def _parse_oniom_line(line_splits):
"""C-CT--0.2 0 1.000 1.100 1.200 L H-HC 123 0.0"""
mm_info, mask, x, y, z, temp = line_splits[0:6]
layer, link_splits = temp[0], temp[1:].split()
# create atom and MM_obj
el, mm_obj = _parse_mm_info(mm_info)
atom = atoms.Atom(el, (float(x), float(y), float(z)))
if mm_obj:
atom.set_mm(mm_obj) # high layer atoms might not have it
# create Oniom object
oniom_obj = atoms.Oniom(int(mask), layer)
# process link atom
if len(link_splits) == 1:
raise RuntimeError('missing bound_to in link atom: %s' % (
' '.join(link_splits)))
elif len(link_splits) > 1:
link_splits.append('0.0') # HAMMERATION
link_mm_info, bound_to, scale1 = link_splits[:3]
link_el, link_mm_obj = _parse_mm_info(link_mm_info)
link_atom = atoms.Atom(link_el, (0, 0, 0)) # empty coords
if link_mm_obj:
link_atom.set_mm(link_mm_obj)
oniom_obj.set_link(link_atom, int(bound_to), float(scale1))
# add oniom_obj
atom.set_oniom(oniom_obj)
return atom
def _parse_xyz_line(line_splited):
(el, x, y, z) = line_splited
el, mm_obj = _parse_mm_info(el)
atom = atoms.Atom(el, (float(x), float(y), float(z)))
if mm_obj:
atom.set_mm(mm_obj)
return atom
def mol22atom(line):
"Reads a mol2 atom line and returns the atoms indexes and bond order"
"""ex:\
' 1 O1 -0.5240 -0.4910 -0.1630 os 1 MOL -0.196235\n'
"""
words = line.strip().split()
# basic atom info
element = words[5].split('.')[0]
x, y, z = words[2:5]
# mm info
atom_type = words[1]
if len(words) == 9:
charge = words[8]
name = words[1]
atom_type = words[5] #changes the info of the atom_type if mol2 has
# 9 fields
else:
charge = None
atom = atoms.Atom(atom_type,(float(x), float(y), float(z)))
mm_obj = atoms.MM(atom_type, charge)
atom.set_mm(mm_obj)
#resinfo if mol2 has 9 fields
if len(words) == 9:
resinfo_obj = atoms.RESinfo(name, words[7], words[6], 'X')
atom.set_resinfo(resinfo_obj)
return atom
def pdb2atom(line):
# start atom
el = line [76:78].strip()
if el == '':
el = ''.join(i for i in line[12:16].strip() if not i.isdigit())[0] #get from atom name
#after eliminating numbers
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
atom = atoms.Atom(el, (x,y,z))
# residue info
name = line [12:16].strip() # atom name
resName = line [17:20].strip() # Residue name
resNum = spaceint(line[22:26]) # Residue number
chain = line [21:22].strip() # chain
resinfo = atoms.RESinfo(name, resName, resNum, chain)
# pdb info
keyword = line[ 0: 6]
serial = spaceint(line[ 6:11])
pdbinfo = atoms.PDBinfo(keyword, serial,
occupancy = spacefloat(line[54:60]),
bfact = spacefloat(line[60:66]),
altloc = line[16:17],
icode = line[26:27],
formalcharge = line[78:80].strip())
# return
atom.set_resinfo(resinfo)
atom.set_pdbinfo(pdbinfo)
return atom
def _gen_zmat(self, inpcrd_name):
text = ''
chargelist = self.read_flag('CHARGE')
if 'ATOMIC_NUMBER' in self._flags: # old amboniom_elements.py (glycam)
elements = self._guess_elements()
else:
elements = self._read_elements()
total_charge = 0
X, Y, Z = self._coords_from_inpcrd(inpcrd_name)
j = 0
for i in self.atom_sel_idx:
name = self.pdb_atom_name[i].replace('-', '').replace('+', '')
residue_name = self.pdb_resname[i].replace('-',
'').replace('+', '')
residue_number = self.pdb_resid[i]
mm_type = self.upper_atom_types[i]
charge = chargelist[i] / 18.2223
total_charge += charge
mask = '0'
x = X[i]
y = Y[i]
z = Z[i]
chain = ''
layer = 'L'
element = elements[j]
j += 1
link_element = link_mm_type = link_bound_to = link_scale1 = None
# create atom
this_atom = atoms.Atom(element, (x, y, z))
resinfo = atoms.RESinfo(name, residue_name, residue_number, chain)
this_atom.set_resinfo(resinfo)
oniominfo = atoms.Oniom(mask, layer)
this_atom.set_oniom(oniominfo)
mm = atoms.MM(mm_type, charge)
this_atom.set_mm(mm)
# print z-matrix for atom
text += iolines.atom2zmat(this_atom)
# Add stuff to text
header = ''
#header += '%nproc=4\n'
#header += '%mem=2GB\n'
#header += '%chk=chk.chk\n'
header += '# amber=softonly geom=connectivity\n\n'
header += 'Se amanha nao chover vai estar um lindo dia de sol\n\n'
header += 'Sum of partial charges: %f\n' % (total_charge)
return header + text
def read_geometry(self, opt_step, scan_step):
with open(self.name, 'r') as f:
f.seek(self.bytedict['orientation:'][scan_step][opt_step])
atoms_list = []
for _ in range(5):
f.readline()
for model_atom in self.atoms_list:
line = f.readline()
atomic_number = int(line.split()[1])
x, y, z = line.split()[3:6]
element = atoms.PERIODIC_TABLE.GetSymbol(atomic_number)
xyz = (float(x), float(y), float(z))
atom = atoms.Atom(element, xyz)
atoms_list.append(atom)
return atoms_list
def pdbqt2atom(line):
# start atom
atype = line[77:79].strip()
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
ad2el = {'H':'H', 'HD':'H', 'HS':'H', 'C':'C', 'A':'C', 'N':'N', 'NA':'N',
'NS':'N', 'OA':'O', 'OS':'O', 'F':'F', 'Mg':'Mg', 'MG':'Mg', 'P':'P',
'SA':'S', 'S':'S', 'Cl':'Cl', 'CL':'Cl', 'Ca':'Ca', 'CA':'Ca',
'Mn':'Mn', 'MN':'Mn', 'Fe':'Fe', 'FE':'Fe', 'Zn':'Zn', 'ZN':'Zn',
'Br':'Br', 'BR':'Br', 'I':'I', 'W':'O'}
atom = atoms.Atom(ad2el[atype], (x,y,z))
# residue info
name = line [12:16].strip() # atom name
resName = line [17:20].strip() # Residue name
resNum = spaceint(line[22:26]) # Residue number
chain = line [21:22].strip() # chain
resinfo = atoms.RESinfo(name, resName, resNum, chain)
# pdb info
keyword = line[ 0: 6]
serial = spaceint(line[ 6:11])
pdbinfo = atoms.PDBinfo(keyword, serial,
occupancy = spacefloat(line[54:60]),
bfact = spacefloat(line[60:66]),
altloc = line[16:17],
icode = line[26:27],
formalcharge = ' ')
# atype, charge
mm = atoms.MM(atype, float(line[70:76]))
# return
atom.set_mm(mm)
atom.set_resinfo(resinfo)
atom.set_pdbinfo(pdbinfo)
return atom