schrodinger.application.bioluminate.antibody.assembly module

class schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl(model: str, template: str)

Bases: object

model: str
template: str
__init__(model: str, template: str) → None
class schrodinger.application.bioluminate.antibody.assembly.AtomPair(model: str, template: str)

Bases: object

model: str
template: str
__init__(model: str, template: str) → None
class schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction(align_asl: schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair], region_to_replace: str, domain_structure: schrodinger.structure._structure.Structure)

Bases: object

align_asl: AlignmentAsl
bonds: List[AtomPair]
region_to_replace: str
domain_structure: Structure
classmethod fromDict(information_dictionary)
__init__(align_asl: AlignmentAsl, bonds: List[AtomPair], region_to_replace: str, domain_structure: Structure) → None
schrodinger.application.bioluminate.antibody.assembly.assemble_domains(template_structure: Structure, assembly_instructions: List[DomainAssemblyInstruction], scheme=AntibodyCDRScheme.Chothia) → Structure

Assemble the built model domains onto the template structure.

Parameters:

  • template_structure – the structure to replace the domains of

  • assembly_instructions – a list of instructions specifying which domains to apply to which regions of the template

Returns:

a copy of the template structure with any instruction-specified domains inserted to replace the corresponding template domains

schrodinger.application.bioluminate.antibody.assembly.align_structures(*, alignment_target: Structure, structure_to_align: Structure, alignment_asl: AlignmentAsl) → Structure

align the domain structure to the specified region of the template

Parameters:

  • alignment_target – template to align the domain of interest to

  • structure_to_align – domain of interest to align to the template

  • alignment_asl – alignment ASLs for template and model

Returns:

a copy of structure_to_align with new aligned coordinates

schrodinger.application.bioluminate.antibody.assembly.replace_domain(*, structure_to_modify: Structure, replacement_domain: Structure, replaced_region_asl: str, bonds: List[AtomPair]) → None

Remove the atoms in the replaced region and merge in the replacement domain

Parameters:

  • structure_to_modify – structure to add the new domain to

  • replacement_domain – modeled structure to merge into the modified structure

  • replaced_region_asl – region on the modified structure to replace

  • bonds – list of AtomPair objects specifying the model and template atoms to use to bond the structures together

schrodinger.application.bioluminate.antibody.assembly.get_map_model_to_template(model_structure: Structure, template_structure: Structure, region_to_replace_asl: str) → Dict[str, Dict[str, str]]

Get a mapping of the model structure to the template structure.

Parameters:

  • model_structure – the structure that is being projected onto the template

  • template_structure – the structure that is being projected onto

  • region_to_replace_asl – the region of the template structure that is being replaced

schrodinger.application.bioluminate.antibody.assembly.get_region_to_replace(template_structure: Structure, region_to_replace_asl: str) → Structure

Get the region of the template structure that is being replaced.

Parameters:

  • template_structure – the structure that is being projected onto

  • region_to_replace_asl – the region of the template structure that is being replaced

schrodinger.application.bioluminate.antibody.assembly.map_chains(st: Structure) → Dict[str, str]

Map the chains in the structure to their chain types.

Parameters:

st – the structure to map the chains of

schrodinger.application.bioluminate.antibody.assembly.rename_chains_in_bonds(bonds: List[AtomPair], map_model_to_template: Dict[str, Dict[str, str]]) → None

Rename the chains in the bonds.

Parameters:

  • bonds – the bonds to rename the chains of

  • map_model_to_template – the mapping of the model structure to the template structure

schrodinger.application.bioluminate.antibody.assembly.rename_chain_in_asl(asl: str, map_old_to_new: Dict[str, str]) → str

Rename the chain name in the ASL if chain name is specified.

Parameters:

  • asl – the ASL to rename the chains of

  • map_old_to_new – the mapping of the old name to the new name

schrodinger.application.bioluminate.antibody.assembly.rename_chains_in_structure(map_model_to_template: Dict[str, Dict[str, str]], model_structure: Structure) → None

Rename the chains in the structure.

Parameters:

  • map_model_to_template – the mapping of the model structure to the template structure

  • model_structure – the structure that is being projected onto

schrodinger.application.bioluminate.antibody.assembly.remove_atoms_by_asl(st: Structure, asl: str) → None
schrodinger.application.bioluminate.antibody.assembly.adjust_resnums(st: Structure, replacement_domain: Structure, bonds: List[AtomPair]) → None

Adjust the resnums in the structure to ensure all res nums are unique.

Parameters:

  • st – the structure to renumber the residues of

  • replacement_domain – the structure that is being projected onto the template

  • bonds – the bonds that will be formed

schrodinger.application.bioluminate.antibody.assembly.get_atom(st: Structure, asl: str) → StructureAtom

Get an atom from the structure.

Parameters:

  • st – the structure to get the atom from

  • asl – the ASL describing the atom

schrodinger.application.bioluminate.antibody.assembly.create_bonds(structure_to_modify: Structure, replacement_domain: Structure, bonds: List[AtomPair]) → None

Create specified bonds within the modeled structure

Parameters:

  • structure_to_modify – the template structure to form the bonds in

  • replacement_domain – the structure of the modelled domain which has been added to the structure_to_modify

  • bonds – AtomPair objects with ASLs relative to the original structures which are being combined

schrodinger.application.bioluminate.antibody.assembly.prepare_atoms_for_bonding(atoms: tuple[schrodinger.structure._structure.StructureAtom]) → None

Prepare atoms for bonding. Figure out if the atom is at the C-terminus or N-terminus. If the C-terminus, remove the hydroxyl group. If the N-terminus, remove the hydrogen.

Parameters:

atoms – the atoms to prepare for bonding

schrodinger.application.bioluminate.antibody.assembly.remove_hydroxyl_group(atom: StructureAtom) → None

Remove the hydroxyl group from the atom.

Parameters:

atom – the atom to remove the hydroxyl group from

schrodinger.application.bioluminate.antibody.assembly.remove_extra_hydrogen(atom: StructureAtom) → None

Remove the extra hydrogen bound to the atom.

Parameters:

atom – the atom to remove the hydrogen from

schrodinger.application.bioluminate.antibody.assembly.minimize_st(st: Structure) → Structure

Minimize the structure.

Parameters:

st – the structure to minimize

Returns:

the minimized structure