7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup
¶
The most important data structure in MDAnalysis is the
AtomGroup
, which contains Atom
instances.
A Universe
is the user-visible entry point and collects all
information needed to analyze a structure or a whole trajectory.
Segments and residues are a way to refer to a collection of atoms. By
convention, a Residue
is a single amino acid, or a water
molecule, ion, or ligand. A Segment
is a collection of
residues such as a whole protein or a chain in a protein or all the
water in the system.
7.2.1. Class Hierarchy¶
A Universe
contains Segments, which contain Residues, which
contain Atoms; all containers are derived from AtomGroup
, and
thus one can always analyze them as a collection of atoms, independent
of the hierarchical level.
Each Atom
can only belong to a single Residue
, and a
Residue
belongs to one specific Segment
. This
hierarchy can be described as
Segment > Residue > Atom
Depending on the use case, it can be more convenient to access data
on, for instance, the basis of residues than atoms, or to write out
individual chains (segments) of a protein. MDAnalysis simply provides
access to these groupings and keeps track of where an atom
belongs. Each object provides three attributes (atoms
,
residues
or residue
, segments
or
segment
) that give access to the tiers in the hierarchy
that the object belongs to.
7.2.2. Manipulating atoms, residues, and segments¶
When working with MDAnalysis it is useful to remember that the fundamental
object is the Atom
. Each particle in the topology is represented by
exactly one Atom
instance. One Atom
, however, can be a member
of multiple AtomGroup
collections, for instance from different
selections even though they all refer to the same Atom
object. Thus,
changing a property of a specific and Atom
in one AtomGroup
changes it “everywhere”.
The same is mostly true for Residue
instances although they are
derived from Atom
instances: all Atom
objects with the same
Atom.resid
are bundled into a single Residue
with
Residue.id
= resid. This means that just changing, say, the residue
name with a command such as
>>> r = u.selectAtoms("resid 99").residues[0]
>>> print(r)
<Residue 'ALA', 99>
>>> r.name = "UNK"
>>> print(r)
<Residue 'UNK', 99>
>>> rnew = u.selectAtoms("resid 99").residues[0]
>>> print(rnew)
<Residue 'UNK', 99>
will typically work as expected. When working with collections such as
AtomGroup
or ResidueGroup
it is generally better to use
provided setter methods such as AtomGroup.set_resname()
or
ResidueGroup.set_resname()
.
There are two cases when it is very important to use the setters:
- changing resid:
AtomGroup.set_resid()
andResidueGroup.set_resid()
- changing segid:
AtomGroup.set_segid()
andResidueGroup.set_segid()
Because residues are determined by the Atom.resid
and segments by
Atom.segid
, the above methods take extra care to rebuild the list of
segments and residues.
Note
AtomGroup.set_resid()
, ResidueGroup.set_resid()
,
AtomGroup.set_segid()
, ResidueGroup.set_segid()
can change the
topology: they can split or merge residues or segments.
Splitting/merging of residues is probably not very useful because no chemical
rearrangements are carried out. Manipulating segments might be more useful in
order to add additional structure to a Universe
and provide instant
segment selectors for interactive work:
u.selectAtoms("protein").set_segid("protein")
u.selectAtoms("resname POPE or resname POPC").set_segid("lipids")
u.selectAtoms("resname SOL").set_segid("water")
u.selectAtoms("resname NA or resname CL").set_segid("ions")
u.protein.numberOfResidues()
water_oxygens = u.water.OW
The setter methods have the additional advantage that they can assign lists. For instance, many MD codes number residues consecutively starting from 1. However, the original structure might be missing a few atoms at the N-terminus. Let’s say that the first residue is really residue 10. In order to store the canonical residue IDs (“resnum”) one could the use
import numpy as np
protein = u.selectAtoms("protein").residues
protein.set_resnum(np.array(protein.resnums()) + 9)
One can then use protein.select("resnum 42")
to select the residue that has
the canonical residue id 42 (instead of resid 33
).
One can also read the resids directly from an original PDB file:
orig = MDAnalysis.Universe("2jln.pdb")
protein.set_resnum(orig.selectAtoms("protein").resids())
7.2.3. Working with Topologies¶
If the topology file given to the Universe had bonding information then this
will have been loaded into the Universe as Universe.bonds
Universe.angles
Universe.torsions
and Universe.impropers
.
If your topology file does not have this information, it is still possible
to construct it based on the positions of the atoms and assumed vdw radii
for these atoms. See MDAnalysis.AtomGroup.guess_bonds()
and
MDAnalysis.topology.core.guess_bonds()
for details.
This Topology information is stored in MDAnalysis.topology.core.TopologyGroup
objects. These are designed to be analogous to the AtomGroup container for Atoms.
For examples working with a box of ethanol:
>>> import MDAnalysis as mda
>>> u = mda.Universe('ethanol.gro', guess_bonds=True)
>>> u.bonds
<TopologyGroup containing 11784 Bonds>
>>> u.bonds.types() # view available types
[('O', 'H'), ('C', 'O'), ('C', 'H'), ('C', 'C')]
>>> u.bonds.selectBonds(('C', 'O')) # return all C-O bonds from the group
<TopologyGroup containing 1473 Bonds>
Bonds are categorised based on the types of atoms. This is done in a way so that type (a, b, c) is equivalent to (c, b, a) ie. bonds are reversible. For example:
>>> u.angles.types()
[('C', 'C', 'H'),
('H', 'C', 'H'),
('C', 'O', 'H'),
('C', 'C', 'O'),
('H', 'C', 'O')]
There is only C-C-H bonds and no H-C-C bonds. Selection however is aware that sometimes types are reversed:
u.angles.selectBonds(('H', 'C', 'C')) # note reversal of type
>>> <TopologyGroup containing 7365 Angles>
TopologyGroups can be combined and indexed:
>>> tg = u.angles.selectBonds(('C', 'C', 'O')) + u.angles.selectBonds(('C', 'O', 'H'))
>>> tg.types()
[('C', 'O', 'H'), ('C', 'C', 'O')]
>>> tg[:100]
<TopologyGroup containing 100 Angles>
Finally, TopologyGroups are linked to some fast Cython calculation methods to determine bond lengths and angle sizes:
>>> tg.angles()
array([ 1.88042373, 1.95928987, 1.74770012, ..., 1.79306789,
1.95522678, 1.88881045])
7.2.4. Combining objects: system building¶
It is often convenient to combined multiple groups of atoms into a single
object. If they are contained in a single Universe
then the methods
described above (especially manipulating the segments) might be
useful. However, if the atoms reside in different universes, the Merge()
function can be used.
7.2.4.1. Merging¶
In the following example for Merge()
, protein, ligand, and solvent were
externally prepared in three different PDB files. They are loaded into separate
Universe
objects (where they could be further manipulated,
e.g. renumbered, relabeled, rotated, ...) The Merge()
command is used to
combine all of them together:
import MDAnalysis
u1 = MDAnalysis.Universe("protein.pdb")
u2 = MDAnalysis.Universe("ligand.pdb")
u3 = MDAnalysis.Universe("solvent.pdb")
u = MDAnalysis.Merge(u1.selectAtoms("protein"), u2.atoms, u3.atoms)
u.atoms.write("system.pdb")
The complete system is then written out to a new PDB file.
7.2.4.2. Replicating¶
It is also possible to replicate a molecule to build a system with multiple copies of the same molecule. In the example, we replicate an AdK molecule and then translate and rotate the second copy:
import MDAnalysis; from MDAnalysis.tests.datafiles import *
u = MDAnalysis.Universe(PSF, DCD)
p = u.selectAtoms("protein")
m = MDAnalysis.Merge(p,p)
# now renumber resids and segids for each copy
# first copy of the protein (need to use atom indices because currently that's the only reliable property in the
merged universe)
p1 = m.selectAtoms("bynum 1:3341")
# second copy
p2 = m.selectAtoms("bynum 3342:6682")
p1.set_segid("A")
p2.set_segid("B")
p2.residues.set_resid(p2.residues.resids() + p1.residues.resids()[-1]) # increment resids for p2 with the last
resid from p1
# you must regenerate the selections after modifying them (see notes in the docs!)
# because the changed resids are not reflected in the selection (due to how residues are referenced internally)
p1 = m.selectAtoms("segid A") # or as before: m.selectAtoms("bynum 1:3341")
p2 = m.selectAtoms("segid B")
# rotate and translate
p2.rotateby(180, [0,0,1])
p2.translate([50,0,0])
Note that we have to manually set the residue numbers (resids) and
segment identifies because Merge()
simply concatenates the
existing atoms and only ensures that all data structures are contained
in the new merged universe.
7.2.5. Classes and functions¶
-
class
MDAnalysis.core.AtomGroup.
Universe
(*args, **kwargs)[source]¶ The MDAnalysis Universe contains all the information describing the system.
The system always requires a topology file — in the simplest case just a list of atoms. This can be a CHARMM/NAMD PSF file or a simple coordinate file with atom informations such as XYZ, PDB, Gromacs GRO, or CHARMM CRD. See Table of Supported Topology Formats for what kind of topologies can be read.
A trajectory provides coordinates; the coordinates have to be ordered in the same way as the list of atoms in the topology. A trajectory can be a single frame such as a PDB, CRD, or GRO file, or it can be a MD trajectory (in CHARMM/NAMD/LAMMPS DCD, Gromacs XTC/TRR, or generic XYZ format). See Table of supported coordinate formats for what can be read as a “trajectory”.
As a special case, when the topology is a XYZ, PDB, GRO or CRD file then the coordinates are immediately loaded from the “topology” file unless a trajectory is supplied.
Examples for setting up a universe:
u = Universe(topology, trajectory) # read system from file(s) u = Universe(pdbfile) # read atoms and coordinates from PDB or GRO u = Universe(topology, [traj1, traj2, ...]) # read from a list of trajectories u = Universe(topology, traj1, traj2, ...) # read from multiple trajectories
Load new data into a universe (replaces old trajectory and does not append):
u.load_new(trajectory) # read from a new trajectory file
Select atoms, with syntax similar to CHARMM (see
selectAtoms
for details):u.selectAtoms(...)
Attributes:
Universe.trajectory
: currently loaded trajectory reader;Universe.trajectory.ts
is the current time stepUniverse.dimensions
: current system dimensions (simulation unit cell, if set in the trajectory)Universe.bonds
: TopologyGroup of bonds in Universe, alsoUniverse.angles
,Universe.dihedrals
, andUniverse.impropers
(low level access throughUniverse._topology
)
Note
If atom attributes such as element, mass, or charge are not explicitly provided in the topology file then MDAnalysis tries to guess them (see
MDAnalysis.topology.tables
). This does not always work and if you require correct values (e.g. because you want to calculate the center of mass) then you need to make sure that MDAnalysis gets all the information needed.Changed in version 0.7.5: Can also read multi-frame PDB files with the
PrimitivePDBReader
.Changed in version 0.8: Parse arbitrary number of arguments as a single topology file and a a sequence of trajectories.
Changed in version 0.9.0: Topology information now loaded lazily, but can be forced with
build_topology()
Changed .bonds attribute to be aTopologyGroup
Added .angles and .torsions attribute asTopologyGroup
Added fragments to Universe cacheInitialize the central MDAnalysis Universe object.
Arguments: - topologyfile
A CHARMM/XPLOR PSF topology file, PDB file or Gromacs GRO file; used to define the list of atoms. If the file includes bond information, partial charges, atom masses, ... then these data will be available to MDAnalysis. A “structure” file (PSF, PDB or GRO, in the sense of a topology) is always required.
- coordinatefile
A trajectory (such as CHARMM DCD, Gromacs XTC/TRR/GRO, XYZ, XYZ.bz2) or a PDB that will provide coordinates, possibly multiple frames. If a list of filenames is provided then they are sequentially read and appear as one single trajectory to the Universe. The list can contain different file formats.
Deprecated since version 0.8: Do not use the coordinatefile keyword argument, just provide trajectories as positional arguments.
- permissive
currently only relevant for PDB files: Set to
True
in order to ignore most errors and read typical MD simulation PDB files; set toFalse
to read with the Bio.PDB reader, which can be useful for real Protein Databank PDB files.None
selects the MDAnalysis default (which is set inMDAnalysis.core.flags
) [None
]- topology_format
provide the file format of the topology file;
None
guesses it from the file extension [None
] Can also pass a subclass ofMDAnalysis.topology.base.TopologyReader
to define a custom reader to be used on the topology file.- format
provide the file format of the coordinate or trajectory file;
None
guesses it from the file extension. Note that this keyword has no effect if a list of file names is supplied because the “chained” reader has to guess the file format for each individual list member. [None
] Can also pass a subclass ofMDAnalysis.coordinates.base.Reader
to define a custom reader to be used on the trajectory file.- guess_bonds
Once Universe has been loaded, attempt to guess the connectivity between atoms. This will populate the .bonds .angles and .torsions attributes of the Universe.
- vdwradii
For use with guess_bonds. Supply a dict giving a vdwradii for each atom type which are used in guessing bonds.
This routine tries to do the right thing:
If a pdb/gro file is provided instead of a psf and no coordinatefile then the coordinates are taken from the first file. Thus you can load a functional universe with
u = Universe('1ake.pdb')
If you want to specify the coordinate file format yourself you can do so using the format keyword:
u = Universe('1ake.ent1', format='pdb')
If only a topology file without coordinate information is provided one will have to load coordinates manually using
Universe.load_new()
. The file format of the topology file can be explicitly set with the topology_format keyword.
Changed in version 0.7.4: New topology_format and format parameters to override the file format detection.
Changed in version 0.10.0: Added
'guess_bonds'
keyword to cause topology to be guessed on Universe creation. Deprecated'bonds'
keyword, use'guess_bonds'
instead.-
angles
¶ Returns a
TopologyGroup
of all angles in the UniverseNew in version 0.9.0.
Changed in version 0.9.2: Now can return empty TopologyGroup
-
bonds
¶ Returns a
TopologyGroup
of all bonds in the Universe.Changed in version 0.9.0: Now a lazily built
TopologyGroup
Changed in version 0.9.2: Now can return empty TopologyGroup
-
build_topology
()[source]¶ Bond angle and torsion information is lazily constructed into the Universe.
This method forces all this information to be loaded.
-
coord
¶ Reference to current timestep and coordinates of universe.
The raw trajectory coordinates are
Universe.coord._pos
, represented as anumpy.float32
array.Because
coord
is a reference to aTimestep
, it changes its contents while one is stepping through the trajectory.Note
In order to access the coordinates it is probably better to use the
AtomGroup.coordinates()
method; for instance, all coordinates of the Universe as a numpy array:Universe.atoms.coordinates()
.
-
dimensions
¶ Current dimensions of the unitcell
-
fragments
¶ Read only tuple of fragments in the Universe
-
impropers
¶ Returns a
TopologyGroup
of all improper torsions in the UniverseNew in version 0.9.0.
Changed in version 0.9.2: Now can return empty TopologyGroup
-
load_new
(filename, **kwargs)[source]¶ Load coordinates from filename, using the suffix to detect file format.
Arguments: - filename
the coordinate file (single frame or trajectory) or a list of filenames, which are read one after another.
- permissive
currently only relevant for PDB files: Set to
True
in order to ignore most errors and read typical MD simulation PDB files; set toFalse
to read with the Bio.PDB reader, which can be useful for real Protein Databank PDB files.None
selects the MDAnalysis default (which is set inMDAnalysis.core.flags
) [None
]- format
provide the file format of the coordinate or trajectory file;
None
guesses it from the file extension. Note that this keyword has no effect if a list of file names is supplied because the “chained” reader has to guess the file format for each individual list member [None
] Can also pass a subclass ofMDAnalysis.coordinates.base.Reader
to define a custom reader to be used on the trajectory file.- kwargs
Other kwargs are passed to the trajectory reader (only for advanced use)
Returns: (filename, trajectory_format) or
None
if filename ==None
Raises: TypeError
if trajectory format can not be determined or no appropriate trajectory reader foundChanged in version 0.8: If a list or sequence that is provided for filename only contains a single entry then it is treated as single coordinate file. This has the consequence that it is not read by the
ChainReader
but directly by its specialized file format reader, which typically has more features than theChainReader
.
-
selectAtoms
(sel, *othersel, **selgroups)[source]¶ Select atoms using a CHARMM selection string.
Returns an
AtomGroup
with atoms sorted according to their index in the psf (this is to ensure that there aren’t any duplicates, which can happen with complicated selections).Existing
AtomGroup
objects can be passed as named arguments, which will then be available to the selection parser.Subselections can be grouped with parentheses.
- Example::
>>> sel = universe.selectAtoms("segid DMPC and not ( name H* or name O* )") >>> sel <AtomGroup with 3420 atoms>
>>> universe.selectAtoms("around 10 group notHO", notHO=sel) <AtomGroup with 1250 atoms>
Note
If exact ordering of atoms is required (for instance, for
angle()
ordihedral()
calculations) then one supplies selections separately in the required order. Also, when multipleAtomGroup
instances are concatenated with the+
operator then the order ofAtom
instances is preserved and duplicates are not removed.See also
Selection Commands for further details and examples.
The selection parser understands the following CASE SENSITIVE keywords:
Simple selections
- protein, backbone, nucleic, nucleicbackbone
- selects all atoms that belong to a standard set of residues; a protein is identfied by a hard-coded set of residue names so it may not work for esoteric residues.
- segid seg-name
- select by segid (as given in the topology), e.g.
segid 4AKE
orsegid DMPC
- resid residue-number-range
- resid can take a single residue number or a range of numbers. A range
consists of two numbers separated by a colon (inclusive) such
as
resid 1:5
. A residue number (“resid”) is taken directly from the topology. - resnum resnum-number-range
- resnum is the canonical residue number; typically it is set to the residue id in the original PDB structure.
- resname residue-name
- select by residue name, e.g.
resname LYS
- name atom-name
- select by atom name (as given in the topology). Often, this is force
field dependent. Example:
name CA
(for Cα atoms) orname OW
(for SPC water oxygen) - type atom-type
- select by atom type; this is either a string or a number and depends on the force field; it is read from the topology file (e.g. the CHARMM PSF file contains numeric atom types). It has non-sensical values when a PDB or GRO file is used as a topology.
- atom seg-name residue-number atom-name
- a selector for a single atom consisting of segid resid atomname,
e.g.
DMPC 1 C2
selects the C2 carbon of the first residue of the DMPC segment - altloc alternative-location
- a selection for atoms where alternative locations are available, which is often the case with high-resolution crystal structures e.g. resid 4 and resname ALA and altloc B selects only the atoms of ALA-4 that have an altloc B record.
Boolean
- not
- all atoms not in the selection, e.g.
not protein
selects all atoms that aren’t part of a protein - and, or
- combine two selections according to the rules of boolean algebra,
e.g.
protein and not (resname ALA or resname LYS)
selects all atoms that belong to a protein, but are not in a lysine or alanine residue
Geometric
- around distance selection
- selects all atoms a certain cutoff away from another selection,
e.g.
around 3.5 protein
selects all atoms not belonging to protein that are within 3.5 Angstroms from the protein - point x y z distance
- selects all atoms within a cutoff of a point in space, make sure
coordinate is separated by spaces, e.g.
point 5.0 5.0 5.0 3.5
selects all atoms within 3.5 Angstroms of the coordinate (5.0, 5.0, 5.0) - prop [abs] property operator value
- selects atoms based on position, using property x, y, or
z coordinate. Supports the abs keyword (for absolute value) and
the following operators: <, >, <=, >=, ==, !=. For example,
prop z >= 5.0
selects all atoms with z coordinate greater than 5.0;prop abs z <= 5.0
selects all atoms within -5.0 <= z <= 5.0.
Connectivity
- byres selection
- selects all atoms that are in the same segment and residue as selection, e.g. specify the subselection after the byres keyword
Index
- bynum index-range
- selects all atoms within a range of (1-based) inclusive indices,
e.g.
bynum 1
selects the first atom in the universe;bynum 5:10
selects atoms 5 through 10 inclusive. All atoms in theMDAnalysis.Universe
are consecutively numbered, and the index runs from 1 up to the total number of atoms.
Preexisting selections
- group group-name
- selects the atoms in the
AtomGroup
passed to the function as an argument named group-name. Only the atoms common to group-name and the instanceselectAtoms()
was called from will be considered. group-name will be included in the parsing just by comparison of atom indices. This means that it is up to the user to make sure they were defined in an appropriateUniverse
. - fullgroup group-name
- just like the
group
keyword with the difference that all the atoms of group-name are included. The resulting selection may therefore have atoms that were initially absent from the instanceselectAtoms()
was called from.
Changed in version 0.7.4: Added resnum selection.
Changed in version 0.8.1: Added group and fullgroup selections.
-
torsions
¶ Returns a
TopologyGroup
of all torsions in the UniverseNew in version 0.9.0.
Changed in version 0.9.2: Now can return empty TopologyGroup
-
trajectory
¶ Reference to trajectory reader object containing trajectory data.
-
MDAnalysis.core.AtomGroup.
Merge
(*args)[source]¶ Return a
Universe
from two or moreAtomGroup
instances.AtomGroup
instances can come from different Universes, or come directly from aselectAtoms()
call.It can also be used with a single
AtomGroup
if the user wants to, for example, re-order the atoms in the Universe.Arguments: One or more AtomGroup
instances.Returns: an instance of Universe
Raises: ValueError
for too few arguments or if an AtomGroup is empty andTypeError
if arguments are notAtomGroup
instances.Example
In this example, protein, ligand, and solvent were externally prepared in three different PDB files. They are loaded into separate
Universe
objects (where they could be further manipulated, e.g. renumbered, relabeled, rotated, ...) TheMerge()
command is used to combine all of them together:u1 = Universe("protein.pdb") u2 = Universe("ligand.pdb") u3 = Universe("solvent.pdb") u = Merge(u1.selectAtoms("protein"), u2.atoms, u3.atoms) u.atoms.write("system.pdb")
The complete system is then written out to a new PDB file.
Note
Merging does not create a full trajectory but only a single structure even if the input consists of one or more trajectories.
-
class
MDAnalysis.core.AtomGroup.
AtomGroup
(atoms)[source]¶ A group of atoms.
ag = universe.selectAtoms(atom-list)The AtomGroup contains a list of atoms; typically, a AtomGroup is generated from a selection. It is build from any list-like collection of
Atom
instances. It is also possible to create an empty AtomGroup from an empty list.An AtomGroup can be indexed and sliced like a list:
ag[0], ag[-1]
will return the first and the last
Atom
in the group whereas the sliceag[0:6:2]
returns every second element, corresponding to indices 0, 2, and 4.
It also supports “advanced slicing” when the argument is a
numpy.ndarray
or alist
:aslice = [0, 3, -1, 10, 3] ag[aslice]
will return a new
AtomGroup
containing (ag[0], ag[3], ag[-1], ag[10], ag[3]).Note
AtomGroups originating from a selection are sorted and duplicate elements are removed. This is not true for AtomGroups produced by slicing. Thus slicing can be used when the order of atoms is crucial (for instance, in order to define angles or dihedrals).
Atoms can also be accessed in a Pythonic fashion by using the atom name as an attribute. For instance,
ag.CA
will provide a
AtomGroup
of all CA atoms in the group. These instant selector attributes are auto-generated for each atom name encountered in the group.Note
The name-attribute instant selector access to atoms is mainly meant for quick interactive work. Thus it either returns a single
Atom
if there is only one matching atom, or a newAtomGroup
for multiple matches. This makes it difficult to use the feature consistently in scripts but it is much better for interactive work.References for analysis methods
[Dima2004] (1, 2) Dima, R. I., & Thirumalai, D. (2004). Asymmetry in the shapes of folded and denatured states of proteins. J Phys Chem B, 108(21), 6564-6570. doi:10.1021/jp037128y Changed in version 0.7.6: An empty AtomGroup can be created and no longer raises a
NoDataError
.Changed in version 0.9.0: The size at which cache is used for atom lookup is now stored as variable _atomcache_size within the class. Added fragments manged property. Is a lazily built, cached entry, similar to residues.
-
_rebuild_caches
()[source]¶ Rebuild all AtomGroup caches.
A number of lists and attributes are cached. These caches are lazily built the first time they are needed. When editing the topology it might happen that not all caches were synced properly (even though that this is supposed to happen eventually). In this case the user can manually force a complete cache rebuild.
Currently the following caches are used:
- atoms (for “in” lookup); cache is only built for large systems with > 10,000 atoms
- indices (
AtomGroup.indices()
) - masses (
AtomGroup.masses()
) - residues (
AtomGroup.residues
) - segments (
AtomGroup.segments
) - bonds (
AtomGroup.bonds
) - angles (
AtomGroup.angles
) - torsions (
AtomGroup.torsions
) - improper torsions (
AtomGroup.impropers
)
See also
New in version 0.7.5.
Changed in version 0.9.0: Added bonds/angles/torsions/impropers to rebuild. Reworked how things are rebuilt to avoid code duplication.
-
_clear_caches
(*args)[source]¶ Clear cache for all args.
If no args are provided, all caches are cleared.
See also
New in version 0.8.
-
align_principalAxis
(axis, vector)[source]¶ Align principal axis with index axis with vector.
Arguments: - axis
Index of the principal axis (0, 1, or 2), as produced by
principalAxes()
.- vector
A 3D vector such as the z-axis (
[0,0,1]
); can be anything that looks like a list with three entries.
To align the long axis of a channel (the first principal axis, i.e. axis = 0) with the z-axis:
u.atoms.align_principalAxis(0, [0,0,1]) u.atoms.write("aligned.pdb")
-
angle
()[source]¶ Returns the angle in degrees between atoms 0, 1, 2.
Angle between atoms 0 and 2 with apex at 1:
2 / / 1------0
New in version 0.7.3.
-
angles
¶ All the angles in this AtomGroup
Note that these angles might extend out of the AtomGroup, to select only angles which are entirely contained by the AtomGroup use u.angles.atomgroup_intersection(ag, strict=True)
New in version 0.9.0.
Changed in version 0.10.0: Now always returns a (possibly empty) TopologyGroup
-
asphericity
(**kwargs)[source]¶ Asphericity.
See [Dima2004] for background information.
Keywords: - pbc
True
: Move all atoms within primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.New in version 0.7.7.
Changed in version 0.8: Added pbc keyword
-
atoms
¶ AtomGroup
of all atoms in this group.If this is a
AtomGroup
then it returns itself. Otherwise, it will return a newAtomGroup
based on allAtom
instances contained.Apply :func:`list to
atoms
or use_atoms
if you really only need a list of individualAtom
instances.
-
bbox
(**kwargs)[source]¶ Return the bounding box of the selection.
The lengths A,B,C of the orthorhombic enclosing box are
L = AtomGroup.bbox() A,B,C = L[1] - L[0]
Keywords: - pbc
True
: Move all atoms within the primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.Returns: [[xmin, ymin, zmin], [xmax, ymax, zmax]] New in version 0.7.2.
Changed in version 0.8: Added pbc keyword
-
bfactors
¶ Crystallographic B-factors (from PDB) in A**2.
-
bond
(pbc=False)[source]¶ Returns the distance between atoms in a 2-atom group.
Distance between atoms 0 and 1:
0---1
Keywords: - pbc
True
: Account for minimum image convention when calculating [False
]
New in version 0.7.3.
Changed in version 0.8: Added pbc keyword
-
bonds
¶ All the bonds in this AtomGroup
Note that these bonds might extend out of the AtomGroup, to select only bonds which are entirely contained by the AtomGroup use u.bonds.atomgroup_intersection(ag, strict=True)
New in version 0.9.0.
Changed in version 0.10.0: Now always returns a (possibly empty) TopologyGroup
-
bsphere
(**kwargs)[source]¶ Return the bounding sphere of the selection.
The sphere is calculated relative to the centre of geometry.
Keywords: - pbc
True
: Move all atoms within primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.Returns: (R, [xcen,ycen,zcen]) New in version 0.7.3.
Changed in version 0.8: Added pbc keyword
-
centerOfGeometry
(**kwargs)[source]¶ Center of geometry (also known as centroid) of the selection.
Keywords: - pbc
True
: Move all atoms within the primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.Changed in version 0.8: Added pbc keyword
-
centerOfMass
(**kwargs)[source]¶ Center of mass of the selection.
Keywords: - pbc
True
: Move all atoms within the primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.Changed in version 0.8: Added pbc keyword
-
centroid
(**kwargs)¶ Center of geometry (also known as centroid) of the selection.
Keywords: - pbc
True
: Move all atoms within the primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.Changed in version 0.8: Added pbc keyword
-
coordinates
(ts=None, copy=False, dtype=<type 'numpy.float32'>)¶ NumPy array of the coordinates.
See also
Deprecated since version 0.7.6: In new scripts use
AtomGroup.get_positions()
preferrably.
-
dihedral
()[source]¶ Calculate the dihedral angle in degrees.
Dihedral angle around axis connecting atoms 1 and 2 (i.e. the angle between the planes spanned by atoms (0,1,2) and (1,2,3)):
3 | 1-----2 / 0
New in version 0.7.0.
-
dimensions
¶ Dimensions of the Universe to which the group belongs, at the current time step.
-
forces
¶ Forces on the atoms in the AtomGroup.
The forces can be changed by assigning an array of the appropriate shape, i.e. either Nx3 to assign individual force or 3, to assign the same force to all atoms (e.g.
ag.forces = array([0,0,0])
will set all forces to (0.,0.,0.)).For more control use the
get_forces()
andset_forces()
methods.New in version 0.7.7.
-
fragments
¶ Read-only list of fragments.
Contains all fragments that any Atom in this AtomGroup is part of, the contents of the fragments may extend beyond the contents of this AtomGroup.
-
get_forces
(ts=None, copy=False, dtype=<type 'numpy.float32'>)[source]¶ Get a NumPy array of the atomic forces (if available). Currently only supported for Gromacs .trr trajectories.
Keywords: - ts
If ts is provided then positions are read from that
Timestep
instead of the one from the current trajectory belonging to this universe. The ts is indexed with the indices returned byindices()
and it is the user’s responsibility to provide a time step that has the appropriate dimensions.- copy
True
: always make a copy (slow),False
: Try to return a array view or reference (faster); note that for passing coordinates to C-code it can be necessary to use a copy [False
]- dtype
NumPy Data type of the array; the default is usually entirely appropriate. Most C-code actually requires the default [
numpy.float32
]
Forces can also be directly obtained from the attribute
forces
.Forces can be directly set with
set_forces()
or by assigning toforces
.New in version 0.7.7.
-
get_positions
(ts=None, copy=False, dtype=<type 'numpy.float32'>)[source]¶ Get a NumPy array of the coordinates.
Keywords: - ts
If ts is provided then positions are read from that
Timestep
instead of the one from the current trajectory belonging to this universe. The ts is indexed with the indices returned byindices()
and it is the user’s responsibility to provide a time step that has the appropriate dimensions.- copy
True
: always make a copy (slow),False
: Try to return a array view or reference (faster); note that for passing coordinates to C-code it can be necessary to use a copy [False
]- dtype
NumPy Data type of the array; the default is usually entirely appropriate. Most C-code actually requires the default [
numpy.float32
]
Coordinates can also be directly obtained from the attribute
positions
.Coordinates can be directly set with
set_positions()
or by assigning topositions
.This method is identical with
coordinates()
but named differently for symmetry with withset_positions()
.New in version 0.7.6.
-
get_velocities
(ts=None, copy=False, dtype=<type 'numpy.float32'>)[source]¶ NumPy array of the velocities.
Raises a
NoDataError
if the underlyingTimestep
does not contain_velocities
.See also
AtomGroup.set_velocities()
and attribute access throughAtomGroup.velocities
.New in version 0.7.6.
-
guess_bonds
(vdwradii=None)[source]¶ Guess all the bonds that exist within this AtomGroup and add to Universe.
Keywords: - vdwradii
Pass a dict relating atom types to vdwradii.
New in version 0.10.0.
-
improper
()[source]¶ Returns the improper dihedral between 4 atoms.
The improper dihedral is calculated in the same way as the proper
dihedral()
: The angle between the planes formed by atoms (0,1,2) and (1,2,3).Note
Only makes sense for a
AtomGroup
with exactly 4Atom
; anything else will raise aValueError
. The interpretation of the angle as an “improper” solely depends on the selection of atoms and thus the user input!New in version 0.7.3.
-
impropers
¶ All the improper torsions in this AtomGroup
Note that these improper torsions might extend out of the AtomGroup, to select only torsions which are entirely contained by the AtomGroup use u.impropers.atomgroup_intersection(ag, strict=True)
New in version 0.9.0.
Changed in version 0.10.0: Now always returns a (possibly empty) TopologyGroup
-
indices
(*args, **kwargs)[source]¶ Array of all
Atom.number
in the group.These indices are 0-based and can be used to directly index
Universe.atoms
or the coordinate arrayMDAnalysis.coordinates.base.Timestep._pos
.
-
momentOfInertia
(**kwargs)[source]¶ Tensor of inertia as 3x3 NumPy array.
Keywords: - pbc
True
: Move all atoms within the primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.Changed in version 0.8: Added pbc keyword
-
names
()[source]¶ Returns a list of atom names.
Changed in version 0.8: Returns a
numpy.ndarray
-
packIntoBox
(box=None, inplace=True)[source]¶ Shift all atoms in this group to be within the primary unit cell.
AtomGroup.packintobox([box, [inplace=True]])
Keywords: - box
Unit cell to move atoms inside of.
- inplace
True
: Change coordinates in place and returnFalse
: Only return the coordinates
All atoms will be moved so that they lie between 0 and boxlength \(L_i\) in all dimensions, i.e. the lower left corner of the simulation box is taken to be at (0,0,0):
\[x_i' = x_i - \left\lfloor\frac{x_i}{L_i}\right\rfloor\]The default is to take unit cell information from the underlying
Timestep
instance. The optional argument box can be used to provide alternative unit cell information (in the MDAnalysis standard format[Lx, Ly, Lz, alpha, beta, gamma]
).Works with either orthogonal or triclinic box types.
By default the coordinates are changed in place and returned
New in version 0.8.
-
positions
¶ Coordinates of the atoms in the AtomGroup.
The positions can be changed by assigning an array of the appropriate shape, i.e. either Nx3 to assign individual coordinates or 3, to assign the same coordinate to all atoms (e.g.
ag.positions = array([0,0,0])
will move all particles to the origin).For more control use the
get_positions()
andset_positions()
methods.New in version 0.7.6.
-
principalAxes
(**kwargs)[source]¶ Calculate the principal axes from the moment of inertia.
e1,e2,e3 = AtomGroup.principalAxes()
The eigenvectors are sorted by eigenvalue, i.e. the first one corresponds to the highest eigenvalue and is thus the first principal axes.
Keywords: - pbc
True
: Move all atoms within primary unit cell before calculation
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.Returns: numpy.array v
withv[0]
as first,v[1]
as second, andv[2]
as third eigenvector.Changed in version 0.8: Added pbc keyword
-
radiusOfGyration
(**kwargs)[source]¶ Radius of gyration.
Keywords: - pbc
True
: Move all atoms within the primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.Changed in version 0.8: Added pbc keyword
-
resids
()[source]¶ Returns a list of residue numbers.
Changed in version 0.8: Returns a
numpy.ndarray
-
residues
¶ Read-only list of
Residue
objects.A
ResidueGroup
of all residues that contain atoms in this group.Changed in version 0.9.0: Now returns strictly a ResidueGroup of the unique Residues that Atoms in this group belong to.
-
resnames
()[source]¶ Returns a list of residue names.
Changed in version 0.8: Returns a
numpy.ndarray
-
resnums
()[source]¶ Returns a list of canonical residue numbers.
New in version 0.7.4.
Changed in version 0.8: Returns a
numpy.ndarray
-
rotate
(R)[source]¶ Apply a rotation matrix R to the selection’s coordinates.
AtomGroup.rotate(R)
\(\mathsf{R}\) is a 3x3 orthogonal matrix that transforms a vector \(\mathbf{x} \rightarrow \mathbf{x}'\):
\[\mathbf{x}' = \mathsf{R}\mathbf{x}\]
-
rotateby
(angle, axis, point=None)[source]¶ Apply a rotation to the selection’s coordinates.
AtomGroup.rotateby(angle,axis[,point])
The transformation from current coordinates \(\mathbf{x}\) to new coordinates \(\mathbf{x}'\) is
\[\mathbf{x}' = \mathsf{R}\,(\mathbf{x}-\mathbf{p}) + \mathbf{p}\]where \(\mathsf{R}\) is the rotation by angle around the axis going through point \(\mathbf{p}\).
Arguments: - angle
rotation angle in degrees
- axis
rotation axis vector, a 3-tuple, list, or array, or a 2-tuple of two MDAnalysis objects from which the axis is calculated as the vector from the first to the second center of geometry.
- point
point on the rotation axis; by default (
None
) the center of geometry of the selection is chosen, or, if axis is a tuple of selections, it defaults to the first point of the axis. point can be a 3-tuple, list, or array or a MDAnalysis object (in which case itscentroid()
is used).
Returns: The 4x4 matrix which consists of the rotation matrix
M[:3,:3]
and the translation vectorM[:3,3]
.
-
segids
()[source]¶ Returns a list of segment ids (=segment names).
Changed in version 0.8: Returns a
numpy.ndarray
-
segments
¶ Read-only list of
Segment
objects.A
SegmentGroup
of all segments that contain atoms in this group.Changed in version 0.9.0: Now strictly returns a
SegmentGroup
of a set of theSegment
instances from thisAtomGroup
-
selectAtoms
(sel, *othersel, **selgroups)[source]¶ Selection of atoms using the MDAnalysis selection syntax.
AtomGroup.selectAtoms(selection[,selection[,...]], [groupname=atomgroup[,groupname=atomgroup[,...]]])
See also
-
sequence
(**kwargs)[source]¶ Returns the amino acid sequence.
The format of the sequence is selected with the keyword format:
format description ‘SeqRecord’ Bio.SeqRecord.SeqRecord
(default)‘Seq’ Bio.Seq.Seq
‘string’ string The sequence is returned by default (keyword
format = 'SeqRecord'
) as aBio.SeqRecord.SeqRecord
instance, which can then be further processed. In this case, all keyword arguments (such as the id string or the name or the description) are directly passed toBio.SeqRecord.SeqRecord
.If the keyword format is set to
'Seq'
, all kwargs are ignored and aBio.Seq.Seq
instance is returned. The difference to the record is that the record also contains metadata and can be directly used as an input for other functions inBio
.If the keyword format is set to
'string'
, all kwargs are ignored and a Python string is returned.Example: Write FASTA file
Use
Bio.SeqIO.write()
, which takes sequence records:import Bio.SeqIO # get the sequence record of a protein component of a Universe protein = u.selectAtoms("protein") record = protein.sequence(id="myseq1", name="myprotein") Bio.SeqIO.write(record, "single.fasta", "fasta")
A FASTA file with multiple entries can be written with
Bio.SeqIO.write([record1, record2, ...], "multi.fasta", "fasta")
Keywords: - format
"string"
: return sequence as a string of 1-letter codes"Seq"
: return aBio.Seq.Seq
instance"SeqRecord"
: return aBio.SeqRecord.SeqRecord
instance
Default is
"SeqRecord"
- id
Sequence ID for SeqRecord (should be different for different sequences)
- name
Name of the protein.
- description
Short description of the sequence.
- kwargs
Any other keyword arguments that are understood by
Bio.SeqRecord.SeqRecord
.
Raises: ValueError
if a residue name cannot be converted to a 1-letter IUPAC protein amino acid code; make sure to only select protein residues. RaisesTypeError
if an unknown format is selected.New in version 0.9.0.
-
set
(name, value, **kwargs)¶ Set attribute name to value for all atoms in the
AtomGroup
.If value is a sequence of the same length as the
AtomGroup
then eachAtom
‘s property name is set to the corresponding value. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.New in version 0.7.4.
Changed in version 0.8: Can set atoms to distinct values by providing a sequence or iterable.
-
set_bfactor
(bfactor)[source]¶ Set the atom bfactor to float bfactor for all atoms in the AtomGroup.
New in version 0.7.4.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_charge
(charge)[source]¶ Set the partial charge to float charge for all atoms in the AtomGroup.
New in version 0.7.4.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_forces
(forces, ts=None)[source]¶ Set the forces for all atoms in the group.
Arguments: - forces
a Nx3 NumPy
numpy.ndarray
where N is the number of atoms in this atom group.
Keywords: - ts
Timestep
, defaults toNone
and then the current time step is used.
Note
If the group contains N atoms and force is a single vector (i.e. an array of length 3) then all N atom positions are set to force (due to NumPy’s broadcasting rules), as described for
forces
.See also
get_forces()
and attribute access throughforces
.New in version 0.7.7.
-
set_mass
(mass)[source]¶ Set the atom mass to float mass for all atoms in the AtomGroup.
New in version 0.7.4.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_name
(name)[source]¶ Set the atom name to string for all atoms in the AtomGroup.
If value is a sequence of the same length as the
AtomGroup
then eachAtom.name
is set to the corresponding value. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.New in version 0.7.4.
Changed in version 0.8: Can set atoms to distinct values by providing a sequence or iterable.
-
set_positions
(coords, ts=None)[source]¶ Set the positions for all atoms in the group.
Arguments: - coords
a Nx3 NumPy
numpy.ndarray
where N is the number of atoms in this atom group.
Keywords: - ts
Timestep
, defaults toNone
and then the current time step is used.
Note
If the group contains N atoms and coord is a single point (i.e. an array of length 3) then all N atom positions are set to coord (due to NumPy’s broadcasting rules), as described for
positions
.See also
get_positions()
and attribute access throughpositions
.New in version 0.7.6.
-
set_radius
(radius)[source]¶ Set the atom radius to float radius for all atoms in the AtomGroup.
New in version 0.7.4.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_resid
(resid)[source]¶ Set the resid to integer resid for all atoms in the
AtomGroup
.If resid is a sequence of the same length as the
AtomGroup
then eachAtom.resid
is set to the corresponding value together with theResidue.id
of the residue the atom belongs to. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.Note
Changing resids can change the topology.
Assigning the same resid to multiple residues will merge these residues. Assigning different resid to atoms in the same residue will split a residue (and potentially merge with another one).
New in version 0.7.4.
Changed in version 0.7.5: Also changes the residues.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable and can change the topology via
MDAnalysis.topology.core.build_residues()
.
-
set_resname
(resname)[source]¶ Set the resname to string resname for all atoms in the
AtomGroup
.If resname is a sequence of the same length as the
AtomGroup
then eachAtom.resname
is set to the corresponding value together with theResidue.name
of the residue the atom belongs to. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.New in version 0.7.4.
Changed in version 0.7.5: Also changes the residues.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_resnum
(resnum)[source]¶ Set the resnum to resnum for all atoms in the
AtomGroup
.If resnum is a sequence of the same length as the
AtomGroup
then eachAtom.resnum
is set to the corresponding value together with theResidue.resnum
of the residue the atom belongs to. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.Note
Changing resnum will not affect the topology: you can have multiple residues with the same resnum.
See also
New in version 0.7.4.
Changed in version 0.7.5: Also changes the residues.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_segid
(segid, buildsegments=True)[source]¶ Set the segid to segid for all atoms in the
AtomGroup
.If segid is a sequence of the same length as the
AtomGroup
then eachAtom.segid
is set to the corresponding value together with theSegment.id
of the residue the atom belongs to. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.Note
set_segid()
can change the topology.With the default buildsegments =
True
it can be used to join segments or to break groups into multiple disjoint segments. Note that eachAtom
can only belong to a singleSegment
.For performance reasons, buildsegments can be set to
False
. Then one needs to runUniverse._build_segments()
manually later in order to update the list ofSegment
instances and regenerate the segid instant selectors.New in version 0.7.4.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_type
(atype)[source]¶ Set the atom type to atype for all atoms in the AtomGroup.
New in version 0.7.4.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_velocities
(v, ts=None)[source]¶ Assign the velocities v to the timestep.
Raises a
NoDataError
if the underlyingTimestep
does not contain_velocities
.See also
AtomGroup.get_velocities()
andAtomGroup.velocities
for attribute access.New in version 0.7.6.
-
shapeParameter
(**kwargs)[source]¶ Shape parameter.
See [Dima2004] for background information.
Keywords: - pbc
True
: Move all atoms within the primary unit cell before calculation [False
]
Note
The
MDAnalysis.core.flags
flag use_pbc when set toTrue
allows the pbc flag to be used by default.New in version 0.7.7.
Changed in version 0.8: Added pbc keyword
-
split
(level)[source]¶ Split atomgroup into a list of atomgroups by level.
level can be “atom”, “residue”, “segment”.
New in version 0.9.0.
-
torsions
¶ All the torsions in this AtomGroup
Note that these torsions might extend out of the AtomGroup, to select only torsions which are entirely contained by the AtomGroup use u.torsions.atomgroup_intersection(ag, strict=True)
New in version 0.9.0.
Changed in version 0.10.0: Now always returns a (possibly empty) TopologyGroup
-
transform
(M)[source]¶ Apply homogenous transformation matrix M to the coordinates.
The matrix M must be a 4x4 matrix, with the rotation in R = `M[:3,:3]` and the translation in
t = M[:3,3]
.The rotation \(\mathsf{R}\) is applied before the translation \(\mathbf{t}\):
\[\mathbf{x}' = \mathsf{R}\mathbf{x} + \mathbf{t}\]
-
translate
(t)[source]¶ Apply translation vector t to the selection’s coordinates.
>>> AtomGroup.translate(t) >>> AtomGroup.translate((A, B))
The method applies a translation to the AtomGroup from current coordinates \(\mathbf{x}\) to new coordinates \(\mathbf{x}'\):
\[\mathbf{x}' = \mathbf{x} + \mathbf{t}\]The translation can also be given as a tuple of two MDAnalysis objects such as two selections (selA, selB), i.e. two
AtomGroup
, or twoAtom
. The translation vector is computed as the difference between the centers of geometry (centroid) of B and A:t = B.centroid() - A.centroid()
-
ts
¶ Temporary Timestep that contains the selection coordinates.
A
Timestep
instance, which can be passed to a trajectory writer.If
ts
is modified then these modifications will be present until the frame number changes (which typically happens when the underlying trajectory frame changes).It is not possible to assign a new
Timestep
to theAtomGroup.ts
attribute; change attributes of the object.
-
universe
¶ The universe to which the atoms belong (read-only).
-
velocities
¶ NumPy array of the velocities of the atoms in the group.
If the trajectory does not contain velocity information then a
NoDataError
is raised.New in version 0.7.5.
Deprecated since version 0.7.6: In 0.8 this will become an attribute! You can already use
get_velocities()
andset_velocities()
.Changed in version 0.8: Became an attribute.
-
wrap
(compound='atoms', center='com', box=None)[source]¶ Shift the contents of this AtomGroup back into the unit cell.
This is a more powerful version of
packIntoBox()
, allowing groups of atoms to be kept together through the process.Keywords: - compound
The group which will be kept together through the shifting process. [
atoms
] Possible options:atoms
group
- This AtomGroupresidues
segments
fragments
- center
How to define the center of a given group of atoms [
com
]- box
Unit cell information. If not provided, the values from Timestep will be used.
When specifying a compound, the translation is calculated based on each compound. The same translation is applied to all atoms within this compound, meaning it will not be broken by the shift. This might however mean that all atoms from the compound are not inside the unit cell, but rather the center of the compound is. Compounds available for use are atoms, residues, segments and fragments
center allows the definition of the center of each group to be specified. This can be either ‘com’ for center of mass, or ‘cog’ for center of geometry.
box allows a unit cell to be given for the transformation. If not specified, an the dimensions information from the current Timestep will be used.
Note
wrap with all default keywords is identical to
packIntoBox()
New in version 0.9.2.
-
write
(filename=None, format='PDB', filenamefmt='%(trjname)s_%(frame)d', **kwargs)[source]¶ Write AtomGroup to a file.
AtomGroup.write(filename[,format])
Keywords: - filename
None
: create TRJNAME_FRAME.FORMAT from filenamefmt [None
]- format
PDB, CRD, GRO, VMD (tcl), PyMol (pml), Gromacs (ndx) CHARMM (str); case-insensitive and can also be supplied as the filename extension [PDB]
- filenamefmt
format string for default filename; use substitution tokens ‘trjname’ and ‘frame’ [“%(trjname)s_%(frame)d”]
- bonds
how to handle bond information, especially relevant for PDBs; default is
"conect"
."conect"
: write only the CONECT records defined in the original file"all"
: write out all bonds, both the original defined and those guessed by MDAnalysisNone
: do not write out bonds
Changed in version 0.9.0: Merged with write_selection. This method can now write both selections out.
-
write_selection
(filename=None, format='vmd', filenamefmt='%(trjname)s_%(frame)d', **kwargs)[source]¶ Write AtomGroup selection to a file to be used in another programme.
Keywords: - filename
None
: create TRJNAME_FRAME.FORMAT from filenamefmt- format
output file format: VMD (tcl), PyMol (pml), Gromacs (ndx), CHARMM (str); can also be supplied as the filename extension. Case insensitive. [vmd]
- filenamefmt
format string for default filename; use ‘%(trjname)s’ and ‘%(frame)s’ placeholders; the extension is set according to the format [“%(trjname)s_%(frame)d”]
- kwargs
additional keywords are passed on to the appropriate
SelectionWriter
Deprecated since version 0.9.0: Use
write()
-
-
class
MDAnalysis.core.AtomGroup.
Atom
(number, name, type, resname, resid, segid, mass, charge, residue=None, segment=None, radius=None, bfactor=None, resnum=None, serial=None, altLoc=None, universe=None)[source]¶ A class representing a single atom.
Atom
is the basic building block of all larger data structures in MDAnalysis, in particular of theAtomGroup
.An
Atom
is typically generated by a topology reader fromMDAnalysis.topology
.For performance reasons, only a predefined number of attributes are included (and thus it is not possible to add attributes “on the fly”; they have to be included in the class definition).
-
number
¶ atom number
-
segid
¶ name of the segment
-
resid
¶ residue number
-
resnum
¶ canonical residue number as, for instance, used in the original PDB file
New in version 0.7.4.
-
resname
¶ residue name
-
id
¶ atom number inside the residue
-
name
¶ string, short name
-
type
¶ string or number (from force field), describing the atom type; stored as a string.
Changed in version 0.7.6: The
Atom.type
attribute is always stored as a string.
-
mass
¶ float, in atomic mass units (u)
-
charge
¶ float, in electron charges (e)
-
radius
¶ Born-radius for electrostatic calculations. (Only if read from a PQR file with the
PQRReader
.)
-
altLoc
¶ Alternate location indicator (as used in ATOM_ records in PDB files)
New in version 0.9.0.
-
bonds
¶ List of
Bond
instances that contains all the bonds that this atom participates in.New in version 0.8.1.
-
angles
¶ List of
Angle
instances that contains all the angles that this atom participates in.New in version 0.8.1.
-
torsions
¶ List of
Torsion
instances that contains all the dihedral torsions that this atom participates in.New in version 0.8.1.
-
angles
A list of the angles that this Atom is in
Changed in version 0.9.0: Changed to managed property
-
bonded_atoms
¶ An AtomGroup of the Atoms that this Atom is bonded to.
New in version 0.9.
-
bonds
A list of the bonds that this Atom is in
Changed in version 0.9.0: Changed to managed property
-
dihedrals
¶ A list of the torsions/dihedrals that this Atom is in
Changed in version 0.9.0: Changed to managed property
-
force
¶ Current force of the atom.
Returns: a (3,) shape numpy array A
NoDataError
is raised if the trajectory does not contain velocities.New in version 0.9.2.
-
fragment
¶ The fragment that this Atom is part of
New in version 0.9.0.
-
impropers
¶ A list of the improper torsions that this Atom is in
Changed in version 0.9.0: Changed to managed property
-
pos
¶ coordinates of the atom
Get the current cartesian coordinates of the atom (read-only).
Deprecated since version 0.8: use
position
-
position
¶ coordinates of the atom
Get the current cartesian coordinates of the atom.
Returns: a (3,) shape numpy array
-
torsions
A list of the torsions/dihedrals that this Atom is in
Changed in version 0.9.0: Changed to managed property
-
universe
¶ a pointer back to the Universe
-
velocity
¶ Current velocity of the atom.
Returns: a (3,) shape numpy array A
NoDataError
is raised if the trajectory does not contain velocities.New in version 0.7.5.
-
-
class
MDAnalysis.core.AtomGroup.
Residue
(name, id, atoms, resnum=None)[source]¶ A group of atoms corresponding to a residue.
- Pythonic access to atoms:
Using a atom name as attribute returns the matching atom (a
Atom
instance), i.e.r.name
. Example:>>> from MDAnalysis.tests.datafiles import PSF,DCD >>> u = Universe(PSF,DCD) >>> print(u.s4AKE.r1.CA) # C-alpha of M1 < Atom 5: name 'CA' of type '22' of resname 'MET', resid 1 and segid '4AKE'>
r['name']
orr[id]
- returns the atom corresponding to that name
Data: Residue.name
Three letter residue name.
Residue.id
Numeric (integer) resid, taken from the topology.
Residue.resnum
Numeric canonical residue id (e.g. as used in the PDB structure).
Note
Creating a
Residue
modifies the underlyingAtom
instances. EachAtom
can only belong to a singleResidue
.Changed in version 0.7.4: Added
Residue.resnum
attribute and resnum keyword argument.-
chi1_selection
()[source]¶ AtomGroup corresponding to the chi1 sidechain dihedral N-CA-CB-CG.
Returns: 4-atom selection in the correct order. If no CB and/or CG is found then this method returns None
.New in version 0.7.5.
-
omega_selection
()[source]¶ AtomGroup corresponding to the omega protein backbone dihedral CA-C-N’-CA’.
omega describes the -C-N- peptide bond. Typically, it is trans (180 degrees) although cis-bonds (0 degrees) are also occasionally observed (especially near Proline).
Returns: 4-atom selection in the correct order. If no C’ found in the previous residue (by resid) then this method returns None
.
-
class
MDAnalysis.core.AtomGroup.
ResidueGroup
(residues)[source]¶ A group of residues.
- Pythonic access to atoms:
Using a atom name as attribute returns a list of all atoms (a
AtomGroup
) of the same name. Example:>>> from MDAnalysis.tests.datafiles import PSF,DCD >>> u = Universe(PSF,DCD) >>> print(u.s4AKE.MET.CA) # C-alpha of all Met <AtomGroup with 6 atoms>
Data: ResidueGroup._residues
Initialize the ResidueGroup with a list of
Residue
instances.-
set
(name, value, **kwargs)¶ Set attribute name to value for all residues in the
ResidueGroup
.If value is a sequence of the same length as the
ResidueGroup
(AtomGroup.residues
) then eachResidue
‘s property name is set to the corresponding value. If value is neither of length 1 (or a scalar) nor of the length of theResidueGroup
then aValueError
is raised.New in version 0.7.5.
Changed in version 0.8: Can set residues to distinct values by providing a sequence or iterable.
-
set_resid
(resid)[source]¶ Set the resid to integer resid for all residues in the
ResidueGroup
.If resid is a sequence of the same length as the
ResidueGroup
then eachAtom.resid
is set to the corresponding value together with theResidue.id
of the residue the atom belongs to. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.Note
Changing resids can change the topology.
Assigning the same resid to multiple residues will merge these residues. The new residue name will be the name of the first old residue in the merged residue.
Warning
The values of this
ResidueGroup
are not being changed. You must create a newResidueGroup
from theUniverse
— onlyAtom
instances are changed, everything else is derived from these atoms.New in version 0.8.
-
set_resname
(resname)[source]¶ Set the resname to string resname for all residues in the
ResidueGroup
.If resname is a sequence of the same length as the
ResidueGroup
then eachAtom.resname
is set to the corresponding value together with theResidue.name
of the residue the atom belongs to. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.New in version 0.7.4.
Changed in version 0.7.5: Also changes the residues.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
set_resnum
(resnum)[source]¶ Set the resnum to resnum for all residues in the
ResidueGroup
.If resnum is a sequence of the same length as the
ResidueGroup
then eachAtom.resnum
is set to the corresponding value together with theResidue.resnum
of the residue the atom belongs to. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.Note
Changing resnum will not affect the topology: you can have multiple residues with the same resnum.
See also
New in version 0.7.4.
Changed in version 0.7.5: Also changes the residues.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
class
MDAnalysis.core.AtomGroup.
Segment
(name, residues)[source]¶ A group of residues corresponding to one segment of the topology.
Pythonic access to residues:
The attribute rN returns the N-th residue
Residue
of the segment (numbering starts at N=1). Example:>>> from MDAnalysis.tests.datafiles import PSF,DCD >>> u = Universe(PSF,DCD) >>> print(u.s4AKE.r1) <Residue 'MET', 1>
Using a residue name as attribute returns a list of all residues (a
ResidueGroup
) of the same name. Example:>>> from MDAnalysis.tests.datafiles import PSF,DCD >>> u = Universe(PSF,DCD) >>> print(u.s4AKE.CYS) <ResidueGroup [<Residue 'CYS', 77>]> >>> print(u.s4AKE.MET) <ResidueGroup [<Residue 'MET', 1>, <Residue 'MET', 21>, <Residue 'MET', 34>, <Residue 'MET', 53>, <Residue 'MET', 96>, <Residue 'MET', 174>]>
Data: Segment.name
is the segid from the topology or the chain identifier when loaded from a PDBInitialize a Segment with segid name from a list of
Residue
instances.-
id
¶ Segment id (alias for
Segment.name
)
-
class
MDAnalysis.core.AtomGroup.
SegmentGroup
(segments)[source]¶ A group of segments.
- Pythonic access to segments:
Using a segid as attribute returns the segment. Because of python language rule, any segid starting with a non-letter character is prefixed with ‘s’, thus ‘4AKE’ –> ‘s4AKE’.
Example:
>>> from MDAnalysis.tests.datafiles import PSF,DCD >>> u = Universe(PSF,DCD) >>> print(u.atoms.segments.s4AKE) # segment 4AKE <AtomGroup with 3314 atoms>
Indexing the group returns the appropriate segment.
Data: SegmentGroup._segments
Initialize the SegmentGroup with a list of
Segment
instances.-
set
(name, value, **kwargs)¶ Set attribute name to value for all
Segment
in thisAtomGroup
.If value is a sequence of the same length as the
SegmentGroup
(AtomGroup.residues
) then eachSegment
‘s property name is set to the corresponding value. If value is neither of length 1 (or a scalar) nor of the length of theSegmentGroup
then aValueError
is raised.New in version 0.8.
-
set_segid
(segid, buildsegments=True)[source]¶ Set the segid to segid for all atoms in the
SegmentGroup
.If segid is a sequence of the same length as the
SegmentGroup
then eachAtom.segid
is set to the corresponding value together with theSegment.id
of the segment the atom belongs to. If value is neither of length 1 (or a scalar) nor of the length of theAtomGroup
then aValueError
is raised.Note
set_segid()
can change the topology.With the default buildsegments =
True
it can be used to join segments or to break groups into multiple disjoint segments. Note that eachAtom
can only belong to a singleSegment
.For performance reasons, buildsegments can be set to
False
. Then one needs to runUniverse._build_segments()
manually later in order to update the list ofSegment
instances and regenerate the segid instant selectors.Warning
The values of this
SegmentGroup
are not being changed (i.e. if you assign multiple segids this instance will not be broken in multiple segments, rather you will have oneSegmentGroup
that groups multiple segments together). You must create a newSegmentGroup
from theUniverse
— onlyAtom
instances are changed, everything else is derived from these atoms.New in version 0.7.4.
Changed in version 0.8: Can set atoms and residues to distinct values by providing a sequence or iterable.
-
MDAnalysis.core.AtomGroup.
asUniverse
(*args, **kwargs)[source]¶ Return a universe from the input arguments.
If the first argument is a universe, just return it:
as_universe(universe) --> universe
Otherwise try to build a universe from the first or the first and second argument:
asUniverse(PDB, **kwargs) --> Universe(PDB, **kwargs) asUniverse(PSF, DCD, **kwargs) --> Universe(PSF, DCD, **kwargs) asUniverse(*args, **kwargs) --> Universe(*args, **kwargs)
Returns: an instance of Universe