def get_atom_lines_from_input(input_file, tags=['ATOM ', 'HETATM']):
lines = propka.lib.open_file_for_reading(input_file).readlines()
conformation = ''
atoms = {}
numbers = []
for line in lines:
tag = line[0:6]
# set the conformation
if tag == 'MODEL ':
conformation = line[6:].strip()
# found an atom - save it
if tag in tags:
atom = Atom(line=line)
atom.get_input_parameters()
atom.groups_extracted = 1
atom.is_protonated = True
atoms[atom.numb] = atom
numbers.append(atom.numb)
# found bonding information - apply it
if tag == 'CONECT' and len(line) > 14:
conect_numbers = [
line[i:i + 5] for i in range(6,
len(line) - 1, 5)
]
center_atom = atoms[int(conect_numbers[0])]
for n in conect_numbers[1:]:
b = atoms[int(n)]
# remember to check for cysteine bridges
if center_atom.element == 'S' and b.element == 'S':
center_atom.cysteine_bridge = True
b.cysteine_bridge = True
# set up bonding
if not b in center_atom.bonded_atoms:
center_atom.bonded_atoms.append(b)
if not center_atom in b.bonded_atoms:
b.bonded_atoms.append(center_atom)
# found info on covalent coupling
if tag == 'CCOUPL' and len(line) > 14:
conect_numbers = [
line[i:i + 5] for i in range(6,
len(line) - 1, 5)
]
center_atom = atoms[int(conect_numbers[0])]
for n in conect_numbers[1:]:
cg = atoms[int(n)]
center_atom.group.couple_covalently(cg.group)
# found info on non-covalent coupling
if tag == 'NCOUPL' and len(line) > 14:
conect_numbers = [
line[i:i + 5] for i in range(6,
len(line) - 1, 5)
]
center_atom = atoms[int(conect_numbers[0])]
for n in conect_numbers[1:]:
cg = atoms[int(n)]
center_atom.group.couple_non_covalently(cg.group)
# this conformation is done - yield the atoms
if tag == 'ENDMDL':
for n in numbers:
yield (conformation, atoms[n])
# prepare for next conformation
atoms = {}
numbers = []
return
def get_atom_lines_from_input(input_file, tags = ['ATOM ','HETATM']):
lines = propka.lib.open_file_for_reading(input_file).readlines()
conformation = ''
atoms = {}
numbers = []
for line in lines:
tag = line[0:6]
# set the conformation
if tag == 'MODEL ':
conformation = line[6:].strip()
# found an atom - save it
if tag in tags:
atom = Atom(line=line)
atom.get_input_parameters()
atom.groups_extracted = 1
atom.is_protonated = True
atoms[atom.numb] = atom
numbers.append(atom.numb)
# found bonding information - apply it
if tag == 'CONECT' and len(line)>14:
conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)]
center_atom = atoms[int(conect_numbers[0])]
for n in conect_numbers[1:]:
b = atoms[int(n)]
# remember to check for cysteine bridges
if center_atom.element == 'S' and b.element == 'S':
center_atom.cysteine_bridge = True
b.cysteine_bridge = True
# set up bonding
if not b in center_atom.bonded_atoms:
center_atom.bonded_atoms.append(b)
if not center_atom in b.bonded_atoms:
b.bonded_atoms.append(center_atom)
# found info on covalent coupling
if tag == 'CCOUPL' and len(line)>14:
conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)]
center_atom = atoms[int(conect_numbers[0])]
for n in conect_numbers[1:]:
cg = atoms[int(n)]
center_atom.group.couple_covalently(cg.group)
# found info on non-covalent coupling
if tag == 'NCOUPL' and len(line)>14:
conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)]
center_atom = atoms[int(conect_numbers[0])]
for n in conect_numbers[1:]:
cg = atoms[int(n)]
center_atom.group.couple_non_covalently(cg.group)
# this conformation is done - yield the atoms
if tag == 'ENDMDL':
for n in numbers:
yield (conformation, atoms[n])
# prepare for next conformation
atoms = {}
numbers = []
return
def get_atom_lines_from_input(input_file, tags=['ATOM ', 'HETATM']):
"""Get atom lines from a PROPKA input file.
Args:
input_file: input file
tags: tags defining atom lines
Yields:
conformation container, list of atoms
"""
lines = open_file_for_reading(input_file).readlines()
conformation = ''
atoms = {}
numbers = []
for line in lines:
tag = line[0:6]
# set the conformation
if tag == 'MODEL ':
conformation = line[6:].strip()
# found an atom - save it
if tag in tags:
atom = Atom(line=line)
atom.get_input_parameters()
initialize_atom_group(atom)
atom.groups_extracted = 1
atom.is_protonated = True
atoms[atom.numb] = atom
numbers.append(atom.numb)
# found bonding information - apply it
if tag == 'CONECT' and len(line) > 14:
conect_numbers = [
line[i:i + 5] for i in range(6,
len(line) - 1, 5)
]
center_atom = atoms[int(conect_numbers[0])]
for num in conect_numbers[1:]:
bond_atom = atoms[int(num)]
# remember to check for cysteine bridges
if center_atom.element == 'S' and bond_atom.element == 'S':
center_atom.cysteine_bridge = True
bond_atom.cysteine_bridge = True
# set up bonding
if not bond_atom in center_atom.bonded_atoms:
center_atom.bonded_atoms.append(bond_atom)
if not center_atom in bond_atom.bonded_atoms:
bond_atom.bonded_atoms.append(center_atom)
# found info on covalent coupling
if tag == 'CCOUPL' and len(line) > 14:
conect_numbers = [
line[i:i + 5] for i in range(6,
len(line) - 1, 5)
]
center_atom = atoms[int(conect_numbers[0])]
for num in conect_numbers[1:]:
cov_atom = atoms[int(num)]
center_atom.group.couple_covalently(cov_atom.group)
# found info on non-covalent coupling
if tag == 'NCOUPL' and len(line) > 14:
conect_numbers = [
line[i:i + 5] for i in range(6,
len(line) - 1, 5)
]
center_atom = atoms[int(conect_numbers[0])]
for num in conect_numbers[1:]:
cov_atom = atoms[int(num)]
center_atom.group.couple_non_covalently(cov_atom.group)
# this conformation is done - yield the atoms
if tag == 'ENDMDL':
for num in numbers:
yield (conformation, atoms[num])
# prepare for next conformation
atoms = {}
numbers = []
