5. scoria.Information module¶

class scoria.Information.Information(parent_molecule_object)¶

A class for storing and accessing information about the elements of a scoria.Molecule object.

assign_elements_from_atom_names(selection=None)¶

Determines the elements of all atoms from the atom names. Note that this will overwrite any existing element assignments, including those explicitly specified in loaded files. Note that this doesn’t populate elements_stripped.

Wrapper function for assign_elements_from_atom_names()

Parameters:	selection (numpy.array) – An optional numpy.array containing the indices of the atoms to consider when calculating the center of mass. If ommitted, all atoms of the scoria.Molecule object will be considered.

assign_masses()¶

Assigns masses to the atoms of the scoria.Molecule object.

Wrapper function for assign_masses()

Note: This will autopopulate the masses according to their element identification and takes no input.

belongs_to_dna(atom_index)¶

Checks if the atom is part of DNA.

Wrapper function for belongs_to_dna()

Parameters:	atom_index (int) – An int, the index of the atom to consider.
Returns:	A boolean. True if part of dna, False if not.

belongs_to_protein(atom_index)¶

Checks if the atom is part of a protein. Taken primarily from Amber residue names.

Wrapper function for belongs_to_protein()

Parameters:	atom_index (int) – An int, the index of the atom to consider.
Returns:	A boolean. True if part of protein, False if not.

belongs_to_rna(atom_index)¶

Checks if the atom is part of RNA.

Wrapper function for belongs_to_rna()

Parameters:	atom_index (int) – An int, the index of the atom to consider.
Returns:	A boolean. True if part of rna, False if not.

define_molecule_chain_residue_spherical_boundaries()¶

Identifies spheres that bound (encompass) the entire molecule, the chains, and the residues. This information is stored in scoria.Molecule.Molecule.hierarchy.

Requires the numpy and scipy libraries.

Wrapper function for define_molecule_chain_residue_spherical_boundaries()

delete_trajectory_frame(index)¶

Removes a given frame from the trajectory.

Wrapper function for delete_trajectory_frame()

Parameters:	index (int) – Integer of the frame to remove.

get_atom_information()¶

Retreives the atomic information for the molecule.

Wrapper function for get_atom_information()

Returns:	A masked array containing the atom information.
Return type:	`numpy.ma.MaskedArray`

The contents of the array are as follows:

member name	dtype	Full Type	Description
record_name	S6	six char string	What the atom belongs to
serial	<i8	64-bit integer	The index of the atom
name	S5	five char string	The atom name
resname	S5	five char string	The residue name
chainid	S1	one char string	The chain identifier
resseq	<i8	64-bit integer	The Residue sequence number
occupancy	<f8	64-bit float	Occupancy of atom
tempfactor	<f8	64-bit float	Tempature Factor
element	S2	two char string	The element symbol
charge	S3	three char string	Charge on the atom
name_stripped	S5	five char string	Atom name without space
resname_stripped	S5	five char string	Residue name without space
chainid_stripped	S1	one char string	Chain identifier without space
element_stripped	S2	two char string	Element symbol without space

An example for printing the elemental symbols of the first five atoms:

>>> atom_info = mol.get_atom_information()
>>> print atom_info['element_stripped'][0:5]
['N' 'C' 'C' 'O' 'C']

get_bonds()¶

Retreives the bonds beteween atoms as a n x n matrix.

Wrapper function for get_bonds()

Returns:	A binary n x n matrix, where bonds are represented by 1.
Return type:	numpy.array

An example for finding all atoms bonded with atom 153:

>>> bonds = mol.get_bonds()
>>> for i in range(0,len(bonds)):
...     if bonds[153][i] == 1:
...             print 153,"-",i
153 - 152
153 - 154
153 - 155

get_bounding_box(selection=None, padding=0.0, frame=None)¶

Calculates a box that bounds (encompasses) a set of atoms.

Wrapper function for get_bounding_box()

Parameters:	selection (numpy.array) – An optional numpy.array containing the indices of the atoms to consider. If ommitted, all atoms of the scoria.Molecule object will be considered. padding (float) – An optional float. The bounding box will extend this many angstroms beyond the atoms being considered. frame (int) – An integer indicating at which timestep the center of mass should be calculated. If ommitted, it defaults to the first frame of the trajectory.
Returns:	A numpy array representing two 3D points, (min_x, min_y, min_z) and (max_x, max_y, max_z), that bound the molecule.
Return type:	numpy.array

get_bounding_sphere(selection=None, padding=0.0, frame=None)¶

Calculates a sphere that bounds (encompasses) a set of atoms.

Requires the numpy and scipy libraries.

Wrapper function for get_bounding_sphere()

Parameters:	selection (numpy.array) – An optional numpy.array containing the indices of the atoms to consider. If ommitted, all atoms of the scoria.Molecule object will be considered. padding (float) – An optional float. The bounding sphere will extend this many angstroms beyond the atoms being considered. frame (int) – An integer indicating at which timestep the center of mass should be calculated. If ommitted, it defaults to the first frame of the trajectory.
Returns:	A tuple containing two elements. The first is a numpy.array representing a 3D point, the (x, y, z) center of the sphere. The second is a float, the radius of the sphere.
Return type:	tuple (numpy.array, float)

get_center_of_mass(selection=None, frame=None)¶

Determines the center of mass.

Wrapper function for get_center_of_mass()

Parameters:	selection (numpy.array) – The indices of the atoms to consider when calculating the center of mass. If ommitted, all atoms of the pymolecule.Molecule object will be considered. frame (int) – The timestep at which the center of mass should be calculated. If ommitted, it defaults to the first frame of the trajectory.
Returns:	The x, y, and z coordinates of the center of mass.
Return type:	numpy.ma

>>> mol = pymolecule.Molecule()
>>> mol.load_pdb_into("single_frame.pdb")
>>> print mol.get_center_of_mass()
[33.0643089093134 19.135747088722564 16.05629867850796]

get_constants()¶

Returns a dictionary containing the constants assumed for the molecular model.

Wrapper function for get_constants()

Returns:	The constants assumed by the model.
Return type:	dict

Dictionary Keys	Value Type	Contains
mass_dict	dict{str:float}	The mass of elements
rna_residues	list(str)	RNA residue names
f8_fields	list(str)	Atom Information floats
vdw_dict	dict{str:float}	Van der Waals force of elements
i8_fields	list(str)	Atom Information integers
protein_residues	list(str)	Protein residue names
bond_length_dict	dict{str:float}	Element-pair bond length
element_names_with_two_letters	list(str)	Element symbols with 2 letters
max_number_of_bonds_permitted	dict{str:int}	Max bonds per element
dna_residues	list(str)	DNA reside names

get_coordinates(frame=None)¶

Returns the set of coordinates from the specified frame.

Wrapper function for get_coordinates()

Parameters:	frame (int) – The timestep from which the coordinates shoule be returned. If ommitted, it defaults to the first frame of the trajectory.
Returns:	The set of coordinates from the specified frame. [[x1, y1, z1], ... [xn, yn, zn]]
Return type:	numpy.array

>>> print mol.get_coordinates()
[[ -30.85199928  -81.45800018  365.05499268]
 [ -31.99500084  -80.69300079  365.66900635]
 [ -32.0530014   -81.13200378  367.18200684]
 ..., 
 [ -27.54199982  -96.25099945  402.83700562]
 [ -23.54199982  -94.7539978   400.41900635]
 [ -22.86100006  -93.72499847  400.55300903]]
 
>>> print mol.get_coordinates(2)
[[ -28.88899994  -80.45700073  365.51699829]
 [ -30.20000076  -79.73699951  365.99700928]
 [ -30.90699959  -80.5510025   367.13000488]
 ..., 
 [ -26.0189991   -97.28099823  403.52600098]
 [ -23.2140007   -94.73999786  400.94699097]
 [ -22.52899933  -93.73300171  400.81399536]]

get_coordinates_undo_point()¶

NEEDS CLARIFICATION. Retreives a previously save set of coordinates to revert to.

Wrapper function for get_coordinates_undo_point()

Returns:	A set of coordinates from which to return to.
Return type:	numpy.array or None

get_default_trajectory_frame()¶

Retreives the default trajectory frame index.

Returns:	An int representing the index of the default trajectory frame.

get_filename()¶

Returns the filename that the molecule was originally loaded from.

Wrapper function for get_filename()

Returns:	The name of the file.
Return type:	`str`

>>> mol = pymolecule.Molecule()
>>> mol.load_pdb_into("single_frame.pdb")
>>> print mol.get_filename()
single_frame.pdb

get_geometric_center(selection=None, frame=None)¶

Determines the geometric center of the molecule.

Wrapper function for get_geometric_center()

Parameters:	selection (numpy.array) – The indices of the atoms to consider when calculating the geometric. If ommitted, all atoms of the pymolecule.Molecule object will be considered. frame (int) – The timestep at which the geometric center should be calculated. If ommitted, it defaults to the first frame of the trajectory.
Returns:	The x, y, and z coordinates of the geometric center.
Return type:	numpy.array

>>> mol = pymolecule.Molecule()
>>> mol.load_pdb_into("single_frame.pdb")
>>> print mol.get_geometric_center()
[ 33.09860848  19.1221197   16.0426808 ]

get_hierarchy()¶

NEEDS CLARIFICATION.

Wrapper function for get_hierarchy()

Returns:	A dictionary?
Return type:	dict

get_remarks()¶

Returns the remarks from the file the molecule was loaded from.

Wrapper function for get_remarks()

Returns:	The remarks from the file an a list of strings.
Return type:	list

>>> mol = pymolecule.Molecule()
>>> mol.load_pdb_into("single_frame.pdb")
>>> print mol.get_remarks()
[' This is a remark.']

get_total_mass(selection=None)¶

Returns the total mass of all atoms within the molecule, or of a given selection.

Wrapper function for get_total_mass()

Parameters:	selection (numpy.array) – The indices of the atoms to consider when calculating the geometric. If ommitted, all atoms of the pymolecule.Molecule object will be considered.
Returns:	The total mass of the atom or selection
Return type:	float

>>> print mol.get_total_mass()
5289.1729999999998

get_total_number_of_atoms(selection=None, frame=None)¶

Counts the number of atoms.

Wrapper function for get_total_number_of_atoms()

Parameters:	selection (numpy.array) – An optional numpy.array containing the indices of the atoms to count. If ommitted, all atoms of the pymolecule.Molecule object will be considered. frame (int) – An integer indicating at which timestep the center of mass should be calculated. If ommitted, it defaults to the first frame of the trajectory.
Returns:	The total number of atoms.
Return type:	int

get_total_number_of_heavy_atoms(selection=None)¶

Counts the number of heavy atoms (i.e., atoms that are not hydrogens).

Wrapper function for get_total_number_of_heavy_atoms()

Parameters:	selection (numpy.array) – An optional numpy.array containing the indices of the atoms to count. If ommitted, all atoms of the pymolecule.Molecule object will be considered.
Returns:	The total number of heavy (non-hydrogen) atoms.
Return type:	int

get_trajectory()¶

Returns the trajectory for the molecule.

Wrapper function for get_trajectory()

Returns:	The set of all coordinates. [[[x11, y11, z11], ... [x1n, y1n, z1n]], ..., [[xm1, ym1, zm1], ... [xmn, ymn, zmn]]]
Return type:	numpy.array

>>> for coord in mol.get_trajectory():
>>>     print coord
>>>     print
[[ -30.85199928  -81.45800018  365.05499268]
 [ -31.99500084  -80.69300079  365.66900635]
 [ -32.0530014   -81.13200378  367.18200684]
 ..., 
 [ -27.54199982  -96.25099945  402.83700562]
 [ -23.54199982  -94.7539978   400.41900635]
 [ -22.86100006  -93.72499847  400.55300903]]

[[ -30.6779995   -81.32499695  365.73199463]
 [ -31.88100052  -80.38600159  366.0289917 ]
 [ -32.40399933  -80.62799835  367.45700073]
 ..., 
 [ -27.44400024  -96.71099854  402.64700317]
 [ -23.79199982  -94.58899689  400.63598633]
 [ -23.10700035  -93.56300354  400.79598999]]
 <more>

get_trajectory_frame_count()¶

Returns the number of frames in __trajectory.

Wrapper function for get_trajectory_frame_count()

Returns:	The number of frames in the trajectory.
Return type:	int

insert_trajectory_frame(index, coordinates)¶

Inserts a new coordinate frame at the end of the trajectory.

Wrapper function for insert_trajectory_frame()

Parameters:	coordinates (numpy.array) – A single frame of coordinates to append. index (int) – The location where the frame should be added.

resseq_reindex()¶

Reindexes the resseq field of the atoms in the molecule, starting with 1.

Wrapper function for resseq_reindex()

serial_reindex()¶

Reindexes the serial field of the atoms in the molecule, starting with 1.

Wrapper function for serial_reindex()

set_atom_information(atom_information)¶

Sets the __atom_information variable. See get_atom_information() for information on the numpy.array structure.

Wrapper function for set_atom_information()

Parameters:	atom_information (numpy.array) – An array containing details on the constituent atoms.

set_bonds(bonds)¶

Sets the __bonds variable. See get_bonds() for additional information.

Wrapper function for set_bonds()

Parameters:	bonds (numpy.array) – A binary n x n matrix containing bonding information.

set_coordinates(coordinates, frame=None)¶

Sets a specified frame of the __trajectory variable.

Wrapper function for set_coordinates()

Parameters:	coordinates (numpy.array) – An array of atomic coordinates. frame (int) – An integer represeting the frame of the trajectory to be modified

set_coordinates_undo_point(coordinates_undo_point)¶

Sets the __coordinates_undo_point variable.

Wrapper function for set_coordinates_undo_point()

Parameters:	coordinates_undo_point (numpy.array) – A coordinate set to revert to after modification.

set_default_trajectory_frame(frame)¶

Se’s the default trajectory frame index for various calculations.

Parameters:	frame (int) – The default frame for coordinate selection.

set_filename(filename)¶

Sets the __filename variable. Note: this does not reload or modify the molecule in anyway.

Wrapper function for set_filename()

Parameters:	filename (str) – String representation of the filename.

set_hierarchy(hierarchy)¶

Sets the __hierarchy variable. DEPRECIATED?

Wrapper function for set_hierarchy()

set_remarks(remarks)¶

Sets the __remarks variable.

Wrapper function for set_remarks()

Parameters:	remarks (list(str)) – List containing remarks.

set_trajectory(trajectory)¶

Sets the __trajectory variable.

Wrapper function for set_trajectory()

Parameters:	trajectory (numpy.array) – An array of atomic coordinates.

5. scoria.Information module¶

Previous topic

Next topic

This Page