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()
# -*- coding: utf-8 -*-
'''
@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])
@author: Naoto Hori
'''
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
ID_DOM_INI = int(sys.argv[3]) - 1 # 重心を求める際に必要
ID_DOM_END = int(sys.argv[4]) - 1
ID_DOM_INI_FIT = int(sys.argv[5]) - 1 # 重心を求める際に必要
ID_DOM_END_FIT = int(sys.argv[6]) - 1
BOXSIZE = float(sys.argv[7])
BOXMAX = 0.5 * BOXSIZE
BOXMIN = -0.5 * BOXSIZE
### Files
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
pdb = PdbFile(sys.argv[2])
pdb.open_to_read()
dcd_out = DcdFile(sys.argv[-1])
dcd_out.open_to_write()
### 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 :
import sys
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:
import math
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
from cafysis.file_io.ninfo import NinfoFile
from cafysis.file_io.pdb import PdbFile
if len(sys.argv) != 4:
print ("Usage: SCRIPT [ninfo file] [pdb file] [output file]")
sys.exit(2)
file_ninfo = NinfoFile(sys.argv[1])
file_ninfo.open_to_read()
ns = NinfoSet()
file_ninfo.read_all(ns)
ns.update_info()
file_ninfo.close()
file_pdb = PdbFile(sys.argv[2])
file_pdb.open_to_read()
chains = file_pdb.read_all()
xyz = []
for c in chains:
for i in range(c.num_atom()):
xyz.append(c.get_atom(i).xyz)
print(("## Confirmation: number of atoms = %i" % len(xyz)))
f_out = open(sys.argv[-1],'w')
f_out.write('#Contacts\n')
for con in ns.contacts:
conid = con.id
imp1 = con.imp1
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()
SEP_B_B = 3 # residue (i) and residue (i+3)
SEP_B_S = 2 # residue (i) and residue (i+2)
SEP_S_S = 2 # residue (i) and residue (i+2)
import sys
from cafysis.file_io.pdb import PdbFile
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet, Fene, LJ
from cafysis.para.BetancourtThirumalai import BTmatrix
if len(sys.argv) != 3:
print('Usage: SCRIPT [input PDB] [output ninfo]')
sys.exit(2)
p = PdbFile(sys.argv[1])
p.open_to_read()
chains = p.read_all()
ns = NinfoSet()
a_BB_pre = None
for ic, c in enumerate(chains):
for r in c.residues:
num_a = len(r.atoms)
a_BB = None
a_SC = None
for a in r.atoms:
# DT5, DA, DC ...., then
SEQ_POSITION = 1
# T5, A, C ...., then
#SEQ_POSITION = 0
ATOMS_P = ('P', 'OP1', 'OP2', "O5'") # "O3'" from the previous nucleotide
ATOMS_P_AMBER = ("P", "O1P", "O2P", "O5*")
ATOMS_S = ("C5'", "C4'", "C3'", "C2'", "C1'", "O4'")
ATOMS_S_AMBER = ("C5*", "C4*", "C3*", "C2*", "C1*", "O4*")
ATOMS_A = ("N9", "C8", "N7", "C5", "C6", "N6", "N1", "C2", "N3", "C4")
ATOMS_G = ("N9", "C8", "N7", "C5", "C6", "O6", "N1", "C2", "N2", "N3", "C4")
ATOMS_C = ("N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6")
ATOMS_T = ("N1", "C2", "O2", "N3", "C4", "O4", "C5", "C7", "C6")
aa = PdbFile(sys.argv[1])
aa.open_to_read()
chains = aa.read_all()
cg_chains = []
atom_id = 0
for c in chains:
c_cg = Chain()
xyz_O3 = None
res_id = 0
for ir, r in enumerate(c.residues):
xyz_P = Coord()
nP = 0