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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,115 @@ | ||
| # This module is here to process the json input of multicomponent.py | ||
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| import os | ||
| import re | ||
| import copy | ||
| import json | ||
| import shutil | ||
|
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| from typing import Iterable, List, Dict, Any, Tuple | ||
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| def convert_cmd_to_dict(argument_dict:Dict[str, Any]) -> Dict[str, Any]: | ||
| special_arguments = ["solute", "solvent"] | ||
| newdata = {} | ||
| for key, value in argument_dict.items(): | ||
| if key not in special_arguments: | ||
| newdata[key] = value | ||
| data = argument_dict | ||
| if "main" in data and data["main"]: | ||
| newdata["solute"] = dict() | ||
| newdata['solute']['xyzfile'] = data["main"] | ||
| if "charge" in data: | ||
| newdata["solute"]["charge"] = data["charge"] | ||
| if "spinmult" in data: | ||
| newdata["solute"]["spinmult"] = data["spinmult"] | ||
| if "solvent" in data and data["solvent"]: | ||
| newdata["solvent"] = dict() | ||
| if "solventoff" in data: | ||
| newdata["solvent"]["off"] = data["solventoff"] | ||
| if "solventfrcmod" in data: | ||
| newdata["solvent"]["frcmod"] = data["solventfrcmod"] | ||
| if "solvent" in data: | ||
| newdata["solvent"]["name"] = data["solvent"] | ||
| return newdata | ||
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| def correct_keyword(data:dict) -> dict: | ||
| """ | ||
| Correct the key in the dictionary to the acceptable keys | ||
| """ | ||
| keyword_dict = { | ||
| "chargemethod": "charge_method", | ||
| "cubesize": "cube_size", | ||
| "fragmentcharge": "fragment_charge", | ||
| "fragmentspinmultiplicity": "fragment_spinmult", | ||
| "fragmentmultiplicity": "fragment_spinmult", | ||
| "spinmultiplicity": "spinmult", | ||
| "multiplicity": "spinmult", | ||
| "output": "prefix", | ||
| } | ||
| newdata = {} | ||
| for key, value in data.items(): | ||
| if key in keyword_dict: | ||
| newdata[keyword_dict[key]] = value | ||
| else: | ||
| newdata[key] = value | ||
| return newdata | ||
|
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| def add_missing_xyzfile_keyword(data:dict, support_input_format:Iterable[str] = ("xyz", "pdb", "mol2", "prep", "off", "lib")) -> dict: | ||
| if "xyzfile" in data: | ||
| return data | ||
| for key, value in data.items(): | ||
| if key in support_input_format and not "xyzfile" in data and isinstance(value, str) and os.path.isfile(value): | ||
| data["xyzfile"] = value | ||
| break | ||
| return data | ||
|
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| def overwrite_keyword(data:dict, arguments:List[Tuple[str, Any]]) -> dict: | ||
| """ | ||
| Overwrite the keyword in the dictionary with the arguments | ||
| """ | ||
| newdata = copy.deepcopy(data) | ||
| ignoredargs = [] | ||
| arguments | ||
| for key, value in arguments: | ||
| if isinstance(value, str) and value == "": | ||
| ignoredargs.append(key) | ||
| for key in ignoredargs: | ||
| arguments.remove((key, "")) | ||
| for key, value in arguments: | ||
| newdata[key] = value | ||
| if "main" in data and data["main"]: | ||
| newdata["solute"] = dict() | ||
| newdata['solute']['xyzfile'] = data["main"] | ||
| if "charge" in data: | ||
| newdata["solute"]["charge"] = data["charge"] | ||
| if "spinmult" in data: | ||
| newdata["solute"]["spinmult"] = data["spinmult"] | ||
| if "solvent" in data and data["solvent"]: | ||
| newdata["solvent"] = dict() | ||
| if "solventoff" in data: | ||
| newdata["solvent"]["off"] = data["solventoff"] | ||
| if "solventfrcmod" in data: | ||
| newdata["solvent"]["frcmod"] = data["solventfrcmod"] | ||
| if "solvent" in data: | ||
| newdata["solvent"]["name"] = data["solvent"] | ||
|
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| return newdata | ||
|
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| def parse_json_input(jsonpath:str): | ||
| with open(jsonpath, "r") as f: | ||
| data = json.load(f) | ||
|
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| def check_inputs(data:dict) -> dict: | ||
| """ | ||
| Check if the input is valid | ||
| """ | ||
| if "solute" not in data and "solutes" not in data: | ||
| raise ValueError("No solute is provided") | ||
| if "solvent" not in data and "solvents" not in data: | ||
| raise ValueError("No solvent is provided") | ||
| if "solute" in data and "solutes" in data: | ||
| raise ValueError("You cannot provide both solute and solutes, only provide the solute argument if you want to use single solute") | ||
| if "solvent" in data and "solvents" in data: | ||
| raise ValueError("You cannot provide both solvent and solvents, only provide the solvent argument if you want to use single solvent") | ||
| if "solutes" in data and (not isinstance(data["solutes"], list) or len(data["solutes"]) == 0): | ||
| raise ValueError("solutes must be a list") | ||
| if "solvents" in data and (not isinstance(data["solvents"], list) or len(data["solvents"]) == 0): | ||
| raise ValueError("solvents must be a list") |
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