.gitignore
AToM-logo.png
LICENSE
MANIFEST.in
README.md
pyproject.toml
.github/workflows/publish.yml
.github/workflows/test.yml
.github/workflows/workflow.yml
atom_openmm/__init__.py
atom_openmm/abfe_explicit.py
atom_openmm/abfe_production.py
atom_openmm/abfe_structprep.py
atom_openmm/async_re.py
atom_openmm/gibbs_sampling.py
atom_openmm/local_openmm_transport.py
atom_openmm/make_atm_system_from_amber.py
atom_openmm/make_atm_system_from_pdb.py
atom_openmm/make_atm_system_from_rcpt_lig.py
atom_openmm/ommreplica.py
atom_openmm/ommsystem.py
atom_openmm/ommworker.py
atom_openmm/openmm_async_re.py
atom_openmm/rbfe_explicit.py
atom_openmm/rbfe_production.py
atom_openmm/rbfe_structprep.py
atom_openmm/temperatureRE_explicit.py
atom_openmm/transport.py
atom_openmm/uwham.py
atom_openmm/utils/AtomUtils.py
atom_openmm/utils/__init__.py
atom_openmm/utils/config.py
atom_openmm/utils/logging.conf
atom_openmm/utils/singal_guard.py
atom_openmm/utils/timer.py
atom_openmm_unofficial.egg-info/PKG-INFO
atom_openmm_unofficial.egg-info/SOURCES.txt
atom_openmm_unofficial.egg-info/dependency_links.txt
atom_openmm_unofficial.egg-info/entry_points.txt
atom_openmm_unofficial.egg-info/requires.txt
atom_openmm_unofficial.egg-info/top_level.txt
examples/README.md
examples/ABFE/fkbp/README.md
examples/ABFE/fkbp/ligands/but.sdf
examples/ABFE/fkbp/ligands/dap.sdf
examples/ABFE/fkbp/ligands/dapp.sdf
examples/ABFE/fkbp/ligands/dmso.sdf
examples/ABFE/fkbp/ligands/dss.sdf
examples/ABFE/fkbp/ligands/prp.sdf
examples/ABFE/fkbp/ligands/thi.sdf
examples/ABFE/fkbp/receptor/fkbp.pdb
examples/ABFE/fkbp/scripts/analyze.sh
examples/ABFE/fkbp/scripts/asyncre_template.cntl
examples/ABFE/fkbp/scripts/create_cntlfile_from_template_abfe.py
examples/ABFE/fkbp/scripts/free_energies_template.sh
examples/ABFE/fkbp/scripts/prep_template.sh
examples/ABFE/fkbp/scripts/run_template.sh
examples/ABFE/fkbp/scripts/setup-atm.sh
examples/ABFE/fkbp/scripts/setup-settings.sh
examples/ABFE/fkbp/scripts/uwham_analysis.R
examples/ABFE/temoa-g1/README.md
examples/ABFE/temoa-g1/analyze.sh
examples/ABFE/temoa-g1/nodefile
examples/ABFE/temoa-g1/temoa-g1.inpcrd
examples/ABFE/temoa-g1/temoa-g1.prmtop
examples/ABFE/temoa-g1/temoa-g1_asyncre.cntl
examples/ABFE/temoa-g1/uwham_analysis.R
examples/RBFE/cdk2/README.md
examples/RBFE/cdk2/ligands/H1Q.sdf
examples/RBFE/cdk2/ligands/H1R.sdf
examples/RBFE/cdk2/ligands/H1S.sdf
examples/RBFE/cdk2/ligands/OI9.sdf
examples/RBFE/cdk2/ligands/OIU.sdf
examples/RBFE/cdk2/ligands/OIY.sdf
examples/RBFE/cdk2/receptor/cdk2.pdb
examples/RBFE/cdk2/scripts/analyze.sh
examples/RBFE/cdk2/scripts/asyncre_template.cntl
examples/RBFE/cdk2/scripts/create_cntlfile_from_template_rbfe.py
examples/RBFE/cdk2/scripts/free_energies_template.sh
examples/RBFE/cdk2/scripts/prep_template.sh
examples/RBFE/cdk2/scripts/run_template.sh
examples/RBFE/cdk2/scripts/setup-atm.sh
examples/RBFE/cdk2/scripts/setup-settings.sh
examples/RBFE/cdk2/scripts/uwham_analysis.R
examples/RBFE/eralpha/README.md
examples/RBFE/eralpha/ligands/2d.mol2
examples/RBFE/eralpha/ligands/2e.mol2
examples/RBFE/eralpha/ligands/3a.mol2
examples/RBFE/eralpha/ligands/3b.mol2
examples/RBFE/eralpha/receptor/eralpha.pdb
examples/RBFE/eralpha/scripts/analyze.sh
examples/RBFE/eralpha/scripts/asyncre_template.cntl
examples/RBFE/eralpha/scripts/create_cntlfile_from_template_rbfe.py
examples/RBFE/eralpha/scripts/free_energies_template.sh
examples/RBFE/eralpha/scripts/nodefile
examples/RBFE/eralpha/scripts/prep_template.sh
examples/RBFE/eralpha/scripts/run_template.sh
examples/RBFE/eralpha/scripts/setup-atm.sh
examples/RBFE/eralpha/scripts/setup-settings.sh
examples/RBFE/eralpha/scripts/uwham_analysis.R
examples/RBFE/protein-peptide/tiam-1/README.md
examples/RBFE/protein-peptide/tiam-1/ligands/sdc1A0F.pdb
examples/RBFE/protein-peptide/tiam-1/ligands/sdc1A0M.pdb
examples/RBFE/protein-peptide/tiam-1/ligands/sdc1A0V.pdb
examples/RBFE/protein-peptide/tiam-1/ligands/sdc1wt.pdb
examples/RBFE/protein-peptide/tiam-1/receptor/tiam1.pdb
examples/RBFE/protein-peptide/tiam-1/receptor/tiam1.pdb~
examples/RBFE/protein-peptide/tiam-1/scripts/analyze.sh
examples/RBFE/protein-peptide/tiam-1/scripts/asyncre_template.cntl
examples/RBFE/protein-peptide/tiam-1/scripts/create_cntlfile_from_template_rbfe.py
examples/RBFE/protein-peptide/tiam-1/scripts/free_energies_template.sh
examples/RBFE/protein-peptide/tiam-1/scripts/make_refvar_atoms.py
examples/RBFE/protein-peptide/tiam-1/scripts/run4_template.sh
examples/RBFE/protein-peptide/tiam-1/scripts/run_template.sh
examples/RBFE/protein-peptide/tiam-1/scripts/setup-atm.sh
examples/RBFE/protein-peptide/tiam-1/scripts/uwham_analysis.R
examples/RBFE/protein-peptide/tiam-1/scripts/vmd_template.in
examples/RBFE/temoa-g1-g4/README.md
examples/RBFE/temoa-g1-g4/analyze.sh
examples/RBFE/temoa-g1-g4/nodefile
examples/RBFE/temoa-g1-g4/temoa-g1-g4.inpcrd
examples/RBFE/temoa-g1-g4/temoa-g1-g4.prmtop
examples/RBFE/temoa-g1-g4/temoa-g1-g4_asyncre.cntl
examples/RBFE/temoa-g1-g4/uwham_analysis.R
tests/QB_A08_A07_asyncre.cntl
tests/QB_A08_A07_asyncre.json
tests/QB_A08_A07_asyncre.yaml
tests/test_atm.py
tests/test_uwham.py
tests/1STP/1STP.pdb
tests/1STP/1STP_asyncre.yaml
tests/1STP/1STP_sys.xml
tests/1STP/nodefile
tests/1STP_equil/1STP.pdb
tests/1STP_equil/1STP_0.pdb
tests/1STP_equil/1STP_0.xml
tests/1STP_equil/1STP_asyncre.yaml
tests/1STP_equil/1STP_sys.xml
tests/1STP_equil/nodefile
tests/3ptb/3ptb.pdb
tests/3ptb/3ptb_sys.pdb
tests/3ptb/3ptb_sys.xml
tests/3ptb/3ptb_sys_2.pdb
tests/3ptb/3ptb_sys_2.xml
tests/3ptb/BEN_ideal.sdf
tests/QB_A08_A07/QB_A08_A07.inpcrd
tests/QB_A08_A07/QB_A08_A07.pdb
tests/QB_A08_A07/QB_A08_A07.prmtop
tests/QB_A08_A07/QB_A08_A07_asyncre.yaml
tests/QB_A08_A07/nodefile
tests/QB_A08_A07_equil/QB_A08_A07.pdb
tests/QB_A08_A07_equil/QB_A08_A07_0.pdb
tests/QB_A08_A07_equil/QB_A08_A07_0.xml
tests/QB_A08_A07_equil/QB_A08_A07_asyncre.yaml
tests/QB_A08_A07_equil/QB_A08_A07_sys.xml
tests/QB_A08_A07_equil/nodefile
tests/QB_A08_A07_equil_sync/QB_A08_A07.pdb
tests/QB_A08_A07_equil_sync/QB_A08_A07_0.pdb
tests/QB_A08_A07_equil_sync/QB_A08_A07_0.xml
tests/QB_A08_A07_equil_sync/QB_A08_A07_asyncre.yaml
tests/QB_A08_A07_equil_sync/QB_A08_A07_sys.xml
tests/QB_A08_A07_equil_sync/nodefile
tests/QB_A08_A07_equil_sync_ats/QB_A08_A07.pdb
tests/QB_A08_A07_equil_sync_ats/QB_A08_A07_0.pdb
tests/QB_A08_A07_equil_sync_ats/QB_A08_A07_0.xml
tests/QB_A08_A07_equil_sync_ats/QB_A08_A07_asyncre.yaml
tests/QB_A08_A07_equil_sync_ats/QB_A08_A07_sys.xml
tests/QB_A08_A07_equil_sync_ats/nodefile
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r0/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r1/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r10/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r11/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r12/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r13/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r14/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r15/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r16/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r17/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r18/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r19/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r2/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r20/QB_A02_A09.out
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tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r3/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_1/r4/QB_A02_A09.out
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tests/TYK2_A02_A09/TYK2_A02_A09_r0_2/r0/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_2/r1/QB_A02_A09.out
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tests/TYK2_A02_A09/TYK2_A02_A09_r0_2/r14/QB_A02_A09.out
tests/TYK2_A02_A09/TYK2_A02_A09_r0_2/r15/QB_A02_A09.out
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