f_pdb_out = PdbFile(sys.argv[-1])
f_pdb_out.open_to_write()
f_pdb_out._file.write('RECORD # SCRIPT: bfactor_write_to_pdb.py\n')
f_pdb_out._file.write('RECORD # argv[1]: ' + sys.argv[1] + '\n')
f_pdb_out._file.write('RECORD # argv[2]: ' + sys.argv[2] + '\n')
f_pdb_out._file.write('RECORD # argv[3]: ' + sys.argv[3] + '\n')
f_pdb_out._file.write('RECORD # argv[4]: ' + sys.argv[4] + '\n')
f_pdb_out._file.write('RECORD # argv[5]: ' + sys.argv[5] + '\n')
scale = float(sys.argv[3])
upper = float(sys.argv[4])
bf = []
for line in f_bf_in:
if line.find('#') != -1:
continue
bf.append(float(line.split()[1]))
imp = 0
for c in chains:
for r in c.residues:
for a in r.atoms:
x = bf[imp] * scale
if x > upper:
x = upper
a.temp_factor = x
imp += 1
f_pdb_out.write_all(chains)
f_pdb_out.close()
for i in range(nmp):
xyz = [0.0, 0.0, 0.0]
ave.append(xyz)
nframe = 0
while dcd.has_more_data():
data = dcd.read_onestep()
nframe += 1
print(nframe)
for i in range(nmp):
ave[i][0] += data[i][0]
ave[i][1] += data[i][1]
ave[i][2] += data[i][2]
dcd.close()
for xyz in ave:
xyz[0] /= float(nframe)
xyz[1] /= float(nframe)
xyz[2] /= float(nframe)
imp = 0
for c in chains:
for i in range(c.num_atom()):
imp += 1
c.get_atom(i).xyz.x = ave[i][0]
c.get_atom(i).xyz.y = ave[i][1]
c.get_atom(i).xyz.z = ave[i][2]
f_out.write_all(chains)
f_out.close()
print('')
print(
' Usage: SCRIPT [input PDB] [The residue number of the first a.a.] [output PDB] [log file]'
)
print('')
sys.exit(2)
pdb_in = PdbFile(sys.argv[1])
pdb_in.open_to_read()
chains = pdb_in.read_all()
pdb_in.close()
res_id = int(sys.argv[2])
f_log = open(sys.argv[4], 'w')
f_log.write('#original -> new\n')
for c in chains:
print(sys.argv[1], '#residues', len(c.residues))
for r in c.residues:
f_log.write('%i %s -> %i\n' %
(r.atoms[0].res_seq, r.atoms[0].ins_code, res_id))
for a in r.atoms:
a.res_seq = res_id
a.ins_code = ' '
res_id += 1
f_log.close()
pdb_out = PdbFile(sys.argv[3])
pdb_out.open_to_write()
pdb_out.write_all(chains)
pdb_out.close()
if tsdata[0][ts.head_col.e_bridge] == '0.0000000':
struct = dcd.read_onestep()
iatom = 0
for c in chains:
for r in c.residues:
for a in r.atoms:
a.xyz.put_as_list(struct[iatom])
iatom += 1
imodel += 1
pdb.modelID = imodel
pdb.set_remark('ORIGINAL_FILE %s' % (dcd_filename,))
pdb.set_remark('ORIGINAL_FRAME %i' % (i_org,))
for iunit, x in enumerate(tsdata):
if iunit == 0:
tsline = 'TS_all'
else:
tsline = 'TS_%i ' % (iunit,)
for y in x:
tsline += ' ' + y
pdb.set_remark(tsline)
pdb.write_all(chains)
else:
dcd.skip_onestep()
i_org += 1
ts.close()
dcd.close()
pdb.close()
chains_cg.append(c_cg)
return chains_cg
if __name__ == '__main__':
from cafysis.file_io.pdb import PdbFile
if len(sys.argv) not in (3, 4):
print(
'Usage: SCRIPT [input aa PDB] [flag to start with P (Y/n)] [output cg PDB]'
)
sys.exit(2)
flg_start_P = False
if len(sys.argv) == 4:
if sys.argv[2] == 'Y':
flg_start_P = True
aa = PdbFile(sys.argv[1], 'r')
chains = aa.read_all()
aa.close()
chains_cg = aa2cg(chains, flg_start_P)
cg = PdbFile(sys.argv[-1], 'w')
cg.write_all(chains_cg)
cg.close()
# matrices[mtx_id].show()
#sys.exit(1)
filename_pdb = sys.argv[1]
''' Read inpout PDB '''
pdb = PdbFile(filename_pdb)
pdb.open_to_read()
chains = pdb.read_all()
pdb.close()
_, ext = os.path.splitext(filename_pdb)
filename_base = os.path.basename(filename_pdb)[:-len(ext)]
''' Rotate and output each assembly unit '''
for mtx_id in assembly_units:
newchains = copy.deepcopy(chains)
for c in newchains:
for r in c.residues:
for a in r.atoms:
#print ('###')
#print (a.xyz.x, a.xyz.y, a.xyz.z)
a.xyz.put_as_list(matrices[mtx_id].do_to_1darray(
a.xyz.get_as_ndarray()))
#print (a.xyz.x, a.xyz.y, a.xyz.z)
outpdb = PdbFile('%s_%s%s' % (filename_base, mtx_id, ext))
outpdb.open_to_write()
outpdb.write_all(newchains)
outpdb.close()
a.serial = atom_id
a.name = ' S '
a.res_name = 'D%s ' % nt[SEQ_POSITION:SEQ_POSITION + 1]
#a.chain_id = 'A'
a.chain_id = '%s' % nchain
a.res_seq = res_id
a.xyz = xyz_S / float(nS)
r_cg.push_atom(a)
atom_id += 1
a = Atom()
a.serial = atom_id
#a.name = ' %sb ' % nt
a.name = ' %sb ' % nt[SEQ_POSITION:SEQ_POSITION + 1]
#a.res_name = 'R%s ' % nt
a.res_name = 'D%s ' % nt[SEQ_POSITION:SEQ_POSITION + 1]
#a.chain_id = 'A'
a.chain_id = '%s' % nchain
a.res_seq = res_id
a.xyz = xyz_B / float(nB)
r_cg.push_atom(a)
c_cg.push_residue(r_cg)
cg_chains.append(c_cg)
cg = PdbFile(sys.argv[-1])
cg.open_to_write()
cg.write_all(cg_chains)
cg.close()
continue
struct = dcd.read_onestep()
""" Move to the origin """
if args.flg_origin:
com = [0.0, 0.0, 0.0]
for v in struct:
com = [com[i]+v[i] for i in range(3)]
com = [com[i]/float(len(struct)) for i in range(3)]
for i in range(len(struct)):
struct[i] = [struct[i][j] - com[j] for j in range(3)]
iatom = 0
for c in chains:
for r in c.residues:
for a in r.atoms:
a.xyz.put_as_list(struct[iatom])
iatom += 1
movie.modelID = iframe + args.id_offset
movie.set_remark('ORIGINAL_FILE %s' % (args.dcd,))
movie.set_remark('ORIGINAL_FRAME %i' % (i_orig,))
movie.write_all(chains)
i_orig += 1
movie.close()
pdb.close()
c_com = Chain()
for r in c.residues:
a_com = Atom()
i_serial += 1
a_com.serial = i_serial
a_com.name = 'NUC'
a_com.res_name = r.atoms[0].res_name
a_com.chain_id = r.atoms[0].chain_id
a_com.res_seq = r.atoms[0].res_seq
mass_sum = 0.0
xyz_sum = Coord()
for a in r.atoms:
if a.element.strip() == 'H':
continue
if a.element.strip() in element2mass:
mass = element2mass[a.element.strip()]
else:
print('Error: no key %s in element2mass.' % (a.element, ))
xyz_sum += a.xyz * mass
mass_sum += mass
a_com.xyz = xyz_sum / float(mass_sum)
r_com = Residue()
r_com.push_atom(a_com)
c_com.push_residue(r_com)
chains_com.append(c_com)
pdb_out.write_all(chains_com)
chains = pdb.read_all()
pdb.close()
for c in chains:
for r in c.residues:
for a in r.atoms:
if a.name.strip() == 'MG':
if check_distance(c_16SCD, a):
r = Residue()
r.push_atom(a)
c_Mg.push_residue(r)
#print(ibundle)
# Only RNA
pdb_out = PdbFile('4y4o_{:s}_16SCD.original.pdb'.format(modelname), 'w')
pdb_out.write_all([
c_16SCD,
])
pdb_out.close()
# RNA and Mg
pdb_out = PdbFile('4y4o_{:s}_16SCD_Mg.original.pdb'.format(modelname), 'w')
pdb_out.write_all([c_16SCD, c_Mg])
pdb_out.close()
chains_cg = aa2cg([
c_16SCD,
])
rmsd, rot = fit(chains_1j5e_cg, chains_cg)
apply_rot([c_16SCD, c_Mg], rot)
# Only RNA
