def atoms_surfnet(osl,
useMesh=True,
interval=1.0,
cutoff=10,
density='Gaussian',
color=None):
try:
atomList = Midas._selectedAtoms(osl)
except (Midas.MidasError, chimera.oslParser.OSLSyntaxError), e:
return str(e)
def interface_surfnet(receptorOSL,
ligandsOSL,
useMesh=True,
interval=1.0,
cutoff=10,
density='Gaussian',
color=None):
try:
receptorAtomList = Midas._selectedAtoms(receptorOSL)
except (Midas.MidasError, chimera.oslParser.OSLSyntaxError), e:
return str(e)
def MethodTwo():
Midas.close("all")
# Parameters
featureNumShells = 6
featureShellThickness = 1.0
# Load Molecule
modelSel = "#0"
[mol] = chimera.openModels.open(pdbfilename)
chimera.viewer.scaleFactor = 4.5
# Draw as Ribbon
Midas.resrepr("smooth", modelSel)
for res in mol.residues:
res.drawMode = chimera.Residue.Ribbon_Edged
# Display Calciums
calciumsSel = modelSel + "::ca"
Midas.vdwdefine("ca", "ca", 0.5, calciumsSel)
Midas.show(calciumsSel)
Midas.represent("sphere", calciumsSel)
# Display Shells
calciums = Midas._selectedAtoms(calciumsSel)
featureModels = []
for calcium in calciums:
location = calcium.coord().xyz.data()
t = apply(newTranslation, location)
f = FeatureShellNode(featureNumShells, featureShellThickness)
t.addChild(f)
featureModels += useVRML(t, name="FEATURE Shell")
# Load hitsfile
import viewhitfile
viewhitfile.loadFile(hitfilename)
def interface_surfnet(receptorOSL,
ligandsOSL,
useMesh=True,
interval=1.0,
cutoff=10,
density='Gaussian',
color=None):
try:
receptorAtomList = Midas._selectedAtoms(receptorOSL)
except (Midas.MidasError, chimera.oslParser.OSLSyntaxError), e:
return str(e)
if not receptorAtomList:
return 'No receptor atoms selected'
try:
ligandsAtomList = Midas._selectedAtoms(ligandsOSL)
except (Midas.MidasError, chimera.oslParser.OSLSyntaxError), e:
return str(e)
if not ligandsAtomList:
return 'No ligand atoms selected'
surfmol = _surfnet.interface_surfnet(receptorAtomList,
ligandsAtomList,
True,
cutoff=cutoff,
threshold=interval)
print '%d spheres' % len(surfmol.atoms)
mList = show_surfnet(surfmol, useMesh, interval, density, color)
for m in mList:
m.name = 'Surfnet for "%s" - "%s"' % (receptorOSL, ligandsOSL)
surfmol.destroy()
return None
def getLocation(specifier):
[atom] = Midas._selectedAtoms(specifier)
return atom.coord().xyz.data()