def get_residues(pdb_fn, restraints, verbose):
residues = set()
for h in restraints:
a = h[0]
b = h[1]
a = a[0] + ':' + a[1:]
residues.add(a) # A19
b = b[0] + ':' + b[1:]
residues.add(b)
# set(['A:41', 'A:9', 'A:10', 'A:16'])
selection = ','.join(residues)
selection_parsed = select_pdb_fragment(selection,
separator=",",
splitting="[,:;]")
residues = parse_pdb(pdb_fn, selection_parsed)
# get mb
for r in residues:
if residues[r].has_key('N9'): # A,G
residues[r]['mb'] = residues[r]['N9'] - (
(residues[r]['N9'] - residues[r]['C6']) / 2)
else: # A,G
residues[r]['mb'] = residues[r]['N1'] - (
(residues[r]['N1'] - residues[r]['C4']) / 2)
for r in residues:
#print 'mb for ' + str(r) + ' is ' + residues[r]['mb']
print ' mb for ', str(r), residues[r]['mb']
return residues
def get_residues(pdb_fn, restraints, verbose):
"""
"""
residues = set()
for h in restraints:
a = h[0]
b = h[1]
a = a[0] + ':' + a[1:]
residues.add(a) # A19
b = b[0] + ':' + b[1:]
residues.add(b)
# set(['A:41', 'A:9', 'A:10', 'A:16'])
selection = ','.join(residues)
selection_parsed = select_pdb_fragment(selection,
separator=",",
splitting="[,:;]")
residues = parse_pdb(pdb_fn, selection_parsed)
# get mb
for r in residues:
if 'N9' in residues[r]: # A,G
residues[r]['mb'] = residues[r]['N9'] - (
(residues[r]['N9'] - residues[r]['C6']) / 2)
else: # A,G
residues[r]['mb'] = residues[r]['N1'] - (
(residues[r]['N1'] - residues[r]['C4']) / 2)
for r in residues:
if verbose:
logger.info(' '.join(['mb for ', str(r), str(residues[r]['mb'])]))
return residues
optparser.add_option("-v", "--verbose",
action="store_true", dest="verbose", default=False,
help="verbose")
(opts, args)=optparser.parse_args()
if len(sys.argv) == 1:
print optparser.format_help() #prints help if no arguments
sys.exit(1)
input_files = args[:] # opts.input_dir
rmsds_fn = opts.rmsds_fn
target_fn = opts.target_fn
method = opts.method
print ' method:', method
target_selection = select_pdb_fragment(opts.target_selection)
model_selection = select_pdb_fragment(opts.model_selection)
if target_selection:
if opts.verbose:
print ' target_selection: #', opts.target_selection, target_selection
ts = target_selection
print ts
resides_in_total = 0
for i in target_selection:
print i, len(ts[i]) # chain string, a list of residues
resides_in_total += len(ts[i])
print 'in total:', resides_in_total
if model_selection:
if opts.verbose:
print ' model_selection: ', len(model_selection), opts.model_selection, model_selection
resides_in_total = 0
def edit_pdb(args):
"""Edit. The function can take `A:3-21>A:1-19` or even syntax like this
`A:3-21>A:1-19,B:22-32>B:20-30` and will do a editing.
The output is printed, line by line. Only ATOM lines are edited!"""
## open a new file
s = StrucFile(args.file)
if not args.no_hr:
add_header()
print 'HEADER --edit ' + args.edit
## --edit 'A:3-21>A:1-19,B:22-32>B:20-30'
if args.edit.find(',') > -1:
# more than one edits
edits = args.edit.split(',') # ['A:3-21>A:1-19', 'B:22-32>B:20-30']
selects = []
for e in edits:
selection_from, selection_to = select_pdb_fragment(
e.split('>')[0]), select_pdb_fragment(e.split('>')[1])
if len(selection_to) != len(selection_from):
raise Exception('len(selection_to) != len(selection_from)')
selects.append([selection_from, selection_to])
print edits
else:
# one edit
e = args.edit
selection_from, selection_to = select_pdb_fragment(
e.split('>')[0]), select_pdb_fragment(e.split('>')[1])
if len(selection_to) != len(selection_from):
raise Exception('len(selection_to) != len(selection_from)')
selects = [[selection_from, selection_to]]
## go ever all edits: ['A:3-21>A:1-19','B:22-32>B:20-30']
for l in s.lines:
if l.startswith('ATOM'):
# get chain and resi
chain = l[21:22].strip()
resi = int(l[22:26].strip())
if_selected_dont_print = False
# for selections
for select in selects:
selection_from, selection_to = select
if selection_from.has_key(chain):
if resi in selection_from[chain]:
# [1,2,3] mapping from [4,5,10], you want to know how to map 1
# 1 is [0] element of first list, so you have to index first list
# to get 0, with this 0 you can get 4 out of second list [4,5,10][0] -> 4
nl = list(l)
chain_new = selection_to.keys()[
0] # chain form second list
nl[21] = chain_new # new chain
index = selection_from[chain].index(
int(resi)) # get index of 1
resi_new = str(selection_to[chain_new][index]).rjust(
4) # 'A' [1,2,3] -> ' 1'
nl[22:26] = resi_new
nl = ''.join(nl)
if_selected_dont_print = True
print nl
if not if_selected_dont_print:
print l
else: # if not atom
print l
s.get_simrna_ready(args.renumber_residues)
print s.get_text()
if args.renumber_residues:
s = StrucFile(args.file)
s.remove_hydrogen()
s.remove_ion()
s.remove_water()
s.get_simrna_ready(args.renumber_residues)
s.renum_atoms()
if not args.no_hr:
add_header()
print s.get_text()
if args.delete:
selection = select_pdb_fragment(args.delete)
s = StrucFile(args.file)
if not args.no_hr:
add_header()
print 'HEADER --delete ' + args.delete #' '.join(str(selection))
for l in s.lines:
if l.startswith('ATOM'):
chain = l[21]
resi = int(l[23:26].strip())
if selection.has_key(chain):
if resi in selection[chain]:
continue # print chain, resi
print l
if args.edit:
selection_from, selection_to = select_pdb_fragment(args.edit.split('>')[0]), select_pdb_fragment(args.edit.split('>')[1])