Changeset 818
- Timestamp:
- Dec 20, 2012 12:15:43 PM (9 years ago)
- Location:
- trunk
- Files:
-
- 6 edited
-
GSASII.py (modified) (1 diff)
-
GSASIIdata.py (modified) (1 diff)
-
GSASIIgrid.py (modified) (2 diffs)
-
GSASIImath.py (modified) (4 diffs)
-
GSASIIplot.py (modified) (5 diffs)
-
GSASIIrestrGUI.py (modified) (32 diffs)
Legend:
- Unmodified
- Added
- Removed
-
trunk/GSASII.py
r817 r818 1085 1085 self.ContourColor = 'Paired' 1086 1086 self.VcovColor = 'RdYlGn' 1087 self.RamaColor = ' RdYlGn'1087 self.RamaColor = 'Blues' 1088 1088 self.Projection = 'equal area' 1089 1089 self.logPlot = False -
trunk/GSASIIdata.py
r817 r818 11 11 import numpy as np 12 12 13 ramachandranDist = np.array([ 14 0,8,15,15,12,9,6,5,6,5,7,13,9,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,1,0,0,0,0,0,0,0,0,0,0, 15 0,1,0,0,3,3,7,5,7,2,3,3,7,4,4,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1, 16 0,0,0,0,1,3,1,2,2,3,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,1,0,0,0,0,0,0,0,0,0, 17 0,0,0,0,0,1,0,0,2,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0, 18 0,0,0,1,1,0,0,0,0,1,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 19 0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,2,2,1,0,0,0,0,0,0,0,0,0,0,0,0, 20 0,0,1,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0, 21 0,0,0,0,0,0,0,1,0,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 22 0,0,0,0,0,0,1,0,0,2,2,2,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 23 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0,0,0,0,0,0,1,0,6,13,20,28,48,66,124,225,357,128,8,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1, 34 0,0,0,0,0,1,1,5,8,29,41,46,52,88,119,177,154,34,7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0, 35 0,0,0,0,0,0,2,1,11,19,32,43,82,121,120,115,39,6,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,2,0,0,1,0,1,0,0,0,0,0, 36 0,0,0,0,0,0,0,4,21,19,42,65,104,108,83,34,8,3,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,8,4,1,0,0,0,0,0,0,0,0,0, 37 0,0,0,0,1,2,5,3,18,30,40,72,98,63,17,6,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,10,5,1,0,0,0,0,0,0,0,0,0, 38 0,1,0,0,0,1,5,10,19,37,42,65,51,22,6,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,18,17,0,0,0,0,0,0,0,0,0,0,1, 39 0,0,0,0,0,1,3,6,10,28,24,32,11,6,1,3,2,0,0,0,0,0,0,0,0,0,0,0,0,0,3,18,24,4,0,0,0,0,0,0,0,0,0,0,0, 40 0,0,0,0,0,1,3,12,12,18,14,5,5,3,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,3,9,31,34,7,1,0,0,0,0,0,0,0,0,0,0, 41 0,0,0,0,0,0,2,4,7,7,6,3,5,1,3,0,1,0,1,0,0,0,0,0,0,0,0,0,0,5,34,50,25,3,0,0,0,0,0,0,0,0,0,1,0, 42 0,0,0,0,0,1,5,2,5,4,5,5,3,0,1,2,0,0,0,0,0,0,0,0,0,0,1,0,1,7,36,33,13,1,1,0,0,0,0,0,0,0,0,0,0, 43 0,0,0,1,0,0,2,10,8,2,1,1,6,10,8,0,0,0,0,0,0,0,0,0,0,0,0,0,1,7,16,14,2,0,0,0,0,0,0,0,0,0,0,0,0, 44 0,0,0,0,0,6,5,8,13,7,3,0,13,5,13,2,0,0,0,0,0,0,0,0,0,0,0,0,0,5,7,6,1,0,0,0,0,0,0,1,0,0,1,0,0, 45 0,0,1,1,4,4,7,15,13,7,4,1,8,21,15,2,0,0,0,0,1,0,0,0,0,0,0,0,1,2,2,3,0,0,1,0,0,0,0,0,0,0,0,0,0, 46 0,0,1,0,2,4,8,13,19,9,8,5,13,16,10,6,2,0,0,0,0,1,0,1,0,0,0,0,0,1,0,1,1,1,0,1,0,0,0,0,0,0,0,0,1, 47 0,0,1,2,2,4,10,12,11,16,8,10,19,16,14,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,3,0,0, 48 1,0,0,2,2,4,3,8,9,27,15,8,17,31,15,3,0,2,0,0,1,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0, 49 0,0,0,4,1,7,12,20,31,40,37,50,54,47,27,11,3,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0, 50 1,0,1,0,5,5,14,21,46,53,88,90,75,58,48,24,19,4,3,1,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 51 0,1,1,4,6,12,15,50,88,130,137,127,113,108,72,61,36,23,10,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,1,0,0,0,0,0,1,0, 52 0,0,0,4,10,28,43,91,131,163,202,142,128,125,135,93,94,73,24,7,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1, 53 0,1,2,5,19,37,73,118,152,164,148,145,119,90,103,145,112,102,27,3,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,1,0,0,0,1,0,0,0,1,0, 54 0,0,2,11,24,52,85,128,110,150,96,91,77,84,124,126,132,65,18,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0, 55 1,0,4,23,43,84,112,146,132,107,86,70,56,74,93,103,85,33,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0, 56 0,2,1,29,67,89,96,123,121,72,53,56,51,49,75,69,36,12,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 57 0,0,8,23,53,67,55,74,68,33,23,26,31,32,61,40,10,5,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 58 1,0,5,10,17,36,33,27,34,24,19,24,16,18,15,6,3,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,1,0,0,0,0,0,0,0,0,0,0,0,0,1, 59 ],dtype=float) 13 ramachandranDist = {'All':np.array([ 14 0,8,15,15,12,9,6,5,6,5,7,13,9,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,1,0,0,0,0,0,0,0,0,0,0, 15 0,1,0,0,3,3,7,5,7,2,3,3,7,4,4,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1, 16 0,0,0,0,1,3,1,2,2,3,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,1,0,0,0,0,0,0,0,0,0, 17 0,0,0,0,0,1,0,0,2,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0, 18 0,0,0,1,1,0,0,0,0,1,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 19 0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,2,2,1,0,0,0,0,0,0,0,0,0,0,0,0, 20 0,0,1,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0, 21 0,0,0,0,0,0,0,1,0,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 22 0,0,0,0,0,0,1,0,0,2,2,2,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 23 0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 24 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'ARG-4':np.array([1,4,1,4,6,18,16,46,50,25,16,24,11,16,6,3,7,16,14,22,38,80,104,84,47,30,19,12,9,7,8,14,15,20,27,39,83,51,31,20,9,5,6,2,2],dtype=float), 1660 'ARG-5':np.array([1,1,1,0,3,5,5,6,18,35,47,43,34,18,26,22,32,25,35,39,49,53,50,58,51,40,34,24,24,19,20,35,33,50,56,37,15,7,7,2,1,1,0,4,1],dtype=float), 1661 'ASN-3':np.array([0,0,0,3,4,7,24,57,59,29,8,1,1,0,1,0,0,1,0,1,13,20,82,97,58,31,19,10,7,7,7,9,13,25,72,150,180,132,60,16,6,4,1,3,0],dtype=float), 1662 'ASP-3':np.array([0,2,0,3,4,23,28,99,77,25,1,4,1,1,1,0,2,0,0,3,12,49,130,130,82,48,22,8,4,6,7,10,10,23,79,195,249,160,45,15,5,2,0,1,1],dtype=float), 1663 'CYS-3':np.array([0,0,1,0,0,3,11,17,19,2,3,1,0,0,0,0,0,1,0,1,12,27,43,35,14,9,2,0,0,2,0,0,4,7,10,54,86,62,41,8,5,1,1,0,0],dtype=float), 1664 'CYS-4':np.array([0,0,0,0,0,0,0,2,6,16,24,32,36,11,6,0,0,0,2,2,0,0,0,0,0,0,0,0,2,0,2,0,12,32,53,32,2,0,0,0,0,0,0,0,0],dtype=float), 1665 'GLN-3':np.array([0,1,4,1,3,8,9,15,16,9,4,1,3,1,0,0,2,1,5,5,16,56,70,71,29,10,14,7,8,10,3,10,8,16,38,77,155,121,61,19,7,5,4,1,0],dtype=float), 1666 'GLU-3':np.array([5,7,2,6,5,10,26,30,25,24,9,3,0,3,0,2,1,3,8,14,33,55,94,107,57,31,19,17,15,8,10,9,10,23,63,147,251,154,81,37,15,11,5,4,8],dtype=float), 1667 'HIS-3':np.array([0,1,0,0,1,11,8,20,15,14,3,1,0,0,0,0,0,0,0,2,10,23,51,41,32,6,5,2,0,1,0,1,3,4,23,53,67,84,43,7,3,1,1,1,1],dtype=float), 1668 'ILE-3':np.array([1,1,2,1,2,6,26,80,53,12,10,5,1,2,3,2,2,1,0,1,3,8,24,38,36,15,5,1,1,6,1,4,3,7,24,126,327,308,150,37,7,2,0,0,0],dtype=float), 1669 'LEU-3':np.array([0,0,0,1,0,1,4,4,4,6,3,0,2,0,0,0,1,0,0,9,32,132,208,136,58,29,32,28,21,15,26,43,52,80,89,182,364,330,143,33,8,1,0,0,1],dtype=float), 1670 'LYS-3':np.array([1,2,2,4,5,8,19,35,28,15,12,2,5,0,3,2,6,6,7,13,24,63,127,106,63,30,22,10,10,16,8,17,27,39,79,152,209,193,84,42,18,6,4,5,2],dtype=float), 1671 'LYS-4':np.array([1,0,3,4,9,7,20,27,33,27,19,9,14,14,11,11,22,27,51,69,93,164,220,168,106,62,48,35,26,10,6,19,13,11,21,31,33,32,13,15,5,2,3,0,0],dtype=float), 1672 'LYS-5':np.array([2,3,8,9,5,16,15,44,43,29,20,17,19,13,7,16,18,40,48,62,91,145,176,129,86,73,40,27,21,10,16,15,13,28,17,41,33,40,28,15,14,6,4,3,5],dtype=float), 1673 'MET-3':np.array([0,0,2,1,1,5,6,7,14,9,5,0,0,1,0,0,1,2,0,5,8,22,37,37,22,10,7,2,4,2,2,3,8,8,18,57,101,79,30,11,0,2,0,0,0],dtype=float), 1674 'MET-4':np.array([1,2,1,1,4,11,7,32,27,40,10,20,18,9,5,1,3,5,3,7,11,15,17,18,16,5,7,6,6,3,5,9,15,20,25,36,35,35,15,6,3,4,5,3,0],dtype=float), 1675 'PHE-3':np.array([1,0,0,1,0,3,29,41,44,16,5,0,0,0,0,0,1,0,0,4,25,68,110,80,44,17,5,0,1,1,2,2,4,12,48,76,169,157,71,17,4,3,2,1,0],dtype=float), 1676 'SER-3':np.array([4,4,5,6,11,30,106,196,196,110,65,21,5,3,4,3,1,5,9,14,36,83,112,84,36,16,9,5,9,7,13,3,9,20,31,76,146,118,89,29,14,3,3,0,4],dtype=float), 1677 'THR-3':np.array([2,3,2,7,9,26,122,218,192,90,20,6,3,0,1,2,4,1,2,1,3,13,24,38,25,6,5,3,1,0,1,8,3,7,10,31,131,288,168,45,16,8,0,1,5],dtype=float), 1678 'TRP-3':np.array([0,0,0,0,0,5,9,24,9,9,4,0,1,0,0,0,0,0,0,2,12,28,35,30,8,2,0,0,2,0,0,1,1,6,14,42,57,31,12,9,3,0,0,0,0],dtype=float), 1679 'TYR-3':np.array([0,0,1,0,2,5,17,43,34,12,5,5,3,0,0,0,1,0,1,6,26,85,106,73,28,8,3,2,0,0,0,0,3,15,28,81,158,145,57,17,2,0,0,1,0],dtype=float), 1680 'VAL-3':np.array([5,5,2,1,4,7,20,26,28,24,9,2,7,8,9,6,6,4,14,53,193,471,420,130,25,4,3,1,3,0,1,4,1,3,7,33,132,133,70,15,7,1,2,7,4],dtype=float), 1681 'OMEG':np.array([31,4,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,29,293,3599,19507,2474,170,13,1,1,0,0,0,0,1,0,1,0,0,0,1,0,0,0,1,4,28],dtype=float), 1682 'OCCO':np.array([442,2960,2076,1320,844,334,154,82,55,39,34,48,76,74,48,47,62,39,49,103,131,330,566,757,706,769, 1683 579,437,385,442,584,629,322,82,33,21,27,35,70,106,145,221,185,101,137])} -
trunk/GSASIIgrid.py
r817 r818 101 101 102 102 [ wxID_RESTRAINTADD, wxID_RESTSELPHASE,wxID_RESTDELETE, wxID_RESRCHANGEVAL, 103 wxID_RESTCHANGEESD,wxID_AARESTRAINTADD, 104 ] = [wx.NewId() for item in range( 6)]103 wxID_RESTCHANGEESD,wxID_AARESTRAINTADD,wxID_AARESTRAINTPLOT, 104 ] = [wx.NewId() for item in range(7)] 105 105 106 106 [ wxID_SAVESEQSEL, … … 458 458 help='Add residue based restraints for macromolecules from macro file') 459 459 self.RestraintEdit.Enable(wxID_AARESTRAINTADD,False) #gets enabled if macromolecule phase 460 self.RestraintEdit.Append(id=wxID_AARESTRAINTPLOT, kind=wx.ITEM_NORMAL,text='Plot residue restraints', 461 help='Plot selected residue based restraints for macromolecules from macro file') 462 self.RestraintEdit.Enable(wxID_AARESTRAINTPLOT,False) #gets enabled if macromolecule phase 460 463 self.RestraintEdit.Append(id=wxID_RESRCHANGEVAL, kind=wx.ITEM_NORMAL,text='Change value', 461 464 help='Change observed value') -
trunk/GSASIImath.py
r817 r818 273 273 return nl.det(VecA) 274 274 275 def getRestTorsion(XYZ,Amat ,Coeff=[]):275 def getRestTorsion(XYZ,Amat): 276 276 VecA = np.empty((3,3)) 277 277 VecA[0] = np.inner(XYZ[1]-XYZ[0],Amat) … … 287 287 Ang = (P12*P23-P13)/(np.sqrt(1.-P12**2)*np.sqrt(1.-P23**2)) 288 288 TOR = (acosd(Ang)*D/abs(D)+720.)%360. 289 return TOR 290 291 def calcTorsionEnergy(TOR,Coeff=[]): 289 292 sum = 0. 290 293 if len(Coeff): … … 293 296 delt = np.where(delt<-180.,delt+360.,delt) 294 297 delt = np.where(delt>180.,delt-360.,delt) 295 # pMax = np.min(cof[0])296 298 term = -cof[2]*delt**2 297 299 val = cof[0]*np.exp(term/1000.0) 298 300 pMax = cof[0][np.argmin(val)] 299 sum = np.sum(val)-pMax 300 return TOR,sum 301 Eval = np.sum(val) 302 sum = Eval-pMax 303 return sum,Eval 301 304 302 305 def getRestRama(XYZ,Amat,Coeff=[]): 303 phi,x = getRestTorsion(XYZ[:5],Amat) 304 psi,x = getRestTorsion(XYZ[1:],Amat) 305 sum = 0 306 phi = getRestTorsion(XYZ[:5],Amat) 307 psi = getRestTorsion(XYZ[1:],Amat) 308 return phi,psi 309 310 def calcRamaEnergy(phi,psi,Coeff=[]): 311 sum = 0. 306 312 if len(Coeff): 307 313 cof = Coeff.T … … 315 321 val = cof[0]*np.exp(val/1000.) 316 322 pMax = cof[0][np.argmin(val)] 317 sum = np.sum(val)-pMax 318 return phi,psi,sum 319 323 Eval = np.sum(val) 324 sum = Eval-pMax 325 return sum,Eval 326 320 327 def getDistDerv(Oxyz,Txyz,Amat,Tunit,Top,SGData): 321 328 -
trunk/GSASIIplot.py
r817 r818 32 32 import GSASIIspc as G2spc 33 33 import GSASIImath as G2mth 34 import GSASIIdata as G2data35 34 import pytexture as ptx 36 35 from OpenGL.GL import * … … 1766 1765 1767 1766 ################################################################################ 1767 ##### PlotTorsion 1768 ################################################################################ 1769 1770 def PlotTorsion(G2frame,phaseName,Torsion,TorName,Names=[],Angles=[],Coeff=[]): 1771 1772 global names 1773 names = Names 1774 sum = np.sum(Torsion) 1775 torsion = np.log(2*Torsion+1.)/sum 1776 tMin = np.min(torsion) 1777 tMax = np.max(torsion) 1778 torsion = 3.*(torsion-tMin)/(tMax-tMin) 1779 X = np.linspace(0.,360.,num=45) 1780 1781 def OnMotion(event): 1782 if event.xdata and event.ydata: #avoid out of frame errors 1783 xpos = event.xdata 1784 ypos = event.ydata 1785 msg = 'torsion,energy: %5.3f %5.3f'%(xpos,ypos) 1786 Page.canvas.SetToolTipString(msg) 1787 G2frame.G2plotNB.status.SetFields(['',msg]) 1788 if len(Angles): 1789 fX = np.where(np.fabs(Angles-xpos)<1.0)[0] 1790 if len(fX): 1791 msg = 'atoms:'+names[fX[0]-1] 1792 Page.canvas.SetToolTipString(msg) 1793 1794 try: 1795 plotNum = G2frame.G2plotNB.plotList.index('Torsion') 1796 Page = G2frame.G2plotNB.nb.GetPage(plotNum) 1797 Page.figure.clf() 1798 Plot = Page.figure.gca() 1799 if not Page.IsShown(): 1800 Page.Show() 1801 except ValueError: 1802 Plot = G2frame.G2plotNB.addMpl('Torsion').gca() 1803 plotNum = G2frame.G2plotNB.plotList.index('Torsion') 1804 Page = G2frame.G2plotNB.nb.GetPage(plotNum) 1805 Page.canvas.mpl_connect('motion_notify_event', OnMotion) 1806 1807 Page.SetFocus() 1808 G2frame.G2plotNB.status.SetFields(['','']) 1809 Plot.plot(X,torsion,'b+') 1810 if len(Coeff): 1811 X2 = np.linspace(0.,360.,45) 1812 Y2 = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in X2]) 1813 Plot.plot(X2,Y2,'r') 1814 if len(Angles): 1815 Eval = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in Angles]) 1816 Plot.plot(Angles,Eval,'ro') 1817 Plot.set_xlim((0.,360.)) 1818 Plot.set_title('Torsion angles for '+TorName+' in '+phaseName) 1819 Plot.set_xlabel('angle',fontsize=16) 1820 Plot.set_ylabel('Energy',fontsize=16) 1821 Page.canvas.draw() 1822 1823 ################################################################################ 1768 1824 ##### PlotRama 1769 1825 ################################################################################ 1770 1826 1771 def PlotRama(G2frame,phaseName): 1772 1773 Data = G2frame.PatternTree.GetItemPyData( 1774 G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Restraints')) 1775 Rama = Data[phaseName]['Rama'] 1776 rama = np.log(G2data.ramachandranDist) 1827 def PlotRama(G2frame,phaseName,Rama,RamaName,Names=[],PhiPsi=[],Coeff=[]): 1828 1829 global names 1830 names = Names 1831 rama = np.log(2*Rama+1.) 1777 1832 ramaMax = np.max(rama) 1778 rama /= float(ramaMax)1779 1833 rama = np.reshape(rama,(45,45)) 1834 global Phi,Psi 1835 Phi = [] 1836 Psi = [] 1780 1837 1781 1838 def OnPlotKeyPress(event): … … 1791 1848 G2frame.RamaColor = 'RdYlGn' 1792 1849 dlg.Destroy() 1793 PlotRama(G2frame,phaseName )1850 PlotRama(G2frame,phaseName,Rama) 1794 1851 1795 1852 def OnMotion(event): … … 1800 1857 Page.canvas.SetToolTipString(msg) 1801 1858 G2frame.G2plotNB.status.SetFields(['',msg]) 1802 1859 if len(Phi): 1860 fPhi = np.where(np.fabs(Phi-xpos)<1.0)[0] 1861 fPsi = np.where(np.fabs(Psi-ypos)<1.0)[0] 1862 if len(fPhi) and len(fPsi) and fPhi[0] == fPsi[0]: 1863 msg = 'atoms:'+names[fPhi[0]-1] 1864 Page.canvas.SetToolTipString(msg) 1865 1803 1866 try: 1804 1867 plotNum = G2frame.G2plotNB.plotList.index('Ramachandran') … … 1820 1883 G2frame.G2plotNB.status.SetFields(['','']) 1821 1884 acolor = mpl.cm.get_cmap(G2frame.RamaColor) 1822 Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest', 1823 extent=[-180,180,-180,180],origin='lower') 1824 colorBar = Page.figure.colorbar(Img) 1825 Plot.set_title('Ramachandran for '+phaseName) 1885 if RamaName == 'All' or '-1' in RamaName: 1886 if len(Coeff): 1887 X,Y = np.meshgrid(np.linspace(-180.,180.,45),np.linspace(-180.,180.,45)) 1888 Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())]) 1889 Plot.contour(X,Y,np.reshape(Z,(45,45))) 1890 Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest', 1891 extent=[-180,180,-180,180],origin='lower') 1892 if len(PhiPsi): 1893 Phi,Psi = PhiPsi.T 1894 Phi = np.where(Phi>180.,Phi-360.,Phi) 1895 Psi = np.where(Psi>180.,Psi-360.,Psi) 1896 Plot.plot(Phi,Psi,'ro',picker=3) 1897 Plot.set_xlim((-180.,180.)) 1898 Plot.set_ylim((-180.,180.)) 1899 else: 1900 if len(Coeff): 1901 X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45)) 1902 Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())]) 1903 Plot.contour(X,Y,np.reshape(Z,(45,45))) 1904 Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest', 1905 extent=[0,360,0,360],origin='lower') 1906 if len(PhiPsi): 1907 Phi,Psi = PhiPsi.T 1908 Plot.plot(Phi,Psi,'ro',picker=3) 1909 Plot.set_xlim((0.,360.)) 1910 Plot.set_ylim((0.,360.)) 1911 Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName) 1826 1912 Plot.set_xlabel(r'$\phi$',fontsize=16) 1827 1913 Plot.set_ylabel(r'$\psi$',fontsize=16) 1914 colorBar = Page.figure.colorbar(Img) 1828 1915 Page.canvas.draw() 1829 1916 -
trunk/GSASIIrestrGUI.py
r817 r818 22 22 import GSASIIgrid as G2gd 23 23 import GSASIIplot as G2plt 24 import GSASIIdata as G2data 24 25 25 26 VERY_LIGHT_GREY = wx.Colour(235,235,235) … … 71 72 Coords += [atom[cx:cx+3] for atom in Atoms] 72 73 Ids += [atom[-1] for atom in Atoms] 74 rama = G2data.ramachandranDist['All'] 75 ramaName = 'All' 73 76 74 77 def OnSelectPhase(event): … … 101 104 return macro #advanced past 1st line 102 105 106 def OnPlotAARestraint(event): 107 page = G2frame.dataDisplay.GetSelection() 108 if 'Torsion' in G2frame.dataDisplay.GetPageText(page): 109 torNames = [] 110 torNames += restrData['Torsion']['Coeff'].keys() 111 dlg = wx.SingleChoiceDialog(G2frame,'Select','Torsion data',torNames) 112 try: 113 if dlg.ShowModal() == wx.ID_OK: 114 torName = torNames[dlg.GetSelection()] 115 torsion = G2data.torsionDist[torName] 116 torCoeff = restrData['Torsion']['Coeff'][torName] 117 torList = restrData['Torsion']['Torsions'] 118 Names = [] 119 Angles = [] 120 for i,[indx,ops,cofName,esd] in enumerate(torList): 121 if cofName == torName: 122 atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) 123 name = '('+atoms[2][1]+atoms[2][0].strip()+atoms[2][2]+')' 124 for atom in atoms: 125 name += ' '+atom[3] 126 XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) 127 angle = G2mth.getRestTorsion(XYZ,Amat) 128 Angles.append(angle) 129 Names.append(name) 130 G2plt.PlotTorsion(G2frame,phaseName,torsion,torName,Names,np.array(Angles),torCoeff) 131 finally: 132 dlg.Destroy() 133 134 elif 'Rama' in G2frame.dataDisplay.GetPageText(page): 135 ramaNames = ['All',] 136 ramaNames += restrData['Rama']['Coeff'].keys() 137 dlg = wx.SingleChoiceDialog(G2frame,'Select','Ramachandran data',ramaNames) 138 try: 139 if dlg.ShowModal() == wx.ID_OK: 140 ramaName = ramaNames[dlg.GetSelection()] 141 rama = G2data.ramachandranDist[ramaName] 142 ramaCoeff = [] 143 if ramaName != 'All': 144 ramaCoeff = restrData['Rama']['Coeff'][ramaName] 145 ramaList = restrData['Rama']['Ramas'] 146 Names = [] 147 PhiPsi = [] 148 for i,[indx,ops,cofName,esd] in enumerate(ramaList): 149 if cofName == ramaName or (ramaName == 'All' and '-1' in cofName): 150 atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) 151 name = '('+atoms[3][1]+atoms[3][0].strip()+atoms[3][2]+')' 152 for atom in atoms: 153 name += ' '+atom[3] 154 XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) 155 phi,psi = G2mth.getRestRama(XYZ,Amat) 156 PhiPsi.append([phi,psi]) 157 Names.append(name) 158 G2plt.PlotRama(G2frame,phaseName,rama,ramaName,Names,np.array(PhiPsi),ramaCoeff) 159 finally: 160 dlg.Destroy() 161 103 162 def OnAddRestraint(event): 104 163 page = G2frame.dataDisplay.GetSelection() 105 restName = G2frame.dataDisplay.GetPageText(page)106 164 if 'Bond' in G2frame.dataDisplay.GetPageText(page): 107 165 AddBondRestraint(restrData['Bond']) … … 291 349 if not macro: 292 350 return 293 atoms = zip(Names, Coords,Ids)351 atoms = zip(Names,Ids) 294 352 macStr = macro.readline() 295 353 while macStr: … … 307 365 pAtms[i] = atm.strip('+') 308 366 ids = np.array([0,0,0]) 309 coords = [[],[],[]]310 367 rNum = -1 311 for name, coord,id in atoms:368 for name,id in atoms: 312 369 names = name.split() 313 370 tNum = int(names[0].split(':')[0]) … … 316 373 ipos = Atms.index(names[2]) 317 374 ids[ipos] = id 318 coords[ipos] = coord319 375 except ValueError: 320 376 continue … … 325 381 rNum = int(names[0].split(':')[0]) 326 382 ids[ipos] = id 327 coords[ipos] = coord328 383 except ValueError: 329 384 try: … … 331 386 ipos = pAtms.index(names[2]) 332 387 ids[ipos] = id 333 coords[ipos] = coord334 388 except ValueError: 335 389 continue … … 339 393 angleRestData['Angles'].append(angle) 340 394 ids = np.array([0,0,0]) 341 coords = [[],[],[]]342 395 macStr = macro.readline() 343 396 macro.close() 344 397 UpdateAngleRestr(angleRestData) 345 398 346 def AddPlaneRestraint( ):347 origAtoms = []348 dlg = wx.MultiChoiceDialog(G2frame,'Select atom B for angle A-B-C for'+General['Name'],349 'Select angle restraint origin atoms',Names)399 def AddPlaneRestraint(restrData): 400 ids = [] 401 dlg = wx.MultiChoiceDialog(G2frame,'Select 4 or more atoms for plane in '+General['Name'], 402 'Select 4+ atoms',Names[iBeg:]) 350 403 if dlg.ShowModal() == wx.ID_OK: 351 404 sel = dlg.GetSelections() 352 for x in sel: 353 if 'all' in Names[x]: 354 allType = Types[x] 355 for name,Type,coords,id in zip(Names,Types,Coords,Ids): 356 if Type == allType and 'all' not in name: 357 origAtoms.append([id,Type,coords]) 358 else: 359 origAtoms.append([Ids[x],Types[x],Coords[x]]) 405 if len(sel) > 3: 406 for x in sel: 407 ids.append(Ids[x+iBeg]) 408 ops = ['1' for i in range(len(sel))] 409 plane = [ids,ops,0.0,0.01] 410 if plane not in restrData['Planes']: 411 restrData['Planes'].append(plane) 412 else: 413 print '**** ERROR - not enough atoms fro a plane restraint - try again ****' 414 UpdatePlaneRestr(restrData) 360 415 361 416 def AddAAPlaneRestraint(planeRestData): … … 363 418 if not macro: 364 419 return 365 atoms = zip(Names, Coords,Ids)420 atoms = zip(Names,Ids) 366 421 macStr = macro.readline() 367 422 while macStr: … … 379 434 rNum = -1 380 435 ids = np.zeros(len(Atms)) 381 coords = [[] for i in range(len(Atms))]382 436 ops = ['1' for i in range(len(Atms))] 383 for name, coord,id in atoms:437 for name,id in atoms: 384 438 names = name.split() 385 439 tNum = int(names[0].split(':')[0]) … … 388 442 ipos = Atms.index(names[2]) 389 443 ids[ipos] = id 390 coords[ipos] = coord391 444 except ValueError: 392 445 continue … … 397 450 rNum = int(names[0].split(':')[0]) 398 451 ids[ipos] = id 399 coords[ipos] = coord400 452 except ValueError: 401 453 try: … … 403 455 ipos = pAtms.index(names[2]) 404 456 ids[ipos] = id 405 coords[ipos] = coord406 457 except ValueError: 407 458 continue … … 411 462 planeRestData['Planes'].append(plane) 412 463 ids = np.zeros(len(Atms)) 413 coords = [[] for i in range(len(Atms))]414 464 macStr = macro.readline() 415 465 macro.close() … … 423 473 if not macro: 424 474 return 425 atoms = zip(Names, Coords,Ids)475 atoms = zip(Names,Ids) 426 476 macStr = macro.readline() 427 477 while macStr: … … 435 485 Atms = items[4:8] 436 486 ids = np.array([0,0,0,0]) 437 coords = [[],[],[],[]] 438 for name,coord,id in atoms: 487 for name,id in atoms: 439 488 names = name.split() 440 489 if res in names[0]: … … 442 491 ipos = Atms.index(names[2]) 443 492 ids[ipos] = id 444 coords[ipos] = coord445 493 except ValueError: 446 494 pass … … 450 498 chiralRestData['Volumes'].append(chiral) 451 499 ids = np.array([0,0,0,0]) 452 coords = [[],[],[],[]]453 500 macStr = macro.readline() 454 501 macro.close() 455 502 UpdateChiralRestr(chiralRestData) 456 503 457 # def AddTorsionRestraint(): 458 # print 'Torsion restraint' 504 def makeChains(Names,Ids): 505 Chains = {} 506 chain = '' 507 atoms = zip(Names,Ids) 508 for name,id in atoms: 509 items = name.split() 510 rnum,res = items[0].split(':') 511 if items[1] not in Chains: 512 Residues = {} 513 Chains[items[1]] = Residues 514 if int(rnum) not in Residues: 515 Residues[int(rnum)] = [] 516 Residues[int(rnum)].append([res,items[2],id]) 517 return Chains 518 459 519 # 460 520 def AddAATorsionRestraint(torsionRestData): … … 462 522 if not macro: 463 523 return 464 atoms = zip(Names,Coords,Ids)524 Chains = makeChains(Names,Ids) 465 525 macStr = macro.readline()[:-1] 466 526 while macStr: … … 476 536 elif 'S' in items[0]: 477 537 Name = items[1] 478 res = items[2]479 esd = float(items[3])538 Res = items[2] 539 Esd = float(items[3]) 480 540 Atms = items[4:8] 481 541 pAtms = ['','','',''] … … 484 544 pAtms[i] = atm.strip('+') 485 545 ids = np.array([0,0,0,0]) 486 coords = [[],[],[],[]] 487 rNum = -1 488 for name,coord,id in atoms: 489 names = name.split() 490 tNum = int(names[0].split(':')[0]) 491 if res in names[0]: 492 try: 493 ipos = Atms.index(names[2]) 494 ids[ipos] = id 495 coords[ipos] = coord 496 except ValueError: 546 chains = Chains.keys() 547 chains.sort() 548 for chain in chains: 549 residues = Chains[chain].keys() 550 residues.sort() 551 for residue in residues: 552 if residue == residues[-1] and Res == '*': 497 553 continue 498 elif res == '*': 499 try: 500 ipos = Atms.index(names[2]) 501 if not np.all(ids): 502 rNum = int(names[0].split(':')[0]) 503 ids[ipos] = id 504 coords[ipos] = coord 505 except ValueError: 506 try: 507 if tNum == rNum+1: 508 ipos = pAtms.index(names[2]) 554 if Res != '*': 555 for res,name,id in Chains[chain][residue]: 556 if Res == res: 557 try: 558 ipos = Atms.index(name) 559 ids[ipos] = id 560 except ValueError: 561 continue 562 else: 563 for res,name,id in Chains[chain][residue]: 564 try: 565 ipos = Atms.index(name) 509 566 ids[ipos] = id 510 coords[ipos] = coord 511 except ValueError: 512 continue 513 if np.all(ids): 514 torsion = [list(ids),['1','1','1','1'],Name,esd] 515 if torsion not in torsionRestData['Torsions']: 516 torsionRestData['Torsions'].append(torsion) 517 ids = np.array([0,0,0,0]) 518 coords = [[],[],[],[]] 567 except ValueError: 568 continue 569 for res,name,id in Chains[chain][residue+1]: 570 try: 571 ipos = pAtms.index(name) 572 ids[ipos] = id 573 except ValueError: 574 continue 575 if np.all(ids): 576 torsion = [list(ids),['1','1','1','1'],Name,Esd] 577 if torsion not in torsionRestData['Torsions']: 578 torsionRestData['Torsions'].append(torsion) 579 ids = np.array([0,0,0,0]) 519 580 macStr = macro.readline() 520 581 macro.close() 521 582 UpdateTorsionRestr(torsionRestData) 522 583 523 # def AddRamaRestraint():524 # print 'Ramachandran restraint'525 #526 584 def AddAARamaRestraint(ramaRestData): 527 585 macro = getMacroFile('Ramachandran') 528 586 if not macro: 529 587 return 530 atoms = zip(Names,Coords,Ids)588 Chains = makeChains(Names,Ids) 531 589 macStr = macro.readline() 532 590 while macStr: … … 545 603 ramaRestData['Coeff'][name] = coeff 546 604 elif 'S' in items[0]: 547 print items 548 cofname = items[1] 549 res = items[2] 550 esd = float(items[3]) 605 Name = items[1] 606 Res = items[2] 607 Esd = float(items[3]) 551 608 Atms = items[4:9] 552 609 mAtms = ['','','','',''] … … 558 615 mAtms[i] = atm.strip('-') 559 616 ids = np.array([0,0,0,0,0]) 560 coords = [[],[],[],[],[]] 561 rNum = -1 562 for name,coord,id in atoms: 563 names = name.split() 564 tNum = int(names[0].split(':')[0]) 565 if res in names[0]: 566 try: 567 ipos = Atms.index(names[2]) 568 if not np.all(ids): 569 rNum = int(names[0].split(':')[0]) 570 ids[ipos] = id 571 coords[ipos] = coord 572 except ValueError: 573 continue 574 # try: 575 # if tNum == rNum+1: 576 # ipos = Atms.index(names[2]) 577 # ids[ipos] = id 578 # coords[ipos] = coord 579 # except ValueError: 580 # try: 581 # if tNum == rNum+2: 582 # ipos = pAtms.index(names[2]) 583 # ids[ipos] = id 584 # coords[ipos] = coord 585 # except ValueError: 586 # pass 587 print ids 588 if np.all(ids): 589 rama = [list(ids),['1','1','1','1'],cofname,esd] 590 print rama 591 if rama not in ramaRestData['Ramas']: 592 ramaRestData['Ramas'].append(rama) 593 ids = np.array([0,0,0,0,0]) 594 coords = [[],[],[],[],[]] 617 chains = Chains.keys() 618 chains.sort() 619 for chain in chains: 620 residues = Chains[chain].keys() 621 residues.sort() 622 if not (any(mAtms) or any(pAtms)): 623 for residue in residues: 624 for res,name,id in Chains[chain][residue]: 625 if Res == res: 626 try: 627 ipos = Atms.index(name) 628 ids[ipos] = id 629 except ValueError: 630 continue 631 if np.all(ids): 632 rama = [list(ids),['1','1','1','1','1'],Name,Esd] 633 if rama not in ramaRestData['Ramas']: 634 ramaRestData['Ramas'].append(rama) 635 ids = np.array([0,0,0,0,0]) 636 else: 637 for residue in residues[1:-1]: 638 for res,name,id in Chains[chain][residue-1]: 639 try: 640 ipos = mAtms.index(name) 641 ids[ipos] = id 642 except ValueError: 643 continue 644 for res,name,id in Chains[chain][residue+1]: 645 try: 646 ipos = pAtms.index(name) 647 ids[ipos] = id 648 except ValueError: 649 continue 650 for res,name,id in Chains[chain][residue]: 651 if Res == res: 652 try: 653 ipos = Atms.index(name) 654 ids[ipos] = id 655 except ValueError: 656 continue 657 if np.all(ids): 658 rama = [list(ids),['1','1','1','1','1'],Name,Esd] 659 if rama not in ramaRestData['Ramas']: 660 ramaRestData['Ramas'].append(rama) 661 ids = np.array([0,0,0,0,0]) 595 662 macStr = macro.readline() 596 663 macro.close() … … 644 711 Obj.ClearSelection() 645 712 else: 646 for row in range( Bonds.GetNumberRows()):713 for row in range(Obj.GetNumberRows()): 647 714 Obj.SelectRow(row,True) 648 715 elif c < 0: #only row clicks … … 1083 1150 mainSizer.Add((5,5),0) 1084 1151 mainSizer.Add(WtBox(TorsionRestr,torsionRestData),0,wx.ALIGN_CENTER_VERTICAL) 1085 mainSizer.Add(wx.StaticText(TorsionRestr,-1,'Torsion function coefficients:'),0,wx.ALIGN_CENTER_VERTICAL)1086 1152 1087 1153 coeffDict = torsionRestData['Coeff'] 1088 if len(coeffDict): 1154 torsionList = torsionRestData['Torsions'] 1155 mainSizer.Add(wx.StaticText(TorsionRestr,-1,'Torsion restraints:'),0,wx.ALIGN_CENTER_VERTICAL) 1156 if len(torsionList): 1157 table = [] 1158 rowLabels = [] 1159 Types = 2*[wg.GRID_VALUE_STRING,]+4*[wg.GRID_VALUE_FLOAT+':10,2',] 1160 if 'macro' in General['Type']: 1161 colLabels = ['(res) A B C D','coef name','torsion','obs E','restr','esd'] 1162 for i,[indx,ops,cofName,esd] in enumerate(torsionList): 1163 atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) 1164 name = '('+atoms[2][1]+atoms[2][0].strip()+atoms[2][2]+')' 1165 for atom in atoms: 1166 name += ' '+atom[3] 1167 XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) 1168 tor = G2mth.getRestTorsion(XYZ,Amat) 1169 restr,calc = G2mth.calcTorsionEnergy(tor,coeffDict[cofName]) 1170 table.append([name,cofName,tor,calc,restr,esd]) 1171 rowLabels.append(str(i)) 1172 torsionTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) 1173 Torsions = G2gd.GSGrid(TorsionRestr) 1174 Torsions.SetTable(torsionTable, True) 1175 Torsions.AutoSizeColumns(False) 1176 for r in range(len(torsionList)): 1177 for c in range(2): 1178 Torsions.SetReadOnly(r,c,True) 1179 Torsions.SetCellStyle(r,c,VERY_LIGHT_GREY,True) 1180 Torsions.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) 1181 G2frame.dataFrame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2gd.wxID_RESTDELETE) 1182 G2frame.dataFrame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2gd.wxID_RESTCHANGEESD) 1183 mainSizer.Add(Torsions,0,) 1184 1185 mainSizer.Add((5,5)) 1186 mainSizer.Add(wx.StaticText(TorsionRestr,-1,'Torsion function coefficients:'),0,wx.ALIGN_CENTER_VERTICAL) 1089 1187 table = [] 1090 1188 rowLabels = [] … … 1103 1201 Coeff.SetCellStyle(r,c,VERY_LIGHT_GREY,True) 1104 1202 mainSizer.Add(Coeff,0,) 1105 mainSizer.Add((5,5))1106 torsionList = torsionRestData['Torsions']1107 mainSizer.Add(wx.StaticText(TorsionRestr,-1,'Torsion restraints:'),0,wx.ALIGN_CENTER_VERTICAL)1108 if len(torsionList):1109 table = []1110 rowLabels = []1111 Types = 2*[wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,2',]1112 if 'macro' in General['Type']:1113 colLabels = ['(res) A (res) B (res) C (res) D','coef name','torsion','obs E','esd']1114 for i,[indx,ops,cofName,esd] in enumerate(torsionList):1115 atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4)1116 name = ''1117 for atom in atoms:1118 name += '('+atom[1]+atom[0].strip()+atom[2]+') '+atom[3]+' '1119 XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3))1120 tor,calc = G2mth.getRestTorsion(XYZ,Amat,coeffDict[cofName])1121 table.append([name,cofName,tor,calc,esd])1122 rowLabels.append(str(i))1123 torsionTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)1124 Torsions = G2gd.GSGrid(TorsionRestr)1125 Torsions.SetTable(torsionTable, True)1126 Torsions.AutoSizeColumns(False)1127 for r in range(len(torsionList)):1128 for c in range(2):1129 Torsions.SetReadOnly(r,c,True)1130 Torsions.SetCellStyle(r,c,VERY_LIGHT_GREY,True)1131 Torsions.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect)1132 G2frame.dataFrame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2gd.wxID_RESTDELETE)1133 G2frame.dataFrame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2gd.wxID_RESTCHANGEESD)1134 mainSizer.Add(Torsions,0,)1135 1203 else: 1136 1204 mainSizer.Add(wx.StaticText(TorsionRestr,-1,'No torsion restraints for this phase'),0,) … … 1176 1244 mainSizer.Add((5,5),0) 1177 1245 mainSizer.Add(WtBox(RamaRestr,ramaRestData),0,wx.ALIGN_CENTER_VERTICAL) 1246 1247 ramaList = ramaRestData['Ramas'] 1248 coeffDict = ramaRestData['Coeff'] 1249 if len(ramaList): 1250 mainSizer.Add(wx.StaticText(RamaRestr,-1,'Ramachandran restraints:'),0,wx.ALIGN_CENTER_VERTICAL) 1251 table = [] 1252 rowLabels = [] 1253 Types = 2*[wg.GRID_VALUE_STRING,]+5*[wg.GRID_VALUE_FLOAT+':10,2',] 1254 if 'macro' in General['Type']: 1255 colLabels = ['(res) A B C D E','coef name','phi','psi','obs E','restr','esd'] 1256 for i,[indx,ops,cofName,esd] in enumerate(ramaList): 1257 atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) 1258 name = '('+atoms[3][1]+atoms[3][0].strip()+atoms[3][2]+')' 1259 for atom in atoms: 1260 name += ' '+atom[3] 1261 XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) 1262 phi,psi = G2mth.getRestRama(XYZ,Amat) 1263 restr,calc = G2mth.calcRamaEnergy(phi,psi,coeffDict[cofName]) 1264 table.append([name,cofName,phi,psi,calc,restr,esd]) 1265 rowLabels.append(str(i)) 1266 ramaTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) 1267 Ramas = G2gd.GSGrid(RamaRestr) 1268 Ramas.SetTable(ramaTable, True) 1269 Ramas.AutoSizeColumns(False) 1270 for r in range(len(ramaList)): 1271 for c in range(2): 1272 Ramas.SetReadOnly(r,c,True) 1273 Ramas.SetCellStyle(r,c,VERY_LIGHT_GREY,True) 1274 Ramas.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) 1275 G2frame.dataFrame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2gd.wxID_RESTDELETE) 1276 G2frame.dataFrame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2gd.wxID_RESTCHANGEESD) 1277 mainSizer.Add(Ramas,0,) 1278 else: 1279 mainSizer.Add(wx.StaticText(RamaRestr,-1,'No Ramachandran restraints for this phase'),0,) 1280 mainSizer.Add((5,5)) 1178 1281 mainSizer.Add(wx.StaticText(RamaRestr,-1,'Ramachandran function coefficients:'),0,wx.ALIGN_CENTER_VERTICAL) 1179 1180 coeffDict = ramaRestData['Coeff']1181 1282 if len(coeffDict): 1182 1283 table = [] … … 1197 1298 Coeff.SetCellStyle(r,c,VERY_LIGHT_GREY,True) 1198 1299 mainSizer.Add(Coeff,0,) 1199 mainSizer.Add((5,5))1200 ramaList = ramaRestData['Ramas']1201 if len(ramaList):1202 table = []1203 rowLabels = []1204 Types = 2*[wg.GRID_VALUE_STRING,]+4*[wg.GRID_VALUE_FLOAT+':10,2',]1205 if 'macro' in General['Type']:1206 colLabels = ['(res) A (res) B (res) C (res) D (res) E','coef name','phi','psi','obs E','esd']1207 for i,[indx,ops,cofName,esd] in enumerate(ramaList):1208 atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4)1209 name = ''1210 for atom in atoms:1211 name += '('+atom[1]+atom[0].strip()+atom[2]+') '+atom[3]+' '1212 XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3))1213 phi,psi,calc = G2mth.getRestRama(XYZ,Amat,coeffDict[cofName])1214 table.append([name,cofName,phi,psi,calc,esd])1215 rowLabels.append(str(i))1216 ramaTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)1217 Ramas = G2gd.GSGrid(RamaRestr)1218 Ramas.SetTable(ramaTable, True)1219 Ramas.AutoSizeColumns(False)1220 for r in range(len(ramaList)):1221 for c in range(2):1222 Ramas.SetReadOnly(r,c,True)1223 Ramas.SetCellStyle(r,c,VERY_LIGHT_GREY,True)1224 Ramas.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect)1225 G2frame.dataFrame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2gd.wxID_RESTDELETE)1226 G2frame.dataFrame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2gd.wxID_RESTCHANGEESD)1227 mainSizer.Add(Ramas,0,)1228 else:1229 mainSizer.Add(wx.StaticText(RamaRestr,-1,'No Ramachandran restraints for this phase'),0,)1230 1300 1231 1301 RamaRestr.SetSizer(mainSizer) … … 1269 1339 G2frame.dataFrame.RestraintEdit.Enable(G2gd.wxID_RESTRAINTADD,False) 1270 1340 G2frame.dataFrame.RestraintEdit.Enable(G2gd.wxID_RESRCHANGEVAL,False) 1341 G2frame.dataFrame.RestraintEdit.Enable(G2gd.wxID_AARESTRAINTPLOT,True) 1271 1342 torsionRestData = restrData['Torsion'] 1272 1343 UpdateTorsionRestr(torsionRestData) … … 1275 1346 G2frame.dataFrame.RestraintEdit.Enable(G2gd.wxID_RESTRAINTADD,False) 1276 1347 G2frame.dataFrame.RestraintEdit.Enable(G2gd.wxID_RESRCHANGEVAL,False) 1348 G2frame.dataFrame.RestraintEdit.Enable(G2gd.wxID_AARESTRAINTPLOT,True) 1277 1349 ramaRestData = restrData['Rama'] 1278 1350 UpdateRamaRestr(ramaRestData) 1279 G2plt.PlotRama(G2frame,phaseName )1351 G2plt.PlotRama(G2frame,phaseName,rama,ramaName) 1280 1352 event.Skip() 1281 1353 … … 1300 1372 G2frame.dataFrame.RestraintEdit.Enable(G2gd.wxID_AARESTRAINTADD,True) 1301 1373 G2frame.dataFrame.Bind(wx.EVT_MENU, OnAddAARestraint, id=G2gd.wxID_AARESTRAINTADD) 1374 G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotAARestraint, id=G2gd.wxID_AARESTRAINTPLOT) 1302 1375 G2frame.dataDisplay = G2gd.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize()) 1303 1376
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