mutadock 2.1.0__tar.gz → 2.2.2__tar.gz

{mutadock-2.1.0 → mutadock-2.2.2}/.gitignore

@@ -87,14 +87,14 @@ demo/
 # AutoDock result files
 *.dlg
 
-# Docking output PDB files
-*_out.pdb
+# Raw multi-pose Vina output (also covered by *.pdbqt above)
+*_out.pdbqt
 
 # Per-run log files
 *_log.txt
 
-# Vina split SDF output
-*_ligand_*.sdf
+# Extracted best-pose SDF output
+*_out.sdf
 
 # Docking results aggregate
 docking_results.csv
@@ -130,3 +130,11 @@ mutation_*/
 
 # Timestamped backups created by backup()
 backups/
+
+# =============================================================================
+# Project-specific: benchmark cross-validation reference dirs
+# (already covered by the wholesale benchmark/ ignore above; listed explicitly
+# so they stay ignored even if benchmark/ scripts are ever un-ignored)
+# =============================================================================
+benchmark/foldx_ref/
+benchmark/mcsm_lig_ref/

{mutadock-2.1.0 → mutadock-2.2.2}/CHANGELOG.md

@@ -7,12 +7,42 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [2.2.2] - 2026-09-19
+
+### Added
+- Local SDF and MOL2 ligand inputs are now validated for a parseable molecule and usable 3-D coordinates before Meeko preparation.
+
+### Changed
+- RDKit is now an explicit Python dependency rather than an implicit requirement of ligand preparation.
+- Installation, AutoSite, matrix-loading, and generated-output guidance is consistent across the README, Sphinx documentation, environment file, installer scripts, and ignore rules.
+
+## [2.2.1] - 2026-09-18
+
+### Changed
+- Updated the PyPI and GitHub README for the 2.2 release series, including current docking outputs, reproducibility controls, resume behavior, input warnings, matrix caching, and subprocess timeout settings.
+- Removed the stale fixed-score example and hard-coded coverage badge from the README.
+
+## [2.2.0] - 2026-09-18
+
 ### Added
 - **Per-item checkpoint/resume for ΔΔG.** `calc_ddg` / `calc_double_ddg` / `calc_triple_ddg` (and `md_ddg_single` / `md_ddg_double` / `md_ddg_triple` via a new `--resume` flag) can now continue an interrupted run: the output CSV is its own checkpoint, so an interruption partway through keeps the rows already computed and only the missing mutations/combinations are recomputed — instead of discarding everything and starting over. Each completed row is flushed immediately, a torn trailing line from a mid-write kill is dropped and recomputed cleanly, and resume refuses to mix rows written under a different `ddG_protocol` or `n_replicates` (it starts fresh in that case). `md_mutate` uses this automatically (driven by the existing append default), upgrading its previous coarse "skip only if the whole file is complete" check to true per-item resume — the same granularity the docking side already had via `*_completed.txt`.
 - **Subprocess timeouts for external tools.** `mk_prepare_receptor`, AutoSite, and Vina are now each run with a wall-clock timeout so a single hung job can no longer stall an entire batch — a timeout raises the tool's domain error and the batch loop skips that receptor-ligand combination. Defaults are 15 min (receptor prep), 30 min (AutoSite), and 60 min (Vina), each overridable via `MUTADOCK_RECEPTOR_PREP_TIMEOUT` / `MUTADOCK_AUTOSITE_TIMEOUT` / `MUTADOCK_VINA_TIMEOUT` (seconds; set to `0` to disable that timeout).
 - `read_partial_ddg()` helper in `mutation/helpers.py` — reads the complete rows of a partial ΔΔG CSV for resume, dropping any torn trailing line and enforcing a settings match.
 - Regression tests: ΔΔG resume identity for single/double/triple (resumed run reproduces the exact row set, `sr` numbering, and `combination` names of a from-scratch run), `read_partial_ddg` guards, and TimeoutExpired→domain-error routing for all three subprocesses (including a real sleeping-subprocess timeout).
 
+### Changed
+- Docking result rows now record the Vina seed, box centre, box size, and exhaustiveness so every reported affinity retains its run provenance.
+- Vina seed handling is explicit across the CLI and batch workflow; a command-line seed takes precedence over configuration only with a visible warning.
+- Ambiguous simultaneous AutoSite and explicit-config requests are rejected instead of silently selecting one search box.
+- Structure checks now warn about duplicated or highly similar chains that can unintentionally multiply mutation enumeration and docking work.
+
+### Fixed
+- Ligand preparation now adds hydrogens with 3-D coordinates before Meeko conversion, preventing polar hydrogens from being written at the origin and preserving hydrogen-bond donor typing.
+- Per-receptor AutoSite boxes are carried through to the corresponding result row instead of being reported as if one global box had been used.
+- Docking CSV append logic remains compatible with older result files while avoiding ragged rows when new provenance columns are present.
+- AutoSite and Vina subprocess failures now preserve clearer context, and configuration/seed validation rejects invalid or contradictory inputs earlier.
+- Substitution matrices now ship inside the installed package, and additional NCBI matrices are cached in a user-writable directory (`~/.cache/mutadock/matrices`, overridable with `MUTADOCK_DATA_DIR`) instead of attempting to write into `site-packages`.
+
 ## [2.1.0] - 2026-07-03
 
 ### Added

{mutadock-2.1.0 → mutadock-2.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mutadock
-Version: 2.1.0
+Version: 2.2.2
 Summary: MUTADOCK is a comprehensive library designed for mutation studies and multiple receptor-ligand docking. Refer to README for more information.
 Project-URL: Repository, https://github.com/naisarg14/mutadock
 Project-URL: Issues, https://github.com/naisarg14/mutadock/issues
@@ -15,6 +15,7 @@ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
 Requires-Dist: biopython
 Requires-Dist: jinja2
 Requires-Dist: matplotlib
@@ -26,6 +27,7 @@ Requires-Dist: pdbfixer
 Requires-Dist: pyarrow
 Requires-Dist: pyrosetta-installer
 Requires-Dist: python-pptx
+Requires-Dist: rdkit
 Requires-Dist: tqdm
 Provides-Extra: dev
 Requires-Dist: black>=24.0; extra == 'dev'
@@ -48,7 +50,6 @@ Description-Content-Type: text/markdown
 [![PyPI version](https://img.shields.io/pypi/v/mutadock.svg)](https://pypi.org/project/mutadock/)
 [![Python](https://img.shields.io/pypi/pyversions/mutadock.svg)](https://pypi.org/project/mutadock/)
 [![Docs](https://readthedocs.org/projects/mutadock/badge/?version=latest)](https://mutadock.readthedocs.io/en/latest/)
-[![Coverage](https://img.shields.io/badge/coverage-45.45%25-yellow.svg)]()
 
 ## Introduction
 
@@ -71,6 +72,13 @@ MUTADOCK is a comprehensive library for protein mutation studies and multi-recep
 - Simple CLI for each workflow step
 - Python API for scripting and integration into existing pipelines
 
+### What's new in the 2.2 series
+
+- Reproducible docking with a configurable random seed (default `19`) and complete run provenance in `docking_results.csv`
+- Safer input validation, including ligand 3D/hydrogen checks and warnings for multi-model, multi-chain, similar-chain, altloc, and insertion-code structures
+- Resumable mutation and docking workflows plus configurable subprocess timeouts
+- PAM250 and BLOSUM62 bundled in the installed package; additional matrices are cached outside the installation directory
+
 
 ## System Requirements
 
@@ -147,15 +155,12 @@ One command takes a **PDB ID**, a **mutation**, and a **ligand code**, and gives
 md_quick --pdb-id 4QJR --mutation A:386:ASN:HIS --ligand-code imatinib
 ```
 
-```
-  Mutation : ASN-A386-HIS
-  ΔΔG      : -27.30 REU (negative = stabilizing)
-  Affinity : -5.66 kcal/mol
-  Report   : mdquick_4QJR/reports/report.html
-```
-
 It fetches + cleans the structure, computes the ΔΔG for that single mutation, builds the mutant, fetches the ligand, finds the pocket with AutoSite (or pass `-c config.txt`), docks, and writes the standard `reports/` bundle. Use `-i protein.pdb` for a local structure, `--ligand-file lig.sdf` for a local ligand, or `--ligand-code 2244` / `cid:5291` / `name:aspirin` for PubChem. Requires the `autosite` binary (ADFRsuite) on PATH when no config is given.
 
+Scores depend on the input structure and protocol, so treat the values printed by
+the demo as results rather than fixed expected output. Pass `--seed` to reproduce
+a docking run exactly.
+
 The staged tools below give you full control over each step.
 
 ### 1. Generate mutation candidates
@@ -214,14 +219,21 @@ md_mutate -h                         # all options
 
 Provide exactly one of `-i/--input` (a local `.pdb`/`.cif` file) or `--pdb-id` (a
 4-character RCSB accession, downloaded automatically). `md_mutate` also warns when
-the input contains multiple models, alternate conformations (altlocs), or
-insertion codes, since these affect residue numbering.
+the input contains multiple models or chains, similar chain sequences, alternate
+conformations (altlocs), or insertion codes, since these can make chain selection
+and residue numbering ambiguous. Inspect these warnings and isolate the intended
+chain(s) before interpreting results.
 
 By default every output file is written next to the input structure. Pass
 `-o/--output-dir DIR` to collect them in `DIR` instead (created if absent); the
 paths recorded in `*_mutants.txt` point into `DIR`, so they remain valid input
 for `md_dock`.
 
+`md_mutate` appends to its checkpoint CSVs by default and skips completed items,
+so rerunning an interrupted job resumes it. The direct `md_ddg_single`,
+`md_ddg_double`, and `md_ddg_triple` commands also support `--resume`. Use
+`--no-append` when you intentionally want a fresh run.
+
 #### Mutation Output
 
 | # | File | Description |
@@ -241,7 +253,7 @@ for `md_dock`.
 ΔΔG is computed as `score(mutant) − score(wild-type self-mutation reference)`, where **both** sides run the identical repack(+minimization) protocol — so a null WT→WT mutation scores ≈ 0 and the values are not biased toward "stabilizing."
 
 - **Units:** `ddG_value` is in **Rosetta Energy Units (REU), not kcal/mol.** A `ddG_kcal` column is also written, and reports show both. REU ≈ but ≠ kcal/mol.
-- **Scaling factor:** the REU→kcal/mol factor is **`REU_TO_KCAL_SCALE` in `src/mutadock/mutation/predict_ddG.py`** (default `0.34`, ≈ 1/2.94; the ref2015 `cartesian_ddg` convention, Park et al. 2016). **To change it, edit that constant** or pass `--reu-to-kcal FACTOR` per run.
+- **Scaling factor:** the default REU→kcal/mol factor is `0.34` (≈ 1/2.94; the ref2015 `cartesian_ddg` convention, Park et al. 2016). Override it per run with `--reu-to-kcal FACTOR`; modifying installed package code is not required.
 - **Protocol (`--protocol`, default `min`):** the recorded protocol is written to a `ddG_protocol` column, and reports flag screening-only runs.
 
   ```bash
@@ -303,6 +315,7 @@ Output files are named `{stem}_{WTAA}-{CHAIN}{POS}-{NEWAA}.pdb` (e.g. `protein_A
 ```bash
 md_dock -r receptors.txt -l ligands.txt -c config.txt
 md_dock -r receptors.txt -l ligands.txt -c config.txt -o results/  # collect outputs in results/
+md_dock -r receptors.txt -l ligands.txt -c config.txt --seed 19    # reproducible run
 md_dock -h   # all options
 ```
 
@@ -312,17 +325,22 @@ By default docking outputs go to an `out/` folder next to each receptor. Pass
 `-o/--output-dir DIR` to collect poses, logs, `docking_results.csv`, and the
 `*_completed.txt` resume file in a single `DIR` instead. Prepared PDBQT files and
 AutoSite caches still live next to their inputs so they can be reused across runs.
+Completed receptor–ligand pairs are skipped automatically; use
+`--ignore-existing` to dock them again. The default seed is `19`. It can also be
+set as `seed = ...` in the configuration file, while an explicit CLI `--seed`
+takes precedence. The CSV records the search box, exhaustiveness, and seed for
+every result.
 
 #### Docking Output
 
 | # | Output | Description |
 |---|--------|-------------|
 | 1 | PDBQT files | Prepared receptor and ligand files |
-| 2 | Log file | Vina output with binding scores per combination |
-| 3 | Output PDB | Top 5 docking poses per combination |
-| 4 | Output PDBQT | Best pose (Vina split) per combination |
-| 5 | Output SDF | Best pose as SDF for visualization |
-| 6 | `docking_results.csv` | All affinities tabulated for easy analysis |
+| 2 | `*_log.txt` | Vina output with binding scores per combination |
+| 3 | `*_out.pdbqt` | Raw multi-pose Vina output |
+| 4 | `*_out.sdf` | Extracted best pose for visualization |
+| 5 | `docking_results.csv` | Affinities plus search-box, exhaustiveness, and seed provenance |
+| 6 | `*_completed.txt` | Resume checkpoint containing completed receptor–ligand pairs |
 
 ### Reports
 
@@ -398,10 +416,13 @@ generate_csv("data/4QJR.cif")
 # Use BLOSUM62 (downloaded automatically if absent)
 generate_csv("data/4QJR.cif", matrix="BLOSUM62")
 
-# Load a matrix directly
-score_dict = load_matrix("data/PAM250")   # dict[str, dict[str, int]], 3-letter keys
+# Resolve a bundled or downloadable matrix by name
+score_dict = resolve_matrix("PAM250")     # works in source and installed packages
 score_dict = resolve_matrix("PAM30")      # downloads PAM30 from NCBI if needed
 
+# Or load a custom matrix file directly
+score_dict = load_matrix("/path/to/custom_matrix")
+
 # --- Generate mutant PDB ---
 from mutadock.mutation.generate_mutant_pdb import generate_pdb
 
@@ -431,6 +452,7 @@ dock_vina(
     log_file="vina.log",
     center=[10.0, 5.0, 20.0],
     box_size=[20.0, 20.0, 20.0],
+    seed=19,
 )
 ```
 
@@ -466,6 +488,17 @@ If NCBI FTP is unreachable, download the matrix manually and use `--matrix-file`
 md_csv_generator -i protein.pdb --matrix-file /path/to/PAM30
 ```
 
+PAM250 and BLOSUM62 are included with MUTADOCK. Other downloaded matrices are
+cached in `~/.cache/mutadock/matrices`; set `MUTADOCK_DATA_DIR` to use a different
+cache directory.
+
+**An external preparation or docking command times out**
+
+The default limits are 900 seconds for receptor preparation, 1800 seconds for
+AutoSite, and 3600 seconds for Vina. Override them with
+`MUTADOCK_RECEPTOR_PREP_TIMEOUT`, `MUTADOCK_AUTOSITE_TIMEOUT`, and
+`MUTADOCK_VINA_TIMEOUT`, respectively. Set a value to `0` to disable that timeout.
+
 **CIF file not recognized**
 PDBFixer and BioPython both support `.cif` natively. Make sure the file extension is `.cif` or `.pdb` — other extensions are not accepted.
 

{mutadock-2.1.0 → mutadock-2.2.2}/README.md

@@ -4,7 +4,6 @@
 [![PyPI version](https://img.shields.io/pypi/v/mutadock.svg)](https://pypi.org/project/mutadock/)
 [![Python](https://img.shields.io/pypi/pyversions/mutadock.svg)](https://pypi.org/project/mutadock/)
 [![Docs](https://readthedocs.org/projects/mutadock/badge/?version=latest)](https://mutadock.readthedocs.io/en/latest/)
-[![Coverage](https://img.shields.io/badge/coverage-45.45%25-yellow.svg)]()
 
 ## Introduction
 
@@ -27,6 +26,13 @@ MUTADOCK is a comprehensive library for protein mutation studies and multi-recep
 - Simple CLI for each workflow step
 - Python API for scripting and integration into existing pipelines
 
+### What's new in the 2.2 series
+
+- Reproducible docking with a configurable random seed (default `19`) and complete run provenance in `docking_results.csv`
+- Safer input validation, including ligand 3D/hydrogen checks and warnings for multi-model, multi-chain, similar-chain, altloc, and insertion-code structures
+- Resumable mutation and docking workflows plus configurable subprocess timeouts
+- PAM250 and BLOSUM62 bundled in the installed package; additional matrices are cached outside the installation directory
+
 
 ## System Requirements
 
@@ -103,15 +109,12 @@ One command takes a **PDB ID**, a **mutation**, and a **ligand code**, and gives
 md_quick --pdb-id 4QJR --mutation A:386:ASN:HIS --ligand-code imatinib
 ```
 
-```
-  Mutation : ASN-A386-HIS
-  ΔΔG      : -27.30 REU (negative = stabilizing)
-  Affinity : -5.66 kcal/mol
-  Report   : mdquick_4QJR/reports/report.html
-```
-
 It fetches + cleans the structure, computes the ΔΔG for that single mutation, builds the mutant, fetches the ligand, finds the pocket with AutoSite (or pass `-c config.txt`), docks, and writes the standard `reports/` bundle. Use `-i protein.pdb` for a local structure, `--ligand-file lig.sdf` for a local ligand, or `--ligand-code 2244` / `cid:5291` / `name:aspirin` for PubChem. Requires the `autosite` binary (ADFRsuite) on PATH when no config is given.
 
+Scores depend on the input structure and protocol, so treat the values printed by
+the demo as results rather than fixed expected output. Pass `--seed` to reproduce
+a docking run exactly.
+
 The staged tools below give you full control over each step.
 
 ### 1. Generate mutation candidates
@@ -170,14 +173,21 @@ md_mutate -h                         # all options
 
 Provide exactly one of `-i/--input` (a local `.pdb`/`.cif` file) or `--pdb-id` (a
 4-character RCSB accession, downloaded automatically). `md_mutate` also warns when
-the input contains multiple models, alternate conformations (altlocs), or
-insertion codes, since these affect residue numbering.
+the input contains multiple models or chains, similar chain sequences, alternate
+conformations (altlocs), or insertion codes, since these can make chain selection
+and residue numbering ambiguous. Inspect these warnings and isolate the intended
+chain(s) before interpreting results.
 
 By default every output file is written next to the input structure. Pass
 `-o/--output-dir DIR` to collect them in `DIR` instead (created if absent); the
 paths recorded in `*_mutants.txt` point into `DIR`, so they remain valid input
 for `md_dock`.
 
+`md_mutate` appends to its checkpoint CSVs by default and skips completed items,
+so rerunning an interrupted job resumes it. The direct `md_ddg_single`,
+`md_ddg_double`, and `md_ddg_triple` commands also support `--resume`. Use
+`--no-append` when you intentionally want a fresh run.
+
 #### Mutation Output
 
 | # | File | Description |
@@ -197,7 +207,7 @@ for `md_dock`.
 ΔΔG is computed as `score(mutant) − score(wild-type self-mutation reference)`, where **both** sides run the identical repack(+minimization) protocol — so a null WT→WT mutation scores ≈ 0 and the values are not biased toward "stabilizing."
 
 - **Units:** `ddG_value` is in **Rosetta Energy Units (REU), not kcal/mol.** A `ddG_kcal` column is also written, and reports show both. REU ≈ but ≠ kcal/mol.
-- **Scaling factor:** the REU→kcal/mol factor is **`REU_TO_KCAL_SCALE` in `src/mutadock/mutation/predict_ddG.py`** (default `0.34`, ≈ 1/2.94; the ref2015 `cartesian_ddg` convention, Park et al. 2016). **To change it, edit that constant** or pass `--reu-to-kcal FACTOR` per run.
+- **Scaling factor:** the default REU→kcal/mol factor is `0.34` (≈ 1/2.94; the ref2015 `cartesian_ddg` convention, Park et al. 2016). Override it per run with `--reu-to-kcal FACTOR`; modifying installed package code is not required.
 - **Protocol (`--protocol`, default `min`):** the recorded protocol is written to a `ddG_protocol` column, and reports flag screening-only runs.
 
   ```bash
@@ -259,6 +269,7 @@ Output files are named `{stem}_{WTAA}-{CHAIN}{POS}-{NEWAA}.pdb` (e.g. `protein_A
 ```bash
 md_dock -r receptors.txt -l ligands.txt -c config.txt
 md_dock -r receptors.txt -l ligands.txt -c config.txt -o results/  # collect outputs in results/
+md_dock -r receptors.txt -l ligands.txt -c config.txt --seed 19    # reproducible run
 md_dock -h   # all options
 ```
 
@@ -268,17 +279,22 @@ By default docking outputs go to an `out/` folder next to each receptor. Pass
 `-o/--output-dir DIR` to collect poses, logs, `docking_results.csv`, and the
 `*_completed.txt` resume file in a single `DIR` instead. Prepared PDBQT files and
 AutoSite caches still live next to their inputs so they can be reused across runs.
+Completed receptor–ligand pairs are skipped automatically; use
+`--ignore-existing` to dock them again. The default seed is `19`. It can also be
+set as `seed = ...` in the configuration file, while an explicit CLI `--seed`
+takes precedence. The CSV records the search box, exhaustiveness, and seed for
+every result.
 
 #### Docking Output
 
 | # | Output | Description |
 |---|--------|-------------|
 | 1 | PDBQT files | Prepared receptor and ligand files |
-| 2 | Log file | Vina output with binding scores per combination |
-| 3 | Output PDB | Top 5 docking poses per combination |
-| 4 | Output PDBQT | Best pose (Vina split) per combination |
-| 5 | Output SDF | Best pose as SDF for visualization |
-| 6 | `docking_results.csv` | All affinities tabulated for easy analysis |
+| 2 | `*_log.txt` | Vina output with binding scores per combination |
+| 3 | `*_out.pdbqt` | Raw multi-pose Vina output |
+| 4 | `*_out.sdf` | Extracted best pose for visualization |
+| 5 | `docking_results.csv` | Affinities plus search-box, exhaustiveness, and seed provenance |
+| 6 | `*_completed.txt` | Resume checkpoint containing completed receptor–ligand pairs |
 
 ### Reports
 
@@ -354,10 +370,13 @@ generate_csv("data/4QJR.cif")
 # Use BLOSUM62 (downloaded automatically if absent)
 generate_csv("data/4QJR.cif", matrix="BLOSUM62")
 
-# Load a matrix directly
-score_dict = load_matrix("data/PAM250")   # dict[str, dict[str, int]], 3-letter keys
+# Resolve a bundled or downloadable matrix by name
+score_dict = resolve_matrix("PAM250")     # works in source and installed packages
 score_dict = resolve_matrix("PAM30")      # downloads PAM30 from NCBI if needed
 
+# Or load a custom matrix file directly
+score_dict = load_matrix("/path/to/custom_matrix")
+
 # --- Generate mutant PDB ---
 from mutadock.mutation.generate_mutant_pdb import generate_pdb
 
@@ -387,6 +406,7 @@ dock_vina(
     log_file="vina.log",
     center=[10.0, 5.0, 20.0],
     box_size=[20.0, 20.0, 20.0],
+    seed=19,
 )
 ```
 
@@ -422,6 +442,17 @@ If NCBI FTP is unreachable, download the matrix manually and use `--matrix-file`
 md_csv_generator -i protein.pdb --matrix-file /path/to/PAM30
 ```
 
+PAM250 and BLOSUM62 are included with MUTADOCK. Other downloaded matrices are
+cached in `~/.cache/mutadock/matrices`; set `MUTADOCK_DATA_DIR` to use a different
+cache directory.
+
+**An external preparation or docking command times out**
+
+The default limits are 900 seconds for receptor preparation, 1800 seconds for
+AutoSite, and 3600 seconds for Vina. Override them with
+`MUTADOCK_RECEPTOR_PREP_TIMEOUT`, `MUTADOCK_AUTOSITE_TIMEOUT`, and
+`MUTADOCK_VINA_TIMEOUT`, respectively. Set a value to `0` to disable that timeout.
+
 **CIF file not recognized**
 PDBFixer and BioPython both support `.cif` natively. Make sure the file extension is `.cif` or `.pdb` — other extensions are not accepted.
 

{mutadock-2.1.0 → mutadock-2.2.2}/docs/conf.py

@@ -14,6 +14,8 @@ sys.path.insert(0, os.path.abspath("../src"))
 project = "MutaDock"
 copyright = "2026, Naisarg Patel"
 author = "Naisarg Patel"
+version = "2.2"
+release = "2.2.2"
 
 # -- General configuration ---------------------------------------------------
 
@@ -50,8 +52,6 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 # -- Options for HTML output -------------------------------------------------
 
 html_theme = "alabaster"
-html_static_path = ["_static"]
-
 html_theme_options = {
     "description": "Mutation analysis and multi-receptor docking toolkit",
     "github_user": "naisarg14",