def expand_sym_cello(info):
''' using the orthogonal coord! (not used)
'''
xf, yf, zf = info['xf'], info['yf'], info['zf']
xo, yo, zo = info['x'], info['y'], info['z']
boxsize = 5
print 'The space group = %s' % info['spg']
# m1,m2,m3=get_sym_operator(info, 'frac')
m1, m2, m3 = get_sym_operator(info, 'orth')
frac, orth = util.frac_orth_matrix(info['cell']) #get matrix
xmin, xmax = min(xo) - boxsize, max(xo) + boxsize
ymin, ymax = min(yo) - boxsize, max(yo) + boxsize
zmin, zmax = min(zo) - boxsize, max(zo) + boxsize
for i in range(len(yo)): #going through each atom
xi = [info['x'][i], info['y'][i], info['z'][i]]
for ii in (-1, 0, 1):
for jj in (-1, 0, 1):
for kk in (-1, 0, 1):
scode = '%d%d%d' % (ii + 5, jj + 5, kk + 5)
for j in range(len(m1)):
xo0 = m1[j][0] * xi[0] + m1[j][1] * xi[1] + m1[j][
2] * xi[2] + m1[j][3]
xo1 = m2[j][0] * xi[0] + m2[j][1] * xi[1] + m2[j][
2] * xi[2] + m2[j][3]
xo2 = m3[j][0] * xi[0] + m3[j][1] * xi[1] + m3[j][
2] * xi[2] + m3[j][3]
xf = util.matrix_prod(frac, [xo0, xo1, xo2])
xf[0] = xf[0] + ii
xf[1] = xf[1] + jj
xf[2] = xf[2] + kk
xno = util.matrix_prod(orth, [xf[0], xf[1], xf[2]])
if (xno[0] < xmin or xno[0] > xmax or xno[1] < ymin
or xno[1] > ymax or xno[2] < zmin
or xno[2] > zmax):
continue
#print xo, xno
d = math.sqrt((xi[0] - xno[0])**2 +
(xi[1] - xno[1])**2 +
(xi[2] - xno[2])**2)
if d > 0.7: continue
if info['nres'][i] == 2408: print '2408=', d, scode
if ii == 0 and jj == 0 and kk == 0: continue
nop = j
print 'ATOM %5d %4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f%3d %s %.3f' % (
1, info['atom'][i], info['alt'][i],
info['comp'][i], info['chain'][i], info['nres'][i],
info['ins'][i], xno[0], xno[1], xno[2], 0, 0,
info['mtr'][i], scode, d)
def data_from_cif(file, info):
'''load data to dictionary from mmcif format
'''
flist = open(file, 'r').readlines()
cell = parse.cell(flist)
spg = parse.space_group_name(flist)
mtrix = parse.ncs_matrix(flist)
scale = parse.scale(flist)
atom = parse.atom_site(flist) # return a dic
info.update(atom)
info['cell'] = cell
info['spg'] = spg
info['mtrix'] = mtrix
if (cell and cell[0] > 1.1):
frac, orth = util.frac_orth_matrix(cell) #get matrix
n = len(info['x'])
xf, yf, zf, mtr = [], [], [], []
for i in range(n):
xyzf = util.matrix_prod(frac,
[info['x'][i], info['y'][i], info['z'][i]])
xf.append(xyzf[0])
yf.append(xyzf[1])
zf.append(xyzf[2])
mtr.append(1) # allways 1 for the 1st copy
info['xf'] = xf
info['yf'] = yf
info['zf'] = zf
info['mtr'] = mtr
return info
def shift_xyz_into_unitcell(file, outfile):
'''Shift the asu into the unit. file is a PDB file!
'''
if not outfile: outfile = file + '_shifted'
info = get_atominfo(file)
if not info['cell']:
print 'Error: The unit cell is not extracted! check you xyz file.\n'
return
fw = open(outfile, 'w')
frac, orth = util.frac_orth_matrix(info['cell']) #get conversion matrix
xf, yf, zf = info['xf'], info['yf'], info['zf']
xfn, yfn, zfn = shift_xyz2unit(xf, yf, zf)
nxf = len(xf)
fp = open(file, 'r').readlines()
anis = {}
for x in fp:
if 'ATOM' in x[:4] or 'HETA' in x[:4]: anis[x[12:26]] = []
if 'ANISOU' in x[:6]: anis[x[12:26]] = x[26:]
for x in fp: #header
if 'ATOM' in x[:4] or 'HETA' in x[:4]: break
fw.write(x)
sp = ' '
for i in range(nxf):
xff, yff, zff = xfn[i], yfn[i], zfn[i]
xno = util.matrix_prod(orth,
[xff, yff, zff]) #convert franck back to orth.
group, natm, atom_o = info['group'][i], info['natm'][i], info[
'atom_o'][i]
alt, comp, ch = info['alt'][i], info['comp'][i], info['chain'][i]
nres, ins, segid = info['nres'][i], info['ins'][i], info['segid'][i]
occ, biso, symbol = float(info['occ'][i]), float(
info['biso'][i]), info['symbol'][i]
if '.' in alt: alt = ' '
if '.' in ins: ins = ' '
ss='%-6s%5s %4s%1s%3s%2s%4d%1s %8.3f%8.3f%8.3f%6.2f%6.2f%4s %4s%2s \n'\
%(group,natm,atom_o,alt,comp,ch,nres,ins,xno[0],xno[1],xno[2],occ,biso, sp,segid, symbol )
fw.write(ss)
id = '%4s%1s%3s%2s%4d' % (atom_o, alt, comp, ch, nres)
if anis[id]:
ss1 = 'ANISOU%5s %s%s' % (natm, id, anis[id])
fw.write(ss1)
fpr = reversed(fp)
for x in fpr:
if 'ATOM' in x[:4] or 'HETA' in x[:4]: break
fw.write(x)
fw.close()
print 'The new PDB file = %s\n' % outfile
def get_sym_operator(info, idd):
'''read the text (operator converted to numbers) and convert it to matrix
m1= x11,x12,x13,t1; y11,y12,y13,t2; z11,z12,z13,t3;
m1,m2,m3 the same as (REMARK 290) if applying orthogonal
'''
spg = info['spg']
frac, orth = util.frac_orth_matrix(info['cell']) #get matrix
m1, m2, m3 = [], [], []
spg_text = space_group_cif.text
tmp = spg_text.split('\n')
tto = []
mmf = []
for x in tmp:
t = x.split("'")
if "'" in x and t[1] == spg:
# print x
t1 = [float(y) for y in x[22:].split()]
tr = [0, 0, 0]
if t1[10] > 0: tr[0] = t1[9] / float(t1[10])
if t1[12] > 0: tr[1] = t1[11] / float(t1[12])
if t1[14] > 0: tr[2] = t1[13] / float(t1[14])
if idd == 'frac':
m1.append([t1[0], t1[1], t1[2], tr[0]])
m2.append([t1[3], t1[4], t1[5], tr[1]])
m3.append([t1[6], t1[7], t1[8], tr[2]])
continue
to = util.matrix_prod(orth, tr)
mmf = [[t1[0], t1[1], t1[2]], [t1[3], t1[4], t1[5]],
[t1[6], t1[7], t1[8]]]
mmo = util.matrix_prod_(orth, mmf)
mmf = util.matrix_prod_(mmo, frac)
mmf[0].append(to[0])
mmf[1].append(to[1])
mmf[2].append(to[2])
m1.append(mmf[0])
m2.append(mmf[1])
m3.append(mmf[2])
#print 'final=', m1,m2,m3
return m1, m2, m3
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 data_from_pdb(file, info):
'''load data to dictionary from pdb format
'''
fp = open(file, 'r')
chain, nres,comp,atom,symbol,alt, ins,biso,occ=[],[],[],[],[],[],[],[],[]
group, natm, natm_c, atom_o, segid = [], [], [], [], []
mtrix,mtr,symop, xf, yf,zf , x,y,z,spg =[],[],[],[],[],[],[],[],[],''
cell, spg = [], ''
for v in fp: #get header infor
if v[:6] == 'MTRIX1' and '1' not in v[55:].strip():
mt1 = [float(m) for m in v[10:55].split()]
elif v[:6] == 'MTRIX2' and '1' not in v[55:].strip():
mt2 = [float(m) for m in v[10:55].split()]
elif v[:6] == 'MTRIX3' and '1' not in v[55:].strip():
mt3 = [float(m) for m in v[10:55].split()]
mtrix.append([mt1, mt2, mt3])
elif 'CRYST1' in v[:6]:
cell = [float(xx) for xx in v.split()[1:7]]
spg = v[54:65].strip()
elif 'ATOM' in v[:4] or 'HETA' in v[:4]:
break
frac, orth = util.frac_orth_matrix(cell) #get matrix
fp.seek(0)
nat = 0
for v in fp:
if 'ENDMDL' in v[:6]: break
if 'ATOM' in v[:4] or 'HETA' in v[:4]:
xx, yy, zz = float(v[30:38]), float(v[38:46]), float(v[46:54])
oc, bb = float(v[54:60]), float(v[60:66])
x.append(xx)
y.append(yy)
z.append(zz)
biso.append(bb)
occ.append(oc)
if (cell and cell[0] > 1.1): #get the fractional xyz
xyzf = util.matrix_prod(frac, [xx, yy, zz])
xf.append(xyzf[0])
yf.append(xyzf[1])
zf.append(xyzf[2])
if v[70:74].strip():
chain.append(v[70:74].strip())
else:
chain.append(v[20:22].strip())
group.append(v[:6].strip())
natm.append(v[6:11].strip())
natm_c.append(nat)
nres.append(int(v[22:26]))
comp.append(v[17:20].strip())
atom.append(v[12:16].strip())
atom_o.append(v[12:16])
segid.append(v[72:76])
symbol.append(v[76:78].strip())
mtr.append(1)
if v[16:17] == ' ':
alt.append('.')
else:
alt.append(v[16:17])
if v[26:27] == ' ':
ins.append('.')
else:
ins.append(v[26:27])
nat = nat + 1 #counting the atom/hetatm
fp.close()
info = {
'chain': chain,
'nres': nres,
'comp': comp,
'atom': atom,
'biso': biso,
'occ': occ,
'symbol': symbol,
'alt': alt,
'ins': ins,
'x': x,
'y': y,
'z': z,
'xf': xf,
'yf': yf,
'zf': zf,
'mtr': mtr,
'symop': symop,
'spg': spg,
'cell': cell,
'mtrix': mtrix,
'group': group,
'natm': natm,
'natm_c': natm_c,
'atom_o': atom_o,
'segid': segid
}
return info
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