''' SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . ''' import os,sys,string,locale,time import numpy import sassie.sasmol.sasmol as sasmol # CENTER # # 12/17/2004 -- adapted from trehalose project for gag modeling : jc # 12/20/2004 -- align N-terminal of CA in 1L6N and 1E6J : jc # 10/16/2005 -- generic align structures : jc # 11/02/2005 -- generic center : jc # 01/01/2011 -- added SASMOL : jc #LC 1 2 3 4 5 6 7 #LC4567890123456789012345678901234567890123456789012345678901234567890123456789 # * ** ''' CENTER is the module that centers molecules from a dcd/pdb file to the coordinates (0.0,0.0,0.0). This module is called from Center Frames from the main GUI through the graphical_center.py script. ''' def print_failure(message,txtOutput): txtOutput.put("\n\n>>>> RUN FAILURE <<<<\n") txtOutput.put(">>>> RUN FAILURE <<<<\n") txtOutput.put(">>>> RUN FAILURE <<<<\n\n") txtOutput.put(message) return def unpack_variables(variables): runname=variables['runname'][0] infile=variables['infile'][0] refpdb=variables['refpdb'][0] ofile=variables['ofile'][0] path=variables['path'][0] return runname,infile,refpdb,ofile,path def write_frame_to_file(m1,nf,frame,cenpath,ofile,outtype,dcdoutfile,intype): if(outtype == 'dcd'): if(intype == 'dcd'): m1.write_dcd_step(dcdoutfile,0,frame) elif(intype == 'pdb'): m1.write_dcd_step(dcdoutfile,frame,frame) elif(outtype == 'pdb'): if(nf == 1): m1.write_pdb(cenpath+ofile,0,'w') elif(nf > 1 and intype == 'dcd'): m1.write_pdb(cenpath+ofile,0,'a') elif(nf > 1 and intype == 'pdb'): m1.write_pdb(cenpath+ofile,frame,'a') return def check_output_type(ofile): if(ofile[-3:] == 'dcd'): print ' output file will be a DCD file' outtype = 'dcd' elif(ofile[-3:] == 'pdb'): print ' output file will be a PDB file' outtype = 'pdb' else: outtype = 'dcd' message='output filename '+ofile+' needs to end in either ".pdb" (1 frame) or ".dcd" (1 or more frames)\n' message+=' : writing output file as a '+ofile+'.dcd\n' print '\n\n',message,'\n\n' ofile = ofile +'.dcd' return outtype,ofile def center(variables,txtOutput): ''' CENTER is the module that centers molecules from a dcd/pdb file to the coordinates (0.0,0.0,0.0). INPUT: variable descriptions: runname: project name infile: filename of dcd input file refpdb: reference pdb file path: input/output filepath OUTPUT: files stored in runname/center directory ofile: output filename ofile*.minmax: text file with min & max dimensions ''' runname,infile,refpdb,ofile,path=unpack_variables(variables) cenpath=runname+'/center/' direxist=os.path.exists(cenpath) if(direxist==0): os.system('mkdir -p '+cenpath) print 'runname = ',runname minmaxfile=ofile+'.minmax' mmfile=open(cenpath+minmaxfile,'w') ttxt=time.ctime() st=''.join(['=' for x in xrange(60)]) txtOutput.put("\n%s \n" %(st)) txtOutput.put("DATA FROM RUN: %s \n\n" %(ttxt)) m1=sasmol.SasMol(0) try: if(infile[-3:] == 'dcd'): m1.read_pdb(path+refpdb) dcdfile = m1.open_dcd_read(path+infile) nf = dcdfile[2] intype = 'dcd' elif(infile[-3:] =='pdb'): m1.read_pdb(path+infile) nf = m1.number_of_frames() intype = 'pdb' except: message='input filename is a PDB or DCD file but it must end with ".pdb" or ".dcd" ' message+=' : stopping here' print_failure(message,txtOutput) minx=[] ; miny=[] ; minz=[] maxx=[] ; maxy=[] ; maxz=[] outtype,ofile = check_output_type(ofile) dcdoutfile = 'None' if(outtype == 'dcd'): dcdoutfile = m1.open_dcd_write(cenpath+ofile) txtOutput.put("Total number of frames = %d\n\n" % (nf)) for i in range(nf): if(intype == 'dcd'): m1.read_dcd_step(dcdfile,i) m1.center(0) minmax=m1.calcminmax_frame(0) elif(intype == 'pdb'): m1.center(i) minmax=m1.calcminmax_frame(i) write_frame_to_file(m1,nf,i+1,cenpath,ofile,outtype,dcdoutfile,intype) minx.append(minmax[0][0]) ; miny.append(minmax[0][1]) ; minz.append(minmax[0][2]) maxx.append(minmax[1][0]) ; maxy.append(minmax[1][1]) ; maxz.append(minmax[1][2]) if(((i+1)%(float(nf)/10.0)==0 or (nf<10))): fraction_done = (float(i+1)/float(nf)) progress_string='\nCOMPLETED '+str(i+1)+' of '+str(nf)+' : '+str(fraction_done*100.0)+' % done' print('%s\n' % progress_string) report_string='STATUS\t'+str(fraction_done) txtOutput.put(report_string) if(intype == 'dcd'): m1.close_dcd_read(dcdfile[0]) if(outtype == 'dcd'): m1.close_dcd_write(dcdoutfile) min_x = numpy.min(minx) ; min_y = numpy.min(miny) ; min_z = numpy.min(minz) max_x = numpy.max(maxx) ; max_y = numpy.max(maxy) ; max_z = numpy.max(maxz) mmfile.write("%s\n" % ("#min_x,min_y,min_z,max_x,max_y,max_z")) mmfile.write("%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n" % (min_x,min_y,min_z,max_x,max_y,max_z)) mmfile.close() txtOutput.put("Min/Max data written to : %s\n\n" % ('./'+cenpath+minmaxfile)) txtOutput.put("minimum x = %lf\t maximum x = %lf -> range: %lf Angstroms\n" % (min_x,max_x,(max_x-min_x))) txtOutput.put("minimum y = %lf\t maximum y = %lf -> range: %lf Angstroms\n" % (min_y,max_y,(max_y-min_y))) txtOutput.put("minimum z = %lf\t maximum z = %lf -> range: %lf Angstroms\n\n" % (min_z,max_z,(max_z-min_z))) print '\nCentered coordinate data (nf=%i) were written to %s\n' % (nf,'./'+cenpath+ofile) txtOutput.put("\nCentered coordinate data (nf=%i) were written to %s\n\n" % (nf,'./'+cenpath+ofile)) txtOutput.put("\n%s \n" %(st)) time.sleep(0.5) print 'CENTER IS DONE' return()