def cut_map_around_xyz(mapfile, peppdb_in, pepid):
'''using several CCP4 until to cut map around the selected molecule
color: [x800080] [xc00000] [xb0b0b0]
'''
mapout = pepid + '_cut.map'
util.delete_file(mapout)
'''
xyzlim,xyzcomp=find_xyzlim_compound(pepid, peppdb_in)
mapscr=cut_map_bylimit(xyzlim)
arg = mapfile + ' ' + ' ' + mapout
command="chmod +x %s ; ./%s " %(mapscr, mapscr) + arg
os.system(command)
return mapout
'''
peppdb = peppdb_in
if util.is_cif(peppdb_in): peppdb = cif.cif2pdb(peppdb_in)
mapscr = cut_map_scr()
arg = mapfile + ' ' + peppdb + ' ' + mapout
command = "chmod +x %s ; ./%s " % (mapscr, mapscr) + arg
os.system(command)
if util.is_cif(peppdb_in):
util.delete_file('%s.PDB' % peppdb_in)
peppdb = peppdb_in
return mapout
def check_ncs(file):
'''full check of the NCS groups (file in pdb or cif)
'''
if util.is_cif(file):
check_ncs_cif(file)
else:
# print 'Please input a cif file.'
return
def get_atominfo(file):
'''Load atom information (pdb or cif)
'''
atominfo = {
'chain': [],
'nres': [],
'comp': [],
'atom': [],
'symbol': [],
'alt': [],
'ins': [],
'x': [],
'y': [],
'z': [],
'xf': [],
'yf': [],
'zf': [],
'occ': [],
'mtr': [],
'symop': [],
'spg': '',
'cell': [],
'mtrix': [],
'atom_o': [],
'group': [],
'natm': [],
'natm_c': [],
'segid': []
}
#print 'Loading atom information.'
if not util.check_file(100, file):
print('Error: file (%s) not exist' % file)
return atominfo
if util.is_cif(file):
dic = data_from_cif(file, atominfo)
else:
dic = data_from_pdb(file, atominfo)
# print 'spg=', dic['spg'], dic['cell']
atominfo.update(dic)
return atominfo
def assign_alt_id(file, outfile):
'''assign alt id if it is wrong!
'''
info = get_atominfo(file)
netdis = check_dis(info, 1) # dist for alt conformers
atoms = []
for x in netdis:
atoms.append(x[1])
atoms.append(x[2])
atoms.sort()
uatoms = []
for i, x in enumerate(atoms):
if i > 0 and x == atoms[i - 1]: continue
uatoms.append(x)
satom, altidd = [], []
for i, x in enumerate(uatoms):
t = x.split('_')
if i > 0:
t0 = uatoms[i - 1].split('_')
if t[:4] != t0[:4]:
util.gsort(satom, 1, -1)
altid = check_alt(satom)
if altid: altidd.append(altid)
#print satom
satom = []
satom.append([x, info['occ'][int(t[7])]])
if len(altidd):
if util.is_cif(file):
newfile = update_ciffile(file, altidd)
else:
newfile = update_pdbfile(file, altidd)
if outfile:
util.move(newfile, outfile)
print '\nThe updated new file = %s\n' % outfile
else:
print '\nThe updated new file = %s\n' % newfile
def check_special_position(file, outfile, out_xyz):
'''file can be in PDB/mmCIF format.
the tolerance of distanc for 0.25 for refmac, 0.5 for shelx, 1.0 for phenix.
'''
if not outfile: outfile = file + '_occ'
fw = open(outfile, 'w')
dist_limit = 0.5 # the minimum distance for atoms on special positions
extend = 2
info = get_atominfo(file)
print 'Searching atoms on special positions(space group=%s)..' % info['spg']
if not info['cell']:
t = 'Error: the unit cell is not extracted!\n'
fw.write(t)
fw.close()
return
frac, orth = util.frac_orth_matrix(info['cell']) #get conversion matrix
m1, m2, m3 = get_sym_operator(info, 'frac') #get sym
xf, yf, zf = info['xf'], info['yf'], info['zf']
xfn, yfn, zfn = shift_xyz2unit(xf, yf, zf)
# xfc,yfc,zfc=xyz_orig(xf, yf, zf)
# xfc1,yfc1,zfc1=xyz_orig(xfn, yfn, zfn)
# print 'new orig=%.3f %.3f %.3f ; old orig=%.3f %.3f %.3f' %(xfc1,yfc1,zfc1,xfc,yfc,zfc)
xfb = util.matrix_prod(frac, [extend, extend, extend]) #boundary in frac
xmin, xmax = expand_boundary(xfn, yfn, zfn, xfb) #use the shifted
# print xmin, xmax
d = 0
nspecial = []
box = (-3, -2, -1, 0, 1, 2, 3) #7*7*7=125 cell
# box=( -2, -1, 0, 1 ,2) #5*5*5=125 cell
# box=( -1, 0, 1) #3*3*3=27
nop = len(m1)
for ii in box:
for jj in box:
for kk in box:
for j in range(nop): #number of operators
m10, m20, m30 = m1[j][0], m2[j][0], m3[j][
0] #pre-assign 30% faster
m11, m21, m31 = m1[j][1], m2[j][1], m3[j][1]
m12, m22, m32 = m1[j][2], m2[j][2], m3[j][2]
m13, m23, m33 = m1[j][3], m2[j][3], m3[j][3]
nxf = len(xf)
for i in range(nxf):
xi = [xfn[i], yfn[i], zfn[i]] #shifted frac
x, y, z = xfn[i], yfn[i], zfn[i]
xnf0 = m10 * x + m11 * y + m12 * z + m13 + ii
xnf1 = m20 * x + m21 * y + m22 * z + m23 + jj
xnf2 = m30 * x + m31 * y + m32 * z + m33 + kk
if (xnf0 < xmin[0] or xnf0 > xmax[0] or xnf1 < xmin[1]
or xnf1 > xmax[1] or xnf2 < xmin[2]
or xnf2 > xmax[2]):
continue
d = util.distf(xi, [xnf0, xnf1, xnf2], info['cell'])
# if d>0.5 : continue
# xno = util.matrix_prod(orth,[xnf0,xnf1,xnf2])
scode = '%d%d%d' % (ii + 5, jj + 5, kk + 5)
if d < 0.5 and (j != 0 or '555' not in scode
): # atom on special position
s1 = '%s_%s_%s_%s_%s_%s_%s_%d' % (
info['chain'][i], info['comp'][i],
info['nres'][i], info['atom'][i],
info['alt'][i], info['ins'][i],
info['natm'][i], i)
s2 = '%3d %s %d %.3f' % (info['mtr'][i], scode,
j + 1, d)
nspecial.append([s1, s2])
if not nspecial:
print('\nNote: No atoms sit on special position.\n')
fw.write('\nNote: No atoms sit on special position.\n')
return
t = '\nNote: The following atoms sit on special position.\n'
print(t)
fw.write(t)
nspecial.sort(key=lambda v: v[0])
dic = {}
for m, xx in enumerate(nspecial):
if m > 0 and nspecial[m][0] == nspecial[m - 1][0]:
dic[xx[0]].append(xx[1])
else:
dic[xx[0]] = [xx[1]]
swater, l_occ = [], []
for s in sorted(dic.keys()):
nfold = len(dic[s]) + 1
op = ['555 1'] #the first one
for m in dic[s]:
t = m.split()
op.append('%s %s' % (t[1], t[2]))
occ, ss = check_coord_occ(info, s, nfold)
s1 = s.split('_')
s2 = '_'.join(s1[:-1])
t = '\natom id=%s : symmetry fold=%d \n' % (s2, nfold)
if '_' not in s: continue
na = int(s.split('_')[-1])
occ_orig = info['occ'][na]
print t.strip(), ' sym_code=', op, 'occ_orig=%s' % occ_orig
print ss
if ('_HOH_' in ss or '_DOD_' in ss) and float(occ_orig) == 1:
swater.append(s1[:-1])
l_occ.append(occ)
if 'Wrong occupancy' in ss:
fw.write(t)
fw.write(ss)
fw.close()
if (l_occ and util.is_cif(file)):
update_coord(file, swater, l_occ, out_xyz)
print '%d waters are updated with occupancy in the coordinates.' % len(
l_occ)
print 'New coordinate= %s' % out_xyz
else:
print 'Coordinates are not updated (Reason: either not in cif or OCC not 1.00).'
print '\nThe output file =%s\n' % outfile
def matt_coeff(infile, outfile):
'''calculate Matthew_coeff and solven content: file is in pdb format;
'''
if not util.check_file(100, infile):
print('Error: file (%s) not exist' % infile)
return
file = infile
if util.is_cif(infile): file = cif2pdb(infile)
fp = open(file, 'r')
cell = [1, 1, 1, 1, 1, 1]
spt, nop, nmat, sym, res, atom, res = 1, 0, 1, 'X', [], [], []
rmass, amass, armass = 0, 0, 0
hetres, aname, rest = [], [], ''
for x in fp:
if 'REMARK 290 ' in x[:12] and '555' in x and ',' in x[23:32]:
nop = nop + 1
elif 'SEQRES' in x[:6]:
t = x[17:79].split()
res.extend(t)
# elif 'SPLIT' in x[:6] :
# t=x[6:].split()
# spt=len(t)
elif 'MTRIX3' in x[:6] and '1' not in x[55:].strip():
nmat = nmat + 1
elif 'CRYST1' in x[:6]:
c = x[7:54].split()
cell = [float(y) for y in c]
sym = x[54:65].strip()
elif ('ATOM' in x[:4] or 'HETA' in x[:4]):
if ('HOH' in x[17:20] or 'DOD' in x[17:20]): continue
atom.append(x)
occ = float(x[54:60])
amass = amass + atom_mass(x[76:78].strip()) * occ
t = x[17:27] #comp_ch_res_int
aname.append(x[76:78].strip())
if t != rest:
comp = t[:3].strip()
restmp = residue_mass(comp)
if restmp < 1:
hetres.append(comp)
else:
armass = armass + residue_mass(comp)
rest = t
aname = []
elif 'ENDMDL' in x[:6]:
break
fp.close()
cell_vol = cell_volume(cell)
nsym = sg_nsym(sym)
if nsym == -1:
print('Error: space group (%s) is not in the list (%s)' % (sym, file))
nsym = nop
#----------
for x in hetres:
armass = armass + non_standard_res(x, atom)
for x in res:
resm = residue_mass(x)
if resm < 1:
m1 = non_standard_res(x, atom)
rmass = rmass + m1
else:
rmass = rmass + resm
amatt, asolv = calc_matt(cell_vol, amass, nsym, nmat, spt) #by atom, occ
rmatt, rsolv = calc_matt(cell_vol, rmass, nsym, nmat, spt) #by SEQRES
armatt, arsolv = calc_matt(cell_vol, armass, nsym, nmat, spt) #residue
matt, solv = -1, -1
if 2.0 < rmatt < 5:
matt, solv = rmatt, rsolv
elif 2.0 < armatt < 5:
matt, solv = armatt, arsolv
elif 2.0 < amatt < 5:
matt, solv = amatt, asolv
else:
matt, solv = armatt, arsolv
print(
'Warning: packing problem (%s), Matthew_coeff=%.2f; Solvent=%.2f' %
(file, matt, solv))
if util.is_cif(infile): util.delete_file(file)
print('%s : split nsym, nmat= %2d %2d %2d' % (file, spt, nsym, nmat))
print('By ATOM: matt= %6.2f , solvent= %6.2f ' % (amatt, asolv))
print('By SEQRES: matt= %6.2f , solvent= %6.2f ' % (rmatt, rsolv))
print('By residue: matt= %6.2f , solvent= %6.2f ' % (armatt, arsolv))
print('Possible: matt= %6.2f , solvent= %6.2f ' % (matt, solv))
print('\nmass_total_atom=%.1f ; cell_vol=%.1f' % (amass, cell_vol))
error = '?'
if (matt > 8.7 or matt < 1.5):
error = 'Warning: Matthew_coefficient(%.2f) is abnormal. Possible incomplete content of ASU (or a split entry).' % matt
if matt == 0.0 and solv == 1.0: error = '?' #space group problem
if outfile:
fw = open(outfile, 'w')
ss = '''data_matt
#
_packing.Matthew_coefficient %6.2f
_packing.solvent_content %6.2f
_packing.error "%s"\n
''' % (matt, solv, error)
fw.write(ss)
fw.close()
print 'The output file = %s\n' % outfile
return matt, solv
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