Python ReadAmberFiles.rst7の例

コード例 #1

ファイル: uc_water.py プロジェクト: pjanowski/Pawel_PhD_Scripts

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

コード例 #2

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

コード例 #3

ファイル: density.py プロジェクト: pjanowski/Pawel_PhD_Scripts

#! /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

コード例 #4

ファイル: check_failed_volumes.py プロジェクト: pjanowski/Pawel_PhD_Scripts

  #~ 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))

コード例 #5

ファイル: check_failed_volumes.py プロジェクト: handreazz/Pawel_PhD_Scripts

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))