# break
elif (line[0:6] == 'HETATM') & (line[17:20]
== 'MSE'): #Selenomethionine
line_edit = 'ATOM ' + line[6:17] + 'MET' + line[20:]
if (line_edit[12:14] == 'SE'):
line_edit = line_edit[0:12] + ' S' + line_edit[14:]
if len(line_edit) > 75:
if (line_edit[76:78] == 'SE'):
line_edit = line_edit[0:76] + ' S' + line_edit[78:]
if line_edit[0:4] == 'ATOM':
resnum = line_edit[23:26]
if not resnum == oldresnum:
count = count + 1
longname = line_edit[17:20]
if longer_names.has_key(longname):
fastaid.write(longer_names[longname])
else:
fastaid.write('X')
oldresnum = resnum
newnum = '%3d' % count
line_edit = line_edit[0:23] + newnum + line_edit[26:]
if removechain:
line_edit = line_edit[0:21] + ' ' + line_edit[22:]
#outid.write(line_edit)
fastaid.write('\n')
#outid.close()
#fastaid.close()
resn = modres[resn]
line_edit = 'ATOM '+line[6:17]+ resn + line[20:]
if orig_resn == "MSE":
# don't count MSE as modified residues for flagging purposes (because they're so common)
# Also, fix up the selenium atom naming
if (line_edit[12:14] == 'SE'):
line_edit = line_edit[0:12]+' S'+line_edit[14:]
if len(line_edit) > 75:
if (line_edit[76:78] == 'SE'):
line_edit = line_edit[0:76]+' S'+line_edit[78:]
else:
shit_stat_modres = True
# Only process residues we know are valid.
if not longer_names.has_key(resn):
continue
resnum = line_edit[22:27]
# Is this a new residue
if not resnum == oldresnum:
if residue_buffer != []: # is there a residue in the buffer ?
if not check_and_print_pdb(count, residue_buffer, residue_letter):
# if unsuccessful
shit_stat_misdns = True
else:
count = count + 1
residue_buffer = []
residue_letter = longer_names[resn]
# Is thresidue_letter
if not resnum == oldresnum:
if residue_buffer != []: # is there a residue in the buffer ?
if not residue_invalid:
if not check_and_print_pdb(count, residue_buffer, residue_letter):
# if unsuccessful
shit_stat_misdns = True
else:
count = count + 1
residue_buffer = []
residue_letter = ""
residue_invalid = False
longname = line_edit[17:20]
if longer_names.has_key(longname):
residue_letter = longer_names[longname]
else:
residue_letter = 'X'
residue_invalid = True
oldresnum = resnum
# What does this do ?
if line_edit[16:17] == 'A':
line_edit = line_edit[:16]+' '+line_edit[17:]
if line_edit[16:17] != ' ':
continue
if removechain:
resn = modres[resn]
line_edit = "ATOM " + line[6:17] + resn + line[20:]
if orig_resn == "MSE":
# don't count MSE as modified residues for flagging purposes (because they're so common)
# Also, fix up the selenium atom naming
if line_edit[12:14] == "SE":
line_edit = line_edit[0:12] + " S" + line_edit[14:]
if len(line_edit) > 75:
if line_edit[76:78] == "SE":
line_edit = line_edit[0:76] + " S" + line_edit[78:]
else:
shit_stat_modres = True
# Only process residues we know are valid.
if not longer_names.has_key(resn):
continue
resnum = line_edit[22:27]
# Is this a new residue
if not resnum == oldresnum:
if residue_buffer != []: # is there a residue in the buffer ?
if not check_and_print_pdb(count, residue_buffer, residue_letter):
# if unsuccessful
shit_stat_misdns = True
else:
count = count + 1
residue_buffer = []
residue_letter = longer_names[resn]