def update_ciffile(file, altidd):
''' correct alter conformer IDs if it is wrong.
'''
nfile = file + '_new_alt'
fw = open(nfile, 'w')
flist = open(file, "r").readlines()
items, values = cif.cifparse(flist, '_atom_site.') # a loop
rows = cif.get_rows(items, values)
nalt = -1
alt = '_atom_site.label_alt_id'
if alt in items: nalt = items.index(alt)
if nalt < 0:
print 'Warning: cif token for alt_id is not found, no correction is applied.'
return nfile
for x in altidd: #correct alt_ids
for y in x:
n, id = y[0], y[1]
rows[n][nalt] = y[1]
st, nall = 0, len(flist)
for i, ln in enumerate(flist):
if 'loop_' in ln.lstrip()[:5] and '_atom_site.' in flist[
i + 1].lstrip()[:11]:
st = i
break
fw.write(ln)
for i in range(st, nall): #remove _atom_site
if '#' in flist[i].lstrip()[0]:
st = i
break
fw.write('#\nloop_\n')
for x in items:
fw.write('%s \n' % x)
fmt = [] # the writing format
nrow, ncol = len(rows), len(rows[0])
for i in range(ncol): #put column format in a list
tmp = []
for j in range(nrow):
n = len(rows[j][i])
tmp.append(n)
fmt.append(max(tmp))
for x in rows: #re-write atom_site (left formated)
for i, y in enumerate(x):
fw.write(y.ljust(fmt[i] + 1))
fw.write('\n')
for n in range(st, nall): # the last lines.
fw.write(flist[n])
fw.close()
return nfile
def parse_table(alist, table, id):
'''parse the table in the DCC: flist is a list
id=0, input file; id=1. input list
'''
if id==0: # a file
flist=open(alist, 'r').readlines()
else:
flist = alist
items,values = cif.cifparse(flist, table)
rows=cif.get_rows(items,values)
return items, rows
def cif2cif_sf(flist, num):
sf = 'SF-%d.cif' % num
fw = open(sf, 'w')
n1 = 0
n2 = len(flist)
for i, x in enumerate(flist):
if 'loop_' in x.lstrip()[:5] and '_refln.' in flist[i +
1].lstrip()[:7]:
n1 = i
break
sflist = []
for i in range(n1, n2):
sflist.append(flist[i])
t = flist[i].lstrip()
if ('#' in t[:1] or 'data_' in t[:5]
or ('_' in t[:1] and '_refln.' not in t[:7])):
n2 = i
break
for i in range(0, n1):
fw.write(flist[i]) #write the front part
items, values = cif.cifparse(flist[n1:n2], '_refln.')
status_col = items.index('_refln.status')
flag_col = items.index('_refln.pdbx_r_free_flag')
rows = cif.get_rows(items, values)
for i in range(len(rows)): #
if rows[i][status_col] == 'f': rows[i][status_col] = 'o'
for i in range(len(rows)):
if int(rows[i][flag_col]) == num and rows[i][status_col] == 'o':
rows[i][status_col] = 'f'
cif.write_cif_loop(fw, items, rows)
for i in range(n2, len(flist)):
fw.write(flist[i]) #write the end part
fw.close()
return sf
def update_coord(file, swater, occ, out_xyz):
'''
'''
print 'Updating coordinate..\n'
newfile = file + '_new'
if len(out_xyz): newfile = out_xyz
fw = open(newfile, 'w')
fp = open(file, 'r')
flist = []
for x in fp:
if x.strip() == 0: continue
flist.append(x.lstrip())
fp.close()
flist = open(file, 'r').readlines()
n1 = 0
for i, x in enumerate(flist): #get the first, part.
if ('loop_' in x[:5] and '_atom_site.' in flist[i + 1][:11]
and '_atom_site.' in flist[i + 2][:11]):
n1 = i
break
sflist = []
n2 = len(flist)
for i in range(n1, n2): # get last line of coord. (the second part)
sflist.append(flist[i])
t = flist[i].lstrip()
if ('#' in t[:1] or 'data_' in t[:5]
or ('_' in t[:1] and '_atom_site.' not in t[:11])):
n2 = i
break
for i in range(0, n1):
fw.write(flist[i]) #write the front part
items, values = cif.cifparse(flist[n1:n2], '_atom_site.')
ch_col = items.index('_atom_site.auth_asym_id')
comp_col = items.index('_atom_site.label_comp_id')
nres_col = items.index('_atom_site.auth_seq_id')
atom_col = items.index('_atom_site.label_atom_id')
alt_col = items.index('_atom_site.label_alt_id')
ins_col = items.index('_atom_site.pdbx_PDB_ins_code')
natm_col = items.index('_atom_site.id')
occ_col = items.index('_atom_site.occupancy')
#swater=[ch, comp,nres,atom,alt,ins,natom]
rows = cif.get_rows(items, values)
for i in range(len(rows)):
for j, x in enumerate(swater):
if (rows[i][ch_col] == x[0] and rows[i][comp_col] == x[1]
and rows[i][nres_col] == x[2] and rows[i][atom_col] == x[3]
and rows[i][alt_col] == x[4] and rows[i][ins_col] == x[5]
and rows[i][natm_col] == x[6]):
rows[i][occ_col] = '%.2f' % occ[j]
break
cif.write_cif_loop(fw, items, rows)
for i in range(n2, len(flist)):
fw.write(flist[i]) #write the end part
fw.close()
return newfile
def find_xyzlim_compound(compid, coord):
'''find xyzlimit used by mapmask, and write the coord in cif or pdb format.
compid: atom_group_id (model_compound_chainID_resnumber_alter_insertion)
coord: the coordinate file
idd = 0, cif format; =1, the pdb format
'''
comp = 'XXXX'
t1 = compid.split(':')
for i, x in enumerate(t1):
t = x.split('_')
if i == 0: comp = '_'.join([t[0], t[1], t[2], t[3]])
if len(t) != 6:
print(
'Error: in group-id (%d). it should be (model_compound_chainID_resnumber_alter_insertion).'
% (i + 1))
return '', ''
idd = util.is_cif(coord)
xyzcomp = comp + '.pdb'
if idd == 1: xyzcomp = comp + '.cif'
fw = open(xyzcomp, 'w')
border = 1 #extend a little to cover more density
xx, yy, zz = [], [], []
if idd == 1: #input cif format
fw.write('data_xyzcomp\n#\n')
flist = open(coord, 'r').readlines()
items, values = cif.cifparse(flist, '_cell.')
fw.write('\n#\n')
for m, p in enumerate(items):
fw.write("%s %s\n" % (p, values[m]))
cell = cif.get_cell(flist)
items, values = cif.cifparse(flist, '_atom_site.')
comp = cif.parse_values(items, values, "_atom_site.auth_comp_id")
asym = cif.parse_values(items, values, "_atom_site.auth_asym_id")
seq = cif.parse_values(items, values, "_atom_site.auth_seq_id")
alt = cif.parse_values(items, values, "_atom_site.label_alt_id")
ins = cif.parse_values(items, values, "_atom_site.pdbx_PDB_ins_code")
x = cif.parse_values(items, values, "_atom_site.Cartn_x")
y = cif.parse_values(items, values, "_atom_site.Cartn_y")
z = cif.parse_values(items, values, "_atom_site.Cartn_z")
model = cif.parse_values(items, values,
"_atom_site.pdbx_PDB_model_num")
if (not (alt and comp and ins and asym and seq and x and y and z)):
print(
'Error: not enough infor. extraced from (%s). Check ciftokens'
% coord)
sys.exit()
fw.write('\n#\nloop_\n')
for p in items:
fw.write("%s\n" % p)
row = cif.get_rows(items, values)
for i in range(len(x)):
alter, inst, mod = '.', '.', '1'
if model and util.is_number(model[i]): mod = model[i]
if alt and alt[i] != '?': alter = alt[i]
if ins and ins[i] != '?': inst = ins[i]
id1 = '_'.join([mod, comp[i], asym[i], seq[i], alter, inst])
if id1 in compid:
xx.append(float(x[i]))
yy.append(float(y[i]))
zz.append(float(z[i]))
for m in row[i]:
fw.write("%s " % m)
fw.write('\n')
else: #pdb format
fp = open(coord, 'r')
for x1 in fp:
if ('CRYST1' in x1[:6]):
fw.write(x1)
cell = [float(p) for p in x1[8:54].split()]
elif ('ATOM' in x1[:4] or 'HETATM' in x1[:6]):
alt = x1[16:17]
if alt.isspace(): alt = '.'
ins = x1[26:27]
if ins.isspace(): ins = '.'
resname, chid, resnum = x1[17:20].strip(), x1[20:22].strip(
), x1[22:26].strip()
resid = '_'.join([resname, chid, resnum, alt, ins])
if resid in compid:
fw.write(x1) #only write the selected section
xx.append(float(x1[30:38]))
yy.append(float(x1[38:46]))
zz.append(float(x1[46:54]))
fp.close()
if not xx or not yy or not zz:
print('Error: %s can not be found in the coordinate. try a new id. ' %
(compid))
return '', ''
frac, orth = util.frac_orth_matrix(cell) #get matrix
border = 2.0
xx_min, xx_max = min(xx) - border, max(xx) + border
yy_min, yy_max = min(yy) - border, max(yy) + border
zz_min, zz_max = min(zz) - border, max(zz) + border
xf_min = util.matrix_prod(frac, [xx_min, yy_min, zz_min])
xf_max = util.matrix_prod(frac, [xx_max, yy_max, zz_max])
xyzlim = '%.3f %.3f %.3f %.3f %.3f %.3f' % (
xf_min[0], xf_max[0], xf_min[1], xf_max[1], xf_min[2], xf_max[2])
fw.close()
return xyzlim, xyzcomp
def cut_map_around_ligand_peptide(dccfile, dic, mapfile_in, xyzfile_in):
'''It generate a complete set for ligand (map, html, jmol).
dccfile: the density file by dcc.
dic: a directory to hold all the file for webpage (url below).
mapfile_in: a input map file.
xyzfile_in: a input coordinate file.
'''
print('Cutting the density maps for ligands/peptide')
tmpxyz = xyzfile_in
if util.is_cif(xyzfile_in): tmpxyz = cif.cif2pdb(xyzfile_in)
pdbfile = os.path.basename(dic['pdbfile']) + '_new'
if pdbfile != tmpxyz: shutil.copy(tmpxyz, pdbfile)
mapfile = os.path.basename(dic['pdbfile']) + '_2fofc.map'
if dic['ligmapcif']: mapfile = dic['xyzfile_orig'] + '_2fofc.map'
shutil.move(mapfile_in, mapfile)
if dic['ligmapcif']: #pre-parse the cif file.
dic['cif'] = 1
ciffile = dic['xyzfile_orig']
flist = open(ciffile, 'r').readlines()
cell_items, values = cif.cifparse(flist, '_cell.')
cell = cif.get_rows(cell_items, values)
dic['cell_items'], dic['lig_cell'] = cell_items, cell
sym_items, values = cif.cifparse(flist, '_symmetry.')
sym = cif.get_rows(sym_items, values)
dic['sym_items'], dic['lig_sym'] = sym_items, sym
items, values = cif.cifparse(flist, '_atom_site.')
comp = cif.parse_values(items, values, "_atom_site.auth_comp_id")
asym = cif.parse_values(items, values, "_atom_site.auth_asym_id")
seq = cif.parse_values(items, values, "_atom_site.auth_seq_id")
alt = cif.parse_values(items, values, "_atom_site.label_alt_id")
ins = cif.parse_values(items, values, "_atom_site.pdbx_PDB_ins_code")
mod = cif.parse_values(items, values, "_atom_site.pdbx_PDB_model_num")
row = cif.get_rows(items, values)
dic['items'], dic['comp1'], dic['asym'], dic[
'seq'] = items, comp, asym, seq
dic['alt'], dic['ins'], dic['mod'], dic['row'] = alt, ins, mod, row
fw_itool = open('LIG_PEPTIDE.cif',
'w') #a cif file contains table, filenames
fw_itool.write('data_lig_peptide\n')
fw_itool.write(
'\n# A "!" will be given if the residue is bad with real_space_R.\n')
fw_itool.write('\n# Criteria: (CC<0.7 and R>0.4) or CC<0.5 or R>0.5\n')
url = 'http://sf-tool.wwpdb.org/users_data/dir_%s/' % dic['dir']
#url=os.environ['THIS_SERVICE_URL__FIX_ME'] + '/users_data/dir_%s/' %dic['dir']
ch_pep, chr_pep, ch_lig, chr_lig, ch_wat, chr_wat = tls.chain_res_range(
pdbfile)
ligpdb = non_poly_pdb(ch_pep, ch_lig, pdbfile) #get non-poly xyz file
dcc = get_dcc(dccfile) #get a list for dcc of each residue
if not dcc:
util.perror(
'Warning: Failed to parse EDS values! No ligand/peptide maps will be generated. '
)
for k, v in ch_pep.items():
if len(v) < 15: #length of peptide
if not dic['sdsc_map']:
map_around_peptide(fw_itool, dic, mapfile, ligpdb, dcc, ch_pep,
url)
break
if ch_lig:
map_around_ligand(fw_itool, dic, mapfile, ligpdb, dcc, ch_lig, url)
get_html_table_baddcc_general(mapfile, dcc) #for polymer/lig/peptide
fw_itool.close()
if dic['sdsc_map']:
arg = 'rm -f %s %s %s LIG_PEPTIDE.cif ' % (mapfile, mapfile_in,
xyzfile_in)
arg = arg + ' %s_rcc_sum.cif.mtz %s_2fofc.map_all.html ' % (
dic['pdbfile'], dic['pdbfile'])
os.system(arg)
# util.delete_file(pdbfile)
return