From 4ce31c1ffc83a44e7b06e4719a0bc8b6074aa64f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 14 Aug 2021 06:38:57 +0200
Subject: [PATCH 01/16] adding easyconfigs: AlphaFold-2.0.0-foss-2020b.eb

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 76 +++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
new file mode 100644
index 00000000000..aa4d2744649
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -0,0 +1,76 @@
+easyblock = 'PythonBundle'
+
+name = 'AlphaFold'
+version = '2.0.0'
+
+homepage = 'https://deepmind.com/research/case-studies/alphafold'
+description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known"
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+builddependencies = [
+    # required for installing dm-tree
+    ('Bazel', '3.7.2'),
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('PyYAML', '5.3.1'),
+    ('TensorFlow', '2.5.0'),
+    ('Biopython', '1.78'),
+    ('jax', '0.2.19'),  # also provides absl-py
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.11.1', {
+        'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'],
+    }),
+    ('chex', '0.0.8', {
+        'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'],
+    }),
+    ('tabulate', '0.8.9', {
+        'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'],
+    }),
+    ('dm-haiku', '0.0.4', {
+        # source tarball on PyPI is missing requirements.txt,
+        # see https://github.com/deepmind/dm-haiku/issues/44
+        'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'],
+        'modulename': 'haiku',
+    }),
+    ('dm-tree', '0.1.6', {
+        'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'],
+        'modulename': 'tree',
+    }),
+    ('websocket-client', '1.2.1', {
+        'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'],
+        'modulename': 'websocket',
+    }),
+    ('docker', '5.0.0', {
+        'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'],
+    }),
+    ('immutabledict', '2.1.0', {
+        'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.0', {
+        'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'],
+        # see https://github.com/google/ml_collections/issues/7
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 4d65a507ed330f7b71f19a63aa9daec5fb365117 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 14 Aug 2021 08:00:36 +0200
Subject: [PATCH 02/16] stick to TensorFlow 2.4.1 dependency for AlphaFold
 2.0.0 with foss/2020b

---
 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index aa4d2744649..9fe9c5a44e3 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -17,7 +17,7 @@ dependencies = [
     ('Python', '3.8.6'),
     ('SciPy-bundle', '2020.11'),
     ('PyYAML', '5.3.1'),
-    ('TensorFlow', '2.5.0'),
+    ('TensorFlow', '2.4.1'),
     ('Biopython', '1.78'),
     ('jax', '0.2.19'),  # also provides absl-py
 ]

From 75b034f4679c9c20eb352190abb0bd3754d3ee5d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 09:32:29 +0200
Subject: [PATCH 03/16] add patch for AlphaFold to fix setup.py, add OpenMM and
 PDBFixer dependencies, also install scripts and 'alphafold' command

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 25 +++++++++++++-
 .../AlphaFold-2.0.0_fix-packages.patch        | 13 +++++++
 .../p/PDBFixer/PDBFixer-1.7-foss-2020b.eb     | 34 +++++++++++++++++++
 3 files changed, 71 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-packages.patch
 create mode 100644 easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index 9fe9c5a44e3..6da221ba1a7 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -19,6 +19,8 @@ dependencies = [
     ('PyYAML', '5.3.1'),
     ('TensorFlow', '2.4.1'),
     ('Biopython', '1.78'),
+    ('OpenMM', '7.5.1'),  # for simtk
+    ('PDBFixer', '1.7'),
     ('jax', '0.2.19'),  # also provides absl-py
 ]
 
@@ -67,10 +69,31 @@ exts_list = [
     (name, version, {
         'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'],
         'sources': ['v%(version)s.tar.gz'],
-        'checksums': ['78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2'],
+        'patches': ['AlphaFold-%(version)s_fix-packages.patch'],
+        'checksums': [
+            '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
+            '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
+        ],
     }),
 ]
 
+postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    # run_alphafold.py script is missing a shebang...
+    "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
+    "cat %(builddir)s/AlphaFold/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py",
+    "chmod a+x %(installdir)s/bin/run_alphafold.py",
+    "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
+    "cp -a %(builddir)s/AlphaFold/alphafold-%(version)s/scripts %(installdir)s/",
+]
+
+sanity_check_paths = {
+    'files': ['bin/alphafold', 'bin/run_alphafold.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
+}
+
+sanity_check_commands = ["alphafold --help"]
+
 sanity_pip_check = True
 
 moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-packages.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-packages.patch
new file mode 100644
index 00000000000..f42a59513e1
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-packages.patch
@@ -0,0 +1,13 @@
+also include alphafold.data.tools and alphafold.model.tf, which are not picked up by find_packages()
+author: Kenneth Hoste (HPC-UGent)
+--- alphafold-2.0.0/setup.py.orig	2021-08-14 08:42:43.030919330 +0200
++++ alphafold-2.0.0/setup.py	2021-08-14 08:43:59.183245602 +0200
+@@ -26,7 +26,7 @@
+     author_email='alphafold@deepmind.com',
+     license='Apache License, Version 2.0',
+     url='https://github.com/deepmind/alphafold',
+-    packages=find_packages(),
++    packages=find_packages() + ['alphafold/data/tools', 'alphafold/model/tf'],
+     install_requires=[
+         'absl-py',
+         'biopython',
diff --git a/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb b/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb
new file mode 100644
index 00000000000..89173238ef0
--- /dev/null
+++ b/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonPackage'
+
+name = 'PDBFixer'
+version = '1.7'
+
+homepage = 'https://github.com/openmm/pdbfixer'
+description = """PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation
+for simulating them."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+source_urls = ['https://github.com/openmm/pdbfixer/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea']
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('OpenMM', '7.5.1'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+    'files': ['bin/pdbfixer'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["pdbfixer --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 9fb09eeba11c0c47b9d5497cc2b22fb3d40b7690 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 11:34:21 +0200
Subject: [PATCH 04/16] add missing dependencies for AlphaFold + patch to pick
 up on them and take into account $ALPHAFOLD_DATA_DIR, fix sanity check
 command

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 11 ++-
 .../AlphaFold-2.0.0_data-dep-paths.patch      | 96 +++++++++++++++++++
 2 files changed, 105 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index 6da221ba1a7..af15e18801c 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -20,6 +20,9 @@ dependencies = [
     ('TensorFlow', '2.4.1'),
     ('Biopython', '1.78'),
     ('OpenMM', '7.5.1'),  # for simtk
+    ('HH-suite', '3.3.0'),
+    ('HMMER', '3.3.2'),
+    ('Kalign', '3.3.1'),
     ('PDBFixer', '1.7'),
     ('jax', '0.2.19'),  # also provides absl-py
 ]
@@ -69,10 +72,14 @@ exts_list = [
     (name, version, {
         'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'],
         'sources': ['v%(version)s.tar.gz'],
-        'patches': ['AlphaFold-%(version)s_fix-packages.patch'],
+        'patches': [
+            'AlphaFold-%(version)s_fix-packages.patch',
+            'AlphaFold-%(version)s_data-dep-paths.patch',
+        ],
         'checksums': [
             '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
             '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
+            '5a1b17002273cc05a06541297b8017b1928063fe54cffe0b133fa4b39b5435ad',  # AlphaFold-2.0.0_data-dep-paths.patch
         ],
     }),
 ]
@@ -92,7 +99,7 @@ sanity_check_paths = {
     'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
 }
 
-sanity_check_commands = ["alphafold --help"]
+sanity_check_commands = ["alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'"]
 
 sanity_pip_check = True
 
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
new file mode 100644
index 00000000000..96fea848153
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
@@ -0,0 +1,96 @@
+pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data
+pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild
+author: Kenneth Hoste (HPC-UGent)
+diff --git a/run_alphafold.py b/run_alphafold.py
+index 61f7ef2..6d80d38 100644
+--- a/run_alphafold.py
++++ b/run_alphafold.py
+@@ -36,6 +36,45 @@ from alphafold.model import model
+ from alphafold.relax import relax
+ # Internal import (7716).
+ 
++
++data_dir = os.getenv('ALPHAFOLD_DATA_DIR')
++if data_dir:
++    uniref90_database_path = os.path.join(data_dir, 'uniref90')
++    mgnify_database_path = os.path.join(data_dir, 'mgnify')
++    bfd_database_path = os.path.join(data_dir, 'bfd')
++    uniclust30_database_path = os.path.join(data_dir, 'uniclust30')
++    pdb70_database_path = os.path.join(data_dir, 'pdb70')
++    template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif')
++    obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat')
++else:
++    uniref90_database_path = None
++    mgnify_database_path = None
++    bfd_database_path = None
++    uniclust30_database_path = None
++    pdb70_database_path = None
++    template_mmcif_dir = None
++    obsolete_pdbs_path = None
++
++hmmer_root = os.getenv('EBROOTHMMER')
++if hmmer_root:
++    jackhmmer_binary_path = os.path.join(hmmer_root, 'bin', 'jackhmmer')
++else:
++    jackhmmer_binary_path = '/usr/bin/jackhmmer'
++
++hhsuite_root = os.getenv('EBROOTHHMINSUITE')
++if hhsuite_root:
++    hhblits_binary_path = os.path.join(hhsuite_root, 'bin', 'hhblits')
++    hhsearch_binary_path = os.path.join(hhsuite_root, 'bin', 'hhsearch')
++else:
++    hhblits_binary_path = '/usr/bin/hhblits'
++    hhsearch_binary_path = '/usr/bin/hhsearch'
++
++kalign_root = os.getenv('EBROOTKALIGN')
++if kalign_root:
++    kalign_binary_path = os.path.join(kalign_root, 'bin', 'kalign')
++else:
++    kalign_binary_path = '/usr/bin/kalign'
++
+ flags.DEFINE_list('fasta_paths', None, 'Paths to FASTA files, each containing '
+                   'one sequence. Paths should be separated by commas. '
+                   'All FASTA paths must have a unique basename as the '
+@@ -44,30 +83,30 @@ flags.DEFINE_list('fasta_paths', None, 'Paths to FASTA files, each containing '
+ flags.DEFINE_string('output_dir', None, 'Path to a directory that will '
+                     'store the results.')
+ flags.DEFINE_list('model_names', None, 'Names of models to use.')
+-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.')
+-flags.DEFINE_string('jackhmmer_binary_path', '/usr/bin/jackhmmer',
++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.')
++flags.DEFINE_string('jackhmmer_binary_path', jackhmmer_binary_path,
+                     'Path to the JackHMMER executable.')
+-flags.DEFINE_string('hhblits_binary_path', '/usr/bin/hhblits',
++flags.DEFINE_string('hhblits_binary_path', hhblits_binary_path,
+                     'Path to the HHblits executable.')
+-flags.DEFINE_string('hhsearch_binary_path', '/usr/bin/hhsearch',
++flags.DEFINE_string('hhsearch_binary_path', hhsearch_binary_path,
+                     'Path to the HHsearch executable.')
+-flags.DEFINE_string('kalign_binary_path', '/usr/bin/kalign',
++flags.DEFINE_string('kalign_binary_path', kalign_binary_path,
+                     'Path to the Kalign executable.')
+-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 '
++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 '
+                     'database for use by JackHMMER.')
+-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify '
++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify '
+                     'database for use by JackHMMER.')
+-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD '
++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD '
+                     'database for use by HHblits.')
+-flags.DEFINE_string('uniclust30_database_path', None, 'Path to the Uniclust30 '
++flags.DEFINE_string('uniclust30_database_path', uniclust30_database_path, 'Path to the Uniclust30 '
+                     'database for use by HHblits.')
+-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 '
++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 '
+                     'database for use by HHsearch.')
+-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with '
++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with '
+                     'template mmCIF structures, each named <pdb_id>.cif')
+ flags.DEFINE_string('max_template_date', None, 'Maximum template release date '
+                     'to consider. Important if folding historical test sets.')
+-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a '
++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a '
+                     'mapping from obsolete PDB IDs to the PDB IDs of their '
+                     'replacements.')
+ flags.DEFINE_enum('preset', 'full_dbs', ['full_dbs', 'casp14'],

From 7ecf851bb86ef903b28ca3c2afcf8ea7b822c903 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 11:49:08 +0200
Subject: [PATCH 05/16] avoid warnigns about non-default values for required
 options to run_alphafold.py script

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb |  2 +-
 .../AlphaFold-2.0.0_data-dep-paths.patch      | 19 ++++++++++++++++++-
 2 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index af15e18801c..9038dac8d56 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -79,7 +79,7 @@ exts_list = [
         'checksums': [
             '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
             '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
-            '5a1b17002273cc05a06541297b8017b1928063fe54cffe0b133fa4b39b5435ad',  # AlphaFold-2.0.0_data-dep-paths.patch
+            '7e19d944934b8004e4ee114c94f580d899ac503f3147fc7746c960cc5ca18c0d',  # AlphaFold-2.0.0_data-dep-paths.patch
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
index 96fea848153..e7f052dcde7 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
@@ -2,7 +2,7 @@ pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data
 pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild
 author: Kenneth Hoste (HPC-UGent)
 diff --git a/run_alphafold.py b/run_alphafold.py
-index 61f7ef2..6d80d38 100644
+index 61f7ef2..96df783 100644
 --- a/run_alphafold.py
 +++ b/run_alphafold.py
 @@ -36,6 +36,45 @@ from alphafold.model import model
@@ -94,3 +94,20 @@ index 61f7ef2..6d80d38 100644
                      'mapping from obsolete PDB IDs to the PDB IDs of their '
                      'replacements.')
  flags.DEFINE_enum('preset', 'full_dbs', ['full_dbs', 'casp14'],
+@@ -268,16 +307,8 @@ if __name__ == '__main__':
+       'fasta_paths',
+       'output_dir',
+       'model_names',
+-      'data_dir',
+       'preset',
+-      'uniref90_database_path',
+-      'mgnify_database_path',
+-      'uniclust30_database_path',
+-      'bfd_database_path',
+-      'pdb70_database_path',
+-      'template_mmcif_dir',
+       'max_template_date',
+-      'obsolete_pdbs_path',
+   ])
+ 
+   app.run(main)

From b7b1ccdd5b84c4dc9baa3d678301cd5c21eb1f7f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 11:52:30 +0200
Subject: [PATCH 06/16] fix default value for template_mmcif_dir based on
 \ALPHAFOLD_DATA_DIR

---
 .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb     | 2 +-
 .../a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch          | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index 9038dac8d56..cab8b7153a4 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -79,7 +79,7 @@ exts_list = [
         'checksums': [
             '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
             '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
-            '7e19d944934b8004e4ee114c94f580d899ac503f3147fc7746c960cc5ca18c0d',  # AlphaFold-2.0.0_data-dep-paths.patch
+            '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950',  # AlphaFold-2.0.0_data-dep-paths.patch
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
index e7f052dcde7..d23e7c15904 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
@@ -2,7 +2,7 @@ pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data
 pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild
 author: Kenneth Hoste (HPC-UGent)
 diff --git a/run_alphafold.py b/run_alphafold.py
-index 61f7ef2..96df783 100644
+index 61f7ef2..81c97a0 100644
 --- a/run_alphafold.py
 +++ b/run_alphafold.py
 @@ -36,6 +36,45 @@ from alphafold.model import model
@@ -17,7 +17,7 @@ index 61f7ef2..96df783 100644
 +    bfd_database_path = os.path.join(data_dir, 'bfd')
 +    uniclust30_database_path = os.path.join(data_dir, 'uniclust30')
 +    pdb70_database_path = os.path.join(data_dir, 'pdb70')
-+    template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif')
++    template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files')
 +    obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat')
 +else:
 +    uniref90_database_path = None

From c032e63216bc9cac93c566a85ad82f794f1d1ca6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 12:21:02 +0200
Subject: [PATCH 07/16] add patch for HHBlits and JackHmmer scripts to avoid
 hardcoded number of cores to use

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb |  2 +
 .../a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch   | 48 +++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index cab8b7153a4..c3325e0a46a 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -75,11 +75,13 @@ exts_list = [
         'patches': [
             'AlphaFold-%(version)s_fix-packages.patch',
             'AlphaFold-%(version)s_data-dep-paths.patch',
+            'AlphaFold-%(version)s_n-cpu.patch',
         ],
         'checksums': [
             '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
             '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
             '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950',  # AlphaFold-2.0.0_data-dep-paths.patch
+            '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a',  # AlphaFold-2.0.0_n-cpu.patch
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch
new file mode 100644
index 00000000000..a61e8394395
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch
@@ -0,0 +1,48 @@
+don't hardcode number of cores to use by HHBlits and Jackhmmer scripts
+author: Kenneth Hoste (HPC-UGent)
+
+diff --git a/alphafold/data/tools/hhblits.py b/alphafold/data/tools/hhblits.py
+index e0aa098..e624f3a 100644
+--- a/alphafold/data/tools/hhblits.py
++++ b/alphafold/data/tools/hhblits.py
+@@ -27,6 +27,8 @@ from alphafold.data.tools import utils
+ _HHBLITS_DEFAULT_P = 20
+ _HHBLITS_DEFAULT_Z = 500
+ 
++HHBLITS_N_CPU = os.getenv('ALPHAFOLD_HHBLITS_N_CPU', os.getenv('SLURM_CPUS_ON_NODE', 4))
++
+ 
+ class HHBlits:
+   """Python wrapper of the HHblits binary."""
+@@ -35,7 +37,7 @@ class HHBlits:
+                *,
+                binary_path: str,
+                databases: Sequence[str],
+-               n_cpu: int = 4,
++               n_cpu: int = HHBLITS_N_CPU,
+                n_iter: int = 3,
+                e_value: float = 0.001,
+                maxseq: int = 1_000_000,
+diff --git a/alphafold/data/tools/jackhmmer.py b/alphafold/data/tools/jackhmmer.py
+index ae53df9..800bf99 100644
+--- a/alphafold/data/tools/jackhmmer.py
++++ b/alphafold/data/tools/jackhmmer.py
+@@ -24,6 +24,9 @@ from alphafold.data.tools import utils
+ # Internal import (7716).
+ 
+ 
++JACKHMMER_N_CPU = os.getenv('ALPHAFOLD_JACKHMMER_N_CPU', os.getenv('SLURM_CPUS_ON_NODE', 4))
++
++
+ class Jackhmmer:
+   """Python wrapper of the Jackhmmer binary."""
+ 
+@@ -31,7 +34,7 @@ class Jackhmmer:
+                *,
+                binary_path: str,
+                database_path: str,
+-               n_cpu: int = 8,
++               n_cpu: int = JACKHMMER_N_CPU,
+                n_iter: int = 1,
+                e_value: float = 0.0001,
+                z_value: Optional[int] = None,

From 08d29023d21179d62a433f3217926974c70d3fc8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 15:12:33 +0200
Subject: [PATCH 08/16] include stereo_chemical_props.txt in AlphaFold
 installaiton directory, switch to installing AlphaFold via 'components'
 because it now requires multiple source files

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 63 +++++++++++++------
 .../AlphaFold-2.0.0_fix-scp-path.patch        | 23 +++++++
 2 files changed, 68 insertions(+), 18 deletions(-)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index c3325e0a46a..dafa3b16123 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -27,6 +27,44 @@ dependencies = [
     ('jax', '0.2.19'),  # also provides absl-py
 ]
 
+# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
+# see docker/Dockerfile in AlphaFold repository
+local_scp_commit = '7102c6'
+
+components = [
+    (name, version, {
+        'easyblock': 'PythonPackage',
+        'source_urls': [
+            'https://github.com/deepmind/alphafold/archive/refs/tags/',
+            'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
+        ],
+        'sources': [
+            'v%(version)s.tar.gz',
+            {
+                'download_filename': 'stereo_chemical_props.txt',
+                'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
+                'extract_cmd': "cp -a %s .",
+            },
+        ],
+        'patches': [
+            'AlphaFold-%(version)s_fix-packages.patch',
+            'AlphaFold-%(version)s_data-dep-paths.patch',
+            'AlphaFold-%(version)s_n-cpu.patch',
+            'AlphaFold-2.0.0_fix-scp-path.patch',
+        ],
+        'checksums': [
+            '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
+            '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
+            '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
+            '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950',  # AlphaFold-2.0.0_data-dep-paths.patch
+            '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a',  # AlphaFold-2.0.0_n-cpu.patch
+            '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27',  # AlphaFold-2.0.0_fix-scp-path.patch
+        ],
+        'start_dir': 'alphafold-%(version)s',
+        'use_pip': True,
+    }),
+]
+
 use_pip = True
 
 exts_list = [
@@ -69,31 +107,17 @@ exts_list = [
         # see https://github.com/google/ml_collections/issues/7
         'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
     }),
-    (name, version, {
-        'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'],
-        'sources': ['v%(version)s.tar.gz'],
-        'patches': [
-            'AlphaFold-%(version)s_fix-packages.patch',
-            'AlphaFold-%(version)s_data-dep-paths.patch',
-            'AlphaFold-%(version)s_n-cpu.patch',
-        ],
-        'checksums': [
-            '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
-            '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
-            '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950',  # AlphaFold-2.0.0_data-dep-paths.patch
-            '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a',  # AlphaFold-2.0.0_n-cpu.patch
-        ],
-    }),
 ]
 
 postinstallcmds = [
     "mkdir -p %(installdir)s/bin",
     # run_alphafold.py script is missing a shebang...
     "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
-    "cat %(builddir)s/AlphaFold/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py",
+    "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py",
     "chmod a+x %(installdir)s/bin/run_alphafold.py",
     "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
-    "cp -a %(builddir)s/AlphaFold/alphafold-%(version)s/scripts %(installdir)s/",
+    "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/",
+    "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
 ]
 
 sanity_check_paths = {
@@ -101,7 +125,10 @@ sanity_check_paths = {
     'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
 }
 
-sanity_check_commands = ["alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'"]
+sanity_check_commands = [
+    "python -c 'import alphafold'",
+    "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
+]
 
 sanity_pip_check = True
 
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch
new file mode 100644
index 00000000000..c44ee6be008
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch
@@ -0,0 +1,23 @@
+fix path to stereo_chemical_props.txt when AlphaFold is installed with EasyBuild
+author: Kenneth Hoste (HPC-UGent)
+diff --git a/alphafold/common/residue_constants.py b/alphafold/common/residue_constants.py
+index 318b44a..fd840e3 100644
+--- a/alphafold/common/residue_constants.py
++++ b/alphafold/common/residue_constants.py
+@@ -19,6 +19,7 @@ import functools
+ from typing import Mapping, List, Tuple
+ 
+ import numpy as np
++import os
+ import tree
+ 
+ # Internal import (35fd).
+@@ -403,7 +404,7 @@ def load_stereo_chemical_props() -> Tuple[Mapping[str, List[Bond]],
+     residue_bond_angles: dict that maps resname --> list of BondAngle tuples
+   """
+   stereo_chemical_props_path = (
+-      'alphafold/common/stereo_chemical_props.txt')
++      os.path.join(os.getenv('EBROOTALPHAFOLD', 'alphafold/common'), 'stereo_chemical_props.txt'))
+   with open(stereo_chemical_props_path, 'rt') as f:
+     stereo_chemical_props = f.read()
+   lines_iter = iter(stereo_chemical_props.splitlines())

From e82389d431c23a0935d99621865191421fe23622 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 17:19:39 +0200
Subject: [PATCH 09/16] include patched OpenMM as component in AlphaFold
 installation

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 37 +++++++++++++--
 .../a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch  | 45 +++++++++++++++++++
 2 files changed, 79 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index dafa3b16123..f91253267d6 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -9,8 +9,12 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve
 toolchain = {'name': 'foss', 'version': '2020b'}
 
 builddependencies = [
+    # CMake/oxygen/SWIG are required for building OpenMM
+    ('CMake', '3.18.4'),
+    ('Doxygen', '1.8.20'),
     # required for installing dm-tree
     ('Bazel', '3.7.2'),
+    ('SWIG', '4.0.2'),
 ]
 
 dependencies = [
@@ -19,7 +23,6 @@ dependencies = [
     ('PyYAML', '5.3.1'),
     ('TensorFlow', '2.4.1'),
     ('Biopython', '1.78'),
-    ('OpenMM', '7.5.1'),  # for simtk
     ('HH-suite', '3.3.0'),
     ('HMMER', '3.3.2'),
     ('Kalign', '3.3.1'),
@@ -27,11 +30,29 @@ dependencies = [
     ('jax', '0.2.19'),  # also provides absl-py
 ]
 
+local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && "
+local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && "
+
 # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
 # see docker/Dockerfile in AlphaFold repository
 local_scp_commit = '7102c6'
 
 components = [
+    # for simtk
+    ('OpenMM', '7.5.1', {
+        'easyblock': 'CMakeMake',
+        'source_urls': ['https://github.com/openmm/openmm/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')],
+        'checksums': [
+            'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7',  # OpenMM-7.5.1.tar.gz
+            '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6',  # OpenMM-7.5.1_AlphaFold.patch
+        ],
+        'start_dir': 'openmm-%(version)s',
+        'preinstallopts': local_openmm_preinstallopts,
+        # required to install OpenMM Python API
+        'installopts': " && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s",
+    }),
     (name, version, {
         'easyblock': 'PythonPackage',
         'source_urls': [
@@ -39,7 +60,10 @@ components = [
             'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
         ],
         'sources': [
-            'v%(version)s.tar.gz',
+            {
+                'download_filename': 'v%(version)s.tar.gz',
+                'filename': SOURCE_TAR_GZ,
+            },
             {
                 'download_filename': 'stereo_chemical_props.txt',
                 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
@@ -121,15 +145,22 @@ postinstallcmds = [
 ]
 
 sanity_check_paths = {
-    'files': ['bin/alphafold', 'bin/run_alphafold.py'],
+    'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT,
+              'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'],
     'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
 }
 
 sanity_check_commands = [
+    "python -m simtk.testInstallation",
     "python -c 'import alphafold'",
     "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
 ]
 
+modextrapaths = {
+    'OPENMM_INCLUDE_PATH': 'include',
+    'OPENMM_LIB_PATH': 'lib',
+}
+
 sanity_pip_check = True
 
 moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch b/easybuild/easyconfigs/a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch
new file mode 100644
index 00000000000..878ffd11b03
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch
@@ -0,0 +1,45 @@
+custom patch for OpenMM to use in conjunction with AlphaFold
+see https://github.com/deepmind/alphafold/blob/main/docker/openmm.patch
+
+Index: simtk/openmm/app/topology.py
+===================================================================
+--- simtk.orig/openmm/app/topology.py
++++ simtk/openmm/app/topology.py
+@@ -356,19 +356,35 @@
+         def isCyx(res):
+             names = [atom.name for atom in res._atoms]
+             return 'SG' in names and 'HG' not in names
++        # This function is used to prevent multiple di-sulfide bonds from being
++        # assigned to a given atom. This is a DeepMind modification.
++        def isDisulfideBonded(atom):
++            for b in self._bonds:
++                if (atom in b and b[0].name == 'SG' and
++                    b[1].name == 'SG'):
++                    return True
++
++            return False
+ 
+         cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)]
+         atomNames = [[atom.name for atom in res._atoms] for res in cyx]
+         for i in range(len(cyx)):
+             sg1 = cyx[i]._atoms[atomNames[i].index('SG')]
+             pos1 = positions[sg1.index]
++            candidate_distance, candidate_atom = 0.3*nanometers, None
+             for j in range(i):
+                 sg2 = cyx[j]._atoms[atomNames[j].index('SG')]
+                 pos2 = positions[sg2.index]
+                 delta = [x-y for (x,y) in zip(pos1, pos2)]
+                 distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2])
+-                if distance < 0.3*nanometers:
+-                    self.addBond(sg1, sg2)
++                if distance < candidate_distance and not isDisulfideBonded(sg2):
++                    candidate_distance = distance
++                    candidate_atom = sg2
++            # Assign bond to closest pair.
++            if candidate_atom:
++                self.addBond(sg1, candidate_atom)
++
++
+ 
+ class Chain(object):
+     """A Chain object represents a chain within a Topology."""

From 6cf72d7645a5ba9fa064ce330bae693fb68c776f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 17:21:38 +0200
Subject: [PATCH 10/16] don't pick up on \SLURM_CPUS_ON_NODE, only add
 environment variable to avoid hardcoding core count for jackhmmer and hhblits

---
 .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb  | 2 +-
 .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch    | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index f91253267d6..ecfaeb43f03 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -81,7 +81,7 @@ components = [
             '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
             '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
             '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950',  # AlphaFold-2.0.0_data-dep-paths.patch
-            '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a',  # AlphaFold-2.0.0_n-cpu.patch
+            'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',  # AlphaFold-2.0.0_n-cpu.patch
             '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27',  # AlphaFold-2.0.0_fix-scp-path.patch
         ],
         'start_dir': 'alphafold-%(version)s',
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch
index a61e8394395..8849e17462c 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch
@@ -1,4 +1,5 @@
-don't hardcode number of cores to use by HHBlits and Jackhmmer scripts
+don't hardcode number of cores to use by HHBlits and Jackhmmer scripts;
+see https://github.com/deepmind/alphafold/issues/110
 author: Kenneth Hoste (HPC-UGent)
 
 diff --git a/alphafold/data/tools/hhblits.py b/alphafold/data/tools/hhblits.py
@@ -9,7 +10,7 @@ index e0aa098..e624f3a 100644
  _HHBLITS_DEFAULT_P = 20
  _HHBLITS_DEFAULT_Z = 500
  
-+HHBLITS_N_CPU = os.getenv('ALPHAFOLD_HHBLITS_N_CPU', os.getenv('SLURM_CPUS_ON_NODE', 4))
++HHBLITS_N_CPU = os.getenv('ALPHAFOLD_HHBLITS_N_CPU', 4)
 +
  
  class HHBlits:
@@ -31,7 +32,7 @@ index ae53df9..800bf99 100644
  # Internal import (7716).
  
  
-+JACKHMMER_N_CPU = os.getenv('ALPHAFOLD_JACKHMMER_N_CPU', os.getenv('SLURM_CPUS_ON_NODE', 4))
++JACKHMMER_N_CPU = os.getenv('ALPHAFOLD_JACKHMMER_N_CPU', 8)
 +
 +
  class Jackhmmer:

From 0342cb8286b955c06325d27dbf74d51b38a815a1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Aug 2021 17:37:07 +0200
Subject: [PATCH 11/16] fix default paths to downloaded AlphaFold data

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb         |  2 +-
 .../a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch  | 11 ++++++-----
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index ecfaeb43f03..b0ff243dc72 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -80,7 +80,7 @@ components = [
             '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
             '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
             '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
-            '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950',  # AlphaFold-2.0.0_data-dep-paths.patch
+            '1d426748bec4f0f3cc49448ebeb14c4350717f88287afd2aabf6738dea387d81',  # AlphaFold-2.0.0_data-dep-paths.patch
             'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',  # AlphaFold-2.0.0_n-cpu.patch
             '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27',  # AlphaFold-2.0.0_fix-scp-path.patch
         ],
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
index d23e7c15904..0dcbedcdce8 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
@@ -1,4 +1,5 @@
 pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data
+(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py);
 pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild
 author: Kenneth Hoste (HPC-UGent)
 diff --git a/run_alphafold.py b/run_alphafold.py
@@ -12,11 +13,11 @@ index 61f7ef2..81c97a0 100644
 +
 +data_dir = os.getenv('ALPHAFOLD_DATA_DIR')
 +if data_dir:
-+    uniref90_database_path = os.path.join(data_dir, 'uniref90')
-+    mgnify_database_path = os.path.join(data_dir, 'mgnify')
-+    bfd_database_path = os.path.join(data_dir, 'bfd')
-+    uniclust30_database_path = os.path.join(data_dir, 'uniclust30')
-+    pdb70_database_path = os.path.join(data_dir, 'pdb70')
++    uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta')
++    mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters.fa')
++    bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt')
++    uniclust30_database_path = os.path.join(data_dir, 'uniclust30', 'uniclust30_2018_08', 'uniclust30_2018_08')
++    pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70')
 +    template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files')
 +    obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat')
 +else:

From 178463798adc6db719de7efb506515d26515af3c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Aug 2021 11:38:17 +0200
Subject: [PATCH 12/16] make run_alphafold.py print a warning when
 $ALPHAFOLD_DATA_DIR is not defined

---
 .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb      | 2 +-
 .../a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch           | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index b0ff243dc72..91d5b657e7f 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -80,7 +80,7 @@ components = [
             '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz
             '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
             '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
-            '1d426748bec4f0f3cc49448ebeb14c4350717f88287afd2aabf6738dea387d81',  # AlphaFold-2.0.0_data-dep-paths.patch
+            '7223e297b23f90816219095696bc6453910c617add60b907a0d3e869da8733bb',  # AlphaFold-2.0.0_data-dep-paths.patch
             'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',  # AlphaFold-2.0.0_n-cpu.patch
             '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27',  # AlphaFold-2.0.0_fix-scp-path.patch
         ],
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
index 0dcbedcdce8..674bcd2f935 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch
@@ -6,7 +6,7 @@ diff --git a/run_alphafold.py b/run_alphafold.py
 index 61f7ef2..81c97a0 100644
 --- a/run_alphafold.py
 +++ b/run_alphafold.py
-@@ -36,6 +36,45 @@ from alphafold.model import model
+@@ -36,6 +36,46 @@ from alphafold.model import model
  from alphafold.relax import relax
  # Internal import (7716).
  
@@ -21,6 +21,7 @@ index 61f7ef2..81c97a0 100644
 +    template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files')
 +    obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat')
 +else:
++    sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!")
 +    uniref90_database_path = None
 +    mgnify_database_path = None
 +    bfd_database_path = None

From 0dd5ba041d50c44ca79a48ba19e80c838ca869ce Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 30 Aug 2021 12:12:06 +0200
Subject: [PATCH 13/16] avoid that existing OpenMM Python bindings get wiped +
 run tests for run_alphafold.py script

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb  | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index 91d5b657e7f..084f05c3353 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -33,6 +33,11 @@ dependencies = [
 local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && "
 local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && "
 
+# required to install OpenMM Python API;
+# avoid that setup.py partially uninstalls existing OpenMM Python bindings...
+local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && "
+local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s"
+
 # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
 # see docker/Dockerfile in AlphaFold repository
 local_scp_commit = '7102c6'
@@ -50,8 +55,7 @@ components = [
         ],
         'start_dir': 'openmm-%(version)s',
         'preinstallopts': local_openmm_preinstallopts,
-        # required to install OpenMM Python API
-        'installopts': " && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s",
+        'installopts': local_openmm_installopts,
     }),
     (name, version, {
         'easyblock': 'PythonPackage',
@@ -142,12 +146,16 @@ postinstallcmds = [
     "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
     "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/",
     "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
+    # run tests for run_alphafold.py script;
+    # shouldn't do this in sanity check to avoid breaking use of --module-only
+    "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
+    "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py",
 ]
 
 sanity_check_paths = {
     'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT,
               'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts', 'stereo_chemical_props.txt'],
 }
 
 sanity_check_commands = [
@@ -156,11 +164,11 @@ sanity_check_commands = [
     "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
 ]
 
+sanity_pip_check = True
+
 modextrapaths = {
     'OPENMM_INCLUDE_PATH': 'include',
     'OPENMM_LIB_PATH': 'lib',
 }
 
-sanity_pip_check = True
-
 moduleclass = 'bio'

From a53f6c809eb2401b3d417c6369db7d0e3c52f330 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 30 Aug 2021 13:47:17 +0200
Subject: [PATCH 14/16] fix AlphaFold sanity check (stereo_chemical_props.txt
 is a file, not a directory)

---
 .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index 084f05c3353..68e9ef8b855 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -154,8 +154,8 @@ postinstallcmds = [
 
 sanity_check_paths = {
     'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT,
-              'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts', 'stereo_chemical_props.txt'],
+              'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
 }
 
 sanity_check_commands = [

From bf7ab99cb86b28677dcff6e9e27f0df8dd74bb04 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 30 Aug 2021 15:13:06 +0200
Subject: [PATCH 15/16] collapse PDBFixer easyconfig as extension into
 AlphaFold easyconfig, to avoid depending on two variants of OpenMM

---
 .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb |  9 +++--
 .../p/PDBFixer/PDBFixer-1.7-foss-2020b.eb     | 34 -------------------
 2 files changed, 7 insertions(+), 36 deletions(-)
 delete mode 100644 easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index 68e9ef8b855..624edcc5ab5 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -26,7 +26,6 @@ dependencies = [
     ('HH-suite', '3.3.0'),
     ('HMMER', '3.3.2'),
     ('Kalign', '3.3.1'),
-    ('PDBFixer', '1.7'),
     ('jax', '0.2.19'),  # also provides absl-py
 ]
 
@@ -96,6 +95,11 @@ components = [
 use_pip = True
 
 exts_list = [
+    ('PDBFixer', '1.7', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'],
+    }),
     ('toolz', '0.11.1', {
         'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'],
     }),
@@ -153,12 +157,13 @@ postinstallcmds = [
 ]
 
 sanity_check_paths = {
-    'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT,
+    'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT,
               'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'],
     'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
 }
 
 sanity_check_commands = [
+    "pdbfixer --help",
     "python -m simtk.testInstallation",
     "python -c 'import alphafold'",
     "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
diff --git a/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb b/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb
deleted file mode 100644
index 89173238ef0..00000000000
--- a/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb
+++ /dev/null
@@ -1,34 +0,0 @@
-easyblock = 'PythonPackage'
-
-name = 'PDBFixer'
-version = '1.7'
-
-homepage = 'https://github.com/openmm/pdbfixer'
-description = """PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation
-for simulating them."""
-
-toolchain = {'name': 'foss', 'version': '2020b'}
-
-source_urls = ['https://github.com/openmm/pdbfixer/archive/refs/tags/']
-sources = ['v%(version)s.tar.gz']
-checksums = ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea']
-
-dependencies = [
-    ('Python', '3.8.6'),
-    ('SciPy-bundle', '2020.11'),
-    ('OpenMM', '7.5.1'),
-]
-
-download_dep_fail = True
-use_pip = True
-
-sanity_check_paths = {
-    'files': ['bin/pdbfixer'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages'],
-}
-
-sanity_check_commands = ["pdbfixer --help"]
-
-sanity_pip_check = True
-
-moduleclass = 'bio'

From f9c5efa34b522e5f3c2d5f8ba6da4fcdd9f77591 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 30 Aug 2021 15:19:29 +0200
Subject: [PATCH 16/16] consistently use %(version)s template in list of
 patches for AlphaFold

---
 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
index 624edcc5ab5..bcfc97f3b65 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb
@@ -77,7 +77,7 @@ components = [
             'AlphaFold-%(version)s_fix-packages.patch',
             'AlphaFold-%(version)s_data-dep-paths.patch',
             'AlphaFold-%(version)s_n-cpu.patch',
-            'AlphaFold-2.0.0_fix-scp-path.patch',
+            'AlphaFold-%(version)s_fix-scp-path.patch',
         ],
         'checksums': [
             '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2',  # v2.0.0.tar.gz