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All the changes from Shahlo's copy of FAST and some of mine too #8

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c429ac0
added specific contacts analysis wrapper
Jun 3, 2021
1f827db
new analysis methods and no pocket edge case
Nov 22, 2021
d8e1cf0
added new analysis methods and sasa clustering
Oct 29, 2021
5f36c1b
added analysis script for calculating axial angle defined by referenc…
Nov 30, 2021
301d964
fixed minor bug in top pockets which double summed pocket volumes
Nov 30, 2021
1d9eae9
added case for pbc cluster in gromacs processing
Jan 22, 2023
af12ab5
A few bug fixes
Jan 22, 2023
3f8be96
support for singularity run in gromacs submission and processing
Jan 29, 2023
384490c
add condition for no source command if singularity option enabled
Jan 29, 2023
2c0b1b5
semicolon to colon bug fix
Jan 29, 2023
6ca5e8b
another small bug fix with misspelled variable
Jan 29, 2023
3f2d26a
adding gpu specs to gromax md run commands for nb bonded pme
Jan 29, 2023
87fe20c
bug fix in md run command, missed a space
Jan 29, 2023
1072281
fixed a bug in trjconv commands
Jan 30, 2023
69cf1b0
bug fix
Jan 30, 2023
e0cc010
added center_group to gromax processing, limited support
Mar 15, 2023
f8032b5
Move all the fast stuff into src/fast
Pandapip1 Jul 31, 2025
7bc2e9e
Clean up submission wrappers and add mem_per_cpu support
Pandapip1 Jul 31, 2025
3fef541
And then the treewide reformat
Pandapip1 Jul 31, 2025
e3fedff
Make analysis/pockets.py not abuse the first index
Pandapip1 Jul 31, 2025
b0d6819
Merge the divergent analysis implementations
Pandapip1 Jul 31, 2025
adafbfd
Remove hardcoded absolute path in md_gen/upside.py
Pandapip1 Jul 31, 2025
14bf183
Rewrite gromacs md_gen
Pandapip1 Aug 4, 2025
ddfa62b
Update project to use pyproject.toml instead of setup.py
Pandapip1 Aug 4, 2025
2be78c5
Add enspara to dependencies
Pandapip1 Aug 5, 2025
0e6da1c
Add pocketminer geometric component
Pandapip1 Jul 21, 2025
8c22321
Add addl_analysis_objs option
Pandapip1 Aug 19, 2025
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8 changes: 4 additions & 4 deletions examples/FAST-tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@
"from enspara.cluster import KCenters\n",
"from enspara.msm import MSM\n",
"from fast import AdaptiveSampling\n",
"from fast.md_gen.gromax import Gromax, GromaxProcessing\n",
"from fast.md_gen.gromacs import Gromacs, GromacsProcessing\n",
"from fast.msm_gen import ClusterWrap\n",
"from fast import DistWrap, PocketWrap\n",
"from fast.sampling import rankings, scalings\n",
Expand Down Expand Up @@ -246,12 +246,12 @@
" gro_submission = LSFSub(\n",
" q_name, n_tasks=n_cpus_gromacs, job_name=sim_name, gpu=gpu_info, R='\"span[hosts=1]\"')\n",
" \n",
" gro_processing = GromaxProcessing(\n",
" gro_processing = GromacsProcessing(\n",
" align_group=10, output_group=10, pbc=pbc, ur=ur)\n",
" # In this specific example, 10 is the index for protein. Check your\n",
" # .ndx file and select the index that chooses protein.\n",
" \n",
" sim_obj = Gromax(\n",
" sim_obj = Gromacs(\n",
" top_file=top_filename, mdp_file=mdp_filename, n_cpus=n_cpus_gromacs,\n",
" n_gpus=n_gpus_gromacs, processing_obj=gro_processing,\n",
" submission_obj=gro_submission, pin='on',\n",
Expand Down Expand Up @@ -419,7 +419,7 @@
"gro_submission = LSFSub(\n",
" q_name, n_tasks=n_cpus_gromacs, job_name=sim_name, gpu=gpu_info, R='\"span[hosts=1]\"')\n",
" \n",
"--This gets passed in as a parameter to make a **Gromax** object which will ultimately generate the following:"
"--This gets passed in as a parameter to make a **Gromacs** object which will ultimately generate the following:"
]
},
{
Expand Down
257 changes: 0 additions & 257 deletions md_gen/gromax.py
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41 changes: 41 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"

[project]
name = "fast"
version = "0"
description = ""
readme = "README.md"
requires-python = ">=3.7"
license = { text = "LGPL2.1" }
authors = []
dependencies = [
"enspara",
]

[project.optional-dependencies]
dev = [
"black",
"ruff",
"pytest"
]
pocketminer = [
"pypocketminer",
"scipy",
"trimesh",
"networkx",
"manifold3d" # TODO replace with blender
]

[tool.setuptools]
package-dir = { "" = "src" }

[tool.setuptools.packages.find]
where = ["src"]

[tool.pytest.ini_options]
minversion = "6.0"
testpaths = [
"tests"
]
11 changes: 10 additions & 1 deletion __init__.py → src/fast/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,22 @@
from .analysis.minimize import MinimizeWrap
from .analysis.rmsd import RMSDWrap
from .analysis.pockets import PocketWrap
from .analysis.pockets import SpecificPockets
from .analysis.distances import DistWrap
from .analysis.specific_contacts import SpecificContactsWrap
from .analysis.interface_contacts import InterfaceContactWrap, ContactCountWrap
from .analysis.multi_interface_dissociation import (
MultipleInterfaceDissociationWrap,
ConstrainedTargetInterfaceDissociationWrap,
)
from .analysis.axial_angle import AxialAngleWrap

# simulations wrapper
from .md_gen.gromax import Gromax, GromaxProcessing
from .md_gen.gromacs import Gromacs, GromacsProcessing

# clustering wrapper
from .msm_gen.clustering import ClusterWrap
from .msm_gen.sasa_clustering import SASAClusterWrap

# save states wrapper
from .msm_gen.save_states import SaveWrap
Expand Down
Empty file added src/fast/analysis/__init__.py
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