def test1():
obj = cuemol.createObj("Vector")
obj2 = cuemol.createObj("Vector")
print "Result: ", obj.UID
print "v.x = ", obj.x
obj.x = 123.456
print "v.x = ", obj.x
obj.set4(1, 2, 3, 4)
print "toString() = ", obj.toString()
return
def atomPropCol(mol):
iter = cuemol.createObj("AtomIterator")
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
def atomPropCol(mol):
iter = cuemol.createObj("AtomIterator")
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
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 __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 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 __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 makeSel(self, selstr, uid):
sel = cm.createObj("SelCommand")
if uid:
if not sel.compile(selstr, uid):
return null
else:
if not sel.compile(selstr, 0):
return null
return sel
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
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 readPDB(fname):
# Create Mol & Register to the scene
mol = cuemol.createObj("MolCoord");
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);
return mol
def readPDB(fname):
# Create Mol & Register to the scene
mol = cuemol.createObj("MolCoord")
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)
return mol
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 makeSel(mol, selstr):
selobj = cuemol.createObj("SelCommand");
uid = mol.scene_uid
if (not selobj.compile(selstr, uid)):
return null
return selobj
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"
rend.coloring = cuemol.createObj("AtomPropColoring");
atomPropCol(mol)
pos = rend.getCenter();
view.setViewCenter(pos);
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()
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;
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"
rend.coloring = cuemol.createObj("AtomPropColoring")
atomPropCol(mol)
pos = rend.getCenter()
view.setViewCenter(pos)
def makeSel(mol, selstr):
selobj = cuemol.createObj("SelCommand")
uid = mol.scene_uid
if (not selobj.compile(selstr, uid)):
return null
return selobj
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
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()