schrodinger.application.bioluminate.antibody.assembly module¶
- class schrodinger.application.bioluminate.antibody.assembly.DomainAlignment(model_asl: str, template_asl: str)¶
Bases:
object- model_asl: str¶
- template_asl: str¶
- __init__(model_asl: str, template_asl: str) None¶
- class schrodinger.application.bioluminate.antibody.assembly.AtomPair(model_asl: str, template_asl: str)¶
Bases:
object- model_asl: str¶
- template_asl: str¶
- __init__(model_asl: str, template_asl: str) None¶
- class schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction(align_region: schrodinger.application.bioluminate.antibody.assembly.DomainAlignment, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair], region_to_replace: str, domain_structure: schrodinger.structure._structure.Structure)¶
Bases:
object- region_to_replace: str¶
- domain_structure: schrodinger.structure._structure.Structure¶
- __init__(align_region: schrodinger.application.bioluminate.antibody.assembly.DomainAlignment, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair], region_to_replace: str, domain_structure: schrodinger.structure._structure.Structure) None¶
- schrodinger.application.bioluminate.antibody.assembly.parse_assembly_instruction_from_yaml(yaml_filename: str) List[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction]¶
Parse a (yaml?)-formatted assembly instruction file and return the relevant strings.
- Returns
a list specifying how to align and connect each mode
- schrodinger.application.bioluminate.antibody.assembly.parse_assembly_instruction_from_structure(model_st: schrodinger.structure._structure.Structure, template_st: schrodinger.structure._structure.Structure) List[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction]¶
Extract the DomainAssemblyInstruction to replace the appropriate template_st domain with the specified model_st domain.
- Returns
a list specifying how to align and connect each mode
- schrodinger.application.bioluminate.antibody.assembly.infer_assembly_instruction_from_structures(model_st: schrodinger.structure._structure.Structure, template_st: schrodinger.structure._structure.Structure) List[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction]¶
For specific antibodies, detect the correct regions to align and atoms to bond to replace the appropriate domain of template_st with model_st
- Returns
a list specifying how to align and connect each mode
- schrodinger.application.bioluminate.antibody.assembly.align_structures(*, alignment_target: schrodinger.structure._structure.Structure, structure_to_align: schrodinger.structure._structure.Structure, alignment_instructions: schrodinger.application.bioluminate.antibody.assembly.DomainAlignment) schrodinger.structure._structure.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_instructions – region on the template structure to which the domain of interest will be aligned
- Returns
- schrodinger.application.bioluminate.antibody.assembly.replace_domain(*, structure_to_modify: schrodinger.structure._structure.Structure, replacement_domain: schrodinger.structure._structure.Structure, replaced_region_asl: str) None¶
- schrodinger.application.bioluminate.antibody.assembly.create_bonds(st: schrodinger.structure._structure.Structure, bond_atom_asl_pairs: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair]) None¶
- schrodinger.application.bioluminate.antibody.assembly.assemble_domains(template_structure: schrodinger.structure._structure.Structure, assembly_instructions: List[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction])¶
Assemble the built model domains onto the template structure.
- schrodinger.application.bioluminate.antibody.assembly.get_domain_assembly_info(assembly_info_source) schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction¶
- Infer the correct type of assembly and return appropriate domain
assembly instruction.