#!/usr/bin/env python
from file_pdb import PdbFile
import sys
if len(sys.argv) != 2:
print('Usage: SCRIPT [input PDB]')
sys.exit(2)
pdb_cafemol = PdbFile(sys.argv[1])
pdb_cafemol.open_to_read()
cafe_chains = pdb_cafemol.read_all()
pdb_cafemol.close()
#last_res_nums = []
#sum = 0
#for c in cafe_chains:
# last_res_num = c.get_atom(-1).res_seq
# sum += last_res_num
# last_res_nums.append(last_res_num)
#print last_res_nums
#print sum
offset = 0
print('#ic ires res_c res imp name')
for (ic, c) in enumerate(cafe_chains):
for (ir, r) in enumerate(c.residues):
for (ia, a) in enumerate(r.atoms):
print(('%3i %6i %6i %s %6i %s' %
(ic + 1, a.res_seq + offset, a.res_seq, a.res_name,
a.res_seq, a.name)))
#!/usr/bin/env python
import sys
from file_pdb import PdbFile
from my_element import Coord
if len(sys.argv) != 3:
print('Usage: % SCRIPT [input pdb] [output pdb]')
sys.exit(2)
f_pdb_in = PdbFile(sys.argv[1])
f_pdb_in.open_to_read()
chains = f_pdb_in.read_all()
f_pdb_in.close()
com = Coord()
total_atom = 0
for c in chains:
total_atom += c.num_atom()
for iatom in range(c.num_atom()):
com.move(c.get_atom(iatom).xyz)
com.x = -com.x / float(total_atom)
com.y = -com.y / float(total_atom)
com.z = -com.z / float(total_atom)
for c in chains:
for iatom in range(c.num_atom()):
c.get_atom(iatom).xyz.move(com)
f_pdb_out = PdbFile(sys.argv[2])
#!/usr/bin/env python
import sys
from file_pdb import PdbFile
if not len(sys.argv) in (4, 5):
print('\n make a vector which represent movement from PDB1 to PDB2')
print('\n Usage: [PDB 1] [PDB 2] [output mpvec file]')
print(' Usage: [PDB 1] [PDB 2] [output mpvec file] [output vec file]\n')
sys.exit(2)
f_pdb = PdbFile(sys.argv[1])
f_pdb.open_to_read()
chains1 = f_pdb.read_all()
f_pdb.close()
f_pdb = PdbFile(sys.argv[2])
f_pdb.open_to_read()
chains2 = f_pdb.read_all()
f_pdb.close()
f_out_mpvec = open(sys.argv[3], 'w')
if len(sys.argv) == 5:
f_out_vec = open(sys.argv[4], 'w')
if len(chains1) != len(chains2):
print('Error: len(chains1) != len(chains2)')
sys.exit(2)
for ic, c1 in enumerate(chains1):
c2 = chains2[ic]
if len(sys.argv) < 6:
print(
'\n Usage: % SCRIPT [min] [max] [width] [PDB] [[PDB] ....] [output]\n')
sys.exit(2)
# parameters
HIST_MIN = float(sys.argv[1])
HIST_MAX = float(sys.argv[2])
HIST_WID = float(sys.argv[3])
# Read chains from all input files
chains = []
for arg in sys.argv[4:-1]:
file = PdbFile(arg)
file.open_to_read()
file.flg_HETATM = True
chains += file.read_all()
# Output file preparing
import os
if os.path.exists(sys.argv[-1]):
if input('File %s exists. Rewrite? [Y/n]' % sys.argv[-1]) != 'Y':
sys.exit(2)
file_out = open(sys.argv[-1], 'w')
# Search Mg
MgIds = []
for (i_chain, chain) in enumerate(chains):
for (i_res, res) in enumerate(chain.residues):
for (i_atom, atom) in enumerate(res.atoms):