def parm2pdb(self, f_parm, f_crd, f_out, aatm=0):
"""
Use ambpdb to build PDB from parm and crd.
@param f_parm: existing parm file
@type f_parm: str
@param f_crd: existing crd file
@type f_crd: str
@param f_out: target file name for PDB
@type f_out: str
@return: f_out, target file name for PDB
@rtype: str
@raise AmberError: if ambpdb fail
"""
## cmd = '%s -p %s -aatm < %s > %s' % \
args = '-p %s %s' % (f_parm, '-aatm' * aatm)
x = Executor('ambpdb',
args,
f_in=f_crd,
f_out=f_out,
log=self.log,
verbose=1,
catch_err=1)
output, error, status = x.run()
if not os.path.exists(f_out):
raise AmberError, 'ambpdb failed.'
return f_out
def main(options):
## ## get extra options from external file
## if options.has_key('x'):
## options.update( _parseExternalOptions( options['x'] ) )
fname = options['i'] # input pdb file
outPath = options['o']
chainMask = options.get('cmask', None)
if chainMask: chainMask = toIntList(chainMask)
try:
if options.has_key('h'):
fheader = options['h']
else:
fheader = options['t'] + '/head.inp'
if options.has_key('s'):
fsegment = options['s']
else:
fsegment = options['t'] + '/segment.inp'
if options.has_key('e'):
ftail = options['e']
else:
ftail = options['t'] + '/end.inp'
except:
errWriteln(
"You have to specify either all three template files or\n" +
"(option -t) a folder that contains head.inp, segment.inp, end.inp.\n"
+
"If both -t and -h, -s, or -e are present, files specified with\n"
+ "-h, -s, -e are preferred.")
## check that input pdb file name (stripped of its path and extension)
## is at least 5 characters long and starts with a number
## Prompt user for renaming of the file.
name = stripFilename(fname)
## the filename is OK, but it has the same name as used for the
## XPLOR output therefore we append _original to the input file
if toInt(name[0]) == None or len(name) == 4:
print "##### NOTE: ######"
print "The pdb file name you gave is OK, but exactly"
print "the same name will be used for the output from"
print "the XPLOR script. Therefore '_original' will be"
print "appended to the input pdb file you gave."
base, ext = absfile(fname).split('.')
new_fname = base + '_original.' + ext
os.rename(fname, new_fname)
fname = new_fname
if toInt(name[0]) == None or len(name) < 4:
print "##### WARNING: ######"
print "The pdb file name you gave is either shorter "
print "than 4 characters or it doesn't start with a number."
print "This will cause the X-PLOR job to fail"
msg = "Do you want to rename the file (Y/N)?"
if upper(raw_input(msg)) == 'Y':
new_name = upper(raw_input("Give a new filname:"))
## check that the new name is OK
if toInt(new_name[0]) == None or len(new_name) < 4:
raise StandardError, \
'You gave an incorrect new filename. Exiting'
## create link
else:
new_file = '%s/%s.%s' % (os.path.dirname(
absfile(fname)), new_name, fname.split('.')[-1])
os.link(fname, new_file)
print 'Link from %s to %s created sucessfully'\
%(absfile(fname), new_file)
fname = new_file
## switch on Amber specialities ?
amber = options.has_key('a')
## cap N- and C-term of chain breaks?
capBreaks = options.has_key('cap')
cleaner = ChainCleaner(
ChainSeparator(fname,
outPath,
int(options['c']),
capBreaks=capBreaks,
chainMask=chainMask))
# initialize with output path and base file name for generate.inp file
xplorer = Xplor(outPath,
cleaner,
fheader,
fsegment,
ftail,
amber,
extras=options)
xplorer.generateInp()
## run X-Plor
if options.has_key('exe'):
out, error, returncode = Executor(
'xplor',
strict=0,
f_in=xplorer.cleaner.pdbname + "_generate.inp",
f_out=xplorer.cleaner.pdbname + '_generate.log').run()
## Show structure in pymol
if options.has_key('view'):
pm = Pymoler()
mname = pm.addPdb(xplorer.outname + '.pdb')
pm.add('select xray-wat, segi 1XWW')
pm.add('select added-wat, segi 1WWW')
pm.add('select hydrogens, elem H')
pm.add('hide everything, xray-wat OR added-wat OR hydrogens')
pm.add('select none')
colors = [hex2rgb(c, str) for c in hexColors(len(xplorer.chains))]
i = 0
for c in xplorer.chains:
print colors[i], c.segment_id
pm.add('set_color col_%i, %s' % (i, colors[i]))
pm.add('color col_%i, segi %s and elem c' % (i, c.segment_id))
i += 1
pm.add('zoom all')
pm.show()
