Bio.PDB.mmtf.DefaultParser module

Code handle loading mmtf-python into Biopython’s structures.

class Bio.PDB.mmtf.DefaultParser.StructureDecoder

Bases: object

Class to pass the data from mmtf-python into a Biopython data structure.

__init__()

Initialize the class.

init_structure(total_num_bonds, total_num_atoms, total_num_groups, total_num_chains, total_num_models, structure_id)

Initialize the structure object.

Parameters

  • total_num_bonds – the number of bonds in the structure

  • total_num_atoms – the number of atoms in the structure

  • total_num_groups – the number of groups in the structure

  • total_num_chains – the number of chains in the structure

  • total_num_models – the number of models in the structure

  • structure_id – the id of the structure (e.g. PDB id)

set_atom_info(atom_name, serial_number, alternative_location_id, x, y, z, occupancy, temperature_factor, element, charge)

Create an atom object an set the information.

Parameters

  • atom_name – the atom name, e.g. CA for this atom

  • serial_number – the serial id of the atom (e.g. 1)

  • alternative_location_id – the alternative location id for the atom, if present

  • x – the x coordinate of the atom

  • y – the y coordinate of the atom

  • z – the z coordinate of the atom

  • occupancy – the occupancy of the atom

  • temperature_factor – the temperature factor of the atom

  • element – the element of the atom, e.g. C for carbon. According to IUPAC. Calcium is Ca

  • charge – the formal atomic charge of the atom

set_chain_info(chain_id, chain_name, num_groups)

Set the chain information.

Parameters

  • chain_id – the asym chain id from mmCIF

  • chain_name – the auth chain id from mmCIF

  • num_groups – the number of groups this chain has

set_entity_info(chain_indices, sequence, description, entity_type)

Set the entity level information for the structure.

Parameters

  • chain_indices – the indices of the chains for this entity

  • sequence – the one letter code sequence for this entity

  • description – the description for this entity

  • entity_type – the entity type (polymer,non-polymer,water)

set_group_info(group_name, group_number, insertion_code, group_type, atom_count, bond_count, single_letter_code, sequence_index, secondary_structure_type)

Set the information for a group.

Parameters

  • group_name – the name of this group, e.g. LYS

  • group_number – the residue number of this group

  • insertion_code – the insertion code for this group

  • group_type – a string indicating the type of group (as found in the chemcomp dictionary. Empty string if none available.

  • atom_count – the number of atoms in the group

  • bond_count – the number of unique bonds in the group

  • single_letter_code – the single letter code of the group

  • sequence_index – the index of this group in the sequence defined by the entity

  • secondary_structure_type – the type of secondary structure used (types are according to DSSP and number to type mappings are defined in the specification)

set_model_info(model_id, chain_count)

Set the information for a model.

Parameters

  • model_id – the index for the model

  • chain_count – the number of chains in the model

set_xtal_info(space_group, unit_cell)

Set the crystallographic information for the structure.

Parameters

  • space_group – the space group name, e.g. “P 21 21 21”

  • unit_cell – an array of length 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma

set_header_info(r_free, r_work, resolution, title, deposition_date, release_date, experimnetal_methods)

Set the header information.

Parameters

  • r_free – the measured R-Free for the structure

  • r_work – the measure R-Work for the structure

  • resolution – the resolution of the structure

  • title – the title of the structure

  • deposition_date – the deposition date of the structure

  • release_date – the release date of the structure

  • experimnetal_methods – the list of experimental methods in the structure

set_bio_assembly_trans(bio_assembly_index, input_chain_indices, input_transform)

Set the Bioassembly transformation information. A single bioassembly can have multiple transforms.

Parameters

  • bio_assembly_index – the integer index of the bioassembly

  • input_chain_indices – the list of integer indices for the chains of this bioassembly

  • input_transform – the list of doubles for the transform of this bioassmbly transform.

finalize_structure()

Any functions needed to cleanup the structure.

set_group_bond(atom_index_one, atom_index_two, bond_order)

Add bonds within a group.

Parameters

  • atom_index_one – the integer atom index (in the group) of the first partner in the bond

  • atom_index_two – the integer atom index (in the group) of the second partner in the bond

  • bond_order – the integer bond order

set_inter_group_bond(atom_index_one, atom_index_two, bond_order)

Add bonds between groups.

Parameters

  • atom_index_one – the integer atom index (in the structure) of the first partner in the bond

  • atom_index_two – the integer atom index (in the structure) of the second partner in the bond

  • bond_order – the bond order