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Feature/main menu (Sourcery refactored) #2

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15 changes: 6 additions & 9 deletions src/check_pdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,8 @@ def get_pdb_line_components(pdb_line: str) -> Dict[str, Union[int, float, str]]:
pdb_line_terms: Dict[str, Union[int, float, str]] = {}

if pdb_line:
if (pdb_line.split())[0] == "ATOM" or (pdb_line.split())[0] == "HETATM":
pdb_line_terms["RECORD TYPE"] = pdb_line[0:6].replace(" ", "")
if (pdb_line.split())[0] in ["ATOM", "HETATM"]:
pdb_line_terms["RECORD TYPE"] = pdb_line[:6].replace(" ", "")
Comment on lines -36 to +37
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@sourcery-ai sourcery-ai bot Dec 7, 2022

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Function get_pdb_line_components refactored with the following changes:

pdb_line_terms["ATOM SERIAL NUMBER"] = (
int(pdb_line[6:11].replace(" ", ""))
if pdb_line[6:11].replace(" ", "") != ""
Expand Down Expand Up @@ -82,7 +82,7 @@ def get_pdb_line_components(pdb_line: str) -> Dict[str, Union[int, float, str]]:
pdb_line_terms["SEGMENT ID"] = pdb_line[72:76].replace(" ", "")
pdb_line_terms["ELEMENT SYMBOL"] = pdb_line[76:78].replace(" ", "")
elif (pdb_line.split())[0] == "TER":
pdb_line_terms["RECORD TYPE"] = pdb_line[0:6].replace(" ", "")
pdb_line_terms["RECORD TYPE"] = pdb_line[:6].replace(" ", "")
try:
pdb_line_terms["ATOM SERIAL NUMBER"] = int(
pdb_line[6:11].replace(" ", "")
Expand All @@ -100,7 +100,7 @@ def get_pdb_line_components(pdb_line: str) -> Dict[str, Union[int, float, str]]:
except ValueError:
pass
elif (pdb_line.split())[0] == "CONECT":
pdb_line_terms["RECORD TYPE"] = pdb_line[0:6].replace(" ", "")
pdb_line_terms["RECORD TYPE"] = pdb_line[:6].replace(" ", "")
pdb_line_terms["ATOM SERIAL NUMBER"] = pdb_line[6:11].replace(" ", "")
pdb_line_terms["BONDED ATOM SERIAL NUMBER"] = pdb_line[12:].strip("\n")

Expand All @@ -111,10 +111,7 @@ def assemble_pdb_line_components(
pdb_line_components: Dict[str, Union[int, float, str]]
) -> Optional[str]:
# Length of an ATOM line should have 78 characters
if (
pdb_line_components["RECORD TYPE"] == "ATOM"
or pdb_line_components["RECORD TYPE"] == "HETATM"
):
if pdb_line_components["RECORD TYPE"] in ["ATOM", "HETATM"]:
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Function assemble_pdb_line_components refactored with the following changes:

for key in [
"X COORDINATE",
"Y COORDINATE",
Expand Down Expand Up @@ -170,7 +167,7 @@ def get_missing_terms(pdb_line_terms: Dict[str, Union[int, float, str]]) -> List

return [
key
for key in pdb_line_terms.keys()
for key in pdb_line_terms
Comment on lines -173 to +170
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Function get_missing_terms refactored with the following changes:

if pdb_line_terms[key] == "" and key in important_columns
]

Expand Down
185 changes: 91 additions & 94 deletions src/gmx_ops.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,17 +71,14 @@ def combine_prot_lig_gro(
root_dir: str, ligand_id: str, protein_pdb: str = "PROTEIN"
) -> List[str]:

complex_lines: list[str] = []
with open(f"{root_dir}/{protein_pdb}_processed.gro", "r") as protein_f:
protein_lines = protein_f.readlines()
with open(
f"{root_dir}/{ligand_id}_fix.acpype/{ligand_id}_fix_GMX.gro", "r"
) as ligand_f:
ligand_lines = ligand_f.readlines()
for line in protein_lines[2:-1]:
complex_lines.append(line)
for line in ligand_lines[2:-1]:
complex_lines.append(line)
complex_lines: list[str] = list(protein_lines[2:-1])
complex_lines.extend(iter(ligand_lines[2:-1]))
Comment on lines -74 to +81
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@sourcery-ai sourcery-ai bot Dec 7, 2022

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Function combine_prot_lig_gro refactored with the following changes:

complex_lines.insert(0, protein_lines[0])
complex_lines.insert(1, f"{len(complex_lines) - 1}\n")
complex_lines.append(protein_lines[-1])
Expand Down Expand Up @@ -190,100 +187,100 @@ def write_mdp_file(self) -> Dict[str, Any]:

sim_types = ["ions", "em", "nvt", "npt", "md"]

default_params_for_ions_and_em: Dict[str, Any] = {
"integrator": self.integrator,
"nsteps": self.nsteps,
"emtol": self.emtol,
"emstep": self.emstep,
"cutoff_scheme": self.cutoff_scheme,
"nstlist": self.nstlist,
"pbc": self.pbc,
"ns_type": self.ns_type,
"rlist": self.rlist,
"coulombtype": self.coulombtype,
"rcoulomb": self.rcoulomb,
"rvdw": self.rvdw,
}

default_params_for_nvt_npt_md: Dict[str, Any] = {
"integrator": self.integrator,
"dt": self.dt,
"nsteps": self.nsteps,
"nstlog": self.nstlog,
"nstenergy": self.nstenergy,
"nstxout_compressed": self.nstxout_compressed,
"cutoff_scheme": self.cutoff_scheme,
"nstlist": self.nstlist,
"pbc": self.pbc,
"ns_type": self.ns_type,
"rlist": self.rlist,
"coulombtype": self.coulombtype,
"rcoulomb": self.rcoulomb,
"vdwtype": self.vdwtype,
"vdw_modifier": self.vdw_modifier,
"rvdw_switch": self.rvdw_switch,
"rvdw": self.rvdw,
"DispCorr": self.DispCorr,
"fourierspacing": self.fourierspacing,
"pme_order": self.pme_order,
"tcoupl": self.tcoupl,
"tc_grps": self.tc_grps,
"tau_t": self.tau_t,
"ref_t": self.ref_t,
"pcoupl": self.pcoupl,
"gen_vel": self.gen_vel,
"constraints": self.constraints,
"constraint_algorithm": self.constraint_algorithm,
"continuation": self.continuation,
"lincs_order": self.lincs_order,
"lincs_iter": self.lincs_iter,
}

if self.sim_type in sim_types and self.sim_type == "ions":
return default_params_for_ions_and_em

elif self.sim_type in sim_types and self.sim_type == "em":

additional_params: Dict[str, Any] = {
if self.sim_type in sim_types:
default_params_for_ions_and_em: Dict[str, Any] = {
"integrator": self.integrator,
"nsteps": self.nsteps,
"emtol": self.emtol,
"emstep": self.emstep,
"cutoff_scheme": self.cutoff_scheme,
"nstlist": self.nstlist,
"pbc": self.pbc,
"ns_type": self.ns_type,
"rlist": self.rlist,
"coulombtype": self.coulombtype,
"rcoulomb": self.rcoulomb,
"rvdw": self.rvdw,
}

default_params_for_nvt_npt_md: Dict[str, Any] = {
"integrator": self.integrator,
"dt": self.dt,
"nsteps": self.nsteps,
"nstlog": self.nstlog,
"nstenergy": self.nstenergy,
"nstxout_compressed": self.nstxout_compressed,
"cutoff_scheme": self.cutoff_scheme,
"nstlist": self.nstlist,
"pbc": self.pbc,
"ns_type": self.ns_type,
"rlist": self.rlist,
"coulombtype": self.coulombtype,
"rcoulomb": self.rcoulomb,
"vdwtype": self.vdwtype,
"vdw_modifier": self.vdw_modifier,
"rvdw_switch": self.rvdw_switch,
"rvdw": self.rvdw,
"DispCorr": self.DispCorr,
"fourierspacing": self.fourierspacing,
"pme_order": self.pme_order,
"tcoupl": self.tcoupl,
"tc_grps": self.tc_grps,
"tau_t": self.tau_t,
"ref_t": self.ref_t,
"pcoupl": self.pcoupl,
"gen_vel": self.gen_vel,
"constraints": self.constraints,
"constraint_algorithm": self.constraint_algorithm,
"continuation": self.continuation,
"lincs_order": self.lincs_order,
"lincs_iter": self.lincs_iter,
}

return default_params_for_ions_and_em | additional_params # type: ignore

elif self.sim_type in sim_types and self.sim_type == "nvt":
additional_params: Dict[str, Any] = {
"define": self.define,
"gen_temp": self.gen_temp,
"gen_seed": self.gen_seed,
}

return default_params_for_nvt_npt_md | additional_params # type: ignore

elif self.sim_type in sim_types and self.sim_type == "npt":
additional_params: Dict[str, Any] = {
"define": self.define,
"pcoupltype": self.pcoupltype,
"tau_p": self.tau_p,
"compressibility": self.compressibility,
"ref_p": self.ref_p,
"refcoord_scaling": self.refcoord_scaling,
}

return default_params_for_nvt_npt_md | additional_params # type: ignore

elif self.sim_type in sim_types and self.sim_type == "md":
additional_params: Dict[str, Any] = {
"pcoupltype": self.pcoupltype,
"tau_p": self.tau_p,
"compressibility": self.compressibility,
"ref_p": self.ref_p,
# "freezegrps": self.freezegrps,
# "freezedim": self.freezedim,
}

return default_params_for_nvt_npt_md | additional_params # type: ignore
if self.sim_type == "em":
additional_params: Dict[str, Any] = {
"vdwtype": self.vdwtype,
"vdw_modifier": self.vdw_modifier,
"rvdw_switch": self.rvdw_switch,
"DispCorr": self.DispCorr,
}

return default_params_for_ions_and_em | additional_params # type: ignore

elif self.sim_type == "ions":
return default_params_for_ions_and_em

elif self.sim_type == "md":
additional_params: Dict[str, Any] = {
"pcoupltype": self.pcoupltype,
"tau_p": self.tau_p,
"compressibility": self.compressibility,
"ref_p": self.ref_p,
# "freezegrps": self.freezegrps,
# "freezedim": self.freezedim,
}

return default_params_for_nvt_npt_md | additional_params # type: ignore

elif self.sim_type == "npt":
additional_params: Dict[str, Any] = {
"define": self.define,
"pcoupltype": self.pcoupltype,
"tau_p": self.tau_p,
"compressibility": self.compressibility,
"ref_p": self.ref_p,
"refcoord_scaling": self.refcoord_scaling,
}

return default_params_for_nvt_npt_md | additional_params # type: ignore

elif self.sim_type == "nvt":
additional_params: Dict[str, Any] = {
"define": self.define,
"gen_temp": self.gen_temp,
"gen_seed": self.gen_seed,
}

return default_params_for_nvt_npt_md | additional_params # type: ignore
Comment on lines -193 to +284
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@sourcery-ai sourcery-ai bot Dec 7, 2022

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Function MDP.write_mdp_file refactored with the following changes:


return {}
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