Pmv.hbondCommands

1 2 ############################################################################ 3 # 4 # Author: Ruth HUEY 5 # 6 # Copyright: M. Sanner TSRI 2000 7 # 8 ############################################################################# 9 10 # $Header 11 # 12 # $Id: hbondCommands.py,v 1.84.4.2 2007/09/21 22:30:06 sargis Exp $ 13 # 14 15 16 from ViewerFramework.VFCommand import CommandGUI 17 from ViewerFramework.VF import AddAtomsEvent 18 from mglutil.gui.BasicWidgets.Tk.colorWidgets import ColorChooser 19 20 from mglutil.gui.InputForm.Tk.gui import InputFormDescr 21 from mglutil.util.callback import CallBackFunction 22 from mglutil.gui.BasicWidgets.Tk.customizedWidgets \ 23 import ExtendedSliderWidget, ListChooser 24 from mglutil.gui.BasicWidgets.Tk.thumbwheel import ThumbWheel 25 26 from Pmv.mvCommand import MVCommand, MVAtomICOM, MVBondICOM 27 from Pmv.measureCommands import MeasureAtomCommand 28 29 from MolKit.molecule import Atom, AtomSet, Bond 30 from MolKit.molecule import BondSet, HydrogenBond, HydrogenBondSet 31 from MolKit.distanceSelector import DistanceSelector 32 from MolKit.hydrogenBondBuilder import HydrogenBondBuilder 33 from MolKit.pdbWriter import PdbWriter 34 35 from DejaVu.Geom import Geom 36 from DejaVu.Spheres import Spheres 37 from DejaVu.Points import CrossSet 38 from DejaVu.Cylinders import Cylinders 39 from DejaVu.spline import DialASpline, SplineObject 40 from DejaVu.GleObjects import GleExtrude, GleObject 41 from DejaVu.Shapes import Shape2D, Triangle2D, Circle2D, Rectangle2D,\ 42 Square2D, Ellipse2D 43 44 from Pmv.stringSelectorGUI import StringSelectorGUI 45 from PyBabel.util import vec3 46 47 import Tkinter, Numeric, math, string, os 48 from string import strip, split 49 from types import StringType 50 51 from opengltk.OpenGL import GL 52 53 from DejaVu.glfLabels import GlfLabels 54 55

56 -def check_hbond_geoms(VFGUI):

57 hbond_geoms_list = VFGUI.VIEWER.findGeomsByName('hbond_geoms') 58 if hbond_geoms_list==[]: 59 hbond_geoms = Geom("hbond_geoms", shape=(0,0), protected=True) 60 VFGUI.VIEWER.AddObject(hbond_geoms, parent=VFGUI.miscGeom) 61 hbond_geoms_list = [hbond_geoms] 62 return hbond_geoms_list[0]

63 64 65 66 # lists of babel_types for donor-acceptor 67 # derived from MacDonald + Thornton 68 # 'Atlas of Side-Chain + Main-Chain Hydrogen Bonding' 69 # plus sp2Acceptor Nam 70 71 sp2Donors = ['Nam', 'Ng+', 'Npl'] 72 sp3Donors = ['N3+', 'O3','S3'] 73 allDonors = [] 74 allDonors.extend(sp2Donors) 75 allDonors.extend(sp3Donors) 76 #added Nam because of bdna cytidine N3 77 #NB: Npl cannot be an acceptor if the sum of its bonds' bondOrder>2 78 sp2Acceptors = ['O2', 'O-', 'Npl', 'Nam'] 79 sp3Acceptors = ['S3', 'O3'] 80 allAcceptors = [] 81 allAcceptors.extend(sp2Acceptors) 82 allAcceptors.extend(sp3Acceptors) 83 a_allAcceptors = [] 84 for n in allAcceptors: 85 a_allAcceptors.append('a'+n) 86 87

88 -def dist(c1, c2):

89 d = Numeric.array(c2) - Numeric.array(c1) 90 ans = math.sqrt(Numeric.sum(d*d)) 91 return round(ans, 3)

92 93

94 -def getAngle(ac, hat, don ):

95 acCoords = getTransformedCoords(ac) 96 hCoords = getTransformedCoords(hat) 97 dCoords = getTransformedCoords(don) 98 pt1 = Numeric.array(acCoords, 'f') 99 pt2 = Numeric.array(hCoords, 'f') 100 pt3 = Numeric.array(dCoords, 'f') 101 #pt1 = Numeric.array(ac.coords, 'f') 102 #pt2 = Numeric.array(hat.coords, 'f') 103 #pt3 = Numeric.array(don.coords, 'f') 104 v1 = Numeric.array(pt1 - pt2) 105 v2 = Numeric.array(pt3 - pt2) 106 dist1 = math.sqrt(Numeric.sum(v1*v1)) 107 dist2 = math.sqrt(Numeric.sum(v2*v2)) 108 sca = Numeric.dot(v1, v2)/(dist1*dist2) 109 if sca>1.0: 110 sca = 1.0 111 elif sca<-1.0: 112 sca = -1.0 113 ang = math.acos(sca)*180./math.pi 114 return round(ang, 5)

115 116

117 -def applyTransformation(pt, mat):

118 pth = [pt[0], pt[1], pt[2], 1.0] 119 return Numeric.matrixmultiply(mat, pth)[:3]

120 121

122 -def getTransformedCoords(atom):

123 # when there is no viewer, the geomContainer is None 124 if atom.top.geomContainer is None: 125 return atom.coords 126 g = atom.top.geomContainer.geoms['master'] 127 c = applyTransformation(atom.coords, g.GetMatrix(g)) 128 return c.astype('f')

129 130 131

132 -class GetHydrogenBondDonors(MVCommand):

133 """This class allows user to get AtomSets of sp2 hydridized and sp3 hybridized hydrogenBond Donors able. 134 \nPackage : Pmv 135 \nModule : bondsCommands 136 \nClass : GetHydrogenBondDonors 137 \nCommand :getHBDonors 138 \nSynopsis:\n 139 sp2Donors, sp3Donors <- getHBDonors(nodes, donorList, **kw) 140 \nRequired Arguments:\n 141 nodes --- 142 donorList --- 143 """ 144

145 - def __init__(self, func=None):

146 MVCommand.__init__(self, func) 147 self.flag = self.flag | self.objArgOnly

148

149 - def onAddCmdToViewer(self):

150 if not self.vf.commands.has_key('typeAtoms'): 151 self.vf.loadCommand('editCommands', 'typeAtoms', 'Pmv', 152 topCommand=0)

153 154

155 - def __call__(self, nodes, donorList=allDonors,**kw):

156 """sp2Donors, sp3Donors <- getHBDonors(nodes, donorList, **kw) """ 157 if type(nodes) is StringType: 158 self.nodeLogString = "'"+nodes+"'" 159 nodes = self.vf.expandNodes(nodes) 160 if not len(nodes): return 'ERROR' 161 ats = nodes.findType(Atom) 162 try: 163 ats.babel_type 164 except AttributeError: 165 tops = ats.top.uniq() 166 for t in tops: 167 self.vf.typeAtoms(t.allAtoms, topCommand=0) 168 return apply(self.doitWrapper, (ats, donorList), kw)

169 170

171 - def checkForPossibleH(self, ats, blen):

172 #check that if at has all bonds, at least one is to a hydrogen 173 # have to do this by element?? 174 probAts = AtomSet(ats.get(lambda x, blen=blen: len(x.bonds)==blen)) 175 #probOAts = ats.get(lambda x, blen=blen: len(x.bonds)==blen) 176 #probSAts = ats.get(lambda x, blen=blen: len(x.bonds)==blen) 177 if probAts: 178 rAts = AtomSet([]) 179 for at in probAts: 180 if not len(at.findHydrogens()): 181 rAts.append(at) 182 if len(rAts): 183 ats = ats.subtract(rAts) 184 return ats

185 186

187 - def doit(self, ats, donorList):

188 #getHBDonors 189 sp2 = [] 190 sp3 = [] 191 for item in sp2Donors: 192 if item in donorList: sp2.append(item) 193 for item in sp3Donors: 194 if item in donorList: sp3.append(item) 195 196 dAts2 = ats.get(lambda x, l=sp2: x.babel_type in l) 197 if not dAts2: dAts2=AtomSet([]) 198 else: 199 dAts2 = self.checkForPossibleH(dAts2, 3) 200 201 dAts3 = ats.get(lambda x, l=sp3: x.babel_type in l) 202 if not dAts3: dAts3=AtomSet([]) 203 else: dAts3 = self.checkForPossibleH(dAts3, 4) 204 205 return dAts2, dAts3

206 207 208

209 -class GetHydrogenBondAcceptors(MVCommand):

210 """This class allows user to get AtomSets of sp2 hydridized and sp3 hybridized 211 hydrogenBond Acceptors. 212 \nPackage : Pmv 213 \nModule : hbondCommands 214 \nClass : GetHydrogenBondEnergies 215 \nCommand : getHBondEnergies 216 \nSynopsis:\n 217 sp2Acceptors, sp3Acceptors <- getHBAcceptors(nodes, acceptorList, **kw) 218 """ 219

220 - def __init__(self, func=None):

221 MVCommand.__init__(self, func) 222 self.flag = self.flag | self.objArgOnly

223

224 - def onAddCmdToViewer(self):

225 if not self.vf.commands.has_key('typeAtoms'): 226 self.vf.loadCommand('editCommands', 'typeAtoms', 'Pmv', 227 topCommand=0)

228 229

230 - def __call__(self, nodes, acceptorList=allAcceptors,**kw):

231 """sp2Acceptors, sp3Acceptors <- getHBAcceptors(nodes, acceptorList, **kw) """ 232 if type(nodes) is StringType: 233 self.nodeLogString = "'"+nodes+"'" 234 nodes = self.vf.expandNodes(nodes) 235 if not len(nodes): return 'ERROR' 236 ats = nodes.findType(Atom) 237 #no way to know if typeBonds has been called on each molecule! 238 try: 239 ats._bndtyped 240 except: 241 tops = ats.top.uniq() 242 for t in tops: 243 self.vf.typeBonds(t.allAtoms, topCommand=0) 244 return apply(self.doitWrapper, (ats, acceptorList), kw)

245 246

247 - def filterAcceptors(self, accAts):

248 ntypes = ['Npl', 'Nam'] 249 npls = accAts.get(lambda x, ntypes=ntypes: x.babel_type=='Npl') 250 nams = accAts.get(lambda x, ntypes=ntypes: x.babel_type=='Nam') 251 #nAts = accAts.get(lambda x, ntypes=ntypes: x.babel_type in ntypes) 252 restAts = accAts.get(lambda x, ntypes=ntypes: x.babel_type not in ntypes) 253 if not restAts: restAts = AtomSet([]) 254 #if nAts: 255 if npls: 256 #for at in nAts: 257 for at in npls: 258 s = 0 259 for b in at.bonds: 260 if b.bondOrder=='aromatic': 261 s = s + 2 262 else: s = s + b.bondOrder 263 #if s<3: 264 #apparently this is wrong 265 if s<4: 266 restAts.append(at) 267 if nams: 268 #for at in nAts: 269 for at in nams: 270 s = 0 271 for b in at.bonds: 272 if b.bondOrder=='aromatic': 273 s = s + 2 274 else: s = s + b.bondOrder 275 #s = s + b.bondOrder 276 if s<3: 277 restAts.append(at) 278 return restAts

279 280 281

282 - def doit(self, ats, acceptorList):

283 #getHBAcceptors 284 sp2 = [] 285 sp3 = [] 286 for item in sp2Acceptors: 287 if item in acceptorList: sp2.append(item) 288 for item in sp3Acceptors: 289 if item in acceptorList: sp3.append(item) 290 291 dAts2 = AtomSet(ats.get(lambda x, l=sp2: x.babel_type in l)) 292 if dAts2: 293 dAts2 = self.filterAcceptors(dAts2) 294 dAts3 = AtomSet(ats.get(lambda x, l=sp3: x.babel_type in l)) 295 return dAts2, dAts3

296 297 298

299 -class GetHydrogenBondEnergies(MVCommand):

300 """This class allows user to get a list of energies of HydrogenBonds. For this calculation, the bond must have a hydrogen atom AND it must know its type. 301 Energy calculation based on "Protein Flexibility and dynamics using constraint 302 theory", J. Molecular Graphics and Modelling 19, 60-69, 2001. MF Thorpe, Ming 303 Lei, AJ Rader, Donald J.Jacobs and Leslie A. Kuhn. 304 \nPackage : Pmv 305 \nModule : hbondCommands 306 \nClass : GetHydrogenBondEnergies 307 \nCommand : getHBondEnergies 308 \nSynopsis:\n 309 [energies] <- getHBondEnergies(nodes, **kw) 310 \nRequired Arguments:\n 311 nodes --- TreeNodeSet holding the current selection 312 """ 313

314 - def __init__(self, func=None):

315 MVCommand.__init__(self, func) 316 self.flag = self.flag | self.objArgOnly

317

318 - def onAddCmdToViewer(self):

319 self.vf.loadModule('measureCommands', 'Pmv', log=0) 320 if not self.vf.commands.has_key('typeAtoms'): 321 self.vf.loadCommand('editCommands', 'typeAtoms', 'Pmv', 322 topCommand=0, log=0)

323 324

325 - def __call__(self, nodes, **kw):

326 """[energies] <- getHBondEnergies(nodes, **kw) 327 \nnodes --- TreeNodeSet holding the current selection 328 """ 329 if type(nodes) is StringType: 330 self.nodeLogString = "'"+nodes+"'" 331 nodes = self.vf.expandNodes(nodes) 332 if not len(nodes): return 'ERROR' 333 ats = nodes.findType(Atom) 334 hats = AtomSet([]) 335 for at in ats: 336 if hasattr(at, 'hbonds'): hats.append(at) 337 if not len(hats): 338 self.warningMsg('no hbonds in specified nodes') 339 return 'ERROR' 340 return apply(self.doitWrapper, (hats,), kw)

341 342

343 - def getEnergy(self, b):

344 accAt = b.accAt 345 b0 = accAt.bonds[0] 346 acN = b0.atom1 347 if id(acN)==id(accAt): acN = b0.atom2 348 b.acN = acN 349 #b.acN = b.accAt.bonds[0].neighborAtom(b.accAt) 350 if b.dlen is None: 351 b.dlen = dist(getTransformedCoords(b.donAt), 352 getTransformedCoords(b.accAt)) 353 #b.dlen = dist(b.donAt.coords, b.accAt.coords) 354 r = 2.8/b.dlen 355 if b.phi is None: b.phi = self.vf.measureAngle(b.hAt, b.accAt, 356 acN, topCommand=0) 357 if b.theta is None: b.theta = self.vf.measureAngle(b.donAt, b.hAt, 358 b.accAt, topCommand=0) 359 b.gamma = self.vf.measureTorsion(b.donAt, b.hAt, b.accAt, 360 acN, topCommand=0) 361 #make all angles into radians 362 theta = b.theta * math.pi/180. 363 newAngle = math.pi - theta 364 gamma = b.gamma * math.pi/180. 365 phi = b.phi * math.pi/180. 366 n = 109.5*math.pi/180. 367 368 if b.type is None: 369 #get # of donAt+# of accAt 370 try: 371 b.donAt.babel_type 372 b.accAt.babel_type 373 except AttributeError: 374 b_ats = AtomSet([b.donAt, b.accAt]) 375 tops = b_ats.top.uniq() 376 for t in tops: 377 self.vf.typeAtoms(t.allAtoms, topCommand=0) 378 if b.donAt.babel_type in sp2Donors: 379 d1=20 380 else: 381 d1=30 382 if b.accAt.babel_type in sp2Acceptors: 383 d2=2 384 else: 385 d2=3 386 b.type = d1+d2 387 388 389 if b.type==33: 390 f = (math.cos(theta)**2)*\ 391 (math.e**(-(newAngle)**6))*(math.cos(phi-n)**2) 392 elif b.type==32: 393 f = (math.cos(theta)**2)*\ 394 (math.e**(-(newAngle)**6))*(math.cos(phi)**2) 395 elif b.type==23: 396 f = ((math.cos(theta)**2)*\ 397 (math.e**(-(newAngle)**6)))**2 398 else: 399 f = (math.cos(theta)**2)*\ 400 (math.e**(-(newAngle)**6))*(math.cos(max(theta, gamma))**2) 401 newVal = 8.*(5.*(r**12) - 6.*(r**10))*f 402 b.energy = round(newVal, 3) 403 return b.energy

404 405

406 - def doit(self, hats):

407 #getHBondEnergies 408 energyList = [] 409 hbonds = hats.hbonds 410 #SHOULD hbonds be checked for type??? HERE??????? 411 for b in hbonds: 412 if b.energy: 413 energyList.append(b.energy) 414 elif b.hAt is None: 415 energyList.append(None) 416 else: 417 energyList.append(self.getEnergy(b)) 418 #print 'returning ', len(energyList), ' hbond energies: ', energyList 419 return energyList

420 421 422

423 -class ShowHBDonorsAcceptors(MVCommand):

424 """This class allows user to show AtomSets of HydrogenBond donors and acceptors. 425 \nPackage : Pmv 426 \nModule : hbondCommands 427 \nClass : ShowHBDonorsAcceptors 428 \nCommand : showHBDA 429 \nSynopsis:\n 430 None <- showHBDA(dnodes, anodes, donorList, acceptorList, **kw) 431 """ 432 433

434 - def onAddCmdToViewer(self):

435 self.vf.loadModule('editCommands', 'Pmv', log=0) 436 self.vf.loadCommand('interactiveCommands','setICOM', 'Pmv', log=0) 437 #setup geoms 438 miscGeom = self.vf.GUI.miscGeom 439 hbond_geoms = check_hbond_geoms(self.vf.GUI) 440 self.masterGeom = Geom('hbondDonorAcceptorGeoms',shape=(0,0), 441 pickable=0, protected=True) 442 self.masterGeom.isScalable = 0 443 self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=hbond_geoms) 444 self.hbdonor2=CrossSet('hbSP2Donors', 445 materials=((0.,1.,1.),), offset=0.4, lineWidth=2, 446 inheritMaterial=0, protected=True) 447 self.hbdonor2.Set(visible=1, tagModified=False) 448 self.hbdonor2.pickable = 0 449 self.hbdonor3=CrossSet('hbSP3Donors', 450 materials=((0.,.3,1.),), offset=0.4, lineWidth=2, 451 inheritMaterial=0, protected=True) 452 self.hbacceptor2=Spheres('hbSP2Acceptors', shape=(0,3), 453 radii=0.2, quality=15, materials=((1.,.8,0.),), inheritMaterial=0, protected=True) 454 self.hbacceptor3=Spheres('hbSP3Acceptors', shape=(0,3), 455 radii=0.2, quality=15, materials=((1.,.2,0.),), inheritMaterial=0, protected=True) 456 for item in [self.hbdonor2, self.hbdonor3, self.hbacceptor2,\ 457 self.hbacceptor3]: 458 item.Set(visible=1, tagModified=False) 459 item.pickable = 0 460 self.vf.GUI.VIEWER.AddObject(item, parent=self.masterGeom) 461 #setup Tkinter variables 462 varNames = ['hideDSel', 'N3', 'O3','S3','Nam', 'Ng', 'Npl',\ 463 'hideASel', 'aS3', 'aO3', 'aO2', 'aO', 'aNpl', 464 'aNam', 'sp2D', 'sp3D', 'sp2A', 'sp3A','useSelection'] 465 466 for n in varNames: 467 exec('self.'+n+'=Tkinter.IntVar()') 468 exec('self.'+n+'.set(1)') 469 self.showDTypeSel = Tkinter.IntVar() 470 self.showATypeSel = Tkinter.IntVar()

471 472

473 - def __call__(self, dnodes, anodes, donorList=allDonors, 474 acceptorList=allAcceptors, **kw):

475 """None <- showHBDA(dnodes, anodes, donorList, acceptorList, **kw) """ 476 477 dnodes = self.vf.expandNodes(dnodes) 478 donats = dnodes.findType(Atom) 479 anodes = self.vf.expandNodes(anodes) 480 acats = anodes.findType(Atom) 481 if not (len(donats) or len(acats)): return 'ERROR' 482 apply(self.doitWrapper, (donats, acats, donorList, acceptorList), kw)

483 484

485 - def doit(self, donats, acats, donorList, acceptorList):

486 #showHBDA 487 if len(donats): 488 dAts2, dAts3 = self.vf.getHBDonors(donats, 489 donorList=donorList, topCommand=0) 490 msg = '' 491 if dAts2: 492 newVerts = [] 493 for at in dAts2: 494 newVerts.append(getTransformedCoords(at).tolist()) 495 self.hbdonor2.Set(vertices=newVerts, visible=1, 496 tagModified=False) 497 #self.hbdonor2.Set(vertices = dAts2.coords, visible=1, 498 # tagModified=False) 499 else: 500 msg = msg + 'no sp2 donors found ' 501 dAts2 = AtomSet([]) 502 self.hbdonor2.Set(vertices=[], tagModified=False) 503 if dAts3: 504 newVerts = [] 505 for at in dAts3: 506 newVerts.append(getTransformedCoords(at).tolist()) 507 self.hbdonor3.Set(vertices=newVerts, visible=1, 508 tagModified=False) 509 #self.hbdonor3.Set(vertices = dAts3.coords, visible=1, tagModified=False 510 else: 511 if len(msg): msg = msg + ';' 512 msg = msg + 'no sp3 donors found' 513 dAts3 = AtomSet([]) 514 self.hbdonor3.Set(vertices=[], tagModified=False) 515 if len(msg): 516 self.warningMsg(msg) 517 else: 518 dAts2 = AtomSet([]) 519 dAts3 = AtomSet([]) 520 self.hbdonor2.Set(vertices=[], tagModified=False) 521 self.hbdonor3.Set(vertices=[], tagModified=False) 522 #NOW THE ACCEPTORS: 523 if len(acats): 524 acAts2, acAts3 = self.vf.getHBAcceptors(acats, 525 acceptorList=acceptorList, topCommand=0) 526 msg = '' 527 if acAts2: 528 newVerts = [] 529 for at in acAts2: 530 newVerts.append(getTransformedCoords(at).tolist()) 531 self.hbacceptor2.Set(vertices = newVerts, visible=1, 532 tagModified=False) 533 #self.hbacceptor2.Set(vertices = acAts2.coords, visible=1, tagModified=False) 534 else: 535 msg = msg + 'no sp2 acceptors found ' 536 acAts2 = AtomSet([]) 537 self.hbacceptor2.Set(vertices=[], tagModified=False) 538 if acAts3: 539 newVerts = [] 540 for at in acAts3: 541 newVerts.append(getTransformedCoords(at).tolist()) 542 self.hbacceptor3.Set(vertices = newVerts, visible=1, 543 tagModified=False) 544 #self.hbacceptor3.Set(vertices = acAts3.coords, visible=1, tagModified=False) 545 else: 546 if len(msg): msg = msg + ';' 547 msg = msg + 'no sp3 acceptors found' 548 acAts3 = AtomSet([]) 549 self.hbacceptor3.Set(vertices=[], tagModified=False) 550 if len(msg): self.warningMsg(msg) 551 else: 552 acAts2 = AtomSet([]) 553 acAts3 = AtomSet([]) 554 self.hbacceptor2.Set(vertices=[], tagModified=False) 555 self.hbacceptor3.Set(vertices=[], tagModified=False) 556 self.vf.GUI.VIEWER.Redraw() 557 #PUT UP A FORM TO TOGGLE Visibility etc (?) 558 # show/hide sp2/sp3 559 # select, save 560 if not len(dAts2) and not len(dAts3) and not len(acAts2)\ 561 and not len(acAts3): 562 self.warningMsg('no donors or acceptors found') 563 return 564 ifd2 = self.ifd2 = InputFormDescr(title = "Show/Hide Donors and Acceptors") 565 if len(dAts2): 566 ifd2.append({'name':'donor2', 567 'widgetType':Tkinter.Checkbutton, 568 'wcfg':{'text':'sp2 donors ', 569 'variable': self.sp2D, 570 'command': CallBackFunction(self.showGeom, 571 self.hbdonor2, self.sp2D), 572 }, 573 'gridcfg':{'sticky':'w'}}) 574 if len(dAts3): 575 ifd2.append({'name':'donor3', 576 'widgetType':Tkinter.Checkbutton, 577 'wcfg':{'text':'sp3 donors ', 578 'variable': self.sp3D, 579 'command': CallBackFunction(self.showGeom, 580 self.hbdonor3, self.sp3D), 581 }, 582 'gridcfg':{'sticky':'w'}}) 583 # 'gridcfg':{'sticky':'w', 'row':-1, 'column':1}}) 584 if len(acAts2): 585 ifd2.append({'name':'accept2', 586 'widgetType':Tkinter.Checkbutton, 587 'wcfg':{'text':'sp2 acceptors ', 588 'variable': self.sp2A, 589 'command': CallBackFunction(self.showGeom, 590 self.hbacceptor2, self.sp2A), 591 }, 592 'gridcfg':{'sticky':'w'}}) 593 if len(acAts3): 594 ifd2.append({'name':'accept3', 595 'widgetType':Tkinter.Checkbutton, 596 'wcfg':{'text':'sp3 acceptors ', 597 'variable': self.sp3A, 598 'command': CallBackFunction(self.showGeom, 599 self.hbacceptor3, self.sp3A), 600 }, 601 'gridcfg':{'sticky':'w'}}) 602 #'gridcfg':{'sticky':'w', 'row':-1, 'column':1}}) 603 ifd2.append({'widgetType': Tkinter.Button, 604 'text':'Select', 605 'wcfg':{'bd':6}, 606 'gridcfg':{'sticky':'ew' }, 607 'command':CallBackFunction(self.select_cb,dAts2,dAts3,acAts2,acAts3)}) 608 ifd2.append({'widgetType': Tkinter.Button, 609 'text':'Cancel', 610 'wcfg':{'bd':6}, 611 'gridcfg':{'sticky':'ew', 'column':1,'row':-1}, 612 'command':self.cancel_cb}) 613 self.form2 = self.vf.getUserInput(self.ifd2, modal=0, blocking=0) 614 self.form2.root.protocol('WM_DELETE_WINDOW',self.cancel_cb)

615 616 617

618 - def showGeom(self, geom, var, event=None):

619 geom.Set(visible=var.get(), tagModified=False) 620 self.vf.GUI.VIEWER.Redraw()

621 622

623 - def select_cb(self, dAts2, dAts3, acAts2, acAts3):

624 #NB need to set level to Atom 625 self.vf.setIcomLevel(Atom) 626 vars = [self.sp2D, self.sp2D, self.sp2A, self.sp3A] 627 atL = [dAts2, dAts3, acAts2, acAts3] 628 for i in range(4): 629 if vars[i].get() and len(atL[i]): 630 self.vf.select(atL[i])

631 632

633 - def cancel_cb(self, event=None):

634 for g in [self.hbdonor2, self.hbdonor3, self.hbacceptor2,\ 635 self.hbacceptor3]: 636 g.Set(vertices=[], tagModified=False) 637 self.vf.GUI.VIEWER.Redraw() 638 self.form2.destroy()

639 640

641 - def buildForm(self):

642 ifd = self.ifd = InputFormDescr(title = "Select nodes + types of donor-acceptors:") 643 ifd.append({'name':'DkeyLab', 644 'widgetType':Tkinter.Label, 645 'text':'For Hydrogen Bonds Donors:', 646 'gridcfg':{'sticky':'w','columnspan':3}}) 647 ifd.append({'name':'selDRB0', 648 'widgetType':Tkinter.Radiobutton, 649 'wcfg':{'text':'Use all atoms', 650 'variable': self.hideDSel, 651 'value':1, 652 'command':self.hideDSelector 653 }, 654 'gridcfg':{'sticky':'w'}}) 655 ifd.append({'name':'selDRB1', 656 'widgetType':Tkinter.Radiobutton, 657 'wcfg':{'text':'Set atoms to use', 658 'variable': self.hideDSel, 659 'value':0, 660 'command':self.hideDSelector 661 }, 662 'gridcfg':{'sticky':'w', 'row':-1, 'column':1}}) 663 ifd.append({'name': 'keyDSelector', 664 'wtype':StringSelectorGUI, 665 'widgetType':StringSelectorGUI, 666 'wcfg':{ 'molSet': self.vf.Mols, 667 'vf': self.vf, 668 'all':1, 669 'crColor':(0.,1.,.2), 670 }, 671 'gridcfg':{'sticky':'we', 'columnspan':2 }}) 672 ifd.append({'name':'limitDTypes', 673 'widgetType':Tkinter.Checkbutton, 674 'wcfg':{'text':'Limit donor types ', 675 'variable': self.showDTypeSel, 676 'command':self.hideDTypes 677 }, 678 'gridcfg':{'sticky':'w', 'columnspan':2}}) 679 ifd.append({'name':'N3+', 680 'widgetType':Tkinter.Checkbutton, 681 'wcfg':{'text':'N3+', 682 'variable': self.N3, }, 683 'gridcfg':{'sticky':'w'}}) 684 ifd.append({'name':'O3', 685 'widgetType':Tkinter.Checkbutton, 686 'wcfg':{'text':'O3', 687 'variable': self.O3, }, 688 'gridcfg':{'sticky':'w','row':-1, 'column':1}}) 689 ifd.append({'name':'S3', 690 'widgetType':Tkinter.Checkbutton, 691 'wcfg':{'text':'S3', 692 'variable': self.S3, }, 693 'gridcfg':{'sticky':'w','row':-1, 'column':2}}) 694 ifd.append({'name':'Nam', 695 'widgetType':Tkinter.Checkbutton, 696 'wcfg':{'text':'Nam', 697 'variable': self.Nam, }, 698 'gridcfg':{'sticky':'w'}}) 699 ifd.append({'name':'Ng+', 700 'widgetType':Tkinter.Checkbutton, 701 'wcfg':{'text':'Ng+', 702 'variable': self.Ng, }, 703 'gridcfg':{'sticky':'w','row':-1, 'column':1}}) 704 ifd.append({'name':'Npl', 705 'widgetType':Tkinter.Checkbutton, 706 'wcfg':{'text':'Npl', 707 'variable': self.Npl, }, 708 'gridcfg':{'sticky':'w','row':-1, 'column':2}}) 709 #now the acceptors 710 ifd.append({'name':'AkeyLab', 711 'widgetType':Tkinter.Label, 712 'text':'For Hydrogen Bonds Acceptors:', 713 'gridcfg':{'sticky':'w','columnspan':3}}) 714 ifd.append({'name':'selARB0', 715 'widgetType':Tkinter.Radiobutton, 716 'wcfg':{'text':'Use all atoms', 717 'variable': self.hideASel, 718 'value':1, 719 'command':self.hideASelector 720 }, 721 'gridcfg':{'sticky':'w'}}) 722 ifd.append({'name':'selARB1', 723 'widgetType':Tkinter.Radiobutton, 724 'wcfg':{'text':'Set atoms to use', 725 'variable': self.hideASel, 726 'value':0, 727 'command':self.hideASelector 728 }, 729 'gridcfg':{'sticky':'w', 'row':-1, 'column':1}}) 730 ifd.append({'name': 'keyASelector', 731 'wtype':StringSelectorGUI, 732 'widgetType':StringSelectorGUI, 733 'wcfg':{ 'molSet': self.vf.Mols, 734 'vf': self.vf, 735 'all':1, 736 'crColor':(0.,1.,.2), 737 }, 738 'gridcfg':{'sticky':'we', 'columnspan':2 }}) 739 ifd.append({'name':

Source Code for Module Pmv.hbondCommands