schrodinger.livedesign.biologics.modeling module

This model contains necessary logic to: 1. Convert a HELM input structure the corresponding atomistic antibody modeling input arguments (i.e. fasta file, antibody construct format) 2. Call the antibody modeling script (currently $SCHRODINGER/run -FROM biolumiante build_antibody.py), which writes the file to the local working directory.

schrodinger.livedesign.biologics.modeling.run_antibody_model(entity_name: str, rdmol_binary: str) → str

Top-level function to parse the rdmol binary into HELM, translate the HELM data into appropriate build_antibody.py arguments, and execute build_antibody.py with those arguments under JobControl.

Parameters

  • entity_name – name of the antibody entity, used for file naming

  • rdmol_binary – binary string of the antibody structure

schrodinger.livedesign.biologics.modeling.get_bispecific_model_job(entity_name: str, helm_model: schrodinger.protein.helm._helm_parser.HelmModel)

Make a JobControlJob to run build_antibody.py and build a bispecific antibody model.

Parameters

  • entity_name – name of the antibody entity, used for file naming

  • helm_model – HELM model of the antibody structure

schrodinger.livedesign.biologics.modeling.get_simple_model_job(entity_name: str, entity_class: schrodinger.livedesign.entity_type.EntityClass, fasta_name: str, helm_model: schrodinger.protein.helm._helm_parser.HelmModel)

Generate a JobControlJob to run build_antibody.py and build a “simple” (one-arm or symmetric arm) antibody model.

Parameters

  • entity_name – name of the antibody entity, used for file naming

  • entity_class – class of the antibody entity

  • fasta_name – name of the FASTA file to write

  • helm_model – HELM model of the antibody structure

schrodinger.livedesign.biologics.modeling.write_antibody_modeling_fasta(helm_model: schrodinger.protein.helm._helm_parser.HelmModel, fasta_name: str)

” Write the HELM sequences of a helm model to a single deduplicated FASTA file.

Parameters

  • helm_model – HELM model of the antibody structure

  • fasta_name – name of the FASTA file to write

schrodinger.livedesign.biologics.modeling.deduplicate_sequences(sequences: schrodinger.protein.alignment.ProteinAlignment) → schrodinger.protein.alignment.ProteinAlignment

Remove duplicate sequences from a FASTA string.

Parameters

sequences – ProteinAlignment object containing the sequences to deduplicate

schrodinger.livedesign.biologics.modeling.get_format_arguments(entity_name: str, entity_class: schrodinger.livedesign.entity_type.EntityClass) → str

Get the arguments to pass to build_antibody.py based on the antibody entity class.

Note that the arguments are different for bispecifics, which include the entity name in its arguments.

Parameters

  • entity_name – name of the antibody entity, used for file naming

  • entity_class – class of the antibody entity

schrodinger.livedesign.biologics.modeling.get_outfile_name(entity_name: str, entity_class: schrodinger.livedesign.entity_type.EntityClass) → str
Parameters

  • entity_name – name of the antibody entity, used for file naming

  • entity_class – class of the antibody entity

Returns

the name of the final output file