LICENSE.md
MANIFEST.in
README.md
requirements.txt
setup.py
intermol/__init__.py
intermol/atom.py
intermol/convert.py
intermol/decorators.py
intermol/exceptions.py
intermol/molecule.py
intermol/moleculetype.py
intermol/orderedset.py
intermol/system.py
intermol/utils.py
intermol/version.py
intermol.egg-info/PKG-INFO
intermol.egg-info/SOURCES.txt
intermol.egg-info/dependency_links.txt
intermol.egg-info/not-zip-safe
intermol.egg-info/requires.txt
intermol.egg-info/top_level.txt
intermol/amber/__init__.py
intermol/charmm/__init__.py
intermol/desmond/__init__.py
intermol/desmond/cmap_parameters.py
intermol/desmond/desmond_parser.py
intermol/forces/__init__.py
intermol/forces/abstract_2_virtual_type.py
intermol/forces/abstract_3_virtual_type.py
intermol/forces/abstract_4_virtual_type.py
intermol/forces/abstract_angle_type.py
intermol/forces/abstract_atom_type.py
intermol/forces/abstract_bond_type.py
intermol/forces/abstract_dihedral_type.py
intermol/forces/abstract_nonbonded_type.py
intermol/forces/abstract_pair_type.py
intermol/forces/abstract_type.py
intermol/forces/atom_c_type.py
intermol/forces/atom_sigeps_type.py
intermol/forces/bending_torsion_dihedral_type.py
intermol/forces/buckingham_nonbonded_type.py
intermol/forces/connection_bond_type.py
intermol/forces/constraint.py
intermol/forces/convert_dihedrals.py
intermol/forces/cosine_angle_type.py
intermol/forces/cosine_squared_angle_type.py
intermol/forces/cross_bond_angle_angle_type.py
intermol/forces/cross_bond_bond_angle_type.py
intermol/forces/cubic_bond_type.py
intermol/forces/exclusions.py
intermol/forces/fene_bond_type.py
intermol/forces/fene_expandable_bond_type.py
intermol/forces/forcedata.py
intermol/forces/forcefunctions.py
intermol/forces/four_fdn_virtual_type.py
intermol/forces/fourier_dihedral_type.py
intermol/forces/g96_bond_type.py
intermol/forces/harmonic_angle_type.py
intermol/forces/harmonic_bond_type.py
intermol/forces/harmonic_potential_bond_type.py
intermol/forces/improper_harmonic_dihedral_type.py
intermol/forces/lj_c_nonbonded_type.py
intermol/forces/lj_c_pair_type.py
intermol/forces/lj_default_pair_type.py
intermol/forces/lj_sigeps_nonbonded_type.py
intermol/forces/lj_sigeps_pair_type.py
intermol/forces/ljq_c_pair_type.py
intermol/forces/ljq_default_pair_type.py
intermol/forces/ljq_sigeps_pair_type.py
intermol/forces/make_forces.py
intermol/forces/morse_bond_type.py
intermol/forces/nonlinear_bond_type.py
intermol/forces/proper_periodic_dihedral_type.py
intermol/forces/quartic_angle_type.py
intermol/forces/quartic_bond_type.py
intermol/forces/quartic_breakable_bond_type.py
intermol/forces/rb_dihedral_type.py
intermol/forces/restricted_bending_angle_type.py
intermol/forces/restricted_bending_dihedral_type.py
intermol/forces/rigidwater.py
intermol/forces/three_fad_virtual_type.py
intermol/forces/three_fd_virtual_type.py
intermol/forces/three_linear_virtual_type.py
intermol/forces/three_out_virtual_type.py
intermol/forces/torsion_torsion_cmap.py
intermol/forces/trig_dihedral_type.py
intermol/forces/two_virtual_type.py
intermol/forces/urey_bradley_angle_type.py
intermol/forces/urey_bradley_noharm_angle_type.py
intermol/gromacs/__init__.py
intermol/gromacs/grofile_parser.py
intermol/gromacs/gromacs_parser.py
intermol/lammps/__init__.py
intermol/lammps/lammps_parser.py
intermol/tests/README.md
intermol/tests/__init__.py
intermol/tests/test_all.py
intermol/tests/testing_tools.py
intermol/tests/__pycache__/__init__.cpython-39.pyc
intermol/tests/__pycache__/test_all.cpython-39-pytest-7.2.0.pyc
intermol/tests/__pycache__/testing_tools.cpython-39.pyc
intermol/tests/amber/min.in
intermol/tests/amber/min_vacuum.in
intermol/tests/amber/stress_tests/benzene_cyclohexane/benzene_cyclohexane_10_500.inpcrd
intermol/tests/amber/stress_tests/benzene_cyclohexane/benzene_cyclohexane_10_500.prmtop
intermol/tests/amber/stress_tests/benzene_cyclohexane/benzene_cyclohexane_10_500_from_amber.gro
intermol/tests/amber/stress_tests/benzene_cyclohexane/benzene_cyclohexane_10_500_from_amber.top
intermol/tests/amber/stress_tests/solv/solv.prmtop
intermol/tests/amber/stress_tests/solv/solv.rst7
intermol/tests/amber/unit_tests/abs/abs.inpcrd
intermol/tests/amber/unit_tests/abs/abs.prmtop
intermol/tests/amber/unit_tests/abs/abs_from_amber.gro
intermol/tests/amber/unit_tests/abs/abs_from_amber.top
intermol/tests/amber/unit_tests/biphenyl/biphenyl.crd
intermol/tests/amber/unit_tests/biphenyl/biphenyl.prmtop
intermol/tests/amber/unit_tests/biphenyl/biphenyl_from_amber.gro
intermol/tests/amber/unit_tests/biphenyl/biphenyl_from_amber.top
intermol/tests/amber/unit_tests/phenol/phenol.crd
intermol/tests/amber/unit_tests/phenol/phenol.prmtop
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intermol/tests/amber/unit_tests/trx/trx.inpcrd
intermol/tests/amber/unit_tests/trx/trx.prmtop
intermol/tests/amber/unit_tests/trx/trx_from_amber.gro
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intermol/tests/amber/unit_tests/znf/znf.prmtop
intermol/tests/amber/unit_tests/znf/znf.rst
intermol/tests/amber/unit_tests/znf/znf_from_amber.gro
intermol/tests/amber/unit_tests/znf/znf_from_amber.top
intermol/tests/desmond/onepoint.cfg
intermol/tests/desmond/onepoint_vacuum.cfg
intermol/tests/desmond/stress_tests/2BP4_amber99_bulk/2BP4_amber99_bulk.cms
intermol/tests/desmond/stress_tests/2BP4_charmm27_bulk/2BP4_charmm27_bulk.cms
intermol/tests/desmond/stress_tests/2BP4_opls_bulk/2BP4_opls_bulk.cms
intermol/tests/desmond/stress_tests/DNA_bulk/DNA_bulk.cms
intermol/tests/desmond/stress_tests/HIV_wild_type_bulk/HIV_wild_type_bulk.cms
intermol/tests/desmond/stress_tests/Rilpivirine_bulk/Rilpivirine_bulk.cms
intermol/tests/desmond/stress_tests/lck_complex_bulk/lck_complex_bulk.cms
intermol/tests/desmond/stress_tests/lck_solvent_bulk/lck_solvent_bulk.cms
intermol/tests/desmond/stress_tests/onemol_bulk/onemol_bulk.cms
intermol/tests/desmond/stress_tests/protein_bulk/protein_bulk.cms
intermol/tests/desmond/stress_tests/simulated_annealing_example_bulk/simulated_annealing_example_bulk.cms
intermol/tests/desmond/unit_tests/frag_amber99SB_ILDN_vacuum/frag_amber99SB-ILDN_vacuum.cms
intermol/tests/desmond/unit_tests/frag_charmm_vacuum/frag_charmm_vacuum.cms
intermol/tests/desmond/unit_tests/frag_opls2001_vacuum/frag_opls2001_vacuum.cms
intermol/tests/desmond/unit_tests/harmangle_vacuum/harmangle_vacuum.cms
intermol/tests/desmond/unit_tests/harmbond_vacuum/harmbond_vacuum.cms
intermol/tests/desmond/unit_tests/improperharm_dihedral_vacuum/improperharm_dihedral_vacuum.cms
intermol/tests/desmond/unit_tests/oplsstyle_dihedral_vacuum/oplsstyle_dihedral_vacuum.cms
intermol/tests/desmond/unit_tests/propertrig_dihedral_vacuum/propertrig_dihedral_vacuum.cms
intermol/tests/desmond/unit_tests/ubangle_vacuum/ubangle_vacuum.cms
intermol/tests/gromacs/grompp.mdp
intermol/tests/gromacs/grompp_vacuum.mdp
intermol/tests/gromacs/stress_tests/2PPN_bulk/2PPN_bulk.gro
intermol/tests/gromacs/stress_tests/2PPN_bulk/2PPN_bulk.top
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intermol/tests/gromacs/stress_tests/2PPN_bulk/oplsaa.ff/ffnonbonded.itp
intermol/tests/gromacs/stress_tests/2PPN_bulk/oplsaa.ff/forcefield.itp
intermol/tests/gromacs/stress_tests/2PPN_bulk/oplsaa.ff/gbsa.itp
intermol/tests/gromacs/stress_tests/2PPN_bulk/oplsaa.ff/tip3p.itp
intermol/tests/gromacs/stress_tests/charmm_bilayer/CLA.itp
intermol/tests/gromacs/stress_tests/charmm_bilayer/DPPC.itp
intermol/tests/gromacs/stress_tests/charmm_bilayer/POT.itp
intermol/tests/gromacs/stress_tests/charmm_bilayer/TIP3.itp
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intermol/tests/gromacs/stress_tests/hostguest_bulk/1_GMX.itp
intermol/tests/gromacs/stress_tests/hostguest_bulk/1atomtypes.itp
intermol/tests/gromacs/stress_tests/hostguest_bulk/cucurbit_7_uril_GMX.itp
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intermol/tests/gromacs/stress_tests/hostguest_bulk/amber03.ff/tip3p.itp
intermol/tests/gromacs/stress_tests/micelle_bulk/SDS.itp
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intermol/tests/gromacs/stress_tests/micelle_bulk/ffCADMOLbon.itp
intermol/tests/gromacs/stress_tests/micelle_bulk/ffCADMOLnb.itp
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intermol/tests/gromacs/stress_tests/micelledrug_bulk/SDS.itp
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intermol/tests/gromacs/stress_tests/solutewater_bulk/solutewater_bulk.gro
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intermol/tests/gromacs/stress_tests/spce4_bulk/spce4_bulk.gro
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