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()