def replace_bfactors(self,infile,outfile,options,check_valid=False):
"""
Writes the .vol file 'infile' to 'outfile', but replaces the bfactor
column with either packing density or volume.
Also adds a short remark before the first atom.
"""
extralines_pd="""REMARK
REMARK COLUMNS MODIFIED FROM ORIGINAL PDB FILE:
REMARK PD - LOCAL PACKING DENSITY
REMARK VDWVOL - VOLUME INSIDE VAN-DER-WAALS SPHERE
REMARK SEVOL - VOLUME IN 1.4 ANGSTROM LAYER OUTSIDE VDW-SPHERE
REMARK BUR - INDICATES BURIED ATOMS (1=BURIED, 0=SURFACE)
REMARK
REMARK AT# ELEM RES C RES# X Y Z PD PD VDWVOL SEVOL BUR
"""
extralines_vol="""REMARK
REMARK COLUMNS MODIFIED FROM ORIGINAL PDB FILE:
REMARK VOL - TOTAL ATOMIC VOLUME
REMARK VDWVOL - VOLUME INSIDE VAN-DER-WAALS SPHERE
REMARK SEVOL - VOLUME IN 1.4 ANGSTROM LAYER OUTSIDE VDW-SPHERE
REMARK BUR - INDICATES BURIED ATOMS (1=BURIED, 0=SURFACE)
REMARK
REMARK AT# ELEM RES C RES# X Y Z VOL VOL VDWVOL SEVOL BUR
"""
extralines_z="""REMARK
REMARK COLUMNS MODIFIED FROM ORIGINAL PDB FILE:
REMARK Z - Z-SCORE
REMARK VDWVOL - VOLUME INSIDE VAN-DER-WAALS SPHERE
REMARK SEVOL - VOLUME IN 1.4 ANGSTROM LAYER OUTSIDE VDW-SPHERE
REMARK BUR - INDICATES BURIED ATOMS (1=BURIED, 0=SURFACE)
REMARK
REMARK AT# ELEM RES C RES# X Y Z Z Z VDWVOL SEVOL BUR
"""
f_atom = 0
out = ""
mode = options['bfactor']
if mode == 'zscore':
z = ZScore(AveragePacking(options))
for l in open(infile).readlines():
if re.search('(^ATOM)|(^HETATM)',l):
if not f_atom:
f_atom = 1
if mode == 'packing_density': out += extralines_pd
elif mode == 'volume': out += extralines_vol
elif mode == 'zscore': out += extralines_z
# extract volume data
atom = self.parse_atom(l,options)
if check_valid and not atom['valid']: continue
if mode == 'packing_density': value = atom['packing_density']
elif mode == 'zscore':
value = z.get_z_score(atom,options)
if not value: value = -1
else: value = atom['total_volume']
newline = l[:55] + "%5.2f %5.2f"%(value,value) + l[67:]
out += newline
else:
out += l
open(outfile,'w').writelines(out+'\n')
def write_pdb_file(self,filename,options):
"""
Writes a pdb file containing all valid atoms. The bfactor option
may be set to 'packdens' - substitutes bfactor with packing density.
'volume' - same with total atomic volume
'minuspackdens' - same with 1-packing density
'zscore' - z-score (normalized difference to reference value)
"""
bfactor = options['bfactor']
out = []
# z-score calculation only needed when the b-factor is to
# be replaced with the z-score
# actually, the expensive part is not the ZScore initialization
# but the AveragePacking initialization
if bfactor == 'zscore':
zsc = ZScore(AveragePacking(options))
for i in range(len(self.atoms)):
if not self.valid[i]:continue
atom = self.get_atom(i)
pl = atom['pdb_line']
# now get the value to be inserted as bfactor
#
# For some programs they need to be normalized
#
# Hallo Fiete!
#
# unter 'packdens' kannst Du dich austoben.
# Habe ein Beispiel reingeschrieben,
# in Python sollte etwas Mathe nicht so schwer sein.
# Aber frag mich trotzdem falls Du im Code versumpfst.
# 11.7.06 KR
#
if bfactor == 'packdens':
value = atom['packing_density']
# normalize values from 0.4 to 0.9 to bfactors between 0.0 and 30.
# 'packdens'
vmin = 0.4
vmax = 0.9
bmin = 0.0
bmax = 30.0
value = ((value-vmin)/vmax) * (bmax-bmin) + bmin
#
if bfactor == 'minuspackdens':
value = 1-atom['packing_density']
# normalize values from 0.4 to 0.9 to bfactors between 30.0 and 0.0
# 'minuspackdens'
vmin = 0.4
vmax = 0.9
bmin = 0.0
bmax = 30.0
value = ((value-vmin)/vmax) * (bmax-bmin) + bmin
#
elif bfactor == 'volume':
value = atom['total_volume']
# nomalize
# (insert code on demand)
elif bfactor == 'zscore':
value = zsc.get_z_score(atom,options)
if not value: value=100.0
# normalize
# (insert code on demand)
pl = pl[:60]+"%6.2f"%(value)+pl[66:]
out.append(pl+'\n')
open(filename,'w').writelines(out)
