def get_origin_translation(asu_prmtop_file_name, asu_rst7_file_name): rst7 = raf.rst7(asu_rst7_file_name) coords = rst7.Get_Coords() UCbox = rst7.Get_Box() u,invu = raf.CompXfrm(UCbox) masses = raf.prmtop(asu_prmtop_file_name).Get_Masses() com = raf.COM(coords,masses) frac_com = dot(u, com) origin_translation = array([0.5, 0.5, 0.5]) - frac_com return u, origin_translation
def get_origin_translation(asu_prmtop_file_name, asu_rst7_file_name): rst7 = raf.rst7(asu_rst7_file_name) coords = rst7.Get_Coords() UCbox = rst7.Get_Box() u, invu = raf.CompXfrm(UCbox) masses = raf.prmtop(asu_prmtop_file_name).Get_Masses() com = raf.COM(coords, masses) frac_com = dot(u, com) origin_translation = array([0.5, 0.5, 0.5]) - frac_com return u, origin_translation
#! /usr/bin/env python import ReadAmberFiles as raf iprmtop=raf.prmtop('/net/casegroup2/u2/pjanowsk/Case/4lzt/4lzt_ff12SB/4lztSh_new.prmtop') masses=iprmtop.Get_Masses() totalmass=sum(masses) irst7=raf.rst7('/net/casegroup2/u2/pjanowsk/Case/4lzt/4lzt_ff12SB/4lztSh.rst7') box=irst7.Get_Box() volume=raf.Get_volume(box) density= totalmass/volume*10/6.022 print "density: %8.3f g/cm^3" %density
#~ if line.strip(): #~ fails.append( line.strip().split('/')[0] ) fails=['1a21', '1a8v', '1ba7', '1c03', '1dvm', '1ezs', '1f3u', '1fc3', '1fh5', '1jxo', '1ofp', '1oy3', '1q32', '1q4o', '1r19', '1r1z', '1r52', '1rzi', '1t0j', '1tee', '1tks', '1tw9', '1tzo', '1vh0', '1vr4', '1w3b', '1wp7', '1wp8', '1x13'] dirs=[ name for name in os.listdir('.') if os.path.isdir(name) and name[0]=='1' ] bad=[] good=[] for dir in dirs: if dir in fails: print dir trst=raf.rst7('%s/%s.rst7' %(dir,dir)) box=trst.Get_Box() bad.append( raf.Get_volume(box) ) else: print dir trst=raf.rst7('%s/%s.rst7' %(dir,dir)) box=trst.Get_Box() good.append( raf.Get_volume(box) ) print "BAD: mean %1.0f\n" %(np.mean(bad)) for v in bad: print "%d\n" %v print "\n" print "GOOD: mean %1.0f\n" %(np.mean(good))
fails = [ '1a21', '1a8v', '1ba7', '1c03', '1dvm', '1ezs', '1f3u', '1fc3', '1fh5', '1jxo', '1ofp', '1oy3', '1q32', '1q4o', '1r19', '1r1z', '1r52', '1rzi', '1t0j', '1tee', '1tks', '1tw9', '1tzo', '1vh0', '1vr4', '1w3b', '1wp7', '1wp8', '1x13' ] dirs = [ name for name in os.listdir('.') if os.path.isdir(name) and name[0] == '1' ] bad = [] good = [] for dir in dirs: if dir in fails: print dir trst = raf.rst7('%s/%s.rst7' % (dir, dir)) box = trst.Get_Box() bad.append(raf.Get_volume(box)) else: print dir trst = raf.rst7('%s/%s.rst7' % (dir, dir)) box = trst.Get_Box() good.append(raf.Get_volume(box)) print "BAD: mean %1.0f\n" % (np.mean(bad)) for v in bad: print "%d\n" % v print "\n" print "GOOD: mean %1.0f\n" % (np.mean(good))