Feature/main menu (Sourcery refactored) by sourcery-ai[bot] · Pull Request #2 · yipy0005/AutoPLGMX

sourcery-ai · 2022-12-07T06:12:44Z

Pull Request #1 refactored by Sourcery.

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NOTE: As code is pushed to the original Pull Request, Sourcery will
re-run and update (force-push) this Pull Request with new refactorings as
necessary. If Sourcery finds no refactorings at any point, this Pull Request
will be closed automatically.

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sourcery-ai · 2022-12-07T06:12:46Z

src/check_pdb.py

-        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(" ", "")


Function get_pdb_line_components refactored with the following changes:

Replace multiple comparisons of same variable with in operator (merge-comparisons)

Replace a[0:x] with a[:x] and a[x:len(a)] with a[x:] [×3] (remove-redundant-slice-index)

sourcery-ai · 2022-12-07T06:12:46Z

src/check_pdb.py

-        pdb_line_components["RECORD TYPE"] == "ATOM"
-        or pdb_line_components["RECORD TYPE"] == "HETATM"
-    ):
+    if pdb_line_components["RECORD TYPE"] in ["ATOM", "HETATM"]:


Function assemble_pdb_line_components refactored with the following changes:

Replace multiple comparisons of same variable with in operator (merge-comparisons)

sourcery-ai · 2022-12-07T06:12:46Z

src/check_pdb.py

-        for key in pdb_line_terms.keys()
+        for key in pdb_line_terms


Function get_missing_terms refactored with the following changes:

Remove unnecessary call to keys() (remove-dict-keys)

sourcery-ai · 2022-12-07T06:12:46Z

src/gmx_ops.py

-    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]))


Function combine_prot_lig_gro refactored with the following changes:

Move assignment closer to its usage within a block (move-assign-in-block)

Convert for loop into list comprehension (list-comprehension)

Replace a for append loop with list extend (for-append-to-extend)

Simplify generator expression (simplify-generator)

Replace identity comprehension with call to collection constructor (identity-comprehension)

sourcery-ai · 2022-12-07T06:12:47Z

src/gmx_ops.py

-        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


Function MDP.write_mdp_file refactored with the following changes:

Move assignments closer to their usage [×2] (move-assign)

Lift repeated conditional into its own if statement (lift-duplicated-conditional)

Simplify conditional into switch-like form [×3] (switch)

sourcery-ai · 2022-12-07T06:12:48Z

src/utils.py

-        key_missing_numbers.append(int("0"))
-        key_missing_numbers.append(int("9999"))
-
+        key_missing_numbers.extend((int("0"), int("9999")))


Function checkConsecutive refactored with the following changes:

Merge consecutive list appends into a single extend (merge-list-appends-into-extend)

sourcery-ai · 2022-12-07T06:12:48Z

src/utils.py

-        if first_line != "":
-            if first_line in lines_lst[line_idx]:
-                output_lst.append(lines_lst[line_idx])
-                try:
-                    while len(lines_lst[line_idx]) != 0:
-                        line_idx += 1
-                        if len(lines_lst[line_idx]) != 0:
-                            output_lst.append(lines_lst[line_idx])
-                        else:
-                            break
-                except IndexError:
-                    pass
+        if first_line != "" and first_line in lines_lst[line_idx]:
+            output_lst.append(lines_lst[line_idx])
+            try:
+                while len(lines_lst[line_idx]) != 0:
+                    line_idx += 1
+                    if len(lines_lst[line_idx]) != 0:
+                        output_lst.append(lines_lst[line_idx])
+                    else:
+                        break
+            except IndexError:
+                pass


Function get_lines refactored with the following changes:

Merge nested if conditions (merge-nested-ifs)

sourcery-ai · 2022-12-07T06:12:48Z

src/utils.py

-        if pdb_type == "COMPLEX" or pdb_type == "PROTEIN":
+        if pdb_type in {"COMPLEX", "PROTEIN"}:


Function read_topol refactored with the following changes:

Replace multiple comparisons of same variable with in operator [×2] (merge-comparisons)

Replace a for append loop with list extend (for-append-to-extend)

Simplify generator expression (simplify-generator)

Use set when checking membership of a collection of literals [×2] (collection-into-set)

sourcery-ai · 2022-12-07T06:12:48Z

src/utils.py

-        lig_itp_contents = lines[0:1] + lines[10:]
-
-        return lig_itp_contents
+        return lines[:1] + lines[10:]


Function write_prm_file refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

Replace a[0:x] with a[:x] and a[x:len(a)] with a[x:] (remove-redundant-slice-index)

sourcery-ai · 2022-12-07T06:12:48Z

src/utils.py

-    else:
-        count = 0
-        for item in resname_lst:
-            if item in amino_acids_3_letter_codes:
-                count += 1
-        if count == 0:
-            return "LIGAND"
-        else:
-            return "COMPLEX"
+    count = sum(item in amino_acids_3_letter_codes for item in resname_lst)
+    return "LIGAND" if count == 0 else "COMPLEX"


Function check_pdb_type refactored with the following changes:

Remove unnecessary else after guard condition (remove-unnecessary-else)

Convert for loop into call to sum() (sum-comprehension)

Replace if statement with if expression (assign-if-exp)

Remove unnecessary casts to int, str, float or bool (remove-unnecessary-cast)

Simplify constant sum() call (simplify-constant-sum)

sourcery-ai · 2022-12-07T06:12:53Z

Sourcery Code Quality Report

✅ Merging this PR will increase code quality in the affected files by 3.36%.

Quality metrics	Before	After	Change
Complexity	21.61 😞	17.21 🙂	-4.40 👍
Method Length	135.15 😞	131.51 😞	-3.64 👍
Working memory	11.55 😞	11.33 😞	-0.22 👍
Quality	44.68% 😞	48.04% 😞	3.36% 👍

Other metrics	Before	After	Change
Lines	1541	1481	-60

Changed files	Quality Before	Quality After	Quality Change
src/check_pdb.py	39.86% 😞	41.57% 😞	1.71% 👍
src/gmx_ops.py	66.25% 🙂	67.38% 🙂	1.13% 👍
src/main_BAK.py	22.69% ⛔	22.95% ⛔	0.26% 👍
src/protprep.py	45.33% 😞	55.16% 🙂	9.83% 👍
src/utils.py	58.35% 🙂	61.33% 🙂	2.98% 👍

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
src/main_BAK.py	main	46 ⛔	954 ⛔	19 ⛔	8.76% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
src/check_pdb.py	get_pdb_line_components	32 😞	558 ⛔	11 😞	23.30% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
src/main_BAK.py	mdp_type	20 😞	361 ⛔	13 😞	28.57% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
src/protprep.py	get_bound_ligand	23 😞	232 ⛔	14 😞	29.72% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
src/check_pdb.py	assemble_pdb_line_components	5 ⭐	167 😞	30 ⛔	40.73% 😞	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

⭐ excellent
🙂 good
😞 poor
⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

'Refactored by Sourcery'

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sourcery-ai bot requested a review from yipy0005 December 7, 2022 06:12

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Feature/main menu (Sourcery refactored)#2

Feature/main menu (Sourcery refactored)#2
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		if pdb_type == "COMPLEX" or pdb_type == "PROTEIN":
		if pdb_type in {"COMPLEX", "PROTEIN"}:

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