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()
from cafysis.file_io.pdb import PdbFile
if len(sys.argv) != 6:
print(
'\n Usage: SCRIPT [bfactor file] [PDB file] [scale] [Upper] [output PDB file]\n'
)
sys.exit(2)
f_bf_in = open(sys.argv[1], 'r')
f_pdb = PdbFile(sys.argv[2])
f_pdb.open_to_read()
chains = f_pdb.read_all()
f_pdb.close()
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]))
if len(sys.argv) != 4:
print(' Usage: % SCRIPT [input DCD] [input PDB] [output PDB] ')
sys.exit(2)
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
dcd.read_header()
nmp = dcd.get_header().nmp_real
f_pdb = PdbFile(sys.argv[2])
f_pdb.open_to_read()
chains = f_pdb.read_all()
f_pdb.close()
f_out = PdbFile(sys.argv[3])
f_out.open_to_write()
ave = []
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]
from cafysis.file_io.ts import TsFile
from cafysis.file_io.pdb import PdbFile
if len(sys.argv) != 5:
print('Usage: % SCRIPT [input DCD] [ts file] [reference PDB] [output movie]')
sys.exit(2)
# Read the reference PDB
pdb = PdbFile(sys.argv[-2])
pdb.open_to_read()
chains = pdb.read_all()
pdb.close()
# Output PDB
pdb = PdbFile(sys.argv[-1])
pdb.open_to_write()
# Open DCD and read the header
dcd_filename = sys.argv[1]
dcd = DcdFile(dcd_filename)
dcd.open_to_read()
dcd.read_header()
# Open TS and read the header
ts = TsFile(sys.argv[2])
ts.open_to_read()
ts.read_header()
# read and write
imodel = 0
i_org = 0
# 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()
print('Error: Beginning frame must be > 0')
sys.exit(2)
if args.frame_stride <= 0:
print('Error: Frame stride must be > 0')
sys.exit(2)
# Read the reference PDB
pdb = PdbFile(args.pdb)
pdb.open_to_read()
chains = pdb.read_all()
pdb.close()
# Output PDB
movie = PdbFile(args.out)
movie.open_to_write()
# Open DCD and read the header
dcd = DcdFile(args.dcd)
dcd.open_to_read()
dcd.read_header()
num_dcd_frames = dcd.count_frame()
if args.frame_end == -1:
frame_end = num_dcd_frames - 1
elif args.frame_end > num_dcd_frames - 1:
print('Warning: There are only %i frames found in the dcd while you specified --to %i' % (num_dcd_frames, args.frame_end))
print(' Output only %i frames.' % (num_dcd_frames))
frame_end = num_dcd_frames - 1
