parmed.amber.AmoebaParm

class parmed.amber.AmoebaParm(prm_name=None, xyz=None, box=None, rst7_name=None)

Tinker Topology (parm7 format) class defining the AMOEBA force field. Gives low, and some high, level access to topology data. You can interact with the raw data in the topology file directly or interact with some of the high-level classes comprising the system topology and parameters.

Parameters

prm_namestr=None

If provided, this file is parsed and the data structures will be loaded from the data in this file

rst7_namestr=None

If provided, the coordinates and unit cell dimensions from the provided Amber inpcrd/restart file will be loaded into the molecule

Attributes

parm_datadict {str

A dictionary that maps FLAG names to all of the data contained in that section of the Amber file.

formatsdict {str

A dictionary that maps FLAG names to the FortranFormat instance in which the data is stored in that section

parm_commentsdict {str

A dictionary that maps FLAG names to the list of COMMENT lines that were stored in the original file

flag_listlist

An ordered list of all FLAG names. This must be kept synchronized with parm_data, formats, and parm_comments such that every item in flag_list is a key to those 3 dicts and no other keys exist

versionstr

The VERSION string from the Amber file

namestr

The file name of the originally parsed file (set to the fname parameter)

atomsAtomList(Atom)

List of all atoms in the system

residuesResidueList(Residue)

List of all residues in the system

bondsTrackedList(Bond)

List of bonds between two atoms in the system

anglesTrackedList(Angle)

List of regular angles between three atoms in the system

dihedralsTrackedList(Angle)

List of all proper torsions between 4 atoms in the system

urey_bradleysTrackedList(UreyBradley)

List of all Urey-Bradley terms between 2 atoms connected by an angle

trigonal_anglesTrackedList(TrigonalAngle)

List of all trigonal angle terms

out_of_plane_bendsTrackedList(OutOfPlaneBend)

List of all out-of-plane bending terms

pi_torsionsTrackedList(PiTorsion)

List of all pi-torsion terms

stretch_bendsTrackedList(StretchBend)

List of all stretch-bending terms

torsion_torsionsTrackedList(TorsionTorsion)

List of all coupled torsion-torsion terms

chiral_framesTrackedList(ChiralFrame)

List of all chiral centers

multipole_framesTrackedList(MultipoleFrame)

List of all multipole frames of reference

adjustsTrackedList(NonbondedException)

List of all nonbonded exception parameters used for adjusting nonbonded interactions between particular pairs of atoms

boxlist of 6 floats

Periodic boundary unit cell dimensions and angles

bond_typesTrackedList(BondType)

The bond types containing the parameters for each bond stretching term

angle_typesTrackedList(AngleType)

The angle types containing the parameters for each angle bending term

dihedral_typesTrackedList(DihedralType)

The dihedral types containing the parameters for each torsional term

urey_bradley_typesTrackedList(BondType)

The Urey-Bradley types containing the parameters for each term

trigonal_angle_typesTrackedList(AngleType)

The trigonal angle types containing the parameters for each term

out_of_plane_bend_typesTrackedList(AngleType)

The out-of-plane bending angle type containing parameters for each term

pi_torsion_typesTrackedList(DihedralType)

The pi-torsion type containing parameters for each torsional term

stretch_bend_typesTrackedList(StretchBendType)

The stretch-bend type containing parameters for each term

torsion_torsion_typesTrackedList(TorsionTorsionType)

The coupled torsion-torsion type containing parameters for coupled torsions

adjust_typesTrackedList(NonbondedExceptionType)

The nonbonded exception scaling factors for pairs of particles

bonds_inc_hiterator(Bond)

All bonds including hydrogen

bonds_without_hiterator(Bond)

All bonds without hydrogen

angles_inc_hiterator(Angle)

All angles including hydrogen

angles_without_hiterator(Angle)

All angles including hydrogen

dihedrals_inc_hiterator(Dihedral)

All dihedrals including hydrogen

dihedrals_without_hiterator(Dihedral)

All dihedrals including hydrogen

chamberbool=False

Whether this instance uses the CHARMM force field

amoebabool=False

Whether this instance uses the Amoeba force field

has_cmapbool=False

Whether this instance has correction map terms or not

Methods

add_atom(atom, resname, resnum[, chain, …])	Adds a new atom to the Structure, adding a new residue to residues if it has a different name or number as the last residue added and adding it to the atoms list.
add_atom_to_residue(atom, residue)	Adds a new atom to the Structure at the end if the given residue
add_flag(flag_name, flag_format[, data, …])	Adds a new flag with the given flag name and Fortran format string and initializes the array with the values given, or as an array of 0s of length num_items
assign_bonds(*reslibs)	Assigns bonds to all atoms based on the provided residue template libraries.
copy(cls[, split_dihedrals])	Makes a copy of the current structure as an instance of a specified subclass
createSystem([nonbondedMethod, …])	Construct an OpenMM System representing the topology described by the prmtop file.
delete_flag(flag_name)	Removes a flag from the topology file
fill_LJ()	Calculates the Lennard-Jones parameters (Rmin/2 and epsilon) for each atom type by computing their values from the A and B coefficients of each atom interacting with itself.
from_rawdata(rawdata)	Take the raw data from a AmberFormat object and initialize an AmberParm from that data.
from_structure(struct[, copy])	Take a Structure instance and initialize an AmberParm instance from that data.
get_box([frame])	In some cases, multiple conformations may be stored in the Structure.
get_coordinates([frame])	In some cases, multiple conformations may be stored in the Structure.
has_1012()	This routine determines whether there are any defined 10-12 Lennard-Jones interactions that are non-zero
has_NBFIX()	This routine determines whether there are any off-diagonal Lennard-Jones modifications (i.e., if any two atoms have a L-J pair interaction that does not match the combined L-J parameters for that pair).
id_format(filename)	Identifies the file type as either Amber-format file (like prmtop) or an old-style topology file.
initialize_topology([xyz, box])	Initializes topology data structures, like the list of atoms, bonds, etc., after the topology file has been read.
is_changed()	Determines if any of the topological arrays have changed since the last upload
join_dihedrals()	Joins multi-term torsions into a single term and makes all of the parameters DihedralTypeList instances.
load_atom_info()	Loads atom properties into the atoms that have been loaded.
load_dataframe(df)	Loads atomic properties from an input DataFrame
load_pointers()	Loads the data in POINTERS section into a pointers dictionary with each key being the pointer name according to http://ambermd.org/formats.html
load_rst7(rst7)	Loads coordinates into the AmberParm class
load_structure()	Loads all of the topology instance variables.
mdin_skeleton()	Returns the skeleton of an mdin file with the &amoeba namelist set up correctly for the potential terms that are present in this topology file.
omm_add_constraints(system, constraints, …)	Adds constraints to a given system
omm_angle_force([constraints, …])	Creates an OpenMM HarmonicAngleForce object (or AmoebaAngleForce if the angles are for an Amoeba-parametrized system)
omm_bond_force([constraints, rigidWater, …])	Creates an OpenMM Bond Force object (or AmoebaBondForce if the bonds are for an Amoeba-parametrized system)
omm_cmap_force()	Creates the OpenMM CMAP torsion force
omm_dihedral_force([split])	Creates the OpenMM PeriodicTorsionForce modeling dihedrals
omm_gbsa_force(implicitSolvent[, …])	Creates a Generalized Born force for running implicit solvent calculations
omm_improper_force()	Creates the OpenMM improper torsion force (quadratic bias)
omm_nonbonded_force([nonbondedMethod, …])	Creates the OpenMM NonbondedForce (and CustomNonbondedForce if necessary) to define the nonbonded interatomic potential for this system.
omm_out_of_plane_bend_force()	Creates the Amoeba out-of-plane bend force
omm_pi_torsion_force()	Creates the Amoeba pi-torsion force
omm_rb_torsion_force()	Creates the OpenMM RBTorsionForce for Ryckaert-Bellemans torsions
omm_set_virtual_sites(system)	Sets the virtual sites in a given OpenMM System object from the extra points defined in this system
omm_stretch_bend_force()	Create the OpenMM Amoeba stretch-bend force for this system
omm_torsion_torsion_force()	Create the OpenMM Amoeba coupled-torsion (CMAP) force
omm_trigonal_angle_force()	Creates the Amoeba trigonal-angle force
omm_urey_bradley_force()	Creates the OpenMM Urey-Bradley force
parse(filename, *args, **kwargs)	Meant for use with the automatic file loader, this will automatically return a subclass of AmberFormat corresponding to what the information in the prmtop file contains (i.e., either an AmberParm, ChamberParm, AmoebaParm, or AmberFormat)
prune_empty_terms()	Looks through all of the topological lists and gets rid of terms in which at least one of the atoms is None or has an idx attribute set to -1 (indicating that it has been removed from the atoms atom list)
ptr(pointer)	Returns the value of the given pointer, and converts to upper-case so it’s case-insensitive.
rdparm(fname[, slow])	Parses the Amber format file
rdparm_old(prmtop_lines[, check])	This reads an old-style topology file and stores the results in the same data structures as a new-style topology file
rdparm_slow(fname)	Parses the Amber format file.
recalculate_LJ()	Fills the LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF arrays in the parm_data raw data dictionary by applying the canonical Lorentz-Berthelot combining rules to the values in LJ_radius and LJ_depth.
rediscover_molecules([solute_ions, fix_broken])	This determines the molecularity and sets the ATOMS_PER_MOLECULE and SOLVENT_POINTERS sections of the prmtops.
remake_parm()	Recomputes the topology file parameters and fills parm_data
save(fname[, format, overwrite])	Saves the current Structure in the requested file format.
set_version()	Sets the version string
split()	Split the current Structure into separate Structure instances for each unique molecule.
strip(selection)	Deletes a subset of the atoms corresponding to an atom-based selection.
to_dataframe()	Generates a DataFrame from the current Structure’s atomic properties
unchange()	Toggles all lists so that they do not indicate any changes
update_dihedral_exclusions()	Nonbonded exclusions and exceptions have the following priority:
view_as(cls)	Returns a view of the current object as another object.
visualize(*args, **kwargs)	Use nglview for visualization.
write_cif(dest[, renumber, coordinates, …])	Write a PDB file from the current Structure instance
write_parm(name)	Writes the current data in parm_data into a new topology file with a given name.
write_pdb(dest[, renumber, coordinates, …])	Write a PDB file from a Structure instance
write_psf(dest[, vmd])	Writes a PSF file from the stored molecule
write_rst7(name[, netcdf])	Writes a restart file with the current coordinates and velocities and box info if it’s present

__init__(prm_name=None, xyz=None, box=None, rst7_name=None)

Instantiates an AmberParm object from data in prm_name and establishes validity based on presence of POINTERS and CHARGE sections. In general, you should use LoadParm from the readparm module instead. LoadParm will correctly dispatch the object to the ‘correct’ flavor of AmberParm

Methods

__init__([prm_name, xyz, box, rst7_name])	Instantiates an AmberParm object from data in prm_name and establishes validity based on presence of POINTERS and CHARGE sections.
add_atom(atom, resname, resnum[, chain, …])	Adds a new atom to the Structure, adding a new residue to residues if it has a different name or number as the last residue added and adding it to the atoms list.
add_atom_to_residue(atom, residue)	Adds a new atom to the Structure at the end if the given residue
add_flag(flag_name, flag_format[, data, …])	Adds a new flag with the given flag name and Fortran format string and initializes the array with the values given, or as an array of 0s of length num_items
assign_bonds(*reslibs)	Assigns bonds to all atoms based on the provided residue template libraries.
copy(cls[, split_dihedrals])	Makes a copy of the current structure as an instance of a specified subclass
createSystem([nonbondedMethod, …])	Construct an OpenMM System representing the topology described by the prmtop file.
delete_flag(flag_name)	Removes a flag from the topology file
fill_LJ()	Calculates the Lennard-Jones parameters (Rmin/2 and epsilon) for each atom type by computing their values from the A and B coefficients of each atom interacting with itself.
from_rawdata(rawdata)	Take the raw data from a AmberFormat object and initialize an AmberParm from that data.
from_structure(struct[, copy])	Take a Structure instance and initialize an AmberParm instance from that data.
get_box([frame])	In some cases, multiple conformations may be stored in the Structure.
get_coordinates([frame])	In some cases, multiple conformations may be stored in the Structure.
has_1012()	This routine determines whether there are any defined 10-12 Lennard-Jones interactions that are non-zero
has_NBFIX()	This routine determines whether there are any off-diagonal Lennard-Jones modifications (i.e., if any two atoms have a L-J pair interaction that does not match the combined L-J parameters for that pair).
id_format(filename)	Identifies the file type as either Amber-format file (like prmtop) or an old-style topology file.
initialize_topology([xyz, box])	Initializes topology data structures, like the list of atoms, bonds, etc., after the topology file has been read.
is_changed()	Determines if any of the topological arrays have changed since the last upload
join_dihedrals()	Joins multi-term torsions into a single term and makes all of the parameters DihedralTypeList instances.
load_atom_info()	Loads atom properties into the atoms that have been loaded.
load_dataframe(df)	Loads atomic properties from an input DataFrame
load_pointers()	Loads the data in POINTERS section into a pointers dictionary with each key being the pointer name according to http://ambermd.org/formats.html
load_rst7(rst7)	Loads coordinates into the AmberParm class
load_structure()	Loads all of the topology instance variables.
mdin_skeleton()	Returns the skeleton of an mdin file with the &amoeba namelist set up correctly for the potential terms that are present in this topology file.
omm_add_constraints(system, constraints, …)	Adds constraints to a given system
omm_angle_force([constraints, …])	Creates an OpenMM HarmonicAngleForce object (or AmoebaAngleForce if the angles are for an Amoeba-parametrized system)
omm_bond_force([constraints, rigidWater, …])	Creates an OpenMM Bond Force object (or AmoebaBondForce if the bonds are for an Amoeba-parametrized system)
omm_cmap_force()	Creates the OpenMM CMAP torsion force
omm_dihedral_force([split])	Creates the OpenMM PeriodicTorsionForce modeling dihedrals
omm_gbsa_force(implicitSolvent[, …])	Creates a Generalized Born force for running implicit solvent calculations
omm_improper_force()	Creates the OpenMM improper torsion force (quadratic bias)
omm_nonbonded_force([nonbondedMethod, …])	Creates the OpenMM NonbondedForce (and CustomNonbondedForce if necessary) to define the nonbonded interatomic potential for this system.
omm_out_of_plane_bend_force()	Creates the Amoeba out-of-plane bend force
omm_pi_torsion_force()	Creates the Amoeba pi-torsion force
omm_rb_torsion_force()	Creates the OpenMM RBTorsionForce for Ryckaert-Bellemans torsions
omm_set_virtual_sites(system)	Sets the virtual sites in a given OpenMM System object from the extra points defined in this system
omm_stretch_bend_force()	Create the OpenMM Amoeba stretch-bend force for this system
omm_torsion_torsion_force()	Create the OpenMM Amoeba coupled-torsion (CMAP) force
omm_trigonal_angle_force()	Creates the Amoeba trigonal-angle force
omm_urey_bradley_force()	Creates the OpenMM Urey-Bradley force
parse(filename, *args, **kwargs)	Meant for use with the automatic file loader, this will automatically return a subclass of AmberFormat corresponding to what the information in the prmtop file contains (i.e., either an AmberParm, ChamberParm, AmoebaParm, or AmberFormat)
prune_empty_terms()	Looks through all of the topological lists and gets rid of terms in which at least one of the atoms is None or has an idx attribute set to -1 (indicating that it has been removed from the atoms atom list)
ptr(pointer)	Returns the value of the given pointer, and converts to upper-case so it’s case-insensitive.
rdparm(fname[, slow])	Parses the Amber format file
rdparm_old(prmtop_lines[, check])	This reads an old-style topology file and stores the results in the same data structures as a new-style topology file
rdparm_slow(fname)	Parses the Amber format file.
recalculate_LJ()	Fills the LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF arrays in the parm_data raw data dictionary by applying the canonical Lorentz-Berthelot combining rules to the values in LJ_radius and LJ_depth.
rediscover_molecules([solute_ions, fix_broken])	This determines the molecularity and sets the ATOMS_PER_MOLECULE and SOLVENT_POINTERS sections of the prmtops.
remake_parm()	Recomputes the topology file parameters and fills parm_data
save(fname[, format, overwrite])	Saves the current Structure in the requested file format.
set_version()	Sets the version string
split()	Split the current Structure into separate Structure instances for each unique molecule.
strip(selection)	Deletes a subset of the atoms corresponding to an atom-based selection.
to_dataframe()	Generates a DataFrame from the current Structure’s atomic properties
unchange()	Toggles all lists so that they do not indicate any changes
update_dihedral_exclusions()	Nonbonded exclusions and exceptions have the following priority:
view_as(cls)	Returns a view of the current object as another object.
visualize(*args, **kwargs)	Use nglview for visualization.
write_cif(dest[, renumber, coordinates, …])	Write a PDB file from the current Structure instance
write_parm(name)	Writes the current data in parm_data into a new topology file with a given name.
write_pdb(dest[, renumber, coordinates, …])	Write a PDB file from a Structure instance
write_psf(dest[, vmd])	Writes a PSF file from the stored molecule
write_rst7(name[, netcdf])	Writes a restart file with the current coordinates and velocities and box info if it’s present

Attributes

ANGLE_FORCE_GROUP
BOND_FORCE_GROUP
CMAP_FORCE_GROUP
DIHEDRAL_FORCE_GROUP
IMPROPER_FORCE_GROUP
NONBONDED_FORCE_GROUP
OUT_OF_PLANE_BEND_FORCE_GROUP
PI_TORSION_FORCE_GROUP
RB_TORSION_FORCE_GROUP
STRETCH_BEND_FORCE_GROUP
TORSION_TORSION_FORCE_GROUP
TRIGONAL_ANGLE_FORCE_GROUP
UREY_BRADLEY_FORCE_GROUP
amoeba	Whether this instance uses the Amoeba force field
angles_inc_h	All angles including hydrogen
angles_without_h	All angles including hydrogen
bonds_inc_h	All bonds including hydrogen
bonds_without_h	All bonds without hydrogen
box
box_vectors	3, 3-element tuple of unit cell vectors that are Quantity objects of dimension length
chamber	Whether this instance uses the CHARMM force field
combining_rule
coordinates
dihedrals_inc_h	All dihedrals including hydrogen
dihedrals_without_h	All dihedrals including hydrogen
has_cmap	Whether this instance has correction map terms or not
positions	A list of 3-element Quantity tuples of dimension length representing the atomic positions for every atom in the system.
topology	The OpenMM Topology object.
velocities
view	Returns an indexable object that can be indexed like a standard Structure, but returns a view rather than a copy