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@carlocamilloni
carlocamilloni committed Dec 7, 2024
1 parent c12de65 commit 3c89a5b
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Showing 10 changed files with 51,330 additions and 51,377 deletions.
23 changes: 22 additions & 1 deletion src/multiego/ensemble.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1278,6 +1278,28 @@ def generate_LJ(meGO_ensemble, train_dataset, parameters):
consistency_checks(meGO_LJ)
consistency_checks(meGO_LJ_14)

final_fields = [
"ai",
"aj",
"type",
"c6",
"c12",
"sigma",
"epsilon",
"probability",
"rc_probability",
"md_threshold",
"rc_threshold",
"rep",
"cutoff",
"same_chain",
"source",
"number_ai",
"number_aj",
]

meGO_LJ = meGO_LJ[final_fields]

et = time.time()
elapsed_time = et - st
print("\t- Done in:", elapsed_time, "seconds")
Expand Down Expand Up @@ -1355,7 +1377,6 @@ def make_pairs_exclusion_topology(meGO_ensemble, meGO_LJ_14):
pairs.loc[(pairs["check"].isin(p14) & (pairs["same_chain"])), "remove"] = "No"
mask = pairs.remove == "Yes"
pairs = pairs[~mask]

pairs["func"] = 1
# Intermolecular interactions are excluded
pairs.loc[(~pairs["same_chain"]), "c6"] = 0.0
Expand Down
107 changes: 47 additions & 60 deletions src/multiego/io.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,28 +6,6 @@
import git
import time

final_fields = [
"ai",
"aj",
"type",
"c6",
"c12",
"sigma",
"epsilon",
"probability",
"rc_probability",
"md_threshold",
"rc_threshold",
"rep",
"cutoff",
"molecule_name_ai",
"molecule_name_aj",
"same_chain",
"source",
"number_ai",
"number_aj",
]


def read_config(file, args_dict):
"""
Expand Down Expand Up @@ -86,7 +64,6 @@ def combine_configurations(yml, args, args_dict):
setattr(args, key, value)
else:
if hasattr(args, element):
print(element, yml)
setattr(args, element, True)

return args
Expand Down Expand Up @@ -382,7 +359,12 @@ def write_nonbonded(topology_dataframe, meGO_LJ, parameters, output_folder):
file.write(" 1 1 no 1.0 1.0\n\n")

file.write("[ atomtypes ]\n")
atomtypes = topology_dataframe[["sb_type", "atomic_number", "mass", "charge", "ptype", "c6", "c12"]].copy()
if parameters.egos == "rc":
atomtypes = topology_dataframe[["sb_type", "atomic_number", "mass", "charge", "ptype", "c6", "c12"]].copy()
atomtypes.rename(columns={"rc_c6": "c6", "rc_c12": "c12"}, inplace=True)
else:
atomtypes = topology_dataframe[["sb_type", "atomic_number", "mass", "charge", "ptype", "c6", "c12"]].copy()

atomtypes["c6"] = atomtypes["c6"].map(lambda x: "{:.6e}".format(x))
atomtypes["c12"] = atomtypes["c12"].map(lambda x: "{:.6e}".format(x))
file.write(dataframe_to_write(atomtypes))
Expand All @@ -392,7 +374,6 @@ def write_nonbonded(topology_dataframe, meGO_LJ, parameters, output_folder):
meGO_LJ["c6"] = meGO_LJ["c6"].map(lambda x: "{:.6e}".format(x))
meGO_LJ["c12"] = meGO_LJ["c12"].map(lambda x: "{:.6e}".format(x))
meGO_LJ.insert(5, ";", ";")
meGO_LJ.drop(columns=["molecule_name_ai", "molecule_name_aj"], inplace=True)
file.write(dataframe_to_write(meGO_LJ))


Expand All @@ -415,7 +396,6 @@ def write_model(meGO_ensemble, meGO_LJ, meGO_LJ_14, parameters):
f"{parameters.root_dir}/outputs/{parameters.system}", parameters.explicit_name, parameters.egos
)
create_output_directories(parameters, output_dir)
meGO_LJ_out = meGO_LJ[final_fields].copy()
write_topology(
meGO_ensemble["topology_dataframe"],
meGO_ensemble["molecule_type_dict"],
Expand All @@ -424,7 +404,7 @@ def write_model(meGO_ensemble, meGO_LJ, meGO_LJ_14, parameters):
parameters,
output_dir,
)
write_nonbonded(meGO_ensemble["topology_dataframe"], meGO_LJ_out, parameters, output_dir)
write_nonbonded(meGO_ensemble["topology_dataframe"], meGO_LJ, parameters, output_dir)
write_output_readme(meGO_LJ, parameters, output_dir)
print("\t- " f"Output files written to {output_dir}")

Expand All @@ -448,38 +428,45 @@ def write_output_readme(meGO_LJ, parameters, output_dir):
for key, value in vars(parameters).items():
f.write(f" - {key}: {value}\n")

# write contents of the symmetry file
if parameters.symmetry:
f.write("\nSymmetry file contents:\n")
# symmetry = read_symmetry_file(parameters.symmetry)
for line in parameters.symmetry:
f.write(f" - {' '.join(line)}\n")

f.write("\nContact parameters:\n")
# write average data intra
f.write("- Intramolecular contacts:\n")
f.write(
f"- epsilon: {meGO_LJ.loc[(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)]['epsilon'].mean():.3f} kJ/mol\n"
)
f.write(f"- sigma: {meGO_LJ.loc[(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)]['sigma'].mean():.3f} nm\n")
f.write(f"- number of attractive contacts: {len(meGO_LJ.loc[(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)])}\n")
f.write(f"- number of repulsive contacts: {len(meGO_LJ.loc[(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] < 0.0)])}\n")

# write average data inter
f.write("- Intermolecular contacts:\n")
f.write(
f"- epsilon: {meGO_LJ.loc[~(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)]['epsilon'].mean():.3f} kJ/mol\n"
)
f.write(f"- sigma: {meGO_LJ.loc[~(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)]['sigma'].mean():.3f} nm\n")
f.write(
f"- number of attractive contacts: {len(meGO_LJ.loc[~(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)])}\n"
)
f.write(f"- number of repulsive contacts: {len(meGO_LJ.loc[~(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] < 0.0)])}\n")

# mdp parameters
f.write("Cutoff MDP parameters:\n")
f.write(f"- Suggested rlist value: {1.1*2.5*meGO_LJ['sigma'].max():4.2f} nm\n")
f.write(f"- Suggested cut-off value: {2.5*meGO_LJ['sigma'].max():4.2f} nm\n")
if parameters.egos == "production":
# write contents of the symmetry file
if parameters.symmetry:
f.write("\nSymmetry file contents:\n")
# symmetry = read_symmetry_file(parameters.symmetry)
for line in parameters.symmetry:
f.write(f" - {' '.join(line)}\n")

f.write("\nContact parameters:\n")
# write average data intra
f.write("- Intramolecular contacts:\n")
f.write(
f"- epsilon: {meGO_LJ.loc[(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)]['epsilon'].mean():.3f} kJ/mol\n"
)
f.write(f"- sigma: {meGO_LJ.loc[(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)]['sigma'].mean():.3f} nm\n")
f.write(
f"- number of attractive contacts: {len(meGO_LJ.loc[(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)])}\n"
)
f.write(
f"- number of repulsive contacts: {len(meGO_LJ.loc[(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] < 0.0)])}\n"
)

# write average data inter
f.write("- Intermolecular contacts:\n")
f.write(
f"- epsilon: {meGO_LJ.loc[~(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)]['epsilon'].mean():.3f} kJ/mol\n"
)
f.write(f"- sigma: {meGO_LJ.loc[~(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)]['sigma'].mean():.3f} nm\n")
f.write(
f"- number of attractive contacts: {len(meGO_LJ.loc[~(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] > 0.0)])}\n"
)
f.write(
f"- number of repulsive contacts: {len(meGO_LJ.loc[~(meGO_LJ['same_chain']) & (meGO_LJ['epsilon'] < 0.0)])}\n"
)

# mdp parameters
f.write("Cutoff MDP parameters:\n")
f.write(f"- Suggested rlist value: {1.1*2.5*meGO_LJ['sigma'].max():4.2f} nm\n")
f.write(f"- Suggested cut-off value: {2.5*meGO_LJ['sigma'].max():4.2f} nm\n")


def print_stats(meGO_LJ):
Expand Down Expand Up @@ -787,7 +774,7 @@ def check_files_existence(args):
FileNotFoundError
If any of the files or directories does not exist
"""
md_ensembles = args.reference + args.train
md_ensembles = args.reference + args.train if args.egos == "production" else []

for ensemble in md_ensembles:
ensemble = f"{args.root_dir}/inputs/{args.system}/{ensemble}"
Expand Down
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