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- region_to_replace: str¶
- domain_structure: schrodinger.structure._structure.Structure¶
- __init__(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) None¶
- schrodinger.application.bioluminate.antibody.assembly.assemble_domains(template_structure: schrodinger.structure._structure.Structure, assembly_instructions: List[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction]) schrodinger.structure._structure.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: schrodinger.structure._structure.Structure, structure_to_align: schrodinger.structure._structure.Structure, alignment_asl: schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl) 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_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: schrodinger.structure._structure.Structure, replacement_domain: schrodinger.structure._structure.Structure, replaced_region_asl: str, bonds: List[schrodinger.application.bioluminate.antibody.assembly.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.remove_atoms_by_asl(st: schrodinger.structure._structure.Structure, asl: str) None¶
- schrodinger.application.bioluminate.antibody.assembly.create_bonds(structure_to_modify: schrodinger.structure._structure.Structure, replacement_domain: schrodinger.structure._structure.Structure, bonds: List[schrodinger.application.bioluminate.antibody.assembly.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