def ssm_fit(aRefMol, aRefSel, aMovMol, aMovSel):
mgr = cuemol.getService("MolAnlManager");
refMol = cuemol.obj(aRefMol)
refSel = cuemol.sel(aRefSel, refMol.getScene())
movMol = cuemol.obj(aMovMol)
movSel = cuemol.sel(aMovSel, movMol.getScene())
mgr.superposeSSM1(refMol, refSel, movMol, movSel, False);
def create_default_paint_coloring():
rval = cm.createObj("PaintColoring")
rval.append(cm.sel("sheet"), cm.col("SteelBlue"))
rval.append(cm.sel("helix"), cm.col("khaki"))
rval.append(cm.sel("nucleic"), cm.col("yellow"))
rval.append(cm.sel("*"), cm.col("FloralWhite"))
return rval
def calc_rmsd(aRefMol, aRefSel, aMovMol, aMovSel):
mgr = cuemol.getService("MolAnlManager")
refMol = cuemol.obj(aRefMol)
refSel = cuemol.sel(aRefSel, refMol.getScene())
movMol = cuemol.obj(aMovMol)
movSel = cuemol.sel(aMovSel, movMol.getScene())
rmsd = mgr.calcRMSD(refMol, refSel, movMol, movSel, "")
return rmsd
def rotateZ(aMol, aCen, aDeg, aSel=None):
sel=aSel
if sel is None:
sel = cuemol.sel("*")
else:
sel = cuemol.sel(aSel)
mat = cuemol.createObj("Matrix")
mat.setRotate(aCen, cuemol.vec(0,0,1), aDeg)
aMol.xformByMat(mat, sel)
def shift(aMol, aShift, aSel=None, aNotify=True):
sel = aSel
if sel is None:
sel = cuemol.sel("*")
else:
sel = cuemol.sel(aSel)
mat = cuemol.createObj("Matrix")
mat.setTranslate(aShift)
aMol.xformByMat(mat, sel)
if aNotify:
aMol.fireAtomsMoved()
def rotate(aMol, aCen, aAxis, aDeg, aSel=None, aNotify=True):
sel = aSel
if sel is None:
sel = cuemol.sel("*")
else:
sel = cuemol.sel(aSel)
mat = cuemol.createObj("Matrix")
mat.setRotate(aCen, aAxis, aDeg)
aMol.xformByMat(mat, sel)
if aNotify:
aMol.fireAtomsMoved()
def merge(aToMol, aFromMol, aFromSel, aCopy=False):
mgr = cuemol.getService("MolAnlManager");
toMol = cuemol.obj(aToMol)
fromMol = cuemol.obj(aFromMol)
fromSel = cuemol.sel(aFromSel, fromMol.getScene())
mgr.copyAtoms(toMol, fromMol, fromSel);
if not aCopy:
mgr.deleteAtoms(fromMol, fromSel);
def __init__(self, aMol, aSel):
molObj = cuemol.obj(aMol)
selObj = cuemol.sel(aSel, molObj.scene_uid)
self.mIter = cuemol.createObj("ResidIterator");
self.mIter.target = molObj;
self.mIter.sel = selObj;
self.mIter.first()
def __init__(self, aMol, aSel="*"):
molObj = cuemol.obj(aMol)
#uid = molObj.uid
selObj = cuemol.sel(aSel, molObj.scene_uid)
self.mIter = cuemol.createObj("AtomIterator")
self.mIter.target = molObj
self.mIter.sel = selObj
self.mIter.first()
def forEachResid(aMol, aSel, aFn):
molObj = cuemol.obj(aMol)
selObj = cuemol.sel(aSel, molObj.scene_uid)
iter = cuemol.createObj("ResidIterator");
iter.target = molObj;
iter.sel = selObj;
iter.first()
while True:
if not iter.hasMore():
break
resid = iter.get()
if aFn(resid):
break
iter.next()
def setupDefaultRenderer(obj):
"""
Setup default renderer for object loaded by CUI's load() function
"""
rend = None
scene = obj.getScene()
## EDIT TXN START ##
with cm.UndoTxn("Create default renderer", scene):
rend = obj.createRenderer("simple")
rend.applyStyles("DefaultCPKColoring")
rend.name = "simple1"
rend.sel = cm.sel("*")
print("active view ID="+str(scene.activeViewID))
view = cm.view(scene)
if view is None:
print("setupDefault renderer: view is null, cannot recenter")
else:
pos = rend.getCenter()
view.setViewCenter(pos)
## EDIT TXN END ##
return rend
def chg_chain(aFromMol, aFromSel, aNewChName):
mgr = cuemol.getService("MolAnlManager");
fromMol = cuemol.obj(aFromMol)
fromSel = cuemol.sel(aFromSel, fromMol.getScene())
mgr.changeChainName(fromMol, fromSel, aNewChName);
def del_atoms(aMol, aSel):
mgr = cuemol.getService("MolAnlManager");
mol = cuemol.obj(aMol)
sel = cuemol.sel(aSel, mol.getScene())
mgr.deleteAtoms(mol, sel);
