def find_similar_atomtype_params(cls, atom_type, tried):
"""
:Description: If some atom_type is not found in the SGB_paramaters() func
the param/similarity.param is parsed to look for the next most
similar atom type.
If that is not found as well, we append the tried
atom_types to tried [] for efficiency and keep looking for
other similar atom types.
:Input:
-atom_type: atom_type of the atom not found.
- tried: similar atom_types that we try to obtain its parameters
but they are not contained in the f14_sgbnp.param file.
:Output:
- new_params: [
similar_atom_type,
SGB_radius,
Van der Waals radius,
Solvatation gamma factor,
Solvatation alpha factor
]
"""
new_atom_type = False
similarity = 0
#Search for the most similar atom
lines = preproces_file_lines(SIMILARITY_PATH)
for line in lines:
line = line.split()
if (line[0] == atom_type and float(line[2]) > float(similarity)
and line[1] not in tried):
similarity = line[2]
new_atom_type = line[1]
elif (line[1] == atom_type and float(line[2]) > float(similarity)
and line[0] not in tried):
similarity = line[2]
new_atom_type = line[0]
if new_atom_type:
tried.append(new_atom_type)
lines = preproces_file_lines(PARAM_PATH)
for line in lines:
if not line.startswith('#'):
line = line.split()
atom_type_file = line[1]
if (atom_type == atom_type_file):
return (line)
new_params = cls.find_similar_atomtype_params(new_atom_type, tried)
return new_params
else:
return []
def retrieve_atom_names(OPLS_CONVERSION_FILE):
"""
:Description: parse the param.data and retrieve
the atom names of the molecule
:Input: OPLS_CONVERSION_FILE: ffldserver output file
cointaining the system parameters
:Output: atom_names: Atom_names of the systems
:Author: Daniel Soler
"""
atom_names = []
lines = preproces_file_lines(OPLS_CONVERSION_FILE)
start_found_NBND = False
for line in lines:
if not line.startswith("----------"):
if (line.startswith("atom type vdw")):
start_found_NBND = True
elif (start_found_NBND):
try:
line = line.split()
atom_names.append(line[0])
except IndexError:
return atom_names
def SGB_paramaters(cls, atom_types, tried=[]):
"""
:Description: Parse the param/f14_sgbnp.param file
to obtain all the SGB Nonbonded parameters
to build the template file.
If some atom_type is not found the param/similarity.param
is parsed to look for the next most similar atom type.
If that is not found as well, we append the tried
atom_types to tried [] for efficiency and keep looking for
other similar atom types.
:Arguments:
- atom_types: atom_types of the system
- tried: atom_types that we try to obtain its parameters
but they are not contained in the f14_sgbnp.param file.
:Returns:
- radius: Atoms SGB radius
- vdw_r: Atoms Van der Waals
- gammas: Atoms gamma solvatation factor
- alphas: Atoms alpha solvatation factor
For more information on this parameters refer
to the PELE documentation.
Example with one atom_type (ONN):
1- We look whether or not its in the conversion atom dictionary
1.1- If it is we change the atom type to the one in the dict
2- We search the SGB parameters in the PARAM_PATH file
2.1- If found return them separately
2.2 -If not found call find_similar_atomtype_params to look
for similar atom types parameters
3- We return the similar SGB parameters or a default
if they were not found
:Author: Daniel Soler
"""
radius = []
vdw_r = []
gammas = []
alphas = []
lines = preproces_file_lines(PARAM_PATH)
for atom_type in atom_types:
if atom_type in CONVERSION:
atom_type = CONVERSION[atom_type]
found = False
for line in lines:
if not line.startswith('#'):
line = line.split()
atom_type_file = line[1]
if (atom_type == atom_type_file):
radius.append(line[4])
vdw_r.append(line[5])
gammas.append(line[6])
alphas.append(line[7])
found = True
break
if not found:
new_params = cls.find_similar_atomtype_params(atom_type,
tried=[])
if (new_params):
radius.append(new_params[4])
vdw_r.append(new_params[5])
gammas.append(new_params[6])
alphas.append(new_params[7])
# warnings.warn("Paramaters of {} used for {}.".format(
# new_params[1], atom_type))
else:
# warnings.warn("Defaults Paramaters used for{}.".format(atom_type))
radius.append(DEFAULT_ATOMTYPE[2])
vdw_r.append(DEFAULT_ATOMTYPE[3])
gammas.append(DEFAULT_ATOMTYPE[4])
alphas.append(DEFAULT_ATOMTYPE[5])
return (radius, vdw_r, gammas, alphas)