TEMPy.protein.prot_rep_biopy

class TEMPy.protein.prot_rep_biopy.Atom(atom_name, coords, record_name='ATOM', serial=None, temp_factor=None, alt_loc=None, icode='', charge='', element='', occ=None, res=None, model=None, chain=None, res_no=None)

A generic atomic class. Subclass should ensure desired fields are set.

change_init_position()

Change initial position co-ordinates of atom to current position.

Returns:

new initial position co-ordinates of atom.

copy()

Returns:

Copy of the Atom instance.

distance_from_atom(atom)

Returns:

Distance from another atom.

distance_from_init_position()

Returns:

Distance from initial position.

get_id_no()

Returns:

string of atom serial number.

get_mass()

Returns:

Atom mass.

get_name()

atom name (ie. ‘CA’ or ‘O’)

Returns:

atom name.

get_pos_mass()

Returns:

An array containing Vector instances containing 3D coordinates of the atom and and its corresponding mass.

get_pos_vector()

Returns:

Vector instance containing 3D coordinates of the atom.

get_res()

Returns:

three letter residue code corresponding to the atom (i.e ‘ARG’).

get_res_no()

Returns:

residue number corresponding to the atom.

get_x()

Returns:

x co-ordinate of atom.

get_y()

Returns:

y co-ordinate of atom.

get_z()

Returns:

z co-ordinate of atom.

gridpoints_around_atom(densmap, radius=0.0, dx=0, dy=0, dz=0)

Get the x,y,z box boundaries of a set radius around an atom If radius is set, dx, dy, and dz will be calculated using radius, if not dx, dy, and dz given will be used. :param *densmap*: Map instance containing the grid :param *radius*: Cutoff radius around atom (Angstroms) :param *dx*: gridpoint distance along x (in integers) :param *dy*: gridpoint distance along y (in integers) :param *dz*: gridpoint distance along z (in integers)

Returns:

Minimum and maximum grid index along each direction of x, y, z e.g. [minx, maxx, miny, maxy, minz, maxz]

map_grid_position(densMap, index=True)

Parameters:

• *densMap* – EM map object consisting the 3D grid of density values.

• *index* – Boolean to return co-ordinates of grid as integer index. If false co-ordinates are returned as floats. Default: True

Returns:

The co-ordinates and density value of the grid point in a density map closest to this atom. Return 0 if atom is outside of map.

matrix_transform(rot_mat)

Transform atom using a 3x3 matrix

Parameters:

*rot_mat* – a 3x3 matrix instance.

Returns:

Transformed position of atom object

reset_position()

Translate atom back in its initial position.

Returns:

initial position co-ordinates of atom.

set_x(mod)

Change the x co-ordinate of an atom based on the argument.

Parameters:

*mod* – float value

Returns:

new x co-ordinate

set_y(mod)

Change the y co-ordinate of an atom based on the argument.

Parameters:

*mod* – float value

Returns:

new y co-ordinate

set_z(mod)

Change the z co-ordinate of an atom based on the argument.

Parameters:

*mod* – float value

Returns:

new x co-ordinate

translate(x, y, z)

Translate the atom.

Parameters:

• *x – distance in Angstroms in respective directions to move atom.

• y – distance in Angstroms in respective directions to move atom.

• z* – distance in Angstroms in respective directions to move atom.

Returns:

Translate atom object.

write_to_PDB()

Writes a PDB ATOM record based in the atom attributes to a file.

class TEMPy.protein.prot_rep_biopy.BioPy_Structure(atomList, filename='Unknown', header='', footer='')

A class representing a Structure object.

RMSD_from_init_position(CA=False)

Return RMSD of structure from initial position after translation.

Parameters:

*CA* – True will consider only CA atoms. False will consider all atoms.

Returns:

RMSD in angstrom

RMSD_from_same_structure(otherStruct, CA=False, write=True)

Return the RMSD between two structure instances.

Parameters:

• *otherStruct* – Structure instance to compare, containing the same number of atoms as the target instance.

• *CA* – True will consider only CA atoms. False will consider all atoms.

Returns:

RMSD in angstrom

break_into_segments(rigid_list, chain='')

Return a list of Structure instance based on the rigid body list.

Parameters:

list* (*rigid) –

list of rigid body defined as:

[[riA,rfA],..,[riB,rfB]]

where:

riA is the starting residues number of segment A. rfA is the final residues number of segment A.

Returns:

List of TEMPy Structure instance

calculate_centre_of_mass()

Returns:

Center of mass of structure as a Vector instance.

calculate_centroid()

Return centre of mass of structure as a Vector instance.

change_init_position()

Change initial position of structure to current position.

combine_SSE_structures(structList)

Combine a list of Structure instance into one and return a new Structure instance.

Parameters:

*structList* – list of Structure instance

Returns:

New Structure Instance

combine_structures(structList)

Add a list of Structure instance to the existing structure.

Parameters:

*structList* – list of Structure instance

Returns:

New Structure Instance

copy()

Returns:

Copy of Structure instance.

find_same_atom(atom_index, otherStruct)

Find if an atom exists in the compared structure, based on atom index.

Parameters:

• *atom_index* – atom number

• *otherStruct* – a structure object to compare

Returns:

If a match is found, it returns the atom object; else it returns a string reporting the mismatch.

get_CAonly()

Returns:

Structure instance with only the backbone atoms in structure.

get_atom(index)

Return specific atom in Structure instance.

Parameters:

*index* – Index of the atom

Returns:

Returns an Atom instance.

get_atom_list()

Returns:

[(RES 1 A: x,y,z), … ,(RES2 1 A: x1,y1,z1)].

Return type:

An array containing Atom instances of positions of all atoms as

get_atoms_in_chains()

TODO - reformat for BioPy_Structure

get_backbone()

Returns:

Structure instance with only the backbone atoms in structure.

get_chain(chainID)

Returns:

New Structure instance with only the requested chain.

get_chain_list()

Returns:

A list of chain ID.

get_extreme_values()

Returns:

A 6-tuple containing the minimum and maximum of x, y and z co-ordinates of the structure. Given in order (min_x, max_x, min_y, max_y, min_z, max_z).

get_next_chain_id(chain_id, chain_list=False)

Renames chains based on mmCIF convention i.e. A -> B, Z -> 0 or g -> h See the ALPHABET list for standard sequence, however any string can be used for chain labelling.

For structures with more than 62 chains, the labels are increased in length, i.e. z -> AA, zz -> AAA, AAA -> BBB

Input: chain_id -> old chain id Output: new_chain_id

get_pos_mass_list()

Returns:

Array containing Vector instances of positions of all atoms and mass.

get_prot_mass_from_atoms()

Calculates Mass (kDa) of the Structure instance, from average mass. Atoms based use get_prot_mass_from_res is more accurate.

get_prot_mass_from_res(Termini=False)

# ADD by IF 22-4-2013 #from Harpal code calculation of mass from seq. Calculates Mass (kDa) of the Structure instance, from average mass #based on http://web.expasy.org/findmod/findmod_masses.html

get_residue(resNo)

Get the residue corresponding to the residue number.

Parameters:

*resNo* – Residues number

Returns:

Returns a Residues instance.

get_residue_indexes()

Get the atom indexes for each residues from atomList in the structure

Returns:

a dictionary containing the index positions for all atoms from each residue in the structure. Items have format: [list, of, atom, indexes, as, ints] Keys have format: (str(chain_label), int(residue_number))

Return type:

residue_indexes

get_selection(startRes, finishRes, chain='')

Get a new Structure instance for the selected residues range without considering residues chain.

Parameters:

• *startRes* – Start residue number

• *finishRes* – End residue number

Returns:

New Structure instance

get_selection_less_than(endRes)

Get a Structure instance comprising all residues with their residue numbers less than endRes.

Parameters:

*endRes* – a residue number

Returns:

A Structure instance

get_selection_more_than(startRes)

Get a Structure instance comprising all residues with their residue numbers greater than startRes.

Parameters:

*startRes* – a residue number

Returns:

A Structure instance

get_torsion_angles()

Returns:

List of torsion angles in Structure instance.

get_vector_list()

Returns:

Array containing 3D Vector instances of positions of all atoms.

iter_asym_id(asym_id)

Function to increase the chain “numbering” by one e.g. from D -> E or from HA -> IA. Uses the chr() and ord() functions to convert between int and ASCII str One should run rename_chains before to ensure all chain_ids are letters

Input: capital letter from A -> Z Output: Next letter in alphabet e.g. from A -> B. For input Z, ouput is

AA, for input ZZ output is AAA etc..

matrix_transform(matrix)

Transform Structure using a 3x3 transformation matrix

Parameters:

*rot_mat* – a 3x3 matrix instance.

Returns:

Transformed position of Structure object

no_of_chains()

Returns:

the number of chains in the Structure object

number_of_residues()

Return the number of residues (and/or nucleotide bases) in the model

randomise_position(max_trans, max_rot, v_grain=30, rad=False, verbose=False)

Randomise the position of the Structure instance using random rotations and translations.

Parameters:

• *max_trans* – Maximum translation permitted

• *max_rot* – Maximum rotation permitted (in degree if rad=False)

• *v_grain* – Graning Level for the generation of random vetors (default=30)

Returns:

Transformed position of Structure object

rename_chains(chain_list=False)

TODO - reformat for BioPy_Structure

renumber_atoms(start_num=1)

Renumber the atoms in the structure. After renumbering the starting atom number will be 1 unless start_num

renumber_residues(startRes=1, missingRes=[])

Renumber the structure starting from startRes. Missing number list to add.

Parameters:

• *startRes* – Starting residue number for renumbering

• *missingRes* – A list of missing residue numbers to add

reorder_residues()

Order residues in atom list by residue number. (NOTE: Does not check for chain information - split by chain first).

reset_position()

Translate structure back into initial position.

rotate_by_axis_angle(x, y, z, turn, x_trans=0, y_trans=0, z_trans=0, rad=False, com=False)

Rotate the Structure instance around its centre.

Parameters:

• *turn* – angle (in radians if rad == True, else in degrees) to rotate map.

• *x – axis to rotate about, ie. x,y,z = 0,0,1 rotates the structure round the xy-plane.

• y – axis to rotate about, ie. x,y,z = 0,0,1 rotates the structure round the xy-plane.

• z* – axis to rotate about, ie. x,y,z = 0,0,1 rotates the structure round the xy-plane.

• *x_trans – extra translational movement if required.

• y_trans – extra translational movement if required.

• z_trans* – extra translational movement if required.

• *com* – centre of mass around which to rotate the structure. If False, rotates around centre of mass of structure.

rotate_by_euler(x_turn, y_turn, z_turn, x_trans=0, y_trans=0, z_trans=0, rad=False, com=False)

Rotate this Structure instance around its centre.

Parameters:

• *x_turn – Euler angles (in radians if rad == True, else in degrees) used to rotate structure, in order XYZ.

• y_turn – Euler angles (in radians if rad == True, else in degrees) used to rotate structure, in order XYZ.

• z_turn* – Euler angles (in radians if rad == True, else in degrees) used to rotate structure, in order XYZ.

• *x_trans – extra translational movement if required.

• y_trans – extra translational movement if required.

• z_trans* – extra translational movement if required.

• *com* – centre of mass around which to rotate the structure. If False, rotates around centre of mass of structure.

split_into_chains()

Split the structure into separate chains and returns the list of Structure instance for each chain.

translate(x, y, z)

Translate the structure.

Parameters:

• *x – distance in Angstroms in respective directions to move structure.

• y – distance in Angstroms in respective directions to move structure.

• z* – distance in Angstroms in respective directions to move structure.

Returns:

Translated Structure instance

write_to_PDB(filename, hetatom=False)

Write Structure instance to PDB file.

Parameters:

*filename* – output filename.

class TEMPy.protein.prot_rep_biopy.gemmiAtom(chain, entity, residue, atom)

Class representing an atom as read from a PDB/mmCIF file using gemmi

gemmi docs here: https://gemmi.readthedocs.io/

get_atom_vals()

returns list ready for parsing by gemmi for file writing

get_col_labels()

returns list ready for parsing by gemmi for file writing

get_str_atom_vals()

returns list ready for parsing by gemmi for file writing

class TEMPy.protein.prot_rep_biopy.gemmi_Structure(atomList, gemmi_structure, filename='Unknown', header='', tempy_scores=[])

Class for representing a protein structure.

Extends BioPy_Structure to deal with additional mmCif labels for dividing atoms into entities, asym units and chains.

add_structure(filename, integrate=False, hetatm=False, water=False)

Add structure from file

add_structure_instance(new_structure, integrate=False)

Add a seperate structure instance to self

Arguements:

new_structure

the new structure instance which will be incorpoated into self

Optional Arguments:

integrate

If True, atoms from the new_structure will be incorporated into chains with the same name in self.

combine_structures(structList)

Combine a list of structure instances with self and returns the new structure as a seperate instance.

Note: this function does not mutate self.

Arguments:

structList

List of Structure instances

Returns:

combined_struct

New gemmi_Structure instance

copy()

Returns:

Copy of Structure instance.

get_chain(chainID)

Returns:

New Structure instance with only the requested chain.

get_global_score(score_name)

return global score

no_of_chains()

Returns:

the number of chains in the Structure object

rename_asym_labels(label_list=False, starting_val=False)

Renames asym_id for each atom in alphabetical order

For structures with more than 26 models the ids switch to doulbe lettering (i.e. from Z -> AA and from ZZZ -> AAAA)

rename_chains(chain_list=False, starting_val=False)

Rename chain labels based on the list of new chain names

Optional Arguments:

chain_list

List of chain names If False rename in alphabetical order.

rename_entity_labels(starting_val=1)

Renames asym_id for each atom in alphabetical order - for structures with more than 26 models the ids switch to doulbe lettering (i.e. from Z -> AA and from ZZZ -> AAAA)

set_atom_labels()

Sets chain, asym_id and entity_id labels for the atoms in atomList

Important to run this before file writing

set_global_score(score_name, score)

Function to incorporate global scores into the structure instance so these values can be written into the cif file as label-value pairs

set_local_score(score_name, scores, verbose=False)

Function to incorporate local scores into structure instance, so that these values can be written into new cif files

This would be efficiently handled using a pandas library

split_into_chains()

Overrides BioPy_Structure method

Split the structure into separate chains and returns the list of Structure instance for each chain.

write_to_mmcif(filename, hetatom=False, save_all_metadata=False)

Write Structure instance to new mmCif file.

Parameters:

*filename* – output filename.