Molecules

This page describes how molecular models are handled in HARP.

atomcollection

class harp.molecule.atomcollection (atomid, resid, resname, atomnamechain, element, conf, xyz, occupancy, bfactor, hetatom, modelnum, authresid=None)

An atomcollection object stores all information about the molecular models and the methods to manipulate them in HARP.

Attributes

The attributes are named following the PDB naming convention

Variable	Descrption
self.natoms	int Number of atoms in the molecule.
self.atomid	numpy.ndarray A 1-D int array of size natoms, containing a numerical id for each individual atom in the molecule.
self.ind	numpy.ndarray A 1-D int array of size natoms, containing the index for each individual atom in the molecule. Is equal to numpy.arange(natoms). Used internally in HARP for indexing.
self.resid	numpy.ndarray A 1-D int array of size natoms, containing a numerical id for the residue for individual atom in the molecule.
self.resname	numpy.ndarray A 1-D string array of size natoms, containing the identity of the residue for each individual atom in the molecule (e.g., Gly, Ala, etc.).
self.element	numpy.ndarray A 1-D string array of size natoms, containing the element identity for each individual atom in the molecule (e.g., C, H, O, N, etc.).
self.atomname	numpy.ndarray A 1-D string array of size natoms, containing the atom identity of each individual atom in a particular residue in the molecule (e.g., CA, CB, N, etc.).
self.chain	numpy.ndarray A 1-D string array of size natoms, containing the identity of the chain for each individual atom in the molecule.
self.xyz	numpy.ndarray A 2-D double array of size [natoms, 3], containing the Cartesian co-ordinates of each individual atom in the molecule. Note: This must be a double array!
self.occupancy	numpy.ndarray A 1-D double array of size natoms, containing the occupancy for each individual atom in the molecule.
self.bfactor	numpy.ndarray A 1-D double array of size natoms, containing the B-factor for each individual atom in the molecule.
self.hetatom	numpy.ndarray A 1-D bool array of size natoms, indicating whether the atom is a heteroatom entry.
self.authresid	numpy.ndarray A 1-D int array of size natoms, containing the author-provided id for the residue for individual atom in the molecule. Defaults to resid if not provided.
self.conf	numpy.ndarray A 1-D string array of size natoms, containing the conformation for individual atom in the molecule.
self.modelnum	numpy.ndarray A 1-D int array of size natoms, containing the model number for individual atom in the molecule.
self.unique_residues	numpy.ndarray A 1-D int array of the unique resid in the molecule.
self.unique_chains	numpy.ndarray A 1-D string array of the unique chain in the molecule.
self.unique_confs	numpy.ndarray A 1-D string array of the unique conf in the molecule.

Functions

The functions associated with atomcollection are

Function	Descrption
self.get_residue	Returns a particular residue. Input: int number (the specific resid to be returned). Output: atomcollection.
self.get_chain	Returns a particular chain. Input: string chain (the specific chain to be returned). Output: atomcollection.
self.get_chains	Returns multiple chains. Input: numpy.ndarray/list chains (the array/list of chain to be returned). Output: atomcollection.
self.get_atomname	Returns a collection of specific atoms based on their identity in residues. Input: string atomname (the specific atomname to be returned). Output: atomcollection.
self.get_atomids	Returns a collection of specific atoms. Input: numpy.ndarray/list atomids (the array/list of atomid to be returned). Output: atomcollection.
self.get_conformation	Returns a specific conformation of the model. Input: string conf (the specifc conf to be returned). Output: atomcollection.
self.dehydrogen	Removes hydrogens from self Input: None. Output: atomcollection.
self.remove_hetatoms	Removes heteroatoms from self Input: None. Output: atomcollection.
self.split_residue	Splits an atomcollection of a single residue into component parts. For a nucleotide, returns a list of phosphate, sugar, and base. For an amino-acid, returns backbone and sidechain. Input: None (Note: self must be a single residue!). Output: A list of atomcollection.
self.com	Returns the Cartesian co-ordinate center-of-mass (centroid) of an atomcollection, i.e. the mean of self.xyz. Input: None. Output: A numpy.ndarray of size 3.

A separate function is involved in loading an atomcollection from a file.

load

harp.molecule.load (fname, only_polymers = False, firstmodel = True, authid = False)

Argument

Variable	Descrption
fname	string The filename of the mmCIF file to load. Note: This function currently only handles the file suffixes .mmcif, .cif, or_ .cif.gz.
only_polymers	bool A flag for whether to only use entities labeled as polymers (i.e. not water, ions, metals, or ligands, etc.).
firstmodel	bool A flag for whether to take the only first model. Useful for an ensemble of models (e.g., as in NMR).
authid	bool A flag for whether to use authid as atomcollection.resid or not. Useful for when people populate the wrong column (e.g., during model building).

Output

Variable	Descrption
atomcollection	atomcollection Contains the molecular model written in the .mmCIF file