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