5.20. AMBER PRMTOP topology parser
Reads an AMBER top file to build the system.
Amber keywords are turned into the following attributes:
AMBER flag |
MDAnalysis attribute |
ATOM_NAME |
names |
CHARGE |
charges |
ATOMIC_NUMBER |
elements |
MASS |
masses |
BONDS_INC_HYDROGEN BONDS_WITHOUT_HYDROGEN |
bonds |
ANGLES_INC_HYDROGEN ANGLES_WITHOUT_HYDROGEN |
angles |
DIHEDRALS_INC_HYDROGEN DIHEDRALS_WITHOUT_HYDROGEN |
dihedrals / improper |
ATOM_TYPE_INDEX |
type_indices |
AMBER_ATOM_TYPE |
types |
RESIDUE_LABEL |
resnames |
RESIDUE_POINTER |
residues |
Note
The Amber charge is converted to electron charges as used in MDAnalysis and other packages. To get back Amber charges, multiply by 18.2223.
Chamber-style Amber topologies (i.e. topologies generated via parmed conversion of a CHARMM topology to an AMBER one) are not currently supported. Support will likely be added in future MDAnalysis releases.
As of version 2.0.0, elements are no longer guessed if ATOMIC_NUMBER records
are missing. In those scenarios, if elements are necessary, users will have
to invoke the element guessers after parsing the topology file. Please see
MDAnalysis.topology.guessers for more details.
5.20.1. Classes
- class MDAnalysis.topology.TOPParser.TOPParser(filename)[source]
Reads topology information from an AMBER top file.
Reads the following Attributes if in topology: - Atomnames - Charges - Masses - Elements - Atomtypes - Resnames - Type_indices - Bonds - Angles - Dihedrals (inc. impropers)
The format is defined in PARM parameter/topology file specification. The reader tries to detect if it is a newer (AMBER 12?) file format by looking for the flag “ATOMIC_NUMBER”.
Notes
Elements are obtained from the atomic numbers (if present). If a given input atomic number does not belong to an element (usually either -1 or 0), the element will be assigned an empty record.
Changed in version 0.7.6: parses both amber10 and amber12 formats
Changed in version 0.19.0: parses bonds, angles, dihedrals, and impropers
Changed in version 1.0.0: warns users that chamber-style topologies are not currently supported
Changed in version 2.0.0: no longer guesses elements if missing
- close()
Close the trajectory file.
- convert_forces_from_native(force, inplace=True)
Conversion of forces array force from native to base units
- Parameters
force (array_like) – Forces to transform
inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.7.
- convert_forces_to_native(force, inplace=True)
Conversion of force array force from base to native units.
- Parameters
force (array_like) – Forces to transform
inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.7.
- convert_pos_from_native(x, inplace=True)
Conversion of coordinate array x from native units to base units.
- Parameters
x (array_like) – Positions to transform
inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
Changed in version 0.7.5: Keyword inplace can be set to
Falseso that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
- convert_pos_to_native(x, inplace=True)
Conversion of coordinate array x from base units to native units.
- Parameters
x (array_like) – Positions to transform
inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
Changed in version 0.7.5: Keyword inplace can be set to
Falseso that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
- convert_time_from_native(t, inplace=True)
Convert time t from native units to base units.
- Parameters
t (array_like) – Time values to transform
inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided.
Changed in version 0.7.5: Keyword inplace can be set to
Falseso that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
- convert_time_to_native(t, inplace=True)
Convert time t from base units to native units.
- Parameters
t (array_like) – Time values to transform
inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to
Falseso that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
- convert_velocities_from_native(v, inplace=True)
Conversion of velocities array v from native to base units
- Parameters
v (array_like) – Velocities to transform
inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.5.
- convert_velocities_to_native(v, inplace=True)
Conversion of coordinate array v from base to native units
- Parameters
v (array_like) – Velocities to transform
inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data
Note
By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.5.
- parse(**kwargs)[source]
Parse Amber PRMTOP topology file filename.
- Return type
A MDAnalysis Topology object
- parse_bonded(num_per_record, numlines)[source]
Extracts bond information from PARM7 format files
- Parameters
Note
For the bond/angle sections of parm7 files, the atom numbers are set to coordinate array index values. As detailed in http://ambermd.org/formats.html to recover the actual atom number, one should divide the values by 3 and add 1. Here, since we want to satisfy zero-indexing, we only divide by 3.
- parse_chunks(data, chunksize)[source]
Helper function to parse AMBER PRMTOP bonds/angles.
- Parameters
data (list of int) – Input list of the parm7 bond/angle section, zero-indexed
num_per_record (int) – The number of entries for each record in the input list
- Returns
vals – A list of tuples containing the atoms involved in a given bonded interaction
- Return type
list of int tuples
Note
In the parm7 format this information is structured in the following format: [ atoms 1:n, internal index ] Where 1:n represent the ids of the n atoms involved in the bond/angle and the internal index links to a given set of FF parameters. Therefore, to extract the required information, we split out the list into chunks of size num_per_record, and only extract the atom ids.
- parse_dihedrals(diha, dihh)[source]
Combines hydrogen and non-hydrogen containing AMBER dihedral lists and extracts sublists for conventional dihedrals and improper angles
- Parameters
diha (list of tuples) – The atom ids of dihedrals not involving hydrogens
dihh (list of tuples) – The atom ids of dihedrals involving hydrogens
- Returns
dihedrals (
Dihedrals) – ADihedralsinstance containing a list of all unique dihedrals as defined by the parm7 fileimpropers (
Impropers) – AImpropersinstance containing a list of all unique improper dihedrals as defined by the parm7 file
Note
As detailed in http://ambermd.org/formats.html, the dihedral sections of parm7 files contain information about both conventional dihedrals and impropers. The following must be accounted for: 1) If the fourth atom in a dihedral entry is given a negative value, this indicates that it is an improper. 2) If the third atom in a dihedral entry is given a negative value, this indicates that it 1-4 NB interactions are ignored for this dihedrals. This could be due to the dihedral within a ring, or if it is part of a multi-term dihedral definition or if it is an improper.
- parse_elements(num_per_record, numlines)[source]
Extracts the atomic numbers of each atom and converts to element type
- Parameters
- Returns
attr – A
Elementsinstance containing the element of each atom as defined in the parm7 file- Return type
Elements
Note
If the record contains unknown atomic numbers (e.g. <= 0), these will be treated as unknown elements and assigned an empty string value. See issues #2306 and #2651 for more details.
Changed in version 2.0.0: Unrecognised elements will now return a empty string. The parser will no longer attempt to guess the element by default.
- parse_type_indices(num_per_record, numlines)[source]
Extracts the index of atom types of the each atom involved in Lennard Jones (6-12) interactions.