def line2tertiarystackDT(line):
it = iter(line.split())
num = len(line.split())
if num != 13:
raise MyError("func_line2ninfo", "line2tertiarystackDT", "")
if next(it) != 'tbs-dist':
raise MyError("func_line2ninfo", "line2tertiarystackDT",
"This line is not tbs-dist")
info = TertiaryStackDT()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.factor = float(next(it))
info.native = float(next(it))
info.coef = float(next(it))
info.excess1 = int(next(it))
info.excess2 = int(next(it))
info.ang1_id = None
info.ang2_id = None
info.dih0_id = None
info.dih1_id = None
info.dih2_id = None
return info
def line2dihedral(line):
it = iter(line.split())
num = len(line.split())
if num != 17 and num != 18:
raise MyError("func_line2ninfo", "line2dihedral", "")
if next(it) != 'dihd':
raise MyError("func_line2ninfo", "line2dihedral",
"This line is not dihedral.")
info = Dihedral()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp3 = int(next(it))
info.imp4 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.imp3un = int(next(it))
info.imp4un = int(next(it))
info.native = float(next(it))
info.factor = float(next(it))
info.correct_mgo = float(next(it))
info.coef = float(next(it))
info.coef_3 = float(next(it))
if num == 18:
info.type = next(it)
return info
def read_header(self):
if not self._file:
raise MyError('DcdFile', 'read_header', 'Logical: _file is None')
self._file.seek(0)
# Read kind
num1, num2 = struct.unpack('ii', self._file.read(8))
if num1 == 2:
self._int_kind = 2
int_kind_str = 'h'
elif num1 == 4:
self._int_kind = 4
int_kind_str = 'i'
elif num1 == 8:
self._int_kind = 8
int_kind_str = 'q'
else:
raise MyError('SisbpFile', 'read_header',
'unknown int kind type: ' + '%i' % num1)
if num2 == 4:
self._real_kind = 4
real_kind_str = 'f'
elif num2 == 8:
self._real_kind = 8
real_kind_str = 'd'
else:
raise MyError('SisbpFile', 'read_header',
'unknown real kind type: ' + '%i' % num2)
self._step_byte = 2 * self._int_kind + self._real_kind
self._kind_str = int_kind_str + int_kind_str + real_kind_str
self._seek_data = self._file.tell()
def line2bondangle(line):
it = iter(line.split())
num = len(line.split())
if num != 14 and num != 15:
raise MyError("func_line2ninfo", "line2bondangle", "")
if next(it) != 'angl':
raise MyError("func_line2ninfo", "line2bondangle",
"This line is not bondangle.")
info = BondAngle()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp3 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.imp3un = int(next(it))
info.native = float(next(it))
info.factor = float(next(it))
info.correct_mgo = float(next(it))
info.coef = float(next(it))
if num == 15:
info.type = next(it)
return info
def line2basestackDT(line, fmt=2):
if fmt == 1:
it = iter(line.split())
num = len(line.split())
if num != 12:
raise MyError("func_line2ninfo", "line2basestackDT", "")
if next(it) != 'bs-dist':
raise MyError("func_line2ninfo", "line2basestackDT",
"This line is not bs-dist")
info = BaseStackDT()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.factor = float(next(it))
info.native = float(next(it))
info.coef = float(next(it))
info.type = next(it)
info.dih1_id = None
info.dih2_id = None
return info
elif fmt == 2:
it = iter(line.split())
num = len(line.split())
if num != 14:
raise MyError("func_line2ninfo", "line2basestackDT", "num!=14")
if next(it) != 'bs-dist':
raise MyError("func_line2ninfo", "line2basestackDT",
"This line is not bs-dist")
info = BaseStackDT()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.h = float(next(it))
info.s = float(next(it))
info.Tm = float(next(it))
info.native = float(next(it))
info.coef = float(next(it))
info.type = next(it)
info.dih1_id = None
info.dih2_id = None
return info
else:
raise MyError("func_line2ninfo", "line2basestackDT", "unknown fmt")
def read_header(self):
''' store lines to self.header_lines
store information to self.head_str and self.head_col
'''
if not self._file :
raise MyError('TsFile', 'read_header', 'Logical: _file is None')
self._file.seek(0)
# skip 5 lines
for i in range(5):
self.header_lines.append( self._file.readline() )
# read header
self.header_lines.append( self._file.readline() )
line = self._file.readline()
self.header_lines.append( line )
self.head_str = line.split()[1:]
self.head_col = self._head_str2col(self.head_str)
# skip 2 lines
self.header_lines.append( self._file.readline() )
self.header_lines.append( self._file.readline() )
#### Count the number of units ####
# skip the first line of step 0
self._file.readline()
if self._file.readline().split()[0] == '#all':
self.flg_all = True
#raise MyError('TsFile','read_header','Bad format: #all')
self.num_unit = 0
for l in self._file:
if l[0] == ' ':
break
if l.split()[1][0:1] == '-':
''' unit-unit lines exist'''
self.flg_u_u = True
break
self.num_unit = int(l.split()[0][1:])
if self.num_unit < 0:
raise MyError('TsFile','read_header','Bad format: num_unit <= 0')
###########################################
# skip 9 lines
self._file.seek(0)
for i in range(9):
self._file.readline()
def _line2atom(self, line):
line = line.rstrip()
if line[0:6] != 'ATOM ' and line[0:6] != 'HETATM' :
raise MyError('PdbFile', 'decompose_atom', 'line does not begin with "ATOM"')
atom = Atom()
atom.serial = int(line[6:11])
atom.name = line[12:16]
atom.alt_loc = line[16:17]
atom.res_name = line[17:20]
atom.chain_id = line[21:22]
atom.res_seq = int(line[22:26])
#atom.ins_code = line[26:27]
atom.ins_code = line[26:30]
atom.xyz = Coord(float(line[30:38]), float(line[38:46]), float(line[46:54]))
try :
atom.occupancy = float(line[54:60])
except :
atom.occupancy = 0.0
try :
atom.temp_factor = float(line[60:66])
except :
atom.temp_factor = 0.0
atom.element = line[76:78]
try :
atom.charge = int(line[78:80])
except :
atom.charge = 0
return atom
def line2hbondDT(line):
it = iter(line.split())
num = len(line.split())
if num < 11:
raise MyError("func_line2ninfo", "line2hbondDT", "")
if next(it) != 'hb-dist':
raise MyError("func_line2ninfo", "line2hbondDT",
"This line is not hb-dist")
info = HBondDT()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.factor = float(next(it))
info.native = float(next(it))
info.coef = float(next(it))
if num > 11:
info.sectert = next(it)
info.nHB = int(next(it))
info.atoms1 = []
info.atoms2 = []
try:
while (True):
a = next(it)
info.atoms1.append(a)
a = next(it)
info.atoms2.append(a)
except:
pass
else:
info.sectert = None
info.nHB = None
info.ang1_id = None
info.ang2_id = None
info.dih0_id = None
info.dih1_id = None
info.dih2_id = None
return info
def write_header(self):
if not self._header:
raise MyError('DcdFile', 'write_header',
'Logical: _header is None')
self._file.seek(0)
if self._header.nset is None:
self._header.nset = 0
if self._header.istart is None:
self._header.istart = 0
if self._header.nstep_save is None:
self._header.nstep_save = 0
if self._header.nstep is None:
self._header.nstep = 0
if self._header.nunit_real is None:
self._header.nunit_real = 0
if self._header.delta is None:
self._header.delta = 0.0
if self._header.tempk is None:
self._header.tempk = 0.0
if self._header.lunit2mp is None:
self._header.lunit2mp = []
#first block
form = '4siii5iifi9i'
binary = struct.pack(form, b'CORD', self._header.nset,
self._header.istart, self._header.nstep_save,
self._header.nstep, self._header.nunit_real, 0, 0,
0, 0, self._header.delta, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0)
self._put_data(binary, struct.calcsize(form))
#title block
binary = struct.pack('i' + '80s' * 2, (3 + len(self._header.lunit2mp)),
self._header.title[0], self._header.title[1])
import re
re_null = re.compile(b'\0')
p = struct.pack('80s', bytes('%f' % self._header.tempk, 'utf-8'))
binary += re_null.sub(b' ', p)
for i in range(self._header.nunit_real):
p = struct.pack('80s',
bytes('%i' % self._header.lunit2mp[i], 'utf-8'))
binary += re_null.sub(b' ', p)
form = 'i' + '80s' * (3 + self._header.nunit_real)
self._put_data(binary, struct.calcsize(form))
# nmp_real
binary = struct.pack('i', self._header.nmp_real)
self._put_data(binary, 4)
def line2basestack(line):
it = iter(line.split())
num = len(line.split())
if num != 13:
raise MyError("func_line2ninfo", "line2basestack", "")
if next(it) != 'basestack':
raise MyError("func_line2ninfo", "line2basestack",
"This line is not basestack")
info = BaseStack()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.native = float(next(it))
info.factor = float(next(it))
info.dummy = int(next(it))
info.coef = float(next(it))
info.type = next(it)
return info
def line2contact(line):
it = iter(line.split())
num = len(line.split())
if num != 12 and num != 13:
raise MyError("func_line2ninfo", "line2contact", "")
if next(it) != 'contact':
raise MyError("func_line2ninfo", "line2contact",
"This line is not contact.")
info = Contact()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.native = float(next(it))
info.factor = float(next(it))
info.dummy = int(next(it))
info.coef = float(next(it))
if num == 13:
info.type = next(it)
return info
def line2bondlength(line):
it = iter(line.split())
num = len(line.split())
if num != 12 and num != 13:
raise MyError("func_line2ninfo", "line2bondlength", "")
if next(it) != 'bond':
raise MyError("func_line2ninfo", "line2bondlength",
"This line is not bondlength.")
info = BondLength()
info.id = int(next(it))
info.iunit1 = int(next(it))
info.iunit2 = int(next(it))
info.imp1 = int(next(it))
info.imp2 = int(next(it))
info.imp1un = int(next(it))
info.imp2un = int(next(it))
info.native = float(next(it))
info.factor = float(next(it))
info.correct_mgo = float(next(it))
info.coef = float(next(it))
if num == 13:
info.type = next(it)
return info
def __init__(self, filename, openmode=None, flg_HETATM=False):
self._filename = filename
self._status = 'Closed'
self.flg_HETATM = flg_HETATM
self.modelID = None
self.remark = None
if openmode is not None:
if openmode == 'r':
self.open_to_read()
elif openmode == 'w':
self.open_to_write()
else:
print("openmode has to be either 'r' or 'w'")
raise MyError('PdbFile', '__init__', "openmode has to be either 'r' or 'w'")
def read_header(self):
if not self._file:
raise MyError('DridFile', 'read_header', 'Logical: _file is None')
self._file.seek(0)
# title block (number of line can be changed)
b = self._pick_data()
len_title = struct.unpack('i', b)[0]
b = self._pick_data()
self._header.title = struct.unpack('%ds' % (len_title, ), b)[0]
self._header.version = int(self._header.title[3:])
if self._header.version != 2:
print('Caution: This is not DRID ver.2 format!!')
print(self._header.title)
if self._header.version == 1:
# centroids
b = self._pick_data()
n_centroids = struct.unpack('i', b)[0]
b = self._pick_data()
self._header.centroids = struct.unpack('i' * n_centroids, b)
# atoms
b = self._pick_data()
n_atoms = struct.unpack('i', b)[0]
b = self._pick_data()
self._header.atoms = struct.unpack('i' * n_atoms, b)
# Mask (ver >= 2)
if self._header.version >= 2:
b = self._pick_data()
n_centroids, n_atoms = struct.unpack('ii', b)
self._header.mask = np.empty((n_centroids, n_atoms))
for ic in range(n_centroids):
b = self._pick_data()
self._header.mask[ic, :] = struct.unpack('i' * n_atoms, b)
self._seek_data = self._file.tell()
def write_header(self):
if not self._header:
raise MyError('DcdFile', 'write_header',
'Logical: _header is None')
self._file.seek(0)
# title block
binary = struct.pack('i', len(self._header.title))
self._put_data(binary, 4)
form = '%is' % (len(self._header.title), )
binary = struct.pack(form, self._header.title)
self._put_data(binary, struct.calcsize(form))
if self._header.version == 1:
# centroids
binary = struct.pack('i', len(self._header.centroids))
self._put_data(binary, 4)
binary = struct.pack('i' * len(self._header.centroids),
*(self._header.centroids))
self._put_data(binary, 4 * len(self._header.centroids))
# atoms
binary = struct.pack('i', len(self._header.atoms))
self._put_data(binary, 4)
binary = struct.pack('i' * len(self._header.atoms),
*(self._header.atoms))
self._put_data(binary, 4 * len(self._header.atoms))
# Mask (ver >= 2)
if self._header.version >= 2:
# Dimensions (# of centroids, # of atoms)
form = 'ii'
binary = struct.pack(form, self._header.mask.shape[0],
self._header.mask.shape[1])
self._put_data(binary, struct.calcsize(form))
for ic in range(self._header.n_centroids()):
form = '%ii' % self._header.mask.shape[1]
binary = struct.pack(form, *(self._header.mask[ic, :]))
self._put_data(binary, struct.calcsize(form))
def open_to_write(self):
if self._status != 'Closed':
raise MyError('PsfFile', 'open_for_read', 'file is not closed')
self._file = open(self._filename, 'w')
def read_header(self):
if not self._file:
raise MyError('DcdFile', 'read_header', 'Logical: _file is None')
###########################################
# Check the format reading title lines
###########################################
self._file.seek(0)
# Skip the first block
b = self._pick_data()
# title block
b = self._pick_data()
size = len(b)
nline = (size - 4) // 80
bdata = struct.unpack(('i' + '80s' * nline), b)
try:
if bdata[1].decode("utf-8").find('Git commit') != -1 or bdata[
2].decode("utf-8").find('CafeMol') != -1:
self._header.format = 'cafemol'
else:
self._header.format = 'charmm'
except:
self._header.format = 'charmm'
###########################################
# Load header infomation
###########################################
self._file.seek(0)
if self._header.format == 'cafemol':
# first block
b = self._pick_data()
bdata = struct.unpack('4siii5iifi9i', b)
#bdata = struct.unpack('4siii5iid9i',b)
if bdata[0].decode("utf-8") != 'CORD':
raise MyError('DcdFile', 'read_header',
'%s is not coordinate file' % (self._filename, ))
self._header.nset = bdata[1]
self._header.istart = bdata[2]
self._header.nstep_save = bdata[3]
self._header.nstep = bdata[4]
self._header.nunit_real = bdata[5]
self._header.delta = bdata[10]
# title block (number of line can be changed)
b = self._pick_data()
bdata = struct.unpack(
('i' + '80s' * (3 + self._header.nunit_real)), b)
self._header.title = (bdata[1], bdata[2])
#self._header.tempk = float(bdata[3].strip('\0 '))
self._header.tempk = float(bdata[3])
self._header.lunit2mp = []
for i in range(self._header.nunit_real):
# self._header.lunit2mp.append(int(bdata[i + 4].strip('\0 ')))
self._header.lunit2mp.append(int(bdata[i + 4]))
# nmp_real
b = self._pick_data()
self._header.nmp_real = struct.unpack('i', b)[0]
elif self._header.format == 'charmm':
# first block
b = self._pick_data()
bdata = struct.unpack('4s20i', b)
if (bdata[11] == 1):
self._header.with_unit_cell = True
#bdata = struct.unpack('4siii5iid9i',b)
#if bdata[0] != 'CORD' :
# raise MyError('DcdFile', 'read_header', '%s is not coordinate file' % (self._filename,))
#self._header.nset = bdata[1]
#self._header.istart = bdata[2]
#self._header.nstep_save = bdata[3]
#self._header.nstep = bdata[4]
#self._header.nunit_real = bdata[5]
#self._header.delta = bdata[10]
# title block (number of line can be changed)
b = self._pick_data()
size = len(b)
nline = (size - 4) // 80
bdata = struct.unpack(('i' + '80s' * nline), b)
self._header.title = []
for i in range(nline):
self._header.title.append(bdata[i + 1])
# nmp_real
b = self._pick_data()
self._header.nmp_real = struct.unpack('i', b)[0]
self._seek_data = self._file.tell()
def open_to_read(self):
if self._status != 'Closed':
raise MyError('NinfoFile', 'open_for_read', 'file is not closed')
self._file = open(self._filename, 'r')
def _head_str2col(self, strlist):
th = TsHeader()
for i, str in enumerate(strlist):
if str == 'step':
th.step = i
elif str == 'tempk':
th.temp = i
elif str == 'label':
th.label = i
elif str == 'radg':
th.rg = i
elif str == 'rmsd':
th.rmsd = i
elif str == 'qscore':
th.q = i
# 現状、mgo未対応
#elif str == '':
# th.mgo_kai = i
#elif str == '':
# th.mgo_coef = i
#elif str == '':
# th.mgo_q = i
#elif str == '':
# th.mgo_state = i
elif str == 'etot':
th.e_tot = i
elif str == 'velet':
th.e_velo = i
elif str == 'local':
th.e_local = i
elif str == 'go':
th.e_go = i
elif str == 'morse':
th.e_morse = i
elif str == 'repul':
th.e_repul = i
elif str == 'solv_dna':
th.e_dna_solv = i
elif str == 'base':
th.e_dna_base = i
elif str == 'elect':
th.e_ele = i
elif str == 'hyd_ion':
th.e_ion_hyd = i
elif str == 'hp':
th.e_hp = i
elif str == 'tail':
th.e_lip_tail = i
elif str == 'int':
th.e_lip_int = i
elif str == 'solv_lip':
th.e_lip_solv = i
elif str == 'box':
th.e_box = i
elif str == 'cap':
th.e_cap = i
elif str == 'bridge':
th.e_bridge = i
elif str == 'pulling':
th.e_pull = i
elif str == 'anchor':
th.e_anch = i
elif str == 'rest1d':
th.e_rest1d = i
elif str == 'imp_lig':
th.e_implig = i
elif str == 'window':
th.e_window = i
elif str == 'stack':
th.e_stack = i
elif str == 'hbond':
th.e_hbond = i
elif str == 'tstack':
th.e_tstack = i
elif str == 'thbond':
th.e_thbond = i
else:
raise MyError('ts.py','_head_str2col','str=%s' % (str,))
return th