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oplsaa2lt.py no longer tries to retrieve files using URLs. README.md …
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…updated accordingly.
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@jewettaij
jewettaij committed Oct 26, 2024
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8 changes: 4 additions & 4 deletions moltemplate/force_fields/convert_OPLSAA_to_LT/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -43,10 +43,10 @@ Ethylene inherits OPLSAA {
```
See the examples in the force_field_OPLSAA2023/ subdirectory directory for details.

Note: The `--par` and `--sb` can also be URLs.
The "oplsaa2023.lt" file was generated this way using the published parameters from [this paper](https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602).

The "oplsaa2023.lt" file is normally generated using the published parameters from [this paper](https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602). Unless otherwise specified in the header, the `oplsaa2lt.py` program is run using these arguments:
```
./oplsaa2lt.py --name OPLSAA --out oplsaa2023.lt \
--par https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602/suppl_file/jp3c06602_si_002.txt \
--sb https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602/suppl_file/jp3c06602_si_003.txt
--par ../oplsaa2023_original_format/Jorgensen_et_al-2023-The_Journal_of_Physical_Chemistry_B.sup-2.par \
--sb ../oplsaa2023_original_format/Jorgensen_et_al-2023-The_Journal_of_Physical_Chemistry_B.sup-3.sb
```
253 changes: 117 additions & 136 deletions moltemplate/force_fields/convert_OPLSAA_to_LT/oplsaa2lt.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,6 @@
#!/usr/bin/env python3

import argparse
import io
import urllib.request
import urllib.error
import sys

from oplsaa2lt_utils import (bond_header, file_equivalences_header,
Expand Down Expand Up @@ -172,19 +169,21 @@ def main(argv):
ap.add_argument(
"--par",
dest="infile_name_par",
default="../oplsaa2023_original_format/Jorgensen_et_al-2023-The_Journal_of_Physical_Chemistry_B.sup-2.par",
help="name of the BOSS .par file. (It can be a URL. Example: --par=https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602/suppl_file/jp3c06602_si_002.txt)",
required=True,
# default="../oplsaa2023_original_format/Jorgensen_et_al-2023-The_Journal_of_Physical_Chemistry_B.sup-2.par",
help="name of the BOSS .par file. (Example: \"oplsaa.par\")",
)
ap.add_argument(
"--sb",
dest="infile_name_sb",
default="../oplsaa2023_original_format/Jorgensen_et_al-2023-The_Journal_of_Physical_Chemistry_B.sup-3.sb",
help="name of the BOSS .sb file. (It can be a URL. Example: --par=https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602/suppl_file/jp3c06602_si_003.txt)",
required=True,
# default="../oplsaa2023_original_format/Jorgensen_et_al-2023-The_Journal_of_Physical_Chemistry_B.sup-3.sb",
help="name of the BOSS .sb file. (Example: \"oplsaa.sb\")",
)
ap.add_argument(
"--out",
dest="outfile_name",
default="",
required=True,
help="name of the .lt file you want to create.",
)
ap.add_argument(
Expand All @@ -197,22 +196,6 @@ def main(argv):

args = ap.parse_args(argv[1:])

if args.infile_name_par.startswith("http"):
url = args.infile_name_par
resource = urllib.request.urlopen(url)
text_in = resource.read().decode('utf-8')
infile_par = io.StringIO(text_in)
else:
infile_par = open(args.infile_name_par)

if args.infile_name_sb.startswith("http"):
url = args.infile_name_sb
resource = urllib.request.urlopen(url)
text_in = resource.read().decode('utf-8')
infile_sb = io.StringIO(text_in)
else:
infile_sb = open(args.infile_name_sb)

if args.outfile_name != "":
outfile = open(args.outfile_name, 'w')
else:
Expand All @@ -226,15 +209,15 @@ def main(argv):

# Import bond and angle information from the ".sb" BOSS file.
# (Eg. https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602/suppl_file/jp3c06602_si_003.txt)
lines_sb = infile_sb.readlines()
infile_sb.close()
with open(args.infile_name_sb, "r") as infile_sb:
lines_sb = infile_sb.readlines()
bonds, angles = get_bonds_and_angles(lines_sb)


# Import atom, dihedral, and improper information from the ".par" BOSS file.
# (Eg. https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602/suppl_file/jp3c06602_si_002.txt)
lines_par = infile_par.readlines()
infile_par.close()
with open(args.infile_name_par, "r") as infile_par:
lines_par = infile_par.readlines()
dihedrals, impropers = get_dihedrals_and_impropers(lines_par)


Expand Down Expand Up @@ -313,114 +296,112 @@ def main(argv):
##################### in this way I can keep the comment blocks from the original FF file
################################################################################################
atoms: list[Atom] = []
outfile.write("# This file was generated automatically using:\n")
outfile.write("# " + g_program_name + " " + " ".join(argv[1:]) + "\n")
outfile.write("")
outfile.write(file_header)
outfile.write(" # NOTE2: I tried to maintain the same two-letter 'general' types as from\n")
outfile.write(" # the original FF file. However, some changes had to be made to comply\n")
outfile.write(" # to the inner functioning of moltemplate. Such changes were:\n #\n")
for original, new in TYPE_CONVERSION_TUPLES:
outfile.write(f" # {original} --> {new}\n")

outfile.write("\n # NOTE3: The original FF file had types for different water models,\n")
outfile.write(" # but it was missing the relevant bonded interactions; therefore, I\n")
outfile.write(" # skipped the water types from the original FF, and hardcoded some simple\n")
outfile.write(" # water models, with the relevant bonded parameters\n")

outfile.write("\n # NOTE4: Water TIP*/SPC* models parameters are taken from LAMMPS doc,\n")
outfile.write(" # the user is invited to read the proper sections in the LAMMPS user manual\n")
outfile.write(" # to properly understand how to setup a simulation with the desided model.\n")
outfile.write(" # As for OPC, it seems it could be implemented in LAMMPS similarly to the\n")
outfile.write(" # TIP4P model (where OM distance should be 0.1594 angstrom).\n")

outfile.write('\n\n write_once("In Charges") {\n')
for line in lines_par[2:]:
if line.startswith("# Add more charge and L-J parameters"):
break
if line.startswith("#"):
outfile.write(f" {line}")
else:
atom = parse_atom_line(line)
if atom is not None:
atoms.append(atom)
outfile.write(f" {atom.charge_line}")
for atom in wat_atoms:
outfile.write(f" {atom.charge_line}")
outfile.write(" } # (end of atom partial charges)\n")
outfile.write('\n\n write_once("Data Masses") {\n')
atoms += wat_atoms
for atom in atoms:
outfile.write(f" {atom.mass_line}")
outfile.write(" } # (end of atom masses)\n")

outfile.write(file_equivalences_header)
for atom in atoms:
outfile.write(f" {atom.repl_line}")

outfile.write(nb_header)
outfile.write(' write_once("In Settings") {\n')
for atom in atoms:
outfile.write(f" {atom.nb_line}")
outfile.write(" } # (end of pair_coeffs)\n")

outfile.write("\n\n\n\n")
outfile.write(" # NOTE: all bonded interaction name can't have '*' or '?' characters, so in each\n")
outfile.write(" # bonded sections such characters will be replaced with another character\n")
outfile.write(" # that, at the time of writing, is not used for atom types (* -> £, ? -> €).\n\n")
outfile.write(bond_header)
outfile.write('\n write_once("In Settings") {\n')
for bond in bonds:
if not bond.to_skip:
outfile.write(f" {bond.coeff_line}")
outfile.write(" } # (end of bond_coeffs)\n")
outfile.write('\n write_once("Data Bonds By Type") {\n')
for bond in bonds:
if not bond.to_skip:
outfile.write(f" {bond.bytype_line}")
outfile.write(" } # (end of bonds by type)\n")

outfile.write(angle_header)
outfile.write('\n write_once("In Settings") {\n')
for angle in angles:
if not angle.to_skip:
outfile.write(f" {angle.coeff_line}")
outfile.write(" } # (end of angle_coeffs)\n")
outfile.write('\n write_once("Data Angles By Type") {\n')
for angle in angles:
if not angle.to_skip:
outfile.write(f" {angle.bytype_line}")
outfile.write(" } # (end of angles by type)\n")

outfile.write(dihedral_header)
outfile.write('\n write_once("In Settings") {\n')
for dihedral in dihedrals:
if not dihedral.to_skip:
outfile.write(f" {dihedral.coeff_line}")
outfile.write(" } # (end of dihedral_coeffs)\n")
outfile.write('\n write_once("Data Dihedrals By Type") {\n')
for dihedral in dihedrals:
if not dihedral.to_skip:
outfile.write(f" {dihedral.bytype_line}")
outfile.write(" } # (end of dihedrals by type)\n")

outfile.write(improper_header)
outfile.write('\n write_once("In Settings") {\n')
for improper in impropers:
if not improper.to_skip:
outfile.write(f" {improper.coeff_line}")
outfile.write(" } # (end of improper_coeffs)\n")
outfile.write('\n write_once("Data Impropers By Type (opls_imp.py)") {\n')
for improper in impropers:
if not improper.to_skip:
outfile.write(f" {improper.bytype_line}")
outfile.write(" } # (end of impropers by type)\n")

outfile.write(closing_stuff)
outfile.write("}\n")

if outfile != sys.stdout:
outfile.close()
with open(args.outfile_name, "w") as outfile:
outfile.write("# This file was generated automatically using:\n")
outfile.write("# " + g_program_name + " " + " ".join(argv[1:]) + "\n")
outfile.write("")
outfile.write(file_header)
outfile.write(" # NOTE2: I tried to maintain the same two-letter 'general' types as from\n")
outfile.write(" # the original FF file. However, some changes had to be made to comply\n")
outfile.write(" # to the inner functioning of moltemplate. Such changes were:\n #\n")
for original, new in TYPE_CONVERSION_TUPLES:
outfile.write(f" # {original} --> {new}\n")

outfile.write("\n # NOTE3: The original FF file had types for different water models,\n")
outfile.write(" # but it was missing the relevant bonded interactions; therefore, I\n")
outfile.write(" # skipped the water types from the original FF, and hardcoded some simple\n")
outfile.write(" # water models, with the relevant bonded parameters\n")

outfile.write("\n # NOTE4: Water TIP*/SPC* models parameters are taken from LAMMPS doc,\n")
outfile.write(" # the user is invited to read the proper sections in the LAMMPS user manual\n")
outfile.write(" # to properly understand how to setup a simulation with the desided model.\n")
outfile.write(" # As for OPC, it seems it could be implemented in LAMMPS similarly to the\n")
outfile.write(" # TIP4P model (where OM distance should be 0.1594 angstrom).\n")

outfile.write('\n\n write_once("In Charges") {\n')
for line in lines_par[2:]:
if line.startswith("# Add more charge and L-J parameters"):
break
if line.startswith("#"):
outfile.write(f" {line}")
else:
atom = parse_atom_line(line)
if atom is not None:
atoms.append(atom)
outfile.write(f" {atom.charge_line}")
for atom in wat_atoms:
outfile.write(f" {atom.charge_line}")
outfile.write(" } # (end of atom partial charges)\n")
outfile.write('\n\n write_once("Data Masses") {\n')
atoms += wat_atoms
for atom in atoms:
outfile.write(f" {atom.mass_line}")
outfile.write(" } # (end of atom masses)\n")

outfile.write(file_equivalences_header)
for atom in atoms:
outfile.write(f" {atom.repl_line}")

outfile.write(nb_header)
outfile.write(' write_once("In Settings") {\n')
for atom in atoms:
outfile.write(f" {atom.nb_line}")
outfile.write(" } # (end of pair_coeffs)\n")

outfile.write("\n\n\n\n")
outfile.write(" # NOTE: all bonded interaction name can't have '*' or '?' characters, so in each\n")
outfile.write(" # bonded sections such characters will be replaced with another character\n")
outfile.write(" # that, at the time of writing, is not used for atom types (* -> £, ? -> €).\n\n")
outfile.write(bond_header)
outfile.write('\n write_once("In Settings") {\n')
for bond in bonds:
if not bond.to_skip:
outfile.write(f" {bond.coeff_line}")
outfile.write(" } # (end of bond_coeffs)\n")
outfile.write('\n write_once("Data Bonds By Type") {\n')
for bond in bonds:
if not bond.to_skip:
outfile.write(f" {bond.bytype_line}")
outfile.write(" } # (end of bonds by type)\n")

outfile.write(angle_header)
outfile.write('\n write_once("In Settings") {\n')
for angle in angles:
if not angle.to_skip:
outfile.write(f" {angle.coeff_line}")
outfile.write(" } # (end of angle_coeffs)\n")
outfile.write('\n write_once("Data Angles By Type") {\n')
for angle in angles:
if not angle.to_skip:
outfile.write(f" {angle.bytype_line}")
outfile.write(" } # (end of angles by type)\n")

outfile.write(dihedral_header)
outfile.write('\n write_once("In Settings") {\n')
for dihedral in dihedrals:
if not dihedral.to_skip:
outfile.write(f" {dihedral.coeff_line}")
outfile.write(" } # (end of dihedral_coeffs)\n")
outfile.write('\n write_once("Data Dihedrals By Type") {\n')
for dihedral in dihedrals:
if not dihedral.to_skip:
outfile.write(f" {dihedral.bytype_line}")
outfile.write(" } # (end of dihedrals by type)\n")

outfile.write(improper_header)
outfile.write('\n write_once("In Settings") {\n')
for improper in impropers:
if not improper.to_skip:
outfile.write(f" {improper.coeff_line}")
outfile.write(" } # (end of improper_coeffs)\n")
outfile.write('\n write_once("Data Impropers By Type (opls_imp.py)") {\n')
for improper in impropers:
if not improper.to_skip:
outfile.write(f" {improper.bytype_line}")
outfile.write(" } # (end of impropers by type)\n")

outfile.write(closing_stuff)
outfile.write("}\n")


if __name__ == '__main__':
Expand Down
5 changes: 4 additions & 1 deletion moltemplate/force_fields/oplsaa2023_original_format/README.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
The two files in this directory are BOSS files which were published in [this paper from 2023](https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602)
These files are in the public domain.

These files are in the public domain. They can be downloaded here:
- https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602/suppl_file/jp3c06602_si_002.txt
- https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.3c06602/suppl_file/jp3c06602_si_003.txt

See ../convert_OPLSAA_to_LT/README.md for instructions how to convert these files into moltemplate format.

Expand Down

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