Add missing file changes

docs/features.rst

@@ -0,0 +1,155 @@
+Molecular Design Toolkit Features
+=================================
+
+.. contents::
+  :depth: 5
+
+
+
+Simulation methods
+------------------
+
+Energy models
+^^^^^^^^^^^^^
+
+**Methods**
+
+ - :meth:`Molecule.calculate` Calculate molecular properties using the assigned energy model
+
+ - :meth:`Molecule.minimize` Perform an energy minimization using the assigned energy model
+
+**Classical**
+
+ - :class:`models.Forcefield` Generic Forcefield energy model (automatically chosen implementation)
+
+ - :class:`models.OpenMMEnergyModel` OpenMM energy kernel for Amber/CHARMM-like forcefields
+
+ - :class:`models.SanderEnergyModel` Sander energy kernel (from AmberTools) for Amber/CHARMM-like forcefields
+
+ - :class:`models.Spring` A single harmonic bond 2 atoms (for testing and toy models)
+
+ - :class:`models.HarmonicOscillator` A 1-D Harmonic oscillator centered at x=0 (for testing and toy models)
+
+**Quantum**
+
+ - :class:`models.RHF` Generic restricted Hartree-Fock (automatically chosen implementation)
+
+ - :class:`models.DFT` Generic density functional theories (automatically chosen implementation)
+
+ - :class:`models.Semiempirical` Generic semiempirical theories (automatically chosen implementation)
+
+ - :class:`models.PySCF` PySCF *ab initio* QM energy kernel, includes implementations for a large number of quantum energy models, including RHF, DFT, CASCI, CASSCF, MP2, and coupled cluster
+
+ - :class:`models.SQM` SQM semi-empirical energy kernel (from AmberTools), includes implementations for a large number of semiempirical models, including MNDO, AM1, PM3, PM6, DFTB
+
+
+Integrators
+^^^^^^^^^^^
+
+ - :class:`integrators.VelocityVerlet` Generic Velocity Verlet dynamics (automatically chosen implementation)
+
+ - :class:`integrators.Langevin` Generic Langevin type (automatically chosen implementation)
+
+ - :class:`integrators.OpenMMVerlet` Velocity Verlet dynamics for use with OpenMM energy models
+
+ - :class:`integrators.OpenMMLangevin` Velocity Langevin dynamics for use with OpenMM energy models
+
+ - :class:`integrators.SurfaceHopping` Multi-state surface hopping dynamics using fewest switched. Implementation: internal.
+
+
+Interactive Widgets
+-------------------
+
+ - :class:`viewer.Configurator` Automatically generates user interfaces for configuring simulations
+
+ - :class:`viewer.GeometryViewer` 3D molecular viewer
+
+ - :class:`viewer.ChemicalGraphViewer` 2D molecular viewer
+
+ - :class:`widgets.OrbitalViewer` 3D molecular orbital viewer
+
+ - :class:`widgets.BondSelector` widget for building lists of atoms and/or bonds
+
+ - :class:`widgets.ResidueSelector` widget for building lists of atoms and/or residues
+
+ - :class:`widgets.GeometryBuilder` widget for manipulating internal coordinates
+
+ - :class:`widgets.Symmetrizer` widget for displaying and manipulating molecular symmetry groups
+
+ - :class:`widgets.ParameterizationDisplay` 3D display of issues when assigning forcefield parameters
+
+
+Data analysis
+-------------
+
+Simulation results are stored in numpy arrays with an explicit unit system based on ``pint`` for easy analysis and comparison. A few are shown here as examples:
+
+**Static properties**
+
+ - :meth:`Molecule.potential_energy`, :meth:`Molecule.forces`, :meth:`Molecule.dipole_moment`, :meth:`Molecule.wfn` Molecular properties calcualted by energy models: the potential energy, force array, dipole moment vector, and electronic wavefunction, respectively.
+
+ - :class:`orbitals.ElectronWfn` A data structure storic electronic wavefunction information, as calculated by a quantum energy model.
+
+ - :meth:`ElectronWfn.aobasis.fock` :meth:`ElectronWfn.aobasis.overlaps` The Fock and overlap matrices in the AO basis
+
+ - :meth:`ElectronWfn.canonical.fock` :meth:`ElectronWfn.canonical.overlaps` The Fock and overlap matrices in the canonical orbital basis
+
+ - :meth:`ElectronWfn.canonical.coeffs` The canonical orbital coefficients in the AO basis
+
+**Trajectory properties**
+
+ - :class:`Trajectory` A data structure storing a series of molecular structures with associated properties
+
+ - :meth:`Trajectory.rmsd` Calculate a timeseries of RMSD values over the course of a trajectory
+
+ - :meth:`Trajectory.distance`, :meth:`Trajectory.angle`, :meth:`Trajectory.dihedral` Return a timeseries of distances, angles, or dihedral angles over the course of a trajectory
+
+ - :meth:`Trajectory.time` :meth:`Trajectory.potential_energy` :meth:`Trajectory.kinetic_temperature` ``...`` - Return timeseries of times, energies, temperatures, etc. over the course of a trajectory
+
+
+Conversions
+-----------
+
+**Files and databases**
+
+ - :meth:`read`, :meth:`write` read/write molecular file formats. Supports PDB, mmCIF, SDF, XYZ, MOL2, and pickled objects. Implementations: OpenBabel, BioPython, or internal.
+
+ - :meth:`from_smiles` Convert a SMILES string into an MDT molecule with a 3D structure. Implementation: OpenBabel.
+
+ - :meth:`from_name` Convert an IUPAC chemical name into an MDT molecule with a 3D structure. Implementation: Opsin.
+
+ - :meth:`from_pdb` Download and create a molecule object from a PDB code. Implementation: BioPython.
+
+
+**Python objects**
+
+MDT molecules can also be converted into objects for a variety of other Python chemistry libraries:
+
+ - :meth:`interfaces.mol_to_pybel`, :meth:`interfaces.pybel_to_mol` Convert an MDT molecule to/from a `pybel` (i.e. OpenBabel) molecule object.
+
+ - :meth:`interfaces.mol_to_pyscf`, :meth:`interfaces.pyscf_to_mol` Convert an MDT molecule to/from a PySCF molecule object.
+
+ - :meth:`interfaces.topology_to_mol`, :meth:`interfaces.mol_to_topology`  Convert an OpenMM topology object to/from an MDT molecule
+
+
+Tools
+-----
+
+**Topology manipulation**
+
+ - :meth:`add_hydrogen` Saturate a molecule's valence with hydrogens. Implementation: OpenBabel.
+
+ - :meth:`guess_bond_orders` Assign bond orders based on geometry and/or topology. Implementation: OpenBabel.
+
+ - :meth:`mutate_residues` Mutate DNA bases and amino acid residues. Implementation: PDBFixer.
+
+ - :meth:`add_water_box` Add water box with optional ions. Implementation: PDBFixer.
+
+
+**Forcefields**
+
+ - :meth:`assign_forcefield` Returns a new molecule with forcefield assignments and any missing atoms. Implementation: AmberTools/tLeap.
+
+ - :meth:`parameterize` Assign forcefield parameters to a molecule. Implementation: Ambertools/antechamber.
+
+ - :meth:`calc_am1_bcc_charges` :meth:`calc_gasteiger_charges` :meth:`calc_esp_charges` Calculate partial charges for use with a forcefield. Implementation: Ambertools/antechamber and Ambertools/SQM

moldesign/_static_data/pint_atomic_units.txt

@@ -8,3 +8,4 @@ ps = picosecond = 1.0 * piscosecond
 amu = 1.0 * atomic_mass_units
 ang = 1.0 * angstrom
 eV = electron_volt
+debye = 0.393430307 * elementary_charge * bohr