parmed.amber package

Subpackages

• parmed.amber.mdin package
  • Submodules
    • parmed.amber.mdin.cntrl module
    • parmed.amber.mdin.ewald module
    • parmed.amber.mdin.mdin module
    • parmed.amber.mdin.pb module
    • parmed.amber.mdin.qmmm module
  • Module contents

Submodules

• parmed.amber.amberformat module
• parmed.amber.asciicrd module
• parmed.amber.mask module
• parmed.amber.netcdffiles module
• parmed.amber.offlib module
• parmed.amber.parameters module
• parmed.amber.readparm module
• parmed.amber.titratable_residues module

Module contents

Package that provides an API to Amber-specific files

class parmed.amber.AmberAsciiRestart(fname, mode='r', natom=0, hasbox=None, title=None, time=0.0)

Bases: parmed.amber.asciicrd._AmberAsciiCoordinateFile

Parser for the Amber ASCII inpcrd/restart file format

Parameters

fnamestr

File name to open

modestr={‘r’, ‘w’}

Whether to open this file for ‘r’eading or ‘w’riting

natomint, optional

Number of atoms in the system (necessary when mode=’w’)

hasboxbool, optional

Does the system have PBCs? Necessary when mode=’w’

titlestr, optional

Title to write to a new trajectory (when mode=’w’)

timefloat, optional

The time to write to the restart file in ps. Default is 0.

Attributes

box

Combined cell lengths and cell angles

cell_angles

cell_lengths

coordinates

positions

velocities

Methods

close()	Close the open file handler
id_format(filename)	Identifies the file type as an Amber restart/inpcrd file

parse

CRDS_PER_LINE = 6

DEFAULT_TITLE = 'restart created by ParmEd'

property box

Combined cell lengths and cell angles

property cell_angles

property cell_lengths

property coordinates

static id_format(filename)

Identifies the file type as an Amber restart/inpcrd file

Parameters

filenamestr

Name of the file to check format for

Returns

is_fmtbool

True if it is an Amber restart/inpcrd file. False otherwise

classmethod parse(filename, structure=False)

property velocities

class parmed.amber.AmberFormat(fname=None)

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)

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)

Removes a flag from the topology file

static id_format(filename)

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)

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)

Parses the Amber format file

rdparm_old(prmtop_lines, check=False)

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)

Parses the Amber format file. This parser is written in pure Python and is therefore slower than the C++-optimized version

set_version()

Sets the version string

view_as(cls)

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)

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.AmberMask(parm, mask)

Bases: object

What is hopefully a fully-fledged Amber mask parser implemented in Python.

Parameters

parmStructure

The topology structure for which to select atoms

maskstr

The mask string that selects a subset of atoms

Methods

Selected([invert])	Generator that returns the indexes of selected atoms
Selection([prnlev, invert])	Parses the mask and analyzes the result to return an atom selection array

Selected(invert=False)

Generator that returns the indexes of selected atoms

Parameters

invertbool, optional

If True, all atoms not selected by the mask will be returned

Returns

generator of int

Each iteration will yield the index of the next atom that has been selected by the mask. Atom indices are 0-based

Selection(prnlev=0, invert=False)

Parses the mask and analyzes the result to return an atom selection array

Parameters

prnlevint, optional

Print debug information on the processing of the Amber mask string. This is mainly useful if you are modifying the mask parser. Default value is 0 (no printout), values between 1 and 8 control the level of output (larger values produce more output). Default 0

invertbool, optional

If True, the returned array will invert the selection of the mask (i.e., selected atoms will not be selected and vice-versa)

Returns

masklist of int

A list with length equal to the number of atoms in the assigned Structure instance. Selected atoms will have a value of 1 placed in the corresponding slot in the return list while atoms not selected will be assigned 0.

class parmed.amber.AmberMdcrd(fname, natom, hasbox, mode='r', title=None)

Bases: parmed.amber.asciicrd._AmberAsciiCoordinateFile

A class to parse Amber ASCII trajectory files. This is much slower than parsing NetCDF files (or the equivalent parsing done in a compiled language like C or C++). For large trajectories, this may be significant.

Attributes

box

coordinates

frame

positions

Methods

add_box(stuff)	Prints ‘stuff’ (which must be a 3-element list, array.array, tuple, or np.ndarray) as the box lengths for this frame
add_coordinates(stuff)	Prints ‘stuff’ (which must be either an iterable of 3*natom or have an attribute ‘flatten’ that converts it into an iterable of 3*natom) to the open file handler.
close()	Close the open file handler
id_format(filename)	Identifies the file type as an Amber mdcrd file

CRDS_PER_LINE = 10

DEFAULT_TITLE = 'trajectory created by ParmEd'

add_box(stuff)

Prints ‘stuff’ (which must be a 3-element list, array.array, tuple, or np.ndarray) as the box lengths for this frame

Parameters

stuffarray or iterable

This must be an iterable of length 3 with the box lengths

Raises

If the coordinate file is an old one being parsed or if you are

currently expected to provide coordinates, a RuntimeError is raised.

raised. If the provided box lengths are not length 3, a ValueError is

raised.

add_coordinates(stuff)

Prints ‘stuff’ (which must be either an iterable of 3*natom or have an attribute ‘flatten’ that converts it into an iterable of 3*natom) to the open file handler. Can only be called on a ‘new’ mdcrd, and adds these coordinates to the current end of the file.

Parameters

stuffarray or iterable

This must be an iterable of length 3*natom or a numpy array that can be flattened to a 3*natom-length array

Raises

If the coordinate file is an old one being parsed or if you are

currently expected to provide unit cell dimensions, a RuntimeError is

raised. If the provided coordinate data does not have length 3*natom, or

cannot be ``flatten()``ed to create a 3*natom array, a ValueError is

raised.

property box

property coordinates

extra_args = ('natom', 'hasbox')

property frame

static id_format(filename)

Identifies the file type as an Amber mdcrd file

Parameters

filenamestr

Name of the file to check format for

Returns

is_fmtbool

True if it is an Amber mdcrd file. False otherwise

class parmed.amber.AmberOFFLibrary

Bases: object

Class containing static methods responsible for parsing and writing OFF libraries

Methods

id_format(filename)	Sees if an open file is an OFF library file.
parse(filename)	Parses an Amber OFF library
write(lib, dest)	Writes a dictionary of ResidueTemplate units to a file in OFF format

static id_format(filename)

Sees if an open file is an OFF library file.

Parameters

filenamestr

The name of the file to see if it is an OFF file format

Returns

is_fmtbool

True if it is recognized as OFF, False otherwise

static parse(filename)

Parses an Amber OFF library

Parameters

filenamestr or file-like iterable

The file name or file object to parse. If it is an iterable, it will be exhausted

Returns

residuesOrderedDict {str

Dictionary pairing residue names with their ResidueTemplate objects

Raises

ValueError if the first line does not match the file format. This line

will be consumed

IOError if filename is the name of a file that does not exist

RuntimeError if EOF is reached prematurely or other formatting issues

found

static write(lib, dest)

Writes a dictionary of ResidueTemplate units to a file in OFF format

Parameters

libdict {str

Items can be either ResidueTemplate or ResidueTemplateContainer instances

deststr or file-like

Either a file name or a file-like object to write the file to

class parmed.amber.AmberParameterSet(*filenames)

Bases: parmed.parameters.ParameterSet

Class storing parameters from an Amber parameter set

Parameters

filenamesstr, list of str, file-like, or list of file-like; optional

Either the name of a file or a list of filenames from which parameters should be parsed.

See also

parmed.parameters.ParameterSet

Notes

Order is important in the list of files provided. The parameters are loaded in the order they are provided, and any parameters that are specified in multiple places are overwritten (that is, the last occurrence is the parameter type that is used)

Attributes

combining_rule

Methods

condense([do_dihedrals])	This function goes through each of the parameter type dicts and eliminates duplicate types.
from_leaprc(fname[, search_oldff])	Load a parameter set from a leaprc file
from_structure(struct)	Extracts known parameters from a Structure instance
id_format(filename)	Identifies the file type as either an Amber-style frcmod or parm.dat file.
load_parameters(fname)	Load a set of parameters from a single parameter file
typeify_templates()	Assign atom types to atom names in templates
write(dest[, title, style])	Writes a parm.dat file with the current parameters

classmethod from_leaprc(fname, search_oldff=False)

Load a parameter set from a leaprc file

Parameters

fnamestr or file-like

Name of the file or open file-object from which a leaprc-style file will be read

search_oldffbool, optional, default=False

If True, search the oldff directories in the main Amber leap folders. Default is False

Notes

This does not read all parts of a leaprc file – only those pertinent to defining force field information. For instance, the following sections and commands are processed:

• addAtomTypes

• loadAmberParams

• loadOFF

• loadMol2

• loadMol3

classmethod from_structure(struct)

Extracts known parameters from a Structure instance

Parameters

structparmed.structure.Structure

The parametrized Structure instance from which to extract parameters into a ParameterSet

Returns

paramsParameterSet

The parameter set with all parameters defined in the Structure

static id_format(filename)

Identifies the file type as either an Amber-style frcmod or parm.dat file.

Parameters

filenamestr

Name of the file to check format for

Returns

is_fmtbool

True if it is an Amber-style parameter file. False otherwise.

load_parameters(fname)

Load a set of parameters from a single parameter file

Parameters

fnamestr or file-like

Parameter file to parse

write(dest, title='Created by ParmEd', style='frcmod')

Writes a parm.dat file with the current parameters

Parameters

deststr or file-like

The file name or file-like object to write the parameters to

titlestr, optional

The title of the frcmod to write. Default is ‘Created by ParmEd’

stylestr, optional

If ‘frcmod’, the parameters are written in frcmod-format. If ‘parm’, the parameters are written in parm.dat-format. Default is ‘frcmod’

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

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()

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)

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)

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()

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()

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)

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

load_atom_info()

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()

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

Parameters

rst7str or Rst7

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

load_structure()

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)

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)

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()

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)

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()

Fills parm_data from the data in the parameter and topology arrays (e.g., atoms, bonds, bond_types, …)

strip(selection)

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)

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)

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.AmoebaParm(prm_name=None, xyz=None, box=None, rst7_name=None)

Bases: parmed.amber._amberparm.AmberParm

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

property amoeba

Whether this instance uses the Amoeba force field

property chamber

Whether this instance uses the CHARMM force field

initialize_topology(xyz=None, box=None)

Initializes topology data structures, like the list of atoms, bonds, etc., after the topology file has been read.

Raises

AmberError if it is not an Amoeba-styled topology file

load_atom_info()

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_structure()

Loads all of the topology instance variables. This is necessary if we actually want to modify the topological layout of our system

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.

Returns

str

A skeleton MDIN file with all of the do_* variables in the &amoeba section set correctly. It is commented for easy editing

remake_parm()

Recomputes the topology file parameters and fills parm_data

class parmed.amber.BeemanRestart(fname=None)

Bases: parmed.amber.amberformat.AmberFormat

The restart files written for/by the Beeman integrator has the same type of format as the topology file

Attributes

accelerations

box

coordinates

natom

old_accelerations

velocities

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
from_rawdata(rawdata)	Take the raw data from a AmberFormat object and initialize a BeemanRestart from that data.
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

property accelerations

property box

property coordinates

classmethod from_rawdata(rawdata)

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

Parameters

rawdataAmberFormat

An AmberFormat instance that has already been instantiated

Returns

instBeemanRestart

An instance of this type from the data in rawdata

property natom

property old_accelerations

property velocities

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

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()

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)

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)

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()

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()

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()

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()

Fills parm_data from the data in the parameter and topology arrays (e.g., atoms, bonds, bond_types, …)

parmed.amber.ConvertFromPSF(struct, params, title='')

This function instantiates a ChamberParm instance from a data structure instantiated by a CHARMM PSF.

Parameters

structStructure

The structure object (typically loaded from a PSF file)

paramsCharmmParameterSet

The parameter set describing the parameters of the input struct

titlestr=’’

The title to assign to the topology file

Returns

ChamberParm

ChamberParm instance with all parameters loaded

class parmed.amber.FortranFormat(format_string, strip_strings=True)

Bases: object

Processes Fortran format strings according to the Fortran specification for such formats. This object handles reading and writing data with any valid Fortran format. It does this by using the fortranformat project [https://bitbucket.org/brendanarnold/py-fortranformat].

However, while fortranformat is very general and adheres well to the standard, it is very slow. As a result, simple, common format strings have been optimized and processes reads and writes between 3 and 5 times faster. The format strings (case-insensitive) of the following form (where # can be replaced by any number) are optimized:

• #E#.#

• #D#.#

• #F#.#

• #(F#.#)

• #a#

• #I#

Parameters

format_stringstr

The Fortran Format string to process

strip_stringsbool=True

If True, strings are stripped before being processed by stripping (only) trailing whitespace

Methods

read(line)	Reads the line and returns the converted data
write(items, dest)	Writes an iterable of data (or a single item) to the passed file-like object

floatre = re.compile('(\\d+)?[edf](\\d+)\\.(\\d+)$', re.IGNORECASE)

floatre2 = re.compile('(\\d+)?\\([edf](\\d+)\\.(\\d+)\\)$', re.IGNORECASE)

intre = re.compile('(\\d+)?i(\\d+)$', re.IGNORECASE)

read(line)

Reads the line and returns the converted data

strre = re.compile('(\\d+)?a(\\d+)$', re.IGNORECASE)

write(items, dest)

Writes an iterable of data (or a single item) to the passed file-like object

Parameters

itemsiterable or single float/str/int

These are the objects to write in this format. The types of each item should match the type specified in this Format for that argument

destfile or file-like

This is the file to write the data to. It must have a write method or an AttributeError will be raised

Notes

This method may be replaced with _write_string (for #a#-style formats) or _write_ffwriter in the class initializer if no optimization is provided for this format, but the call signatures and behavior are the same for each of those functions.

parmed.amber.LoadParm(parmname, xyz=None, box=None)

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.NetCDFRestart(fname, mode='r')

Bases: object

Class to read or write NetCDF restart files

Attributes

box

cell_angles

cell_lengths

coordinates

remd_dimtype

remd_indices

temp0

time

velocities

Methods

id_format(filename)	Identifies the file type as an Amber NetCDF restart file
open_new(fname, natom, box, vels[, title, …])	Opens a new NetCDF file and sets the attributes
open_old(fname)	Opens the NetCDF file and sets the global attributes that the file sets
parse(fname)	Opens the NetCDF file and sets the global attributes that the file sets

close
flush

property box

property cell_angles

property cell_lengths

close()

property coordinates

flush()

static id_format(filename)

Identifies the file type as an Amber NetCDF restart file

Parameters

filenamestr

Name of the file to check format for

Returns

is_fmtbool

True if it is an Amber NetCDF restart file. False otherwise

Notes

Remote NetCDF files cannot be loaded

classmethod open_new(fname, natom, box, vels, title='', remd=None, temp=None, remd_dimtypes=None)

Opens a new NetCDF file and sets the attributes

Parameters

fnamestr

Name of the new file to open (overwritten)

natomint

The number of atoms in the system

boxbool

Whether unit cell information is written or not

velsbool

Whether velocity information is written or not

titlestr=’’

The title to write to the NetCDF restart file

remdstr=None

None – No REMD information is written ‘T[emperature]’ – target temperature (or pH) will be written ‘M[ulti-D]’ – remd_dimtypes will be written

remd_dimtypesiterable of int=None

Array of exchange types for each group. The length will be the REMD dimension (if remd above is “M[ulti-D]”)

Notes

remd is case-insensitive, and done based on first-letter matching

classmethod open_old(fname)

Opens the NetCDF file and sets the global attributes that the file sets

Parameters

fnamestr

Name of the file to read

classmethod parse(fname)

Opens the NetCDF file and sets the global attributes that the file sets

Parameters

fnamestr

Name of the file to read

property remd_dimtype

property remd_indices

property temp0

property time

property velocities

class parmed.amber.NetCDFTraj(fname, mode='r')

Bases: object

Class to read or write NetCDF restart files

Parameters

fnamestr

Name of the file to open

modestr

Mode to open in:

• ‘w’ means write-mode

• ‘r’ means read-mode

Notes

You should use the open_new and open_old alternative constructors instead of the default constructor

Attributes

box

cell_lengths_angles

coordinates

forces

remd_dimtype

remd_indices

temp0

time

velocities

Methods

add_box(lengths[, angles])	Adds a new cell length and angle frame to the end of a NetCDF trajectory.
add_cell_lengths_angles(lengths[, angles])	Adds a new cell length and angle frame to the end of a NetCDF trajectory.
add_coordinates(stuff)	Adds a new coordinate frame to the end of a NetCDF trajectory.
add_forces(stuff)	Adds a new coordinate frame to the end of a NetCDF trajectory.
add_remd_indices(stuff)	Add REMD indices to the current frame of the NetCDF file
add_temp0(stuff)	The temperature to add to the current frame of the NetCDF file
add_time(stuff)	Adds the time to the current frame of the NetCDF file
add_velocities(stuff)	Adds a new velocities frame to the end of a NetCDF trajectory.
close()	Closes the NetCDF file
id_format(filename)	Identifies the file type as an Amber NetCDF trajectory file
open_new(fname, natom, box[, crds, vels, …])	Opens a new NetCDF file and sets the attributes
open_old(fname)	Opens the NetCDF file and sets the global attributes that the file sets

flush

add_box(lengths, angles=None)

Adds a new cell length and angle frame to the end of a NetCDF trajectory. This should only be called on objects created with the “open_new” constructor.

Parameters

lengthsarray of 3 (or 6) floats (or Quantities)

This should be a 1-D array of 3 or 6 elements. If 6 elements, angles should be None (below) and the first 3 elements are the box lengths (angstroms) and the last 3 are the box angles (degrees).

angles3-item iterable = None

These are the box angles (if lengths contains only 3 elements) in degrees. Must be a 1-D array of 3 elements or None if lengths includes angles as well.

add_cell_lengths_angles(lengths, angles=None)

Adds a new cell length and angle frame to the end of a NetCDF trajectory. This should only be called on objects created with the “open_new” constructor.

Parameters

lengthsarray of 3 (or 6) floats (or Quantities)

This should be a 1-D array of 3 or 6 elements. If 6 elements, angles should be None (below) and the first 3 elements are the box lengths (angstroms) and the last 3 are the box angles (degrees).

angles3-item iterable = None

These are the box angles (if lengths contains only 3 elements) in degrees. Must be a 1-D array of 3 elements or None if lengths includes angles as well.

add_coordinates(stuff)

Adds a new coordinate frame to the end of a NetCDF trajectory. This should only be called on objects created with the “open_new” constructor.

Parameters

stuffiterable of floats or distance Quantity

This array of floats is converted into a numpy array of shape (natom, 3). It can be passed either in the 2-D format of [ [x1, y1, z1], [x2, y2, z2], … ] or in the 1-D format of [x1, y1, z1, x2, y2, z2, … ].

add_forces(stuff)

Adds a new coordinate frame to the end of a NetCDF trajectory. This should only be called on objects created with the “open_new” constructor.

Parameters

stuffiterable of floats or energy/distance Quantity

This array of floats is converted into a numpy array of shape (natom, 3). It can be passed either in the 2-D format of [ [x1, y1, z1], [x2, y2, z2], … ] or in the 1-D format of [x1, y1, z1, x2, y2, z2, … ].

add_remd_indices(stuff)

Add REMD indices to the current frame of the NetCDF file

Parameters

stuffiterable of int

The indices in each REMD dimension

add_temp0(stuff)

The temperature to add to the current frame of the NetCDF file

Parameters

stufffloat or temperature Quantity

The temperature to add to the current NetCDF file

add_time(stuff)

Adds the time to the current frame of the NetCDF file

Parameters

stufffloat or time-dimension Quantity

The time to add to the current frame

add_velocities(stuff)

Adds a new velocities frame to the end of a NetCDF trajectory. This should only be called on objects created with the “open_new” constructor.

Parameters

stuffiterable of floats or distance/time Quantity

This array of floats is converted into a numpy array of shape (natom, 3). It can be passed either in the 2-D format of [ [x1, y1, z1], [x2, y2, z2], … ] or in the 1-D format of [x1, y1, z1, x2, y2, z2, … ].

property box

property cell_lengths_angles

close()

Closes the NetCDF file

property coordinates

flush()

property forces

static id_format(filename)

Identifies the file type as an Amber NetCDF trajectory file

Parameters

filenamestr

Name of the file to check format for

Returns

is_fmtbool

True if it is an Amber NetCDF trajectory file. False otherwise

Notes

Remote NetCDF files cannot be loaded

classmethod open_new(fname, natom, box, crds=True, vels=False, frcs=False, remd=None, remd_dimension=None, title='')

Opens a new NetCDF file and sets the attributes

Parameters

fnamestr

Name of the new file to open (overwritten)

natomint

Number of atoms in the restart

boxbool

Indicates if cell lengths and angles are written to the NetCDF file

crdsbool=True

Indicates if coordinates are written to the NetCDF file

velsbool=False

Indicates if velocities are written to the NetCDF file

frcsbool=False

Indicates if forces are written to the NetCDF file

remdstr=None

‘T[emperature]’ if replica temperature is written ‘M[ulti]’ if Multi-D REMD information is written None if no REMD information is written

remd_dimensionint=None

If remd above is ‘M[ulti]’, this is how many REMD dimensions exist

titlestr=’’

The title of the NetCDF trajectory file

classmethod open_old(fname)

Opens the NetCDF file and sets the global attributes that the file sets

Parameters

fnamestr

File name of the trajectory to open. It must exist

property remd_dimtype

property remd_indices

property temp0

property time

property velocities

class parmed.amber.Rst7(filename=None, natom=None, title='', time=0.0)

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)

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)

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)

Writes the coordinates and/or velocities to a restart file