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 test2():
scm = cuemol.getService("SceneManager")
scid = scm.activeSceneID
print "Active scene ID=", scid
sc = scm.getScene(scid)
vwid = sc.activeViewID
print "Active view ID=", vwid
color = cuemol.createObj("Color")
color.setCode(0xFFFFFF)
sc.bgcolor = color
import cuemol
import wx
print "wc.veersion= " + wx.version()
print "scene ID = " + str(scene_id)
print "view ID = " + str(view_id)
scm = cuemol.getService("SceneManager")
scene = scm.getScene(scene_id)
print "scene.uid = " + str(scene.uid)
color = cuemol.createObj("Color")
color.setCode(0xFFFFFF)
scene.bgcolor = color
iter.target = mol
iter.first()
i = 0;
col = cuemol.createObj("Color")
while iter.hasMore():
atom = iter.get()
col.setHSB(i/360.0, 1.0, 1.0)
ccode = col.getCode()
atom.setAtomPropInt("col", ccode)
iter.next()
i = i+131
##############################
scm = cuemol.getService("SceneManager")
# scid = scm.activeSceneID;
# scene = scm.getScene(scid);
scene = scm.getScene(scene_id);
# view = scm.getView(scene.activeViewID);
view = scm.getView(view_id);
mol = readPDB(fname)
mol.name = "PLP"
scene.addObject(mol)
mol.applyTopology()
rend = createRend(mol, "simple", "*");
# rend.applyStyles("DefaultCPK,DefaultCPKColoring");
rend.name = "simple1"
def test3():
scm = cuemol.getService("SceneManager")
scid = scm.activeSceneID
print "Active scene ID=", scid
scene = scm.getScene(scid)
#print "scene = "+str(scene)
mol = cuemol.createObj("MolCoord")
fname = '/Users/user/Dropbox/works/test_data/1CRN.pdb'
for line in open(fname):
#print "PDB: ", line;
if line[0:6] in ["ATOM ", "HETATM"]:
aname = line[12:16].strip()
altloc = line[16:17]
resn = line[17:20].strip()
chn = line[21:22]
resid = int(line[22:26])
ins = line[26:27]
posx = float(line[30:38])
posy = float(line[38:46])
posz = float(line[46:54])
occ = float(line[54:60])
bfac = float(line[60:66])
elem = line[76:78].strip()
else:
print "PDB: ", line
continue
# print "name=", aname
atom = cuemol.createObj("MolAtom")
atom.name = aname
atom.element = elem
atom.bfac = bfac
atom.occ = occ
vpos = cuemol.createObj("Vector")
vpos.set3(posx, posy, posz)
atom.pos = vpos
mol.appendAtom1(atom, chn, resid, resn)
# apply topology
mol.applyTopology()
mol.name = "Mol"
# calc 2nry str
mgr = cuemol.getService("MolAnlManager")
mgr.calcProt2ndry2(mol, True, 0.0)
# Register to the scene
scene.addObject(mol)
# Create simple renderer
rend = mol.createRenderer("simple")
rend.name = "simple1"
rend.applyStyles("DefaultCPKColoring")
vwid = scene.activeViewID
print "Active view ID=", vwid
view = scm.getView(vwid)
view.setViewCenter(rend.getCenter())
return
import cuemol
# Create new scene
scm = cuemol.getService("SceneManager")
scene = scm.createScene()
mol = cuemol.createObj("MolCoord")
# Register to the scene
scene.addObject(mol)
#####
fname = '/net3/ishitani/PLP.pdb'
for line in open(fname):
# print "PDB: ", line;
if line[0:6] in ["ATOM ", "HETATM"]:
aname = line[12:16].strip()
altloc = line[16:17]
resn = line[17:20].strip()
chn = line[21:22]
resid = int(line[22:26])
ins = line[26:27]
posx = float(line[30:38])
posy = float(line[38:46])
posz = float(line[46:54])
occ = float(line[54:60])
bfac = float(line[60:66])
elem = line[76:78].strip()
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);
def __init__(self):
self._mgr = cm.getService("ScrEventManager")
self._mgr.addListener(self._listener)
self._slot = {}
print("********** EventManager __init__!!")
import cuemol
# Create new scene
scm = cuemol.getService("SceneManager");
scene = scm.createScene();
mol = cuemol.createObj("MolCoord");
# Register to the scene
scene.addObject(mol);
#####
fname = '/net3/ishitani/PLP.pdb';
for line in open(fname):
# print "PDB: ", line;
if line[0:6] in ["ATOM ", "HETATM"]:
aname = line[12:16].strip( )
altloc = line[16:17]
resn = line[17:20].strip( )
chn = line[21:22]
resid = int( line[22:26] )
ins = line[26:27]
posx = float( line[30:38] )
posy = float( line[38:46] )
posz = float( line[46:54] )
occ = float( line[54:60] )
bfac = float( line[60:66] )
elem = line[76:78].strip()