def dcd_fit(filename_dcd, filename_dcd_out, natom_total, serials,
filename_rmsd):
f_out = open(filename_rmsd, 'w')
# Coord1
pdb = PdbFile('16SCD.cg.pdb')
pdb.open_to_read()
ref_chains = pdb.read_all()
pdb.close()
#num_atom = 0
#for chain in ref_chains :
# for residue in chain.residues :
# num_atom += len(residue.atoms)
ref = zeros((natom_total, 3), dtype=float64, order='C')
i = 0
for chain in ref_chains:
for residue in chain.residues:
for atom in residue.atoms:
(ref[i][0], ref[i][1], ref[i][2]) = atom.xyz.get_as_tuple()
i += 1
mask = []
for i in range(natom_total):
# the serial ID starts from 1, thus i+1 is the serial ID
if i + 1 in serials:
mask.append(1)
else:
mask.append(0)
dcd = DcdFile(filename_dcd)
dcd.open_to_read()
dcd.read_header()
out_dcd = DcdFile(filename_dcd_out)
out_dcd.open_to_write()
out_dcd.set_header(dcd.get_header())
out_dcd.write_header()
#dcd.show_header()
k = 0
while dcd.has_more_data():
k += 1
coords_dcd = dcd.read_onestep_np()
rmsd = superimpose(ref.T, coords_dcd.T, mask)
f_out.write('{:8d} {:6.2f}\n'.format(k, rmsd))
out_dcd.write_onestep(coords_dcd)
dcd.close()
out_dcd.close()
@author: Naoto Hori
'''
import sys
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:
import sys
from cafysis.file_io.pdb import PdbFile
if len(sys.argv) != 5:
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()
### Read the reference pdb
ref_chains = pdb.read_all()
num_atom = 0
for chain in ref_chains :
num_atom += chain.num_atom()
ref = zeros((3, num_atom), dtype=float64, order='F')
i = 0
for chain in ref_chains :
for residue in chain.residues:
for atom in residue.atoms :
(ref[0][i], ref[1][i], ref[2][i]) = atom.xyz.get_as_tuple()
i += 1
pdb.close()
ref_idx = [i for i in range(ID_DOM_INI_FIT, ID_DOM_END_FIT+1)]
pre_idx = [i for i in range(ID_DOM_INI_FIT, ID_DOM_END_FIT+1)]
# header
dcd.read_header()
header = dcd.get_header()
dcd_out.set_header(header)
dcd_out.write_header()
nmp = header.nmp_real
def find_max_min_PBC(d):
if len(v) != num_dimension:
print('len(v) != num_dimension, %i' % num_dimension)
sys.exit(2)
#debug
#for i in xrange(num_ev):
# print '# ev %i' % i
# for value in ev[i] :
# print value
# Calculate principal coordinate
chains = f_pdb.read_all()
for v in ev:
x = 0.0
idx = 0
for c in chains:
for i in range(c.num_atom()):
c.get_atom(i).xyz.x
x += (c.get_atom(i).xyz.x - data_ave[idx]) * v[idx]
idx += 1
x += (c.get_atom(i).xyz.y - data_ave[idx]) * v[idx]
idx += 1
x += (c.get_atom(i).xyz.z - data_ave[idx]) * v[idx]
idx += 1
f_out.write('%12.5f ' % x)
f_out.write('\n')
f_pdb.close()
f_out.close()
a.xyz.transform(rotateQ.mtx)
#ここまでで、QがZ軸上にのった
print("QをZ軸上へ")
print("Q:",Q.get_as_tuple())
print("N:",N.get_as_tuple())
##########################################################
#NをZ軸まわりに回転させ、Nx>0でNy=0な位置へもっていく。
#DEBUG N = Coord(3,-3,-3)
theta = -atan2(N.y,N.x)
#DEBUG print "theta",theta, "(", theta/pi*180.0, "deg)"
rotateN = mtx_crd_transform()
rotateN.rotate_z(theta)
#DEBUG N.transform(rotateN.mtx)
for c in chains:
for r in c.residues:
for a in r.atoms:
a.xyz.transform(rotateN.mtx)
#DEBUG print "N",N.get_as_tuple()
#ここまでで、NをX軸上へ
print("NをX軸上へ")
print("Q:",Q.get_as_tuple())
print("N:",N.get_as_tuple())
pdb_out = PdbFile("20130628.pdb")
pdb_out.open_to_write()
pdb_out.write_all(chains)
pdb_out.close()
import math
from cafysis.file_io.pdb import PdbFile
from cafysis.file_io.ninfo import NinfoFile
from cafysis.para.rnaAform import ARNA
from cafysis.para.rnaDT13 import DT13
from cafysis.elements.ninfo import NinfoSet, BondLength, BondAngle, BaseStackDT, HBondDT
if len(sys.argv) != 4:
print('Usage: SCRIPT [cg pdb] [hb list file] [output ninfo]')
sys.exit(2)
f_in = PdbFile(sys.argv[1])
f_in.open_to_read()
chains = f_in.read_all()
f_in.close()
if len(chains) > 1:
print('%i chains' % len(chains))
n_nt = []
for ic, c in enumerate(chains):
n_nt.append(c.num_res())
print('#nt (chain %i): ', ic + 1, n_nt)
seq = []
for ic, c in enumerate(chains):
s = []
for r in c.residues:
# "RA " ---> "A"
s.append(r.atoms[0].res_name.strip()[1])
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()
from cafysis.file_io.pdb import PdbFile
from cafysis.elements.coord import Coord
if len(sys.argv) not in (2, 3):
print('Usage: SCRIPT [PDB] (score cutoff = 0.5)')
print(' or : SCRIPT [PDB] [score cutoff]')
sys.exit(2)
SCORE_CUT = 0.5
if len(sys.argv) > 2:
SCORE_CUT = float(sys.argv[2])
pf = PdbFile(sys.argv[1])
pf.open_to_read()
chains = pf.read_all()
pf.close()
coms = []
normals = []
locations = []
## Suppose all residues have a base
nres = 0
for ic, c in enumerate(chains):
for ir, r in enumerate(c.residues):
nres += 1
## A,U,G or C
ntd = r.atoms[0].res_name.strip()
imp2_offset += c2.num_res()
imp1_offset += c1.num_res()
return
if __name__ == '__main__':
import sys
if len(sys.argv) != 3:
print ('Usage: %SCRIPT [input PDB] [output ninfo]')
sys.exit(2)
from cafysis.file_io.pdb import PdbFile
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
f = PdbFile(sys.argv[1])
f.open_to_read()
chains = f.read_all()
f.close()
ns = NinfoSet()
generate_FENEs(chains, ns)
generate_LJs(chains, ns)
f_ninfo = NinfoFile(sys.argv[-1])
f_ninfo.open_to_write()
f_ninfo.write_all(ns)
f_ninfo.close()
row_pre = 0
else:
row_pre = row
#TEST
#for mtx_id in assembly_units:
# print (mtx_id)
# 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()))
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()
#if args.flg_fit:
# from Superimpose import superimpose
if args.frame_begin < 0:
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
import sys
from cafysis.file_io.pdb import PdbFile
from cafysis.elements.coord import Coord
from cafysis.elements.pdb import Chain, Residue, Atom
element2mass = {'P': 30.973761, 'O': 15.9994, 'C': 12.0107, 'N': 14.0067}
if __name__ == '__main__':
if len(sys.argv) != 3:
print('Usage: %SCRIPT [input PDB file] [output PDB]')
sys.exit(2)
pdb_in = PdbFile(sys.argv[1])
pdb_in.open_to_read()
chains = pdb_in.read_all()
pdb_in.close()
pdb_out = PdbFile(sys.argv[2])
pdb_out.open_to_write()
pdb_out.write_remark('Generated using cafysis/pdb_rna_nucleotide_com.py')
import time
import datetime
pdb_out.write_remark('At %s' % (datetime.datetime.fromtimestamp(
time.time()).strftime('%Y%m%d %H:%M%S'), ))
chains_com = []
from . import elements
i_serial = 0
