moldesign.interfaces package¶
Submodules¶
moldesign.interfaces.ambertools module¶
-
class
moldesign.interfaces.ambertools.AmberParameters(prmtop, inpcrd, job)¶ Bases:
tuple-
inpcrd¶ Alias for field number 1
-
job¶ Alias for field number 2
-
prmtop¶ Alias for field number 0
-
-
moldesign.interfaces.ambertools.ExtraAmberParameters¶ alias of
GAFFParameters
-
exception
moldesign.interfaces.ambertools.ParameterizationError[source]¶ Bases:
exceptions.Exception
-
moldesign.interfaces.ambertools.assign_forcefield(mol, **kwargs)[source]¶ run_tleap(mol, forcefields=None, parameters=None, engine=None, image=None, wait=True, jobname=None, display=True) Drives tleap to create a prmtop and inpcrd file. Specifically uses the AmberTools 16 tleap distribution.
Defaults are as recommended in the ambertools manual.
Parameters: - mol (moldesign.Molecule) – Molecule to set up
- forcefields (List[str]) – list of the names of forcefields to use (see AmberTools manual for descriptions)
- parameters (List[ExtraAmberParameters]) – (optional) list of amber parameters for non-standard residues
- engine (pyccc.Engine) – Engine to run this job on (default:
moldesign.compute.get_engine()) - image (str) – URL for the docker image
- wait (bool) – if True, block until this function completes and return the function’s return value. Otherwise, return a job object immediately that can be queried later.
- jobname – argument for
moldesign.compute.compute.run_job() - display (bool) – if True, show logging output for this job
References
Ambertools Manual, http://ambermd.org/doc12/Amber16.pdf. See page 33 for forcefield recommendations.
-
moldesign.interfaces.ambertools.build_bdna(sequence, **kwargs)[source]¶ Uses Ambertools’ Nucleic Acid Builder to build a 3D double-helix B-DNA structure.
Parameters: - sequence (str) – DNA sequence for one of the strands (a complementary sequence will automatically be created)
- engine (pyccc.Engine) – Engine to run this job on (default:
moldesign.compute.get_engine()) - image (str) – URL for the docker image
- wait (bool) – if True, block until this function completes and return the function’s return value. Otherwise, return a job object immediately that can be queried later.
- jobname – argument for
moldesign.compute.compute.run_job() - display (bool) – if True, show logging output for this job
Returns: B-DNA double helix
Return type:
-
moldesign.interfaces.ambertools.build_dna_helix(sequence, helix_type='B', **kwargs)[source]¶ Uses Ambertools’ Nucleic Acid Builder to build a 3D DNA double-helix.
Parameters: - sequence (str) – DNA sequence for one of the strands (a complementary sequence will automatically be created)
- helix_type (str) – Type of helix - ‘A’=Arnott A-DNA ‘B’=B-DNA (from standard templates and helical params), ‘LB’=Langridge B-DNA, ‘AB’=Arnott B-DNA, ‘SB’=Sasisekharan left-handed B-DNA
- engine (pyccc.Engine) – Engine to run this job on (default:
moldesign.compute.get_engine()) - image (str) – URL for the docker image
- wait (bool) – if True, block until this function completes and return the function’s return value. Otherwise, return a job object immediately that can be queried later.
- jobname – argument for
moldesign.compute.compute.run_job() - display (bool) – if True, show logging output for this job
All helix types except ‘B’ are taken from fiber diffraction data (see the refernce for details)
Returns: B-DNA double helix Return type: moldesign.Molecule References
See NAB / AmberTools documentation: http://ambermd.org/doc12/Amber16.pdf, pg 771-2
-
moldesign.interfaces.ambertools.calc_am1_bcc_charges(mol, **kwargs)[source]¶ Calculate am1 bcc charges
Parameters: mol (moldesign.Molecule) – assign partial charges to this molecule (they will be stored at mol.properties['am1-bcc'])Note
This will implicity run an AM1 energy minimization before calculating the final partial charges. For more control over this process, use the
moldesign.models.SQMPotentialenergy model to calculate the charges.Returns: AM1-BCC partial charges on each atom Return type: Mapping[moldesign.Atom, units.Scalar[charge]]
-
moldesign.interfaces.ambertools.calc_gasteiger_charges(mol, **kwargs)[source]¶ Calculate gasteiger charges
Parameters: mol (moldesign.Molecule) – assign partial charges to this molecule Returns: - gasteiger partial charges on each atom
- (they will be stored at
mol.properties['gasteiger'])
Return type: Mapping[moldesign.Atom, units.Scalar[charge]]
-
moldesign.interfaces.ambertools.parameterize(mol, charges='esp', ffname='gaff2', **kwargs)[source]¶ Parameterize
mol, typically using GAFF parameters.This will both assign a forcefield to the molecule (at
mol.ff) and produce the parameters so that they can be used in other systems (e.g., so that this molecule can be simulated embedded in a larger protein)Note
‘am1-bcc’ and ‘gasteiger’ partial charges will be automatically computed if necessary. Other charge types must be precomputed.
Parameters: - mol (moldesign.Molecule) –
- charges (str or dict) –
- what partial charges to use? Can be a dict (
{atom:charge}) OR - a string, in which case charges will be read from
mol.properties.[charges name]; typical values will be ‘esp’, ‘mulliken’, ‘am1-bcc’, etc. Use ‘zero’ to set all charges to 0 (for QM/MM and testing) - what partial charges to use? Can be a dict (
- ffname (str) – Name of the gaff-like forcefield file (default: gaff2)
Returns: - Parameters for the molecule; this object can be used to create
forcefield parameters for other systems that contain this molecule
Return type:
-
moldesign.interfaces.ambertools.run_tleap(mol, forcefields=None, parameters=None, **kwargs)[source]¶ Drives tleap to create a prmtop and inpcrd file. Specifically uses the AmberTools 16 tleap distribution.
Defaults are as recommended in the ambertools manual.
Parameters: - mol (moldesign.Molecule) – Molecule to set up
- forcefields (List[str]) – list of the names of forcefields to use (see AmberTools manual for descriptions)
- parameters (List[ExtraAmberParameters]) – (optional) list of amber parameters for non-standard residues
- engine (pyccc.Engine) – Engine to run this job on (default:
moldesign.compute.get_engine()) - image (str) – URL for the docker image
- wait (bool) – if True, block until this function completes and return the function’s return value. Otherwise, return a job object immediately that can be queried later.
- jobname – argument for
moldesign.compute.compute.run_job() - display (bool) – if True, show logging output for this job
References
Ambertools Manual, http://ambermd.org/doc12/Amber16.pdf. See page 33 for forcefield recommendations.
moldesign.interfaces.biopython_interface module¶
-
moldesign.interfaces.biopython_interface.biopy_to_mol(struc)[source]¶ Convert a biopython PDB structure to an MDT molecule.
Note
Biopython doesn’t deal with bond data, so no bonds will be present in the Molecule
Parameters: struc (Bio.PDB.Structure.Structure) – Biopython PDB structure to convert Returns: converted molecule Return type: moldesign.Molecule
-
moldesign.interfaces.biopython_interface.get_mmcif_assemblies(fileobj=None, mmcdata=None)[source]¶ Parse an mmCIF file, return biomolecular assembly specifications
Parameters: - fileobj (file-like) – File-like object for the PDB file (this object will be rewound before returning)
- mmcdata (dict) – dict version of complete mmCIF data structure (if passed, this will not be read again from fileobj)
Returns: dict mapping assembly ids to BioAssembly instances
Return type: Mapping[str, BioAssembly]
-
moldesign.interfaces.biopython_interface.parse_mmcif(f)[source]¶ Parse an mmCIF file (using the Biopython parser) and return a molecule
Note
This routine is not currently called by any part of the user-facing API! The OpenBabel parser appears to give more accurate results for the time being. The molecules created using this routine will NOT have any bond topology!
Parameters: f (file) – file-like object containing the mmCIF file Returns: parsed molecule Return type: moldesign.Molecule
-
moldesign.interfaces.biopython_interface.parse_pdb(f)[source]¶ Parse a PDB file (using the Biopython parser) and return the basic structure
Note
This structure will be missing some key data - most notably bonds, but also any biomolecular assembly information. Therefore, our default parser combines this routine with a few other methods to create the final Molecule object
See also
moldesign.fileio.read_pdb
Parameters: f (file) – file-like object containing the PDB file Returns: parsed molecule Return type: moldesign.Molecule
moldesign.interfaces.nbo_interface module¶
-
moldesign.interfaces.nbo_interface.make_nbo_input_file(mol, requests)[source]¶ Parameters: mol (moldesign.molecules.Molecule) – Returns:
moldesign.interfaces.openbabel module¶
-
moldesign.interfaces.openbabel.add_hydrogen(mol, ph=None, wait=True)[source]¶ Add hydrogens to saturate atomic valences.
Parameters: - mol (moldesign.Molecule) – Molecule to saturate
- ph (float) – Assign formal charges and protonation using pH model; if None (the default), neutral protonation will be assigned where possible.
Returns: New molecule with all valences saturated
Return type:
-
moldesign.interfaces.openbabel.from_smiles(smi, name=None, wait=True)[source]¶ Translate a smiles string to a 3D structure. This method uses OpenBabel to generate a plausible 3D conformation of the 2D SMILES topology. We only use the first result from the conformation generator.
Parameters: Returns: the translated molecule
Return type:
-
moldesign.interfaces.openbabel.guess_bond_orders(mol, wait=True)[source]¶ Use OpenBabel to guess bond orders using geometry and functional group templates.
Parameters: mol (moldesign.Molecule) – Molecule to perceive the bonds of Returns: New molecule with assigned bonds Return type: moldesign.Molecule
-
moldesign.interfaces.openbabel.mol_to_pybel(mdtmol)[source]¶ Translate a moldesign molecule object into a pybel molecule object.
Note
The focus is on translating topology and biomolecular structure - we don’t translate any metadata.
Parameters: mdtmol (moldesign.Molecule) – molecule to translate Returns: translated molecule Return type: pybel.Molecule
-
moldesign.interfaces.openbabel.pybel_to_mol(pbmol, atom_names=True, reorder_atoms_by_residue=False, primary_structure=True, **kwargs)[source]¶ Translate a pybel molecule object into a moldesign object.
Note
The focus is on translating topology and biomolecular structure - we don’t translate any metadata.
Parameters: - pbmol (pybel.Molecule) – molecule to translate
- atom_names (bool) – use pybel’s atom names (default True)
- reorder_atoms_by_residue (bool) – change atom order so that all atoms in a residue are stored contiguously
- primary_structure (bool) – translate primary structure data as well as atomic data
- **kwargs (dict) – keyword arguments to moldesign.Molecule __init__ method
Returns: translated molecule
Return type:
-
moldesign.interfaces.openbabel.read_file(filename, name=None, format=None)[source]¶ Read a molecule from a file
Note
Currently only reads the first conformation in a file
Parameters: Returns: parsed result
Return type:
-
moldesign.interfaces.openbabel.read_stream(filelike, format, name=None)[source]¶ Read a molecule from a file-like object
Note
Currently only reads the first conformation in a file
Parameters: Returns: parsed result
Return type:
-
moldesign.interfaces.openbabel.read_string(molstring, format, name=None, wait=True)[source]¶ Read a molecule from a file-like object
Note
Currently only reads the first conformation in a file
Parameters: Returns: parsed result
Return type:
-
moldesign.interfaces.openbabel.write_file(mol, filename=None, mode='w', format=None)[source]¶ Write molecule to a file
Parameters: - mol (moldesign.Molecule) – molecule to write
- filename (str) – File to write to
- mode (str) – Writing mode (e.g. ‘w’ to overwrite, the default, or ‘a’ to append)
- format (str) – File format: pdb, sdf, mol2, bbll, etc.
-
moldesign.interfaces.openbabel.write_string(mol, format, wait=True)[source]¶ Create a file from the passed molecule
Parameters: - mol (moldesign.Molecule) – molecule to write
- format (str) – File format: pdb, sdf, mol2, bbll, etc.
Returns: contents of the file
Return type:
moldesign.interfaces.openmm module¶
-
moldesign.interfaces.openmm.mol_to_topology(mol)[source]¶ Create an openmm topology object from an MDT molecule
Parameters: mol (moldesign.Molecule) – molecule to copy topology from Returns: topology of the molecule Return type: simtk.openmm.app.Topology
-
moldesign.interfaces.openmm.pint2simtk(quantity)[source]¶ Converts a quantity from the pint to simtk unit system. Note SimTK appears limited, esp for energy units. May need to have pint convert to SI first
-
moldesign.interfaces.openmm.simtk2pint(quantity, flat=False)[source]¶ Converts a quantity from the simtk unit system to a quantity from the pint unit system :param quantity: :param flat: if True, flatten 3xN arrays to 3N
-
moldesign.interfaces.openmm.topology_to_mol(topo, name=None, positions=None, velocities=None, assign_bond_orders=True)[source]¶ Convert an OpenMM topology object into an MDT molecule.
Parameters: - topo (simtk.openmm.app.topology.Topology) – topology to convert
- name (str) – name to assign to molecule
- positions (list) – simtk list of atomic positions
- velocities (list) – simtk list of atomic velocities
- assign_bond_orders (bool) – assign bond orders from templates (simtk topologies do not store bond orders)
moldesign.interfaces.opsin_interface module¶
moldesign.interfaces.parmed_interface module¶
moldesign.interfaces.pdbfixer_interface module¶
-
moldesign.interfaces.pdbfixer_interface.add_water(mol, min_box_size=None, padding=None, ion_concentration=None, neutralize=True, positive_ion='Na+', negative_ion='Cl-', wait=True)[source]¶ Solvate a molecule in a water box with optional ions
Parameters: - mol (moldesign.Molecule) – solute molecule
- min_box_size (u.Scalar[length] or u.Vector[length]) – size of the water box - either
a vector of x,y,z dimensions, or just a uniform cube length. Either this or
padding(or both) must be passed - padding (u.Scalar[length]) – distance to edge of water box from the solute in each dimension
- neutralize (bool) – add ions to neutralize solute charge (in addition to specified ion concentration)
- positive_ion (str) – type of positive ions to add, if needed. Allowed values (from OpenMM modeller) are Cs, K, Li, Na (the default) and Rb
- negative_ion (str) – type of negative ions to add, if needed. Allowed values (from OpenMM modeller) are Cl (the default), Br, F, and I
- ion_concentration (float or u.Scalar[molarity]) – ionic concentration in addition to whatever is needed to neutralize the solute. (if float is passed, we assume the number is Molar)
Returns: new Molecule object containing both solvent and solute
Return type:
moldesign.interfaces.pyscf_interface module¶
-
class
moldesign.interfaces.pyscf_interface.StatusLogger(description, columns, logger)[source]¶ Bases:
object-
LEN= 15¶
-
-
moldesign.interfaces.pyscf_interface.basis_values(mol, basis, coords, coeffs=None, positions=None, wait=True)[source]¶ Calculate the orbital’s value at a position in space
Parameters: - mol (moldesign.Molecule) – Molecule to attach basis set to
- basis (moldesign.orbitals.BasisSet) – set of basis functions
- coords (Array[length]) – List of coordinates (with shape
(len(coords), 3)) - coeffs (Vector) – List of ao coefficients (optional; if not passed, all basis fn values are returned)
Returns: - if
coeffsis not passed, an array of basis fn values at each coordinate. Otherwise, a list of orbital values at each coordinate
Return type: Array[length]
moldesign.interfaces.qmmm module¶
moldesign.interfaces.qtrfit module¶
Interface to quaternion-based atom alignment routines.
This code has been translated from Fortran to Python
-
moldesign.interfaces.qtrfit.qtrfit(mol, pos, ref, massweight=True)[source]¶ Transform the atomic positions in
posto minimize the overall distance to those inrefThis function minimizes the distance between pos and ref. If `massweight`=True, we minimize the mass-weighted distance:
- ..math::
- D = sqrt{ sum_{i=1}^{text{N}} m_i left| mathbf{pos}_i - mathbf{ref}_i right|^2 }
Otherwise, the root-squared distance is used:
- ..math::
- D = sqrt{ sum_{i=1}^{text{N}} left| mathbf{pos}_i - mathbf{ref}_i right|^2 }
Parameters: - mol (moldesign.Molecule) – molecule that these arrays describe
- pos (u.Array) – The Nx3 array to be rotated
- ref (u.Array) – The Nx3 array to match
- massweight (bool) – whether to use mass-weighted coordinates (the default)
Returns: translated and rotated version of pos with minimum RMSD
Return type: u.Array
References
TODO: reference to original qtrfit code (and license, if it exists)