Class MolContainer

The container for the molecular information.

The structural data object for this class is a container possessing a number of different arrays corresponding to different structural information. These objects include:

• atom_num: The atom name.
• atom_name: The atom name.
• bonded: Each element an array of bonded atom indices.
• chain_id: The chain ID.
• element: The element symbol.
• pdb_record: The optional PDB record name (one of ATOM, HETATM, or TER).
• res_name: The residue name.
• res_num: The residue number.
• seg_id: The segment ID.
• x: The x coordinate of the atom.
• y: The y coordinate of the atom.
• z: The z coordinate of the atom.

All arrays should be of equal length so that an atom index can retrieve all the corresponding data. Only the atom identification string is compulsory, all other arrays can contain None.

Instance Methods

__init__(self)
Initialise the molecular container.

int _atom_index(self, atom_num)
Find the atom index corresponding to the given atom number.

str or None _det_pdb_element(self, atom_name)
Try to determine the element from the PDB atom name.

list of str _parse_gaussian_record(self, record)
Parse the Gaussian log record string and return an array of the corresponding atomic information.

list of str _parse_xyz_record(self, record)
Parse the XYZ record string and return an array of the corresponding atomic information.

_sort(self)
Sort all structural data.

_sort_key(self, i)
Return the information for sorting the sequence data.

int atom_add(self, atom_name=None, res_name=None, res_num=None, pos=[None, None, None], element=None, atom_num=None, chain_id=None, segment_id=None, pdb_record=None)
Method for adding an atom to the structural data object.

atom_connect(self, index1=None, index2=None)
Method for connecting two atoms within the data structure object.

fill_object_from_gaussian(self, records)
Method for generating a complete Structure_container object from the given Gaussian log records.

fill_object_from_pdb(self, records, alt_loc_select=None, reset_serial=True)
Method for generating a complete Structure_container object from the given PDB records.

fill_object_from_xyz(self, records)
Method for generating a complete Structure_container object from the given xyz records.

from_xml(self, mol_node, file_version=1)
Recreate the MolContainer from the XML molecule node.

is_empty(self)
Check if the container is empty.

int last_residue(self)
Return the number of the last residue.

str, int loop_residues(self)
Generator method for looping over the individual residues of the molecule.

merge(self, mol_cont=None)
Merge the contents of the given molecule container into here.

to_xml(self, doc, element)
Create XML elements for the contents of this molecule container.

Method Details

_atom_index(self, atom_num)

Find the atom index corresponding to the given atom number.

Parameters:

• atom_num (int) - The atom number to find the index of.

Returns: int

The atom index corresponding to the atom.

_det_pdb_element(self, atom_name)

Try to determine the element from the PDB atom name.

Parameters:

• atom_name (str) - The PDB atom name.

Returns: str or None

The element name, or None if unsuccessful.

_parse_gaussian_record(self, record)

Parse the Gaussian log record string and return an array of the corresponding atomic information.

The format of the Gaussian log records is:

__________________________________________________________________________________________
|         |              |                                                               |
| Columns | Data type    | Description                                                   |
|_________|______________|_______________________________________________________________|
|         |              |                                                               |
|  1      | int          | "Center Number" - the sequential atom number.                 |
|  2      | int          | "Atomic Number" - the atomic number.                          |
|  3      | int          | "Atomic Type" - the atomic type?                              |
|  4      | float        | X coordinate in Angstrom                                      |
|  5      | float        | Y coordinate in Angstrom                                      |
|  6      | float        | Z coordinate in Angstrom                                      |
|_________|______________|_______________________________________________________________|

Parameters:

• record (str) - The single line Gaussian record.

Returns: list of str

The list of atomic information

_parse_xyz_record(self, record)

Parse the XYZ record string and return an array of the corresponding atomic information.

The format of the XYZ records is:

__________________________________________________________________________________________
|         |              |              |                                                |
| Columns | Data type    | Field        | Definition                                     |
|_________|______________|______________|________________________________________________|
|         |              |              |                                                |
|  1      | String       | element      |                                                |
|  2      | Real         | x            | Orthogonal coordinates for X in Angstroms      |
|  3      | Real         | y            | Orthogonal coordinates for Y in Angstroms      |
|  4      | Real         | z            | Orthogonal coordinates for Z in Angstroms      |
|_________|______________|______________|________________________________________________|

Parameters:

• record (str) - The single line PDB record.

Returns: list of str

The list of atomic information

atom_add(self, atom_name=None, res_name=None, res_num=None, pos=[None, None, None], element=None, atom_num=None, chain_id=None, segment_id=None, pdb_record=None)

Method for adding an atom to the structural data object.

This method will create the key-value pair for the given atom.

Parameters:

• atom_name (str or None) - The atom name, e.g. 'H1'.
• res_name (str or None) - The residue name.
• res_num (int or None) - The residue number.
• pos (list (length = 3)) - The position vector of coordinates.
• element (str or None) - The element symbol.
• atom_num (int or None) - The atom number.
• chain_id (str or None) - The chain identifier.
• segment_id (str or None) - The segment identifier.
• pdb_record (str or None) - The optional PDB record name, e.g. 'ATOM' or 'HETATM'.

Returns: int

The index of the added atom.

atom_connect(self, index1=None, index2=None)

Method for connecting two atoms within the data structure object.

This method will append index2 to the array at bonded[index1] and vice versa.

Parameters:

• index1 (int) - The index of the first atom.
• index2 (int) - The index of the second atom.

fill_object_from_gaussian(self, records)

Method for generating a complete Structure_container object from the given Gaussian log records.

Parameters:

• records (list of str) - A list of structural Gaussian log records.

fill_object_from_pdb(self, records, alt_loc_select=None, reset_serial=True)

Method for generating a complete Structure_container object from the given PDB records.

Parameters:

• records (list of str) - A list of structural PDB records.
• alt_loc_select (str or None) - The PDB ATOM record 'Alternate location indicator' field value to select which coordinates to use.
• reset_serial (bool) - A flag which if True will cause the first serial number (or atom number) to be reset to 1, and all other numbers shifted.

fill_object_from_xyz(self, records)

Method for generating a complete Structure_container object from the given xyz records.

Parameters:

• records (list of str) - A list of structural xyz records.

from_xml(self, mol_node, file_version=1)

Recreate the MolContainer from the XML molecule node.

Parameters:

• mol_node (xml.dom.minicompat.NodeList instance) - The molecule XML node.
• file_version (int) - The relax XML version of the XML file.

last_residue(self)

Return the number of the last residue.

Returns: int

The last residue number.

loop_residues(self)

Generator method for looping over the individual residues of the molecule.

Returns: str, int

The residue name and number.

merge(self, mol_cont=None)

Merge the contents of the given molecule container into here.

Parameters:

• mol_cont (MolContainer instance) - The data structure for the molecule to merge.

to_xml(self, doc, element)

Create XML elements for the contents of this molecule container.

Parameters:

• doc (xml.dom.minidom.Document instance) - The XML document object.
• element (XML element object) - The element to add the molecule XML elements to.