The Biopython package is open source software made available under generous terms. If you use Biopython in work contributing to a scientific publication, we ask that you cite our application note below or one of the module specific publications listed on our website : Cock, P. Biopython: freely available Python tools for computational molecular biology and bioinformatics. This means pip install should be quick, and not require a compiler. As a developer or potential contributor, you may wish to download, build and install Biopython yourself. This is described below.
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PDB is a Biopython module that focuses on working with crystal structures of biological macromolecules. Among other things, Bio. PDB includes a PDBParser class that produces a Structure object, which can be used to access the atomic data in the file in a convenient manner. There is limited support for parsing the information contained in the PDB header. If the flag is not present a PDBConstructionException will be generated if any problems are detected during the parse operation.
Note however that many PDB files contain headers with incomplete or erroneous information. Many of the errors have been fixed in the equivalent mmCIF files. The structure object has an attribute called header which is a Python dictionary that maps header records to their values.
In this case you should assume that the molecule used in the experiment has some residues for which no ATOM coordinates could be determined. The list of missing residues will be empty or incomplete if the PDB header does not follow the template from the PDB specification.
The dictionary can also be created without creating a Structure object, ie. Contact the Biopython developers via the mailing list if you need this. By subclassing Select and returning 0 when appropriate you can exclude models, chains, etc.
Cumbersome maybe, but very powerful. Additional stuff is essentially added when needed. Such a data structure is not necessarily best suited for the representation of the macromolecular content of a structure, but it is absolutely necessary for a good interpretation of the data present in a file that describes the structure typically a PDB or MMCIF file. If this hierarchy cannot represent the contents of a structure file, it is fairly certain that the file contains an error or at least does not describe the structure unambiguously.
Parsing a PDB file can thus be used to detect likely problems. We will give several examples of this in section Examples. Structure, Model, Chain and Residue are all subclasses of the Entity base class. The Atom class only partly implements the Entity interface because an Atom does not have children.
For each Entity subclass, you can extract a child by using a unique id for that child as a key e. Disordered atoms and residues are represented by DisorderedAtom and DisorderedResidue classes, which are both subclasses of the DisorderedEntityWrapper base class.
They hide the complexity associated with disorder and behave exactly as Atom and Residue objects. In general, a child Entity object i. Atom, Residue, Chain, Model can be extracted from its parent i. Residue, Chain, Model, Structure, respectively by using an id as a key.
Note that this list is sorted in a specific way e. A full id for a Residue object e. This really should be done via a nice Decorator class that includes integrity checking, but you can take a look at the code Entity. Its id is a user given string. The Structure contains a number of Model children.
Most crystal structures but not all contain a single model, while NMR structures typically consist of several models. Disorder in crystal structures of large parts of molecules can also result in several models.
Crystal structures generally have only one model with id 0 , while NMR files usually have several models. Each Chain in a Model object has a unique id. This scheme is adopted for reasons described in section Associated problems. The sequence identifier resseq , an integer describing the position of the residue in the chain e. The insertion code is sometimes used to preserve a certain desirable residue numbering scheme. A Ser 80 insertion mutant inserted e.
In this way the residue numbering scheme stays in tune with that of the wild type structure. Unsurprisingly, a Residue object stores a set of Atom children. It also contains a string that specifies the residue name e. In most cases, the hetflag and insertion code fields will be blank, e. However, disordered residues are dealt with in a special way, as described in section Point mutations.
The id of an atom is its atom name e. An Atom id needs to be unique in a Residue. Again, an exception is made for disordered atoms, as described in section Disordered atoms. The atom id is simply the atom name eg. In practice, the atom name is created by stripping all spaces from the atom name in the PDB file. However, in PDB files, a space can be part of an atom name.
In cases were stripping the spaces would create problems ie. In a PDB file, an atom name consists of 4 chars, typically with leading and trailing spaces.
Often these spaces can be removed for ease of use e. To generate an atom name and thus an atom id the spaces are removed, unless this would result in a name collision in a Residue i.
In the latter case, the atom name including spaces is tried. This situation can e. The atomic data stored includes the atom name, the atomic coordinates including standard deviation if present , the B factor including anisotropic B factors and standard deviation if present , the altloc specifier and the full atom name including spaces. Less used items like the atom element number or the atomic charge sometimes specified in a PDB file are not stored. To manipulate the atomic coordinates, use the transform method of the Atom object.
Vector implements the full set of 3D vector operations, matrix multiplication left and right and some advanced rotation-related operations as well. As an example of the capabilities of Bio. PDB can handle both disordered atoms and point mutations i. In general, we have tried to encapsulate all the complexity that arises from disorder. On the other hand it should also be possible to represent disorder completely in the data structure.
Therefore, disordered atoms or residues are stored in special objects that behave as if there is no disorder. This is done by only representing a subset of the disordered atoms or residues.
Which subset is picked e. Each Atom object in a DisorderedAtom object can be uniquely indexed using its altloc specifier. The DisorderedAtom object forwards all uncaught method calls to the selected Atom object, by default the one that represents the atom with the highest occupancy.
The user can of course change the selected Atom object, making use of its altloc specifier. In this way atom disorder is represented correctly without much additional complexity. In other words, if you are not interested in atom disorder, you will not be bothered by it. Each disordered atom has a characteristic altloc identifier. This is evidently solved by using DisorderedAtom objects to represent the disordered atoms, and storing the DisorderedAtom object in a Residue object just like ordinary Atom objects.
The DisorderedAtom will behave exactly like an ordinary atom in fact the atom with the highest occupancy by forwarding all uncaught method calls to one of the Atom objects the selected Atom object it contains. Since these residues belong to a different residue type e. In this case, each residue is represented by one Residue object, and both Residue objects are stored in a single DisorderedResidue object see Fig. The DisorderedResidue object forwards all uncaught methods to the selected Residue object by default the last Residue object added , and thus behaves like an ordinary residue.
Each Residue object in a DisorderedResidue object can be uniquely identified by its residue name. The user can select the active Residue object in a DisorderedResidue object via this id.
Example: suppose that a chain has a point mutation at position 10, consisting of a Ser and a Cys residue. Make sure that residue 10 of this chain behaves as the Cys residue. Therefore, to generate a unique id for each hetero residue, waters and other hetero residues are treated in a different way.
Remember that Residue object have the tuple hetfield, resseq, icode as id. The hetfield is blank for amino and nucleic acids, and a string for waters and other hetero residues. The content of the hetfield is explained below. A glucose molecule e. Its residue id could e. You can also use the Selection. You can use this to go up in the hierarchy, e. Extract a hetero residue from a chain e. A Polypeptide object is simply a UserList of Residue objects, and is always created from a single Model in this case model 1.
Note that in the above case only model 0 of the structure is considered by PolypeptideBuilder. However, it is possible to use PolypeptideBuilder to build Polypeptide objects from Model and Chain objects as well. The sequence of each polypeptide can then easily be obtained from the Polypeptide objects. The sequence is represented as a Biopython Seq object, and its alphabet is defined by a ProteinAlphabet object. The neighbor lookup is done using a KD tree module written in C see Bio.