Changeset 1090
- Timestamp:
- Oct 8, 2013 2:33:36 PM (9 years ago)
- File:
-
- 1 edited
-
trunk/exports/G2export_PDB.py (modified) (5 diffs)
Legend:
- Unmodified
- Added
- Removed
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trunk/exports/G2export_PDB.py
r1089 r1090 10 10 '''Code to demonstrate how export routines are created 11 11 ''' 12 import numpy as np 12 13 import os.path 13 14 import GSASIIpath … … 40 41 '''Export as a PDB file 41 42 ''' 43 44 def PDBheader(): 45 self.Write("HEADER phase "+str(phasenam)+" from "+str(self.G2frame.GSASprojectfile)) 46 self.Write("TITLE") 47 self.Write("COMPND") 48 self.Write("SOURCE") 49 self.Write("KEYWDS") 50 self.Write("EXPDTA X-RAY POWDER DIFFRACTION") 51 self.Write("REVDAT") 52 self.Write("JRNL") 53 self.Write("REMARK 1") 54 self.Write("REMARK 2") 55 self.Write("REMARK 2 RESOLUTION. 2.66 ANGSTROMS.") 56 self.Write("REMARK 2 POWDER DIFFRACTION MINIMUM D-SPACING.") 57 58 def PDBremark250(): 59 self.Write('REMARK 250') 60 self.Write('REMARK 250 REFINEMENT.') 61 self.Write('REMARK 250 PROGRAM : GSAS-II') 62 self.Write('REMARK 250 AUTHORS : TOBY & VON DREELE') 63 self.Write('REMARK 250 REFRENCE : J. APPL. CRYST. 46, 544-549(2013)') 64 self.Write('REMARK 250') 65 self.Write('REMARK 250 DATA USED IN REFINEMENT') 66 self.Write('REMARK 250 RESOLUTION RANGE HIGH (ANGSTROMS) : x.xx') 67 self.Write('REMARK 250 RESOLUTION RANGE LOW (ANGSTROMS) : xx.xx') 68 self.Write('REMARK 250 POWDER DIFFRACTION DATA.') 69 self.Write('REMARK 250') 70 self.Write('REMARK 250 FIT TO DATA USED IN REFINEMENT') 71 self.Write('REMARK 250 NUMBER OF POWDER PATTERNS : x') 72 self.Write('REMARK 250 PROFILE R VALUES (%) : x.xx') 73 self.Write('REMARK 250 WEIGHTED PROFILE R VALUES (%) : x.xx') 74 self.Write('REMARK 250 F**2 R VALUES (%) : xx.xx') 75 self.Write('REMARK 250 NUMBERS OF POWDER PATTERN POINTS : xxxx') 76 self.Write('REMARK 250 NUMBERS OF REFLECTIONS : xxxx') 77 self.Write('REMARK 250 TOTAL NUMBER OF POWDER POINTS : xxxx') 78 self.Write('REMARK 250') 79 self.Write('REMARK 250 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.') 80 self.Write('REMARK 250 PROTEIN ATOMS : xxxx') 81 self.Write('REMARK 250 NUCLEIC ACID ATOMS : xxxx') 82 self.Write('REMARK 250 HETEROGEN ATOMS : xxxx') 83 self.Write('REMARK 250 SOLVENT ATOMS : xxxx') 84 self.Write('REMARK 250') 85 self.Write('REMARK 250 MODEL REFINEMENT.') 86 self.Write('REMARK 250 NUMBER OF LEAST-SQUARES PARAMETERS : xxxx') 87 self.Write('REMARK 250 NUMBER OF RESTRAINTS : xxxx') 88 self.Write('REMARK 250') 89 self.Write('REMARK 250 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. NUMBER.') 90 self.Write('REMARK 250 BOND ANGLES (DEG) : x.xx xxx') 91 # self.Write('REMARK 250 ANTI-BUMPING DISTANCE RESTRAINTS (A) :x.xxx xxx') 92 # self.Write('REMARK 250 HYDROGEN BOND DISTANCE RESTRAINTS (A) :x.xxx xxx') 93 self.Write('REMARK 250 INTERATOMIC DISTANCES (A) :x.xxx xxx') 94 self.Write('REMARK 250 DISTANCES FROM RESTRAINT PLANES (A) :x.xxx xxx') 95 self.Write('REMARK 250 TORSION PSEUDOPOTENTIAL RESTRAINTS (E) : x.xx xxx') 96 self.Write('REMARK 250 TORSION ANGLE RESTRAINTS (E) : x.xx xxx') 97 self.Write('REMARK 250') 98 self.Write('REMARK 200') 99 self.Write('DBREF') 100 101 def PDBseqres(seqList): 102 chains = seqList.keys() 103 chains.sort() 104 nSeq = 0 105 for chain in chains: 106 nres = len(seqList[chain]) 107 nrec = (nres-1)/13+1 108 iB = 0 109 for irec in range(nrec): 110 iF = min(iB+13,nres) 111 text = 'SEQRES {:3d}{:2s}{:5d} '+(iF-iB)*'{:4s}' 112 self.Write(text.format(irec+1,chain,nres,*seqList[chain][iB:iF])) 113 nSeq += 1 114 iB += 13 115 return nSeq 116 42 117 # the export process starts here 43 118 # load all of the tree into a set of dicts … … 54 129 print 'not macromolecular phase' 55 130 return 56 print phasedict.keys()57 print General['SGData'].keys()58 131 i = self.Phases[phasenam]['pId'] 59 132 if len(self.phasenam) > 1: # if more than one filename is included, add a phase # … … 63 136 fil = self.filename 64 137 fp = self.OpenFile(fil) 65 self.Write("HEADER phase "+str(phasenam)+" from "+str(self.G2frame.GSASprojectfile)) 66 # get cell parameters 67 pfx = str(phasedict['pId'])+'::' 68 A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict) 69 line = "CRYST1 {:8.3f} {:8.3f} {:8.3f} {:6.2f} {:6.2f} {:6.2f} ".format(*G2lat.A2cell(A)) 138 Atoms = phasedict['Atoms'] 139 cx,ct,cs,cia = General['AtomPtrs'] 140 seqList = {} 141 AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE', 142 'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE'] 143 seq = 0 144 for atom in Atoms: 145 if atom[ct-3] in AA3letter and int(atom[ct-4]) != seq: 146 if atom[ct-2] not in seqList: 147 seqList[atom[ct-2]] = [] 148 seqList[atom[ct-2]].append(atom[ct-3]) 149 seq = int(atom[ct-4]) 150 PDBheader() 151 PDBremark250() 152 nSeq = PDBseqres(seqList) 153 154 # get cell parameters 155 Cell = General['Cell'][1:7] 156 line = "CRYST1 {:8.3f} {:8.3f} {:8.3f} {:6.2f} {:6.2f} {:6.2f} ".format(*Cell) 70 157 line += General['SGData']['SpGrp'].ljust(13) 71 158 line += '%2d'%(len(General['SGData']['SGOps'])*len(General['SGData']['SGCen'])) … … 74 161 self.Write('ORIGX2 0.000000 1.000000 0.000000 0.00000') 75 162 self.Write('ORIGX3 0.000000 0.000000 1.000000 0.00000') 76 G = G2lat.A2Gmat(A)[0] 77 A,B = G2lat.Gmat2AB(G) 163 A,B = G2lat.cell2AB(Cell) 78 164 self.Write('SCALE1 {:9.6f} {:9.6f} {:9.6f} 0.00000'.format(*B[0])) 79 165 self.Write('SCALE2 {:9.6f} {:9.6f} {:9.6f} 0.00000'.format(*B[1])) 80 166 self.Write('SCALE3 {:9.6f} {:9.6f} {:9.6f} 0.00000'.format(*B[2])) 81 Atoms = phasedict['Atoms'] 82 83 167 iatom = 1 168 nHet = 0 169 nTer = 0 170 for atom in Atoms: 171 if atom[cia] == 'I': 172 Biso = atom[cia+1]*8.*np.pi**2 173 xyz = np.inner(A,np.array(atom[cx:cx+3])) 174 if atom[ct-3] in AA3letter: 175 fmt = 'ATOM{:7d} {:4s}{:3s}{:2s}{:4s} '+3*'{:8.3f}'+2*'{:6.2f}'+'{:s}' 176 self.Write(fmt.format(iatom,atom[ct-1],atom[ct-3], \ 177 atom[ct-2],atom[ct-4],xyz[0],xyz[1],xyz[2],atom[cx+3],Biso,atom[ct].rjust(12))) 178 if atom[ct-1] == 'OXT': 179 iatom += 1 180 self.Write('TER {:7d} {:4s}{:3s}'.format(iatom,atom[ct-1],atom[ct-3])) 181 nTer += 1 182 else: 183 nHet += 1 184 fmt = 'HETATM{:5d} {:5s}{:3s}{:2s}{:4s} '+3*'{:8.3f}'+2*'{:6.2f}'+'{:s}' 185 self.Write(fmt.format(iatom,atom[ct-1].ljust(5),atom[ct-3], \ 186 atom[ct-2],atom[ct-4],xyz[0],xyz[1],xyz[2],atom[cx+3],Biso,atom[ct].rjust(12))) 187 iatom += 1 188 189 vals = [3,0,nHet,0,0,0,6,len(Atoms),nTer,0,nSeq] 190 fmt = 'MASTER'+11*'{:5d}' 191 self.Write(fmt.format(*vals)) 192 self.Write('END') 84 193 self.CloseFile() 85 194 print('Phase '+str(phasenam)+' written to file '+str(fil)) 195 196
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