimera.openModels.list(id=modelNo)[0]
residues = mol.residues
residues.sort(lambda a, b: cmp(a.id.position, b.id.position))
for res in residues:
if res.id.chainId.strip() == motif.chainid:
chainRes.append(res)
# Hilight motif
motifSel = "#%d:%d-%d.%s" % (
modelNo, chainRes[motif.start].id.position,
chainRes[motif.end - 1].id.position, motif.chainid)
if gVerbose:
print "MOTIFSEL:", motifSel
print "START RES:", chainRes[motif.start].type,
print "STOP RES:", chainRes[motif.end - 1].type
Midas.color("red", motifSel)
Midas.rescolor("red", motifSel)
if gHaveCore:
# Hilight coreMotif
coreMotifSel = "#%d:%d-%d.%s" % (
modelNo, chainRes[motif.coreStart].id.position,
chainRes[motif.coreEnd - 1].id.position, motif.chainid)
print "CORESEL:", coreMotifSel
Midas.color("yellow", coreMotifSel)
print motif
return group