Major update of dependencies and structure

README.md

@@ -1,5 +1,5 @@
 # AlphaPulldown
-[![Downloads](https://static.pepy.tech/badge/alphapulldown)](https://pepy.tech/project/alphapulldown)  [![python3.10](https://img.shields.io/badge/python-3.8-blue.svg)](https://www.python.org/downloads/release/python-3100/) ![GPL3 license](https://img.shields.io/badge/license-GPLv3-green)
+[![Downloads](https://static.pepy.tech/badge/alphapulldown)](https://pepy.tech/project/alphapulldown)  [![python3.10](https://img.shields.io/badge/python-3.10-blue.svg)](https://www.python.org/downloads/release/python-3100/) ![GPL3 license](https://img.shields.io/badge/license-GPLv3-green)
 
 <span style="color:red">*This is a development version of AlphaPulldown! The stable version is available at [0.30.7 branch](https://github.com/KosinskiLab/AlphaPulldown/tree/temp_main)</span>.
 
@@ -49,14 +49,14 @@ Check if you have downloaded necessary parameters and databases (e.g. BFD, MGnif
 
 **Firstly**, install [Anaconda](https://www.anaconda.com/) and create AlphaPulldown environment, gathering necessary dependencies 
 ```bash
-conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.10 openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base
+conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.10 openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base pytest
 ```
 
 **Secondly**, activate the AlphaPulldown environment and install AlphaPulldown
 ```bash
 source activate AlphaPulldown
-python3 -m pip install alphapulldown==0.30.8
-pip install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+python3 -m pip install alphapulldown==1.00.0
+pip install jax==0.4.19 jaxlib==0.4.19+cuda11.cudnn86 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 ```
 
 **Optionally**, if you do not have these software yet on your system, install [HMMER](http://hmmer.org/documentation.html), [HH-suite](https://github.com/soedinglab/hh-suite) from Anaconda

alphapulldown/__init__.py

@@ -1 +1 @@
-__version__ = "0.30.8"
+__version__ = "1.00.0"

alphapulldown/create_individual_features.py

@@ -4,58 +4,27 @@
 # This script is just to create msa and structural features for each sequences and store them in pickle
 # #
 
-import os
-import pickle
-import sys
+from alphafold import run_alphafold as run_af
 from alphapulldown.objects import MonomericObject
-import importlib
-from absl import app
-from absl import flags
-from absl import logging
-
 from alphafold.data.pipeline import DataPipeline
 from alphafold.data.tools import hmmsearch
 from alphafold.data import templates
-import numpy as np
-import os
 from absl import logging, app
-import numpy as np
-from alphapulldown.utils import *
+from alphapulldown.utils import save_meta_data, create_uniprot_runner, parse_fasta
 import contextlib
 from datetime import datetime
-import alphafold
 from pathlib import Path
 from colabfold.utils import DEFAULT_API_SERVER
+import os
+import sys
+import pickle
 
 @contextlib.contextmanager
 def output_meta_file(file_path):
     """function that create temp file"""
     with open(file_path, "w") as outfile:
         yield outfile.name
 
-
-def load_module(file_name, module_name):
-    spec = importlib.util.spec_from_file_location(module_name, file_name)
-    module = importlib.util.module_from_spec(spec)
-    sys.modules[module_name] = module
-    spec.loader.exec_module(module)
-    return module
-
-
-PATH_TO_RUN_ALPHAFOLD = os.path.join(
-    os.path.dirname(alphafold.__file__), "run_alphafold.py"
-)
-
-try:
-    run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
-except FileNotFoundError:
-    PATH_TO_RUN_ALPHAFOLD = os.path.join(
-        os.path.dirname(os.path.dirname(alphafold.__file__)), "run_alphafold.py"
-    )
-
-    run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
-
-
 flags = run_af.flags
 flags.DEFINE_bool("save_msa_files", False, "save msa output or not")
 flags.DEFINE_bool(

alphapulldown/create_individual_features_with_templates.py

@@ -3,10 +3,10 @@
 # create_individual_features using custom multimeric templates
 #
 
+from alphafold import run_alphafold as run_af
 from alphapulldown.objects import MonomericObject
-from alphapulldown.utils import parse_fasta, save_meta_data, create_uniprot_runner
+from alphapulldown.utils import create_uniprot_runner
 from alphapulldown.create_custom_template_db import create_db
-import alphafold
 from alphafold.data.pipeline import DataPipeline
 from alphafold.data.tools import hmmsearch
 from alphafold.data import templates
@@ -16,16 +16,7 @@
 from pathlib import Path
 import tempfile
 import csv
-from create_individual_features import load_module, create_and_save_monomer_objects, iter_seqs
-
-
-PATH_TO_RUN_ALPHAFOLD = os.path.join(os.path.dirname(alphafold.__file__), "run_alphafold.py")
-
-try:
-    run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
-except FileNotFoundError:
-    PATH_TO_RUN_ALPHAFOLD = os.path.join(os.path.dirname(os.path.dirname(alphafold.__file__)), "run_alphafold.py")
-    run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
+from create_individual_features import create_and_save_monomer_objects, iter_seqs
 
 
 flags = run_af.flags

alphapulldown/objects.py

@@ -6,7 +6,6 @@
 import tempfile
 import os
 import contextlib
-from tracemalloc import start
 import numpy as np
 from alphafold.data import parsers
 from alphafold.data import pipeline_multimer
@@ -16,8 +15,7 @@
 from alphafold.data import templates
 from pathlib import Path as plPath
 from alphafold.data.tools import hhsearch
-from colabfold.batch import get_queries, unserialize_msa, get_msa_and_templates, msa_to_str, build_monomer_feature, \
-    parse_fasta
+from colabfold.batch import unserialize_msa, get_msa_and_templates, msa_to_str, build_monomer_feature
 
 
 @contextlib.contextmanager

alphapulldown/plot_pae.py

@@ -7,7 +7,6 @@
 matplotlib.use("agg")
 import matplotlib.pyplot as plt
 import pickle as pkl
-import numpy as np
 
 
 def plot_pae(seqs: list, order, feature_dir, job_name):

alphapulldown/predict_structure.py

@@ -12,9 +12,7 @@
 from alphafold.common import residue_constants
 from alphafold.relax import relax
 import numpy as np
-from alphapulldown.utils import get_run_alphafold
-
-run_af = get_run_alphafold()
+from alphafold import run_alphafold as run_af
 
 RELAX_MAX_ITERATIONS = run_af.RELAX_MAX_ITERATIONS
 RELAX_ENERGY_TOLERANCE = run_af.RELAX_ENERGY_TOLERANCE

alphapulldown/rename_colab_search_a3m.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python3
-import sys
 import glob, os
 from itertools import groupby
-import re
 
 """
 Rename all .a3m files in the current directory

alphapulldown/run_multimer_jobs.py

@@ -1,23 +1,22 @@
 #!/usr/bin/env python3
 
-
 # Author: Dingquan Yu
 # A script to create region information for create_multimer_features.py
 # #
 
-
 import itertools
-from absl import app, flags, logging
-from alphapulldown.utils import *
+from absl import app, logging
+from alphapulldown.utils import (create_interactors, read_all_proteins, read_custom, make_dir_monomer_dictionary,
+                                 load_monomer_objects, check_output_dir, create_model_runners_and_random_seed,
+                                 create_and_save_pae_plots)
 from itertools import combinations
 from alphapulldown.objects import MultimericObject
 import os
 from pathlib import Path
 from alphapulldown.predict_structure import predict, ModelsToRelax
+from alphafold import run_alphafold as run_af
 
 
-
-run_af = get_run_alphafold()
 flags = run_af.flags
 
 flags.DEFINE_enum(

alphapulldown/utils.py

@@ -21,8 +21,6 @@
 from alphafold.data import parsers
 from pathlib import Path
 import numpy as np
-import importlib
-import alphafold
 import sys
 import datetime
 import re
@@ -518,29 +516,4 @@ def parse_fasta(fasta_string: str):
             continue  # Skip blank lines.
         sequences[index] += line
 
-    return sequences, descriptions
-
-
-def load_module(file_name, module_name):
-    spec = importlib.util.spec_from_file_location(module_name, file_name)
-    module = importlib.util.module_from_spec(spec)
-    sys.modules[module_name] = module
-    spec.loader.exec_module(module)
-    return module
-
-
-def get_run_alphafold():
-    PATH_TO_RUN_ALPHAFOLD = os.path.join(
-        os.path.dirname(alphafold.__file__), "run_alphafold.py"
-    )
-
-    try:
-        run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
-    except FileNotFoundError:
-        PATH_TO_RUN_ALPHAFOLD = os.path.join(
-            os.path.dirname(os.path.dirname(alphafold.__file__)), "run_alphafold.py"
-        )
-
-        run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
-
-    return run_af
+    return sequences, descriptions

setup.cfg

@@ -1,11 +1,11 @@
 [metadata]
-name = alphapulldown 
-version = 1.00.0
+name = alphapulldown
 author = Dingquan Yu
 author_email = [email protected]
 description = Pipeline allows massive screening using alphafold
 url = https://github.com/KosinskiLab/AlphaPulldown
-
+long_description = file: README.md
+long_description_content_type = text/markdown
 classifiers =
     Programming Language :: Python :: 3
     License :: OSI Approved :: MIT License
@@ -18,39 +18,42 @@ packages=
     colabfold
     analysis_pipeline
     af2plots
-package_dir = 
+package_dir =
     alphapulldown = ./alphapulldown
     alphafold = ./alphafold/alphafold
     colabfold = ./alphapulldown/ColabFold/colabfold
     analysis_pipeline = ./alphapulldown/analysis_pipeline
     af2plots = ./alphapulldown/analysis_pipeline/af2plots/af2plots
-
 include_package_data = True
-
 python_requires = ==3.10.*
-install_requires = 
-    absl-py >= 0.13.0 
-    dm-haiku
-    dm-tree>=0.1.6
-    h5py>=3.1.0
-    matplotlib>=3.3.3
-    ml-collections>=0.1.0
+install_requires =
+    alphafold @ git+https://github.com/KosinskiLab/alphafold.git@main
+    colabfold @ git+https://github.com/sokrypton/ColabFold.git@main
+    af2plots @ git+https://gitlab.com/gchojnowski/af2plots.git@main
+    absl-py==1.4.0
+    dm-haiku==0.0.9
+    dm-tree==0.1.8
+    h5py==3.10.0
+    matplotlib
+    ml-collections==0.1.1
     numpy
-    pandas>=1.3.4
-    tensorflow
-    importlib-resources==5.8.0
+    pandas==1.5.3
+    tensorflow==2.14.0
+    importlib-resources==6.1.0
     biopython>=1.78
-    nbformat==5.4.0
-    py3Dmol==2.0.1
-    ipython
-    tqdm
-    appdirs
+    nbformat==5.9.2
+    py3Dmol==2.0.4
+    ipython==8.16.1
+    tqdm==4.66.1
+    appdirs==1.4.4
     jupyterlab
     ipywidgets
-scripts = ./alphapulldown/create_individual_features.py, ./alphapulldown/create_individual_features_with_templates.py, ./alphapulldown/run_multimer_jobs.py, ./alphapulldown/analysis_pipeline/create_notebook.py, ./alphapulldown/rename_colab_search_a3m.py, ./alphapulldown/prepare_seq_names.py
+scripts = ./alphafold/run_alphafold.py, ./alphapulldown/create_individual_features.py, ./alphapulldown/create_individual_features_with_templates.py, ./alphapulldown/run_multimer_jobs.py, ./alphapulldown/analysis_pipeline/create_notebook.py, ./alphapulldown/rename_colab_search_a3m.py, ./alphapulldown/prepare_seq_names.py
+
 [options.packages.find]
 where = ./
 exclude = test*
 
 [options.data_files]
-lib/python3.8/site-packages/alphafold/common/ = stereo_chemical_props.txt
+lib/python3.10/site-packages/alphafold/common/ = stereo_chemical_props.txt
+lib/python3.10/site-packages/alphafold/ = ./alphafold/run_alphafold.py

setup.py

@@ -1,3 +1,4 @@
 from setuptools import setup
+from alphapulldown import __version__
 if __name__ == '__main__':
-    setup()
+    setup(version=__version__)