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 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 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 delete(aObj, aType=None):
tgt = None
if cuemol.iswrapper(aObj):
tgt = aObj
else:
# try renderer name/uid
try:
tgt = cuemol.rend(aObj)
except:
pass
# try object name/uid
if tgt == None:
try:
tgt = cuemol.obj(aObj)
except:
return False
if cuemol.isobj(tgt):
sc = tgt.getScene()
sc.destroyObject(tgt.uid)
return True
elif cuemol.isrend(tgt):
obj = tgt.getClientObj()
obj.destroyRenderer(tgt.uid)
return True
return False
def delete(aObj, aType=None):
tgt = None
if cuemol.iswrapper(aObj):
tgt = aObj
else:
# try renderer name/uid
try:
tgt = cuemol.rend(aObj)
except:
pass
# try object name/uid
if tgt==None:
try:
tgt = cuemol.obj(aObj)
except:
return False
if cuemol.isobj(tgt):
sc = tgt.getScene()
sc.destroyObject(tgt.uid)
return True
elif cuemol.isrend(tgt):
obj = tgt.getClientObj()
obj.destroyRenderer(tgt.uid)
return True
return False
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 saveObject(aObj, aFileName, aFmtName, aOpts=None):
obj = cuemol.obj(aObj)
strMgr = cuemol.svc("StreamManager")
writer = strMgr.createHandler(aFmtName, 1)
writer.setPath(aFileName)
writer.attach(obj)
writer.write()
writer.detach()
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 saveObject(aObj, aFileName, aFmtName, aOpts=None):
obj = cuemol.obj(aObj)
strMgr = cuemol.svc("StreamManager")
writer = strMgr.createHandler(aFmtName, 1)
if aOpts is not None:
for k, v in aOpts.items():
print("writer set prop: k=", k, "v=", v)
ci.setProp(writer, k, v)
writer.setPath(aFileName)
writer.attach(obj)
writer.write()
writer.detach()
def saveObject(aObj, aFileName, aFmtName, aOpts=None):
obj = cm.obj(aObj)
strMgr = cm.strMgr()
writer = strMgr.createHandler(aFmtName, 1)
if aOpts is not None:
for k,v in aOpts.items():
print("writer set prop: k=",k,"v=",v)
ci.setProp(writer._wrapped, k, v)
writer.setPath(aFileName)
writer.attach(obj)
writer.write();
writer.detach();
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 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);