def get_chain_seq(flist):
'''return a dic (each chain has a list nres).
'''
chain = {}
items, values = cif.cifparse(flist, '_atom_site.')
asym = cif.parse_values(items, values, "_atom_site.auth_asym_id")
seq = cif.parse_values(items, values, "_atom_site.auth_seq_id")
if not (asym or seq): return chain
ch_old, ns_old = '', ''
for x in asym:
ch = x
if ch != ch_old:
chain[ch] = []
ch_old = ch
for i, x in enumerate(seq):
ns = x
ch = asym[i]
if ns != ns_old and util.is_number(ns):
chain[ch].append(int(ns))
ns_old = ns
# print chain
return chain
def cell(flist):
'''return cell values as a list of float!
'''
cell = [0, 0, 0, 0, 0, 0]
items, values = cif.cifparse(flist, '_cell.')
if not len(items): return cell
a = cif.parse_values(items, values, '_cell.length_a')
b = cif.parse_values(items, values, '_cell.length_b')
c = cif.parse_values(items, values, '_cell.length_c')
alpha = cif.parse_values(items, values, '_cell.angle_alpha')
beta = cif.parse_values(items, values, '_cell.angle_beta')
gamma = cif.parse_values(items, values, '_cell.angle_gamma')
if (not (a and b and c and alpha and beta and gamma)):
print('Warning: cells not extracted. Check ciftokens')
for i, x in enumerate([a, b, c, alpha, beta, gamma]):
if len(x) == 0 or not util.is_number(x[0]):
print('Error: cell has wrong (%s) values' % x)
continue
cell[i] = float(x[0].strip())
return cell
def space_group_name(flist):
'''get space_group, return a string
'''
spg = ''
items, values = cif.cifparse(flist, '_symmetry.')
symm = cif.parse_values(items, values, '_symmetry.space_group_name_H-M')
if symm:
spg = symm[0].replace("'", '').replace('"', '').strip()
else:
print('Warning: space group not extracted. Check ciftokens')
return spg
def is_bigcif(file):
'''big cif has chainID more than one charactors
return 0: not cif
'''
n=0
flist=open(file, 'r').readlines()
items,values = cif.cifparse(flist, '_atom_site.') # a loop
asym=cif.parse_values(items,values,"_atom_site.auth_asym_id")
if asym :
for x in asym:
if len(x)>1:
n=2
print('Note: Cif file (%s) has chainID >1 charactor.' %file)
break
return n
def remove_bad_water(pdbfile, sffile):
npdb=pdbfile+'_rmwat'
fw=open(npdb, 'w')
dccfile=pdbfile + '_dcc.cif'
arg='%s/bin/dcc -pdb %s -sf %s -no_xtriage -o %s ' %(os.environ['DCCPY'], pdbfile, sffile, dccfile)
os.system(arg)
print 'Removing bad waters from %s' %dccfile
flist=open(dccfile, 'r').readlines()
items,values = cif.cifparse(flist, '_pdbx_rscc_mapman_prob.')
ch=cif.parse_values(items,values, '_pdbx_rscc_mapman_prob.auth_asym_id')
comp=cif.parse_values(items,values, '_pdbx_rscc_mapman_prob.auth_comp_id')
seq=cif.parse_values(items,values ,'_pdbx_rscc_mapman_prob.auth_seq_id')
rsr=cif.parse_values(items,values, '_pdbx_rscc_mapman_prob.real_space_R')
wrsr=cif.parse_values(items,values, '_pdbx_rscc_mapman_prob.RsR_over_correlation')
dcc=cif.parse_values(items,values ,'_pdbx_rscc_mapman_prob.correlation')
nn=len(ch)
fp=open(pdbfile, 'r')
for x in fp:
if (('ATOM' in x[:4] or 'HETATM' in x[:6] or 'ANISOU' in x[:6]) and
x[17:20] == 'HOH' ):
ch1, seq1 = x[20:22].strip(), x[22:26].strip()
id=0
for i, y in enumerate (comp):
if 'HOH' in y and ch1==ch[i] and seq1==seq[i] :
id=1
break
if id==1:
print 'removing water (%s)' %x[:28]
continue
else:
fw.write(x)
else:
fw.write(x)
fw.close()
fp.close()
print 'The new pdb file = %s' %npdb
def ncs_matrix(flist):
'''get NCS matrix, return a list of 3X4 matrix
'''
mtrix = []
items, values = cif.cifparse(flist, "_struct_ncs_oper.")
if not items: return []
id = cif.parse_values(items, values, '_struct_ncs_oper.id')
code = cif.parse_values(items, values, '_struct_ncs_oper.code')
b11 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[1][1]')
b12 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[1][2]')
b13 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[1][3]')
b21 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[2][1]')
b22 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[2][2]')
b23 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[2][3]')
b31 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[3][1]')
b32 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[3][2]')
b33 = cif.parse_values(items, values, '_struct_ncs_oper.matrix[3][3]')
t1 = cif.parse_values(items, values, '_struct_ncs_oper.vector[1]')
t2 = cif.parse_values(items, values, '_struct_ncs_oper.vector[2]')
t3 = cif.parse_values(items, values, '_struct_ncs_oper.vector[3]')
if not (id and code and b11 and b12 and b13 and t1 and b21 and b22 and b23
and t2 and b31 and b32 and b33 and t3):
return []
for i in range(len(b11)):
idd = ' '
if code[i] == 'given': idd = '1'
mt1 = [
float(x) for x in (b11[i], b12[i], b13[i], t1[i])
if util.is_number(x)
]
mt2 = [
float(x) for x in (b21[i], b22[i], b23[i], t2[i])
if util.is_number(x)
]
mt3 = [
float(x) for x in (b31[i], b32[i], b33[i], t3[i])
if util.is_number(x)
]
if not (mt1 and mt2 and mt3):
print 'Error: NCS matrix has wrong values'
continue
mtrix.append([mt1, mt2, mt3])
return mtrix
def get_rsr_database(res, rfact, file):
'''parse the mean and dev of the RsR for the res range for each
residue.
'''
if not util.check_file(30, file):
print('Warning: no RsR data base is found. ')
flist=open(file, 'r').readlines()
items,values = cif.cifparse(flist, '_rsr_shell.') # a loop
resname=cif.parse_values(items,values,"_rsr_shell.residue");
resh=cif.parse_values(items,values,"_rsr_shell.d_res_high");
resl=cif.parse_values(items,values,"_rsr_shell.d_res_low");
rfh=cif.parse_values(items,values,"_rsr_shell.rfact_high");
rfl=cif.parse_values(items,values,"_rsr_shell.rfact_low");
sst=cif.parse_values(items,values,"_rsr_shell.secondary_structure");
mean_all=cif.parse_values(items,values,"_rsr_shell.mean_all");
dev_all= cif.parse_values(items,values,"_rsr_shell.deviation_all");
num_all=cif.parse_values(items,values,"_rsr_shell.number_all");
mean_fil=cif.parse_values(items,values,"_rsr_shell.mean_filter");
dev_fil=cif.parse_values(items,values,"_rsr_shell.deviation_filter");
num_fil=cif.parse_values(items,values,"_rsr_shell.number_filter");
resn={}
for i,x in enumerate (resname) :
# if float(resh[i]) <=res <= float(resl[i]):
id='%s_%s' %(resname[i], sst[i])
# if float(resh[i]) <= res <= float(resl[i]) and float(rfl[i]) <= rfact <= float(rfh[i]):
if float(resh[i]) <= res <= float(resl[i]) :
t= [float(mean_all[i]),float(dev_all[i]),int(num_all[i]),
float(mean_fil[i]),float(dev_fil[i]), int(num_fil[i])]
if id not in resn : resn[ id ] = t
return resn
def parse_dcc(flist, table):
'''parse the table in the DCC: flist is a list
'''
dcc=[]
if table == '_pdbx_rscc_mapman.' :
items,values = cif.cifparse(flist, '_pdbx_rscc_mapman.')
nseq=cif.parse_values(items,values,"_pdbx_rscc_mapman.auth_seq_id");
chid=cif.parse_values(items,values,"_pdbx_rscc_mapman.auth_asym_id");
comp=cif.parse_values(items,values,"_pdbx_rscc_mapman.auth_comp_id");
alt=cif.parse_values(items,values,"_pdbx_rscc_mapman.label_alt_id");
ins=cif.parse_values(items,values,"_pdbx_rscc_mapman.label_ins_code");
cc=cif.parse_values(items,values,"_pdbx_rscc_mapman.correlation");
rsr=cif.parse_values(items,values,"_pdbx_rscc_mapman.real_space_R");
zrsr=cif.parse_values(items,values,"_pdbx_rscc_mapman.real_space_Zscore");
biso=cif.parse_values(items,values,"_pdbx_rscc_mapman.Biso_mean");
occ=cif.parse_values(items,values,"_pdbx_rscc_mapman.occupancy_mean");
modid=cif.parse_values(items,values,"_pdbx_rscc_mapman.model_id");
pdbid=cif.parse_values(items,values,"_pdbx_rscc_mapman.pdb_id");
if not items: return dcc
for i in range(len(chid)):
if (modid and int(modid[i])>1): break
a=[nseq[i], chid[i], comp[i], alt[i], cc[i],
rsr[i], biso[i], occ[i], pdbid[i], zrsr[i], ins[i] ]
dcc.append(a)
elif table == '_pdbx_map.' :
items,values = cif.cifparse(flist, '_pdbx_map.')
nseq=cif.parse_values(items,values,"_pdbx_map.auth_seq_id");
chid=cif.parse_values(items,values,"_pdbx_map.auth_asym_id");
comp=cif.parse_values(items,values,"_pdbx_map.auth_comp_id");
biso=cif.parse_values(items,values,"_pdbx_map.Biso_mean_overall");
cc=cif.parse_values(items,values,"_pdbx_map.density_correlation_overall");
rsr=cif.parse_values(items,values,"_pdbx_map.real_space_R_overall");
zobs=cif.parse_values(items,values,"_pdbx_map.ZOBS_overall");
zdiff=cif.parse_values(items,values,"_pdbx_map.ZDIFF_overall");
zdplus=cif.parse_values(items,values,"_pdbx_map.ZDplus_overall");
zdminus=cif.parse_values(items,values,"_pdbx_map.ZDminus_overall");
cc_m=cif.parse_values(items,values,"_pdbx_map.density_correlation_main_chain");
rsr_m=cif.parse_values(items,values,"_pdbx_map.real_space_R_main_chain");
zobs_m=cif.parse_values(items,values,"_pdbx_map.ZOBS_main_chain");
zdiff_m=cif.parse_values(items,values,"_pdbx_map.ZDIFF_main_chain");
cc_s=cif.parse_values(items,values,"_pdbx_map.density_correlation_side_chain");
rsr_s=cif.parse_values(items,values,"_pdbx_map.real_space_R_side_chain");
zobs_s=cif.parse_values(items,values,"_pdbx_map.ZOBS_side_chain");
zdiff_s=cif.parse_values(items,values,"_pdbx_map.ZDIFF_side_chain");
if not items: return dcc
for i in range(len(chid)):
if zdiff and not zdiff_s:
a=[ comp[i], chid[i], nseq[i], biso[i], cc[i], rsr[i], zobs[i], zdiff[i],zdplus[i],zdminus[i] ]
elif zdiff and zdiff_s:
a=[ comp[i], chid[i], nseq[i], biso[i], cc[i], rsr[i], zobs[i], zdiff[i], zdplus[i],zdminus[i],
cc_m[i], rsr_m[i], zobs_m[i], zdiff_m[i],cc_s[i], rsr_s[i], zobs_s[i], zdiff_s[i]]
dcc.append(a)
return dcc #nseq,chid,comp,alt,cc,rsr,biso,occ,pdid
def parse_cif(flist, table):
dic={}
ciftable='_%s.'%table
items,values = cif.cifparse(flist, ciftable)
if ciftable =='_pdbx_nonpoly_scheme.':
asym=cif.parse_values(items,values,'_pdbx_nonpoly_scheme.asym_id')
monid=cif.parse_values(items,values,'_pdbx_nonpoly_scheme.pdb_mon_id')
nseq=cif.parse_values(items,values,'_pdbx_nonpoly_scheme.pdb_seq_num')
chid=cif.parse_values(items,values,'_pdbx_nonpoly_scheme.pdb_strand_id')
ins=cif.parse_values(items,values,'_pdbx_nonpoly_scheme.pdb_ins_code')
if(monid and nseq and asym):
dic={'monid':monid, 'nseq':nseq, 'asym':asym,'chid':chid, 'ins':ins}
elif ciftable =='_struct_conn.':
id=cif.parse_values(items,values,'_struct_conn.id')
asym1=cif.parse_values(items,values,'_struct_conn.ptnr1_auth_asym_id')
comp1=cif.parse_values(items,values,'_struct_conn.ptnr1_auth_comp_id')
nseq1=cif.parse_values(items,values,'_struct_conn.ptnr1_auth_seq_id')
alt1 =cif.parse_values(items,values,'_struct_conn.pdbx_ptnr1_label_alt_id')
ins1 =cif.parse_values(items,values,'_struct_conn.pdbx_ptnr1_PDB_ins_code')
asym2=cif.parse_values(items,values,'_struct_conn.ptnr2_auth_asym_id')
comp2=cif.parse_values(items,values,'_struct_conn.ptnr2_auth_comp_id')
nseq2=cif.parse_values(items,values,'_struct_conn.ptnr2_auth_seq_id')
alt2 =cif.parse_values(items,values,'_struct_conn.pdbx_ptnr2_label_alt_id')
ins2 =cif.parse_values(items,values,'_struct_conn.pdbx_ptnr2_PDB_ins_code')
if (id and asym1 and comp1 and nseq1 and asym2 and comp2 and nseq2):
dic={'id':id, 'asym1':asym1, 'comp1':comp1, 'nseq1':nseq1, 'alt1':alt1, 'ins1':ins1,
'asym2':asym2, 'comp2':comp2, 'nseq2':nseq2, 'alt2':alt2, 'ins2':ins2}
elif ciftable =='_pdbx_molecule.':
ins_id=cif.parse_values(items,values,'_pdbx_molecule.instance_id')
prd_id=cif.parse_values(items,values,'_pdbx_molecule.prd_id')
asm_id=cif.parse_values(items,values,'_pdbx_molecule.asym_id')
if (ins_id and prd_id and asm_id):
dic={'ins_id':ins_id, 'prd_id':prd_id, 'asm_id':asm_id}
elif ciftable =='_pdbx_poly_seq_scheme.':
asym=cif.parse_values(items,values,'_pdbx_poly_seq_scheme.asym_id')
nseq=cif.parse_values(items,values,'_pdbx_poly_seq_scheme.pdb_seq_num')
monid=cif.parse_values(items,values,'_pdbx_poly_seq_scheme.pdb_mon_id')
chid=cif.parse_values(items,values,'_pdbx_poly_seq_scheme.pdb_strand_id')
ins=cif.parse_values(items,values,'_pdbx_poly_seq_scheme.pdb_ins_code')
if asym and monid :
dic={'monid':monid, 'nseq':nseq, 'asym':asym,'chid':chid, 'ins':ins}
return dic
def get_dcc(dccfile):
'''put dccfile as list of list
'''
dcc = []
if (util.check_file(100, dccfile) == 0): return dcc
flist = open(dccfile, 'r').readlines()
items, values = cif.cifparse(flist, '_pdbx_rscc_mapman.')
nseq = cif.parse_values(items, values, "_pdbx_rscc_mapman.auth_seq_id")
chid = cif.parse_values(items, values, "_pdbx_rscc_mapman.auth_asym_id")
comp = cif.parse_values(items, values, "_pdbx_rscc_mapman.auth_comp_id")
alt = cif.parse_values(items, values, "_pdbx_rscc_mapman.label_alt_id")
ins = cif.parse_values(items, values, "_pdbx_rscc_mapman.label_ins_code")
cc = cif.parse_values(items, values, "_pdbx_rscc_mapman.correlation")
rsr = cif.parse_values(items, values, "_pdbx_rscc_mapman.real_space_R")
zrsr = cif.parse_values(items, values,
"_pdbx_rscc_mapman.real_space_Zscore")
biso = cif.parse_values(items, values, "_pdbx_rscc_mapman.Biso_mean")
occ = cif.parse_values(items, values, "_pdbx_rscc_mapman.occupancy_mean")
#model=cif.parse_values(items,values,"_pdbx_rscc_mapman.model_id");
pdbid = cif.parse_values(items, values, "_pdbx_rscc_mapman.pdb_id")
if not items: return dcc
for i in range(len(chid)):
a = [
nseq[i], chid[i], comp[i], alt[i], cc[i], rsr[i], biso[i], occ[i],
pdbid[i]
]
dcc.append(a)
return dcc
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
def get_list(file):
vlist=[]
if not util.check_file(200, file):
print('Error: file (%s) do not exist' %file)
return vlist
flist=open(file,'r').readlines()
pdbid='XXXX'
for x in flist:
if 'data_' in x:
pdbid=x.split('_')[1].strip()
break
items,values = cif.cifparse(flist, '_pdbx_density.')
sym=cif.parse_values(items,values,'_pdbx_density.space_group_name_H-M')
res=cif.parse_values(items,values,'_pdbx_density.ls_d_res_high');
rw=cif.parse_values(items,values,'_pdbx_density.R_value_R_work');
rf=cif.parse_values(items,values,'_pdbx_density.R_value_R_free');
biso=cif.parse_values(items,values,'_pdbx_density.Biso_mean');
bwil=cif.parse_values(items,values,'_pdbx_density.B_wilson');
l2=cif.parse_values(items,values,'_pdbx_density.Padilla-Yeates_L2_mean');
z=cif.parse_values(items,values,'_pdbx_density.Z_score_L_test');
fom=cif.parse_values(items,values,'_pdbx_density.fom');
isig=cif.parse_values(items,values,'_pdbx_density.I_over_sigI_resh');
isigd=cif.parse_values(items,values,'_pdbx_density.I_over_sigI_diff');
pst=cif.parse_values(items,values,'_pdbx_density.translational_pseudo_symmetry');
bsol=cif.parse_values(items,values,'_pdbx_density.B_solvent');
ksol=cif.parse_values(items,values,'_pdbx_density.K_solvent');
tlst=cif.parse_values(items,values,'_pdbx_density.partial_B_value_correction_success');
ntls=cif.parse_values(items,values,'_pdbx_density.tls_group_number');
nncs=cif.parse_values(items,values,'_pdbx_density.ncs_group_number');
nmtx=cif.parse_values(items,values,'_pdbx_density.mtrix_number');
matt=cif.parse_values(items,values,'_pdbx_density.Matthew_coeff');
solv=cif.parse_values(items,values,'_pdbx_density.solvent_content');
dpix=cif.parse_values(items,values,'_pdbx_density.Cruickshank_dpi_xyz');
rtwin=cif.parse_values(items,values,'_pdbx_density.reflns_twin');
xtwin=cif.parse_values(items,values,'_pdbx_density.twin_by_xtriage');
tmp=cif.parse_values(items,values,'_pdbx_density.iso_B_value_type');
if tmp : btype=tmp[0][0]
ctwin_t=cif.parse_values(items,values,'_pdbx_density.twin_operator');
ctwin='N'
if '2:' in ctwin_t[0] : ctwin='Y'
anis=cif.parse_values(items,values,'_pdbx_density.anisotropy');
# looped
items,values = cif.cifparse(flist, '_pdbx_density_corr.')
prog=cif.parse_values(items,values,'_pdbx_density_corr.program');
resh=cif.parse_values(items,values,'_pdbx_density_corr.ls_d_res_high');
rwork=cif.parse_values(items,values,'_pdbx_density_corr.ls_R_factor_R_work');
rfree=cif.parse_values(items,values,'_pdbx_density_corr.ls_R_factor_R_free');
fcc=cif.parse_values(items,values,'_pdbx_density_corr.correlation_coeff_Fo_to_Fc');
rsr=cif.parse_values(items,values,'_pdbx_density_corr.real_space_R');
dcc=cif.parse_values(items,values,'_pdbx_density_corr.correlation');
detail=cif.parse_values(items,values,'_pdbx_density_corr.details');
nr, nc=0, 0
for i, x in enumerate(detail):
if 'Best' in x :
nc=i
break
rprog, cprog = prog[nr].replace(' ', ''), prog[nc]
crw, crf, fcc, rsr, dcc=rwork[nc], rfree[nc], fcc[nc],rsr[nc],dcc[nc]
rw_crw='?'
if util.is_number(rw[0]) and util.is_number(crw):
t=int (1000*(float(rw[0]) -float(crw)))
rw_crw='%d' %(t)
all=[pdbid, res,rw_crw, rw, rf, crw, crf, fcc, rsr, dcc, fom, biso,bwil,
matt,solv, ksol, bsol, ntls,nncs, nmtx,
tlst,btype, pst, rtwin,xtwin, ctwin, l2, z,anis, isig,isigd, rprog, sym]
all_new=[]
for x in all:
t=x
if not x :
t='?'
else:
if (type(x)==list ):t=x[0]
y=t.replace(' ', '_')
if util.is_number(y) and '.' in y:
y='%.2f' %float(y)
all_new.append(y)
return all_new
def check_ncs_cif(file):
'''check all errors in the cif file:
check the four cif tables agaist the scheme
'''
flist = open(file, 'r').readlines()
ncs = ncs_from_head(flist)
items, values = cif.cifparse(flist, '_struct_ncs_ens.')
ens_id = cif.parse_values(items, values, '_struct_ncs_ens.id')
items, values = cif.cifparse(flist, '_refine_ls_restr_ncs.')
res_ord = cif.parse_values(items, values,
'_refine_ls_restr_ncs.pdbx_ordinal')
res_ref = cif.parse_values(items, values,
'_refine_ls_restr_ncs.pdbx_refine_id')
res_ens = cif.parse_values(items, values,
'_refine_ls_restr_ncs.pdbx_ens_id')
res_dom = cif.parse_values(items, values, '_refine_ls_restr_ncs.dom_id')
res_typ = cif.parse_values(items, values, '_refine_ls_restr_ncs.pdbx_type')
res_asy = cif.parse_values(items, values,
'_refine_ls_restr_ncs.pdbx_auth_asym_id')
res_num = cif.parse_values(items, values,
'_refine_ls_restr_ncs.pdbx_number')
res_rms = cif.parse_values(items, values,
'_refine_ls_restr_ncs.rms_dev_position')
if '?' in res_rms:
res_rms = cif.parse_values(items, values,
'_refine_ls_restr_ncs.pdbx_rms')
res_wgh = cif.parse_values(items, values,
'_refine_ls_restr_ncs.weight_position')
items, values = cif.cifparse(flist, '_struct_ncs_dom.')
dom_ens = cif.parse_values(items, values, '_struct_ncs_dom.pdbx_ens_id')
dom_id = cif.parse_values(items, values, '_struct_ncs_dom.id')
dom_all = cif.parse_values(items, values, '_struct_ncs_dom.details')
items, values = cif.cifparse(flist, '_struct_ncs_dom_lim.')
lim_ens = cif.parse_values(items, values,
'_struct_ncs_dom_lim.pdbx_ens_id')
lim_dom = cif.parse_values(items, values, '_struct_ncs_dom_lim.dom_id')
lim_com = cif.parse_values(items, values,
'_struct_ncs_dom_lim.pdbx_component_id')
lim_basy = cif.parse_values(items, values,
'_struct_ncs_dom_lim.beg_auth_asym_id')
lim_bseq = cif.parse_values(items, values,
'_struct_ncs_dom_lim.beg_auth_seq_id')
lim_easy = cif.parse_values(items, values,
'_struct_ncs_dom_lim.end_auth_asym_id')
lim_eseq = cif.parse_values(items, values,
'_struct_ncs_dom_lim.end_auth_seq_id')
lim_all = cif.parse_values(items, values,
'_struct_ncs_dom_lim.selection_details')
if len(ncs):
if not (res_ens or dom_ens or lim_ens or ens_id):
util.perror(
'Warning: NCS records exist, but no cif tables for it.')
return
else:
if not len(ens_id): return
if not (res_ens or res_dom or res_ord or res_ref or res_asy or res_typ):
util.perror(
'Warning: No cif table (refine_ls_restr_ncs) or missing key items for NCS.'
)
if not (dom_ens or dom_id):
util.perror(
'Warning: No cif table (struct_ncs_dom) or missing key items for NCS.'
)
if not (lim_ens or lim_dom or lim_com):
util.perror(
'Warning: No cif table (struct_ncs_dom_lim) or missing key items for NCS.'
)
if not (ens_id):
util.perror('Warning: No cif table (struct_ncs_ens) for NCS.')
chain = get_chain_seq(flist) #chain is dic for int
def tmp(list1, list2): #put ensemble=key and doms=[] to a dic
tmpd = {}
for j, y in enumerate(list1):
if y not in list(tmpd.keys()): tmpd[y] = []
tmpd[y].append(list2[j])
return tmpd
dom = tmp(dom_ens, dom_id)
lim = tmp(lim_ens, lim_dom)
res = tmp(res_ens, res_dom)
def tmp1(list1, list2, s2):
for n in list1:
if n not in list2:
util.perror('Error: NCS ID (%s) not in table (%s).' % (n, s2))
if dom: tmp1(ens_id, list(dom.keys()), 'struct_ncs_dom')
if lim: tmp1(ens_id, list(lim.keys()), 'struct_ncs_dom_lim')
if res: tmp1(ens_id, list(res.keys()), 'refine_ls_restr_ncs')
# print chain.keys(), chain, dom, lim, res
if (lim_basy and lim_easy and lim_bseq and lim_eseq):
check_lim(lim_ens, chain, lim_basy, lim_easy, lim_bseq, lim_eseq)
check_res(res_ens, chain, res_ref, res_asy, res_typ, res_num, res_rms)
def val_from_dcc(outf):
''' The format of outf can not be changed !!
index (0,1,2,3,4,5,6,7...) corresponds to
(resh,resl,Rwork,Rfree,Comp,FCC, Real_R, Dcc)
res_rep: the reported; res_not: no TLS; res_tls: with TLS
'''
if not util.check_file(500, outf): return '', ''
flist = open(outf, "r").readlines()
items, values = cif.cifparse(flist, '_pdbx_density.')
res = cif.parse_values(items, values, '_pdbx_density.ls_d_res_high')
rw = cif.parse_values(items, values, '_pdbx_density.R_value_R_work')
rf = cif.parse_values(items, values, '_pdbx_density.R_value_R_free')
biso = cif.parse_values(items, values, '_pdbx_density.Biso_mean')
bwil = cif.parse_values(items, values, '_pdbx_density.B_wilson')
l2 = cif.parse_values(items, values,
'_pdbx_density.Padilla-Yeates_L2_mean')
z = cif.parse_values(items, values, '_pdbx_density.Z_score_L_test')
fom = cif.parse_values(items, values, '_pdbx_density.fom')
items, values = cif.cifparse(flist, '_pdbx_density_corr.')
prog = cif.parse_values(items, values, '_pdbx_density_corr.program')
resh = cif.parse_values(items, values, '_pdbx_density_corr.ls_d_res_high')
rwork = cif.parse_values(items, values,
'_pdbx_density_corr.ls_R_factor_R_work')
rfree = cif.parse_values(items, values,
'_pdbx_density_corr.ls_R_factor_R_free')
fcc = cif.parse_values(items, values,
'_pdbx_density_corr.correlation_coeff_Fo_to_Fc')
rsr = cif.parse_values(items, values, '_pdbx_density_corr.real_space_R')
dcc = cif.parse_values(items, values, '_pdbx_density_corr.correlation')
detail = cif.parse_values(items, values, '_pdbx_density_corr.details')
nr, nb = 0, 0
for i, x in enumerate(detail):
if 'Best' in x:
nb = i
break
rep = '%8s %4s %6s %6s %6s ' % (prog[nr], resh[nr], rwork[nr],
rfree[nr], biso[0])
val = '%8s %4s %6s %6s %6s %6s %6s %6s %6s %6s %6s ' % (
prog[nb], resh[nb], rwork[nb], rfree[nb], bwil[0], l2[0], z[0], fom[0],
fcc[nb], rsr[nb], dcc[nb])
return rep, val
def atom_site(flist):
'''get all atom record. return a dictionary
'''
dic = {}
chain, nres, comp, atom, symbol, alt, ins = [], [], [], [], [], [], []
x, y, z, biso, occ = [], [], [], [], []
items, values = cif.cifparse(flist, '_atom_site.') # a loop
group1 = cif.parse_values(items, values, "_atom_site.group_PDB")
natm = cif.parse_values(items, values, "_atom_site.id")
symbol1 = cif.parse_values(items, values, "_atom_site.type_symbol")
if not symbol1:
symbol1 = cif.parse_values(items, values,
"_atom_site.atom_type_symbol")
atom1 = cif.parse_values(items, values, "_atom_site.label_atom_id")
asym1 = cif.parse_values(items, values, "_atom_site.auth_asym_id")
comp1 = cif.parse_values(items, values, "_atom_site.label_comp_id")
nres1 = cif.parse_values(items, values, "_atom_site.auth_seq_id")
x1 = cif.parse_values(items, values, "_atom_site.Cartn_x")
y1 = cif.parse_values(items, values, "_atom_site.Cartn_y")
z1 = cif.parse_values(items, values, "_atom_site.Cartn_z")
biso1 = cif.parse_values(items, values, "_atom_site.B_iso_or_equiv")
occ1 = cif.parse_values(items, values, "_atom_site.occupancy")
ins1 = cif.parse_values(items, values, "_atom_site.pdbx_PDB_ins_code")
if not ins1:
ins1 = cif.parse_values(items, values, "_atom_site.ndb_ins_code")
alt1 = cif.parse_values(items, values, "_atom_site.label_alt_id")
if (not (atom1 and comp1 and asym1 and nres1 and x1 and y1 and z1 and occ1
and biso1)):
print('Error: there is problem to parse atom_site.')
return dic
n = len(x1)
for i in range(n):
chain.append(asym1[i])
nres.append(int(nres1[i]))
comp.append(comp1[i])
atom.append(atom1[i])
if (natm): natm.append(natm[i]) #newly added
symbol.append(symbol1[i])
if not alt1:
alt.append('.')
else:
alt.append(alt1[i])
if not ins1:
ins.append('.')
else:
ins.append(ins1[i])
x.append(float(x1[i]))
y.append(float(y1[i]))
z.append(float(z1[i]))
biso.append(float(biso1[i]))
occ.append(float(occ1[i]))
dic = {
'chain': chain,
'nres': nres,
'comp': comp,
'atom': atom,
'symbol': symbol,
'alt': alt,
'ins': ins,
'x': x,
'y': y,
'z': z,
'biso': biso,
'occ': occ,
'natm': natm
}
return dic
def scale(flist):
'''get SCALE matrix, return a list of 3X4 matrix
'''
scale = []
items, values = cif.cifparse(flist, "_atom_sites.")
if not items: return []
b11 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[1][1]')
b12 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[1][2]')
b13 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[1][3]')
t1 = cif.parse_values(items, values, '_atom_sites.fract_transf_vector[1]')
b21 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[2][1]')
b22 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[2][2]')
b23 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[2][3]')
t2 = cif.parse_values(items, values, '_atom_sites.fract_transf_vector[2]')
b31 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[3][1]')
b32 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[3][2]')
b33 = cif.parse_values(items, values,
'_atom_sites.fract_transf_matrix[3][3]')
t3 = cif.parse_values(items, values, '_atom_sites.fract_transf_vector[3]')
if not (b11 and b12 and b13 and t1 and b21 and b22 and b23 and t2 and b31
and b32 and b33 and t3):
return []
for i in range(len(b11)):
mt1 = [
float(x) for x in (b11[i], b12[i], b13[i], t1[i])
if util.is_number(x)
]
mt2 = [
float(x) for x in (b11[i], b12[i], b13[i], t1[i])
if util.is_number(x)
]
mt3 = [
float(x) for x in (b11[i], b12[i], b13[i], t1[i])
if util.is_number(x)
]
if not (mt1 and mt2 and mt3):
print 'Error: Scale matrix has wrong values'
continue
scale.append([mt1, mt2, mt3])
return scale
