Connectivity

Motivation

The connectivity of atoms is notoriously difficult to come by for biological macromolecules. PDB files, the de facto standard exchange format for structural information allows bonds to be specified in CONECT records. However, they are not mandatory. Many programs, especially the ones not requiring on connectivity of atoms, do not write CONECT records. As a result, programs and structural biology frameworks can’t rely on connectivity information to be present. The connectivity information needs to be derived in the program itself.

Loader heuristics are great if you are the one that implemented them but are problematic if you are just the user of a software that has them. As time goes on, these heuristics become buried in thousands of lines of code and they are often hard yet impossible to trace back.

Different clients of the framework have different requirements. A visualisation software wants to read in a PDB files as is without making any changes. A script in an automated pipeline, however, does want to either strictly reject files that are incomplete or fill-in missing structural features. All these aspects are implemented in the conop module, separated from the loading of the PDB file, giving clients a fine grained control over the loading process. The conop logic can thus be reused in code requiring the presence of

The conop module defines a Processor interface, to run connectivity algorithms, that is to connect the atoms with bonds and perform basic clean up of erroneous structures. The clients of the conop module can specify how the Processor should treat unknown amino acids, missing atoms and chemically infeasible bonds.

Processors

The exact behaviour for a processor is implementation-specific. So far, two classes implement the processor interface: A heuristic and a rule-based processor. The processor mainly differ in the source of their connectivity information. The Heuristicprocessor uses a hard-coded heuristic connectivity table for the 20 standard amino acids as well as nucleotides.For other compounds such as ligands the HeuristicProcessor runs a distance-based connectivity algorithm that connects two atoms if they are closer than a certain threshold. The RuleBasedProcessor uses a connectivity library containing all molecular components present in the PDB files on PDB.org. The library can easily be extended with custom connectivity information, if required. If a compound library is present, the RuleBasedProcessor is enabled by default, otherwise the HeuristicProcessor is used as a fallback.

class Processor
check_bond_feasibility

Whether an additional bond feasibility check is performed. Disabled by default. If turned on, atoms are only connected by bonds if they are within a reasonable distance (as defined by IsBondFeasible()).

Type:

bool

assign_torsions

Whether backbone torsions should be added to the backbone. Enabled by default. If turned on, PHI, PSI and OMEGA torsions are assigned to the peptide residues. See also AssignBackboneTorsions().

Type:

bool

connect

Whether to connect atoms by bonds. Enabled by default. Turn this off if you would like to speed up the loading process and do not require connectivity information to be present in your structures. Note though that peptide_bonds may be ignored if this is turned off.

Type:

bool

peptide_bonds

Whether to connect residues by peptide bonds. Enabled by default. This also sets the is_protein property of residues when peptide bonds are created. Turn this off if you would like to create your own peptide bonds.

Type:

bool

zero_occ_treatment

Controls the behaviour of importing atoms with zero occupancy. By default, this is set to warn.

Type:

ConopAction

Process(ent)

Processess the entity ent according to the current options.

class HeuristicProcessor(check_bond_feasibility=False, assign_torsions=True, connect=True, peptide_bonds=True, zero_occ_treatment=CONOP_WARN)

The HeuristicProcessor implements the Processor interface. Refer to its documentation for methods and accessors common to all processor.

Parameters:
class RuleBasedProcessor(compound_lib, fix_elements=True, strict_hydrogens=False, unknown_res_treatment=CONOP_WARN, unknown_atom_treatment=CONOP_WARN, check_bond_feasibility=False, assign_torsions=True, connect=True, peptide_bonds=True, zero_occ_treatment=CONOP_WARN)

The RuleBasedProcessor implements the Processor interface. Refer to its documentation for methods and accessors common to all processor.

Parameters:
fix_elements

Whether the element of the atom should be changed to the atom defined in the compound library. Enabled by default.

Type:

bool

strict_hydrogens

Whether to use strict hydrogen naming rules outlined in the compound library. Disabled by default.

Type:

bool

unk_atom_treatment

Treatment upon encountering an unknown atom. Warn by default.

Type:

ConopAction

unk_res_treatment

Treatment upon encountering an unknown residue. Warn by default.

Type:

ConopAction

class ConopAction

Defines actions to take when certain events happen during processing. Possible values:

CONOP_WARN, CONOP_SILENT, CONOP_REMOVE, CONOP_REMOVE_ATOM, CONOP_REMOVE_RESIDUE, CONOP_FATAL