parmed.amber.readparm module¶

This module is simply a namespace for all Amber topology-like classes. There are different variants; for instance the standard Amber topology, the chamber-made topology, and the tinker_to_amber-made topology. These classes are all defined in their own private modules, but imported here to simplify the API.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

class parmed.amber.readparm.AmberFormat(fname=None)[source]¶

Bases: object

A class that can parse and print files stored in the Amber topology or MDL format. In particular, these files have the general form:

` %VERSION VERSION_STAMP = V00001.000 DATE = XX/XX/XX XX:XX:XX %FLAG <FLAG_NAME> %COMMENT <comments> %FORMAT(<Fortran_Format>) ... data corresponding to that Fortran Format %FLAG <FLAG_NAME2> %COMMENT <comments> %FORMAT(<Fortran_Format>) ... data corresponding to that Fortran Format `

where the %COMMENT sections are entirely optional

Parameters

fnamestr=None: If provided, this file is parsed and the data structures will be loaded from the data in this file

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
charge_flagstr=’CHARGE’: The name of the name of the FLAG that describes partial atomic charge data. If this flag is found, then its data are multiplied by the ELECTROSTATIC_CONSTANT to convert back to fractions of electrons
versionstr: The VERSION string from the Amber file
namestr: The file name of the originally parsed file (set to the fname parameter)

Methods

`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
`delete_flag`(flag_name)	Removes a flag from the topology file
`id_format`(filename)	Identifies the file type as either Amber-format file (like prmtop) or an old-style topology file.
`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)
`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.
`set_version`()	Sets the version string
`view_as`(cls)	Returns a view of the current object as another object.
`write_parm`(name)	Writes the current data in parm_data into a new topology file with the given name

add_flag(flag_name, flag_format, data=None, num_items=- 1, comments=None, after=None)[source]¶

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

Parameters

flag_namestr: Name of the flag to insert. It is converted to all upper case
flag_formatstr: Fortran format string representing how the data in this section should be written and read. Do not enclose in ()
datalist=None: Sequence with data for the new flag. If None, a list of zeros of length num_items (see below) is given as a holder
num_itemsint=-1: Number of items in the section. This variable is ignored if a set of data are given in data
commentslist of str=None: List of comments to add to this section
afterstr=None: If provided, the added flag will be added after the one with the name given to after. If this flag does not exist, IndexError will be raised

Raises

AmberError if flag already exists
IndexError if the after flag does not exist

delete_flag(flag_name)[source]¶: Removes a flag from the topology file

static id_format(filename)[source]¶

Identifies the file type as either Amber-format file (like prmtop) or an old-style topology file.

Parameters

filenamestr: Name of the file to check format for

Returns

is_fmtbool: True if it is an Amber-style format, False otherwise

static parse(filename, *args, **kwargs)[source]¶: 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)

rdparm(fname, slow=False)[source]¶: Parses the Amber format file

rdparm_old(prmtop_lines, check=False)[source]¶

This reads an old-style topology file and stores the results in the same data structures as a new-style topology file

Parameters

prmtop_lineslist of str: List of all lines in the prmtop file
checkbool, optional: If True, only the first couple sections will be read to determine if this is, in fact, an old-style topology file

rdparm_slow(fname)[source]¶: Parses the Amber format file. This parser is written in pure Python and is therefore slower than the C++-optimized version

set_version()[source]¶: Sets the version string

view_as(cls)[source]¶

Returns a view of the current object as another object.

Parameters

clstype: Class definition of an AmberParm subclass for the current object to be converted into

Returns

instance of cls initialized from data in this object. This is NOT a deep
copy, so modifying the original object may modify this. The copy
function will create a deep copy of any AmberFormat-derived object

write_parm(name)[source]¶

Writes the current data in parm_data into a new topology file with the given name

Parameters

namestr or file-like: Name of the file to write the topology file to or file-like object to write

class parmed.amber.readparm.AmberParm(prm_name=None, xyz=None, box=None, rst7_name=None)[source]¶

Bases: parmed.amber.amberformat.AmberFormat, parmed.structure.Structure

Amber Topology (parm7 format) class. 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, optional: If provided, this file is parsed and the data structures will be loaded from the data in this file
xyzstr or array, optional: If provided, the coordinates and unit cell dimensions from the provided Amber inpcrd/restart file will be loaded into the molecule, or the coordinates will be loaded from the coordinate array
boxarray, optional: If provided, the unit cell information will be set from the provided unit cell dimensions (a, b, c, alpha, beta, and gamma, respectively)

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
charge_flagstr=’CHARGE’: The name of the name of the FLAG that describes partial atomic charge data. If this flag is found, then its data are multiplied by the ELECTROSTATIC_CONSTANT to convert back to fractions of electrons
versionstr: The VERSION string from the Amber file
namestr: The file name of the originally parsed file (set to the fname parameter)
LJ_typesdict {str: A mapping whose keys are atom types paired with the nonbonded index of that type
LJ_radiuslist(float): A list of floats corresponding to the Rmin/2 parameter for every Lennard-Jones type. The indexes are the nonbonded index (nb_idx attribute of the Atom class) minus 1 to account for indexing from 0 in Python. The values are in Angstroms. To get the radius for a particular atom type, you can use LJ_radius[LJ_types[“type”]-1]
LJ_depthlist(float): A list of Lennard-Jones epsilon parameters laid out the same way as LJ_radius, described above.
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 angles between three atoms in the system
dihedralsTrackedList(Angle): List of all proper and improper torsions between 4 atoms in the system
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
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.
`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`()	Fills `parm_data` from the data in the parameter and topology arrays (e.g., `atoms`, `bonds`, `bond_types`, …)
`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

property amoeba¶: Whether this instance uses the Amoeba force field

property angles_inc_h¶: All angles including hydrogen

property angles_without_h¶: All angles including hydrogen

property bonds_inc_h¶: All bonds including hydrogen

property bonds_without_h¶: All bonds without hydrogen

property box¶

property chamber¶: Whether this instance uses the CHARMM force field

property dihedrals_inc_h¶: All dihedrals including hydrogen

property dihedrals_without_h¶: All dihedrals including hydrogen

fill_LJ()[source]¶

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.

This fills the LJ_radius, LJ_depth, and LJ_types data structures.

classmethod from_rawdata(rawdata)[source]¶

Take the raw data from a AmberFormat object and initialize an AmberParm from that data.

Parameters

rawdataAmberFormat: An AmberFormat instance that has already been instantiated

Returns

parmAmberParm: An instance of this type from the data in rawdata

classmethod from_structure(struct, copy=False)[source]¶

Take a Structure instance and initialize an AmberParm instance from that data.

Parameters

structStructure: The input structure from which to construct an AmberParm instance
copybool: If True, the input struct is deep-copied to make sure it does not share any objects with the original struct. Default is False

Returns

instAmberParm: The AmberParm instance derived from the input structure

Raises

TypeError: If the structure has parameters not supported by the standard Amber force field (i.e., standard bond, angle, and dihedral types)

Notes

Due to the nature of the prmtop file, struct almost always returns a deep copy. The one exception is when struct is already of type AmberParm, in which case the original object is returned unless copy is True.

has_1012()[source]¶

This routine determines whether there are any defined 10-12 Lennard-Jones interactions that are non-zero

Returns

has_10_12bool: If True, 10-12 interactions are defined for this particular system

has_NBFIX()[source]¶

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).

Returns

nbfixbool: If True, off-diagonal elements in the combined Lennard-Jones matrix exist. If False, they do not.

property has_cmap¶: Whether this instance has correction map terms or not

initialize_topology(xyz=None, box=None)[source]¶: Initializes topology data structures, like the list of atoms, bonds, etc., after the topology file has been read.

is_changed()[source]¶: Determines if any of the topological arrays have changed since the last upload

load_atom_info()[source]¶: Loads atom properties into the atoms that have been loaded. If any arrays are too short or too long, an IndexError will be raised

load_pointers()[source]¶: 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)[source]¶

Loads coordinates into the AmberParm class

Parameters

rst7str or Rst7: The Amber coordinate file (either ASCII restart or NetCDF restart) object or filename to assign atomic coordinates from.

load_structure()[source]¶: Loads all of the topology instance variables. This is necessary if we actually want to modify the topological layout of our system (like deleting atoms)

omm_nonbonded_force(nonbondedMethod=None, nonbondedCutoff=Quantity(value=8, unit=angstrom), switchDistance=Quantity(value=0, unit=angstrom), ewaldErrorTolerance=0.0005, reactionFieldDielectric=78.5)[source]¶

Creates the OpenMM NonbondedForce (and CustomNonbondedForce if necessary) to define the nonbonded interatomic potential for this system. A CustomNonbondedForce is used for the r^-4 part of the 12-6-4 Lennard-Jones potential as well as any modified off-diagonal (i.e., NBFIX) terms

Parameters

nonbondedMethodcutoff method: This is the cutoff method. It can be either the NoCutoff, CutoffNonPeriodic, CutoffPeriodic, PME, or Ewald objects from the simtk.openmm.app namespace
nonbondedCutofffloat or distance Quantity: The nonbonded cutoff must be either a floating point number (interpreted as nanometers) or a Quantity with attached units. This is ignored if nonbondedMethod is NoCutoff.
switchDistancefloat or distance Quantity: The distance at which the switching function is turned on for van der Waals interactions. This is ignored when no cutoff is used, and no switch is used if switchDistance is 0, negative, or greater than the cutoff
ewaldErrorTolerancefloat=0.0005: When using PME or Ewald, the Ewald parameters will be calculated from this value
reactionFieldDielectricfloat=78.5: If the nonbondedMethod is CutoffPeriodic or CutoffNonPeriodic, the region beyond the cutoff is treated using a reaction field method with this dielectric constant. It should be set to 1 if another implicit solvent model is being used (e.g., GB)

Returns

NonbondedForce [, CustomNonbondedForce]: If a CustomNonbondedForce is necessary, the return value is a 2-element tuple of NonbondedForce, CustomNonbondedForce. If only a NonbondedForce is necessary, that is the return value

ptr(pointer)[source]¶

Returns the value of the given pointer, and converts to upper-case so it’s case-insensitive. A non-existent pointer meets with a KeyError

Parameters

pointerstr: The AMBER pointer for which to extract the value

Returns

int: The returned integer is the value of that pointer

recalculate_LJ()[source]¶

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.

Notes

This will undo any off-diagonal L-J modifications you may have made, so call this function with care.

rediscover_molecules(solute_ions=True, fix_broken=True)[source]¶: This determines the molecularity and sets the ATOMS_PER_MOLECULE and SOLVENT_POINTERS sections of the prmtops. Returns the new atom sequence in terms of the ‘old’ atom indexes if re-ordering was necessary to fix the tleap bug. Returns None otherwise.

remake_parm()[source]¶: Fills parm_data from the data in the parameter and topology arrays (e.g., atoms, bonds, bond_types, …)

strip(selection)[source]¶

Deletes a subset of the atoms corresponding to an atom-based selection.

Parameters

selectionAmberMask, str, or iterable of bool: This is the selection of atoms that will be deleted from this structure. If it is a string, it will be interpreted as an AmberMask. If it is an AmberMask, it will be converted to a selection of atoms. If it is an iterable, it must be the same length as the atoms list.

write_parm(name)[source]¶

Writes the current data in parm_data into a new topology file with a given name.

Parameters

namestr or file-like: The name of the file to write the prmtop to or the file object to write to

write_rst7(name, netcdf=None)[source]¶

Writes a restart file with the current coordinates and velocities and box info if it’s present

Parameters

namestr: Name of the file to write the restart file to
netcdfbool=False: If True, write a NetCDF-format restart file (requires a NetCDF backend; scipy, netCDF4, or ScientificPython; to be installed)

Notes

If netcdf is not specified and the filename extension given by name is .ncrst, the a NetCDF restart file will be written. However, an explicit value for netcdf will override any filename extensions.

class parmed.amber.readparm.ChamberParm(prm_name=None, xyz=None, box=None, rst7_name=None)[source]¶

Bases: parmed.amber._amberparm.AmberParm

Chamber Topology (parm7 format) class.

Gives low, and some high, level access to topology data or interact with some of the high-level classes comprising the system topology and parameters. The ChamberParm class uses the same attributes that the AmberParm class uses, and only the ones unique to ChamberParm will be shown below.

Parameters

prm_namestr, optional: If provided, this file is parsed and the data structures will be loaded from the data in this file
xyzstr or array, optional: If provided, the coordinates and unit cell dimensions from the provided Amber inpcrd/restart file will be loaded into the molecule, or the coordinates will be loaded from the coordinate array
boxarray, optional: If provided, the unit cell information will be set from the provided unit cell dimensions (a, b, c, alpha, beta, and gamma, respectively)

See also

AmberParm

Attributes

LJ_14_radiuslist(float): The same as LJ_radius, except specific for 1-4 nonbonded parameters, which may differ in the CHARMM force field
LJ_14_depthlist(float): The same as LJ_depth, except specific for 1-4 nonbonded parameters, which may differ in the CHARMM force field
urey_bradleysTrackedList(UreyBradley): List of Urey-Bradley terms between two atoms in a valence angle
impropersTrackedList(Improper): List of CHARMM-style improper torsions
cmapsTrackedList(Cmap): List of coupled-torsion correction map parameters
urey_bradley_typesTrackedList(UreyBradleyType): List of parameters defining the Urey-Bradley terms
improper_typesTrackedList(Improper): List of parameters defining the Improper terms
cmap_typesTrackedList(CmapType): List of parameters defining the CMAP terms
chamberbool=True: Whether this instance uses the CHARMM force field
amoebabool=False: Whether this instance uses the Amoeba force field
has_cmapbool: 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`()	Fills the LJ_radius, LJ_depth arrays and LJ_types dictionary with data from LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF sections of the prmtop files, by undoing the canonical combining rules.
`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 a ChamberParm 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.
`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`()	Takes the values of the LJ_radius and LJ_depth arrays and recalculates the LENNARD_JONES_A/BCOEF topology sections from the canonical combining rules.
`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`()	Fills `parm_data` from the data in the parameter and topology arrays (e.g., `atoms`, `bonds`, `bond_types`, …)
`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

property amoeba¶: Whether this instance uses the Amoeba force field

property chamber¶: Whether this instance uses the CHARMM force field

fill_LJ()[source]¶: Fills the LJ_radius, LJ_depth arrays and LJ_types dictionary with data from LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF sections of the prmtop files, by undoing the canonical combining rules.

classmethod from_structure(struct, copy=False)[source]¶

Take a Structure instance and initialize a ChamberParm instance from that data.

Parameters

structStructure: The input structure from which to construct a ChamberParm instance
copybool: If True, the input struct is deep-copied to make sure it does not share any objects with the original struct. Default is False

Returns

instChamberParm: The ChamberParm instance derived from the input structure

Notes

Due to the nature of the prmtop file, struct almost always returns a deep copy. The one exception is when struct is already of type ChamberParm, in which case the original object is returned unless copy is True.

initialize_topology(xyz=None, box=None)[source]¶: Initializes topology data structures, like the list of atoms, bonds, etc., after the topology file has been read. The following methods are called:

load_pointers()[source]¶: 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_structure()[source]¶: Loads all of the topology instance variables. This is necessary if we actually want to modify the topological layout of our system (like deleting atoms)

recalculate_LJ()[source]¶: Takes the values of the LJ_radius and LJ_depth arrays and recalculates the LENNARD_JONES_A/BCOEF topology sections from the canonical combining rules.

remake_parm()[source]¶: Fills parm_data from the data in the parameter and topology arrays (e.g., atoms, bonds, bond_types, …)

parmed.amber.readparm.LoadParm(parmname, xyz=None, box=None)[source]¶

Loads a topology file using the correct class.

Parameters

parmnamestr: The name of the topology file to load
xyzstr or array, optional: If provided, the coordinates and unit cell dimensions from the provided Amber inpcrd/restart file will be loaded into the molecule, or the coordinates will be loaded from the coordinate array
boxarray, optional: If provided, the unit cell information will be set from the provided unit cell dimensions (a, b, c, alpha, beta, and gamma, respectively)

Returns

parmAmberParm (or subclass): This function parses the topology file, determines if it is an Amber-style (i.e., traditional Amber force field), Chamber-style (i.e., CHARMM force field), or Amoeba-style (i.e., Amoeba force field), and then returns an instance of the appropriate type.

class parmed.amber.readparm.Rst7(filename=None, natom=None, title='', time=0.0)[source]¶

Bases: object

Amber input coordinate (or restart coordinate) file. Front-end for the readers and writers, supports both NetCDF and ASCII restarts.

Parameters

filenamestr, optional: If a filename is provided, this file is parsed and the Rst7 data populated from that file. The format (ASCII or NetCDF) is autodetected
natomint, optional: If no filename is provided, this value is required. If a filename is provided, this value is ignored (and instead set to the value of natom from the coordinate file). This is the number of atoms for which we have coordinates. If not provided for a new file, it must be set later.
titlestr, optional: For a file that is to be written, this is the title that will be given to that file. Default is an empty string
timefloat, optional: The time to write to the restart file. This is cosmetic. Default is 0

Attributes

box
box_vectors: Unit cell vectors with units
hasbox: Whether or not this Rst7 has unit cell information
hasvels: Whether or not this Rst7 has velocities
positions: Atomic coordinates with units
velocities: Atomic velocities in units of angstroms/picoseconds

Methods

`copy_from`(thing)	Copies the coordinates, velocities, and box information from another instance
`open`(filename)	Constructor that opens and parses an input coordinate file
`write`(fname[, netcdf])	Writes the coordinates and/or velocities to a restart file

property box¶

property box_vectors¶: Unit cell vectors with units

classmethod copy_from(thing)[source]¶: Copies the coordinates, velocities, and box information from another instance

property hasbox¶: Whether or not this Rst7 has unit cell information

property hasvels¶: Whether or not this Rst7 has velocities

classmethod open(filename)[source]¶

Constructor that opens and parses an input coordinate file

Parameters

filenamestr: Name of the file to parse

property positions¶: Atomic coordinates with units

property velocities¶: Atomic velocities in units of angstroms/picoseconds

write(fname, netcdf=False)[source]¶: Writes the coordinates and/or velocities to a restart file