schrodinger.application.bioluminate.epitope.psc_workflow module¶
- schrodinger.application.bioluminate.epitope.psc_workflow.gen_fastas(spreadsheet_file=None, output_dir=None, overwrite=False)[source]¶
Read an Excel spreadsheet that contains at least 3 columns with the column names, ‘ID’, ‘VH’ and ‘VL’, indicating the names/labels of the antibodies, heavy chain and light chain sequences, respectively.
- class schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow(project_name, fastas_dir, overwrite_data=False)[source]¶
Bases:
object
Class that creates an paratope similarity clustering workflow object
- util_scripts_dir = './utils/'¶
- numbering_scheme = 'EnhancedChothia'¶
- nmodels = 1¶
- S = None¶
- D = None¶
- D1d = None¶
- L = None¶
- N_fab = None¶
- ID_fab = None¶
- plot_width = 7¶
- plot_height = 6¶
- dpi = 300¶
- fastas_dir = None¶
- project_name = None¶
- overwrite_data = None¶
- data_dir = None¶
- fab_dir = None¶
- build_ab_log_dir = None¶
- faux_epi_dir = None¶
- mif_dir = None¶
- gen_jobname(filename)[source]¶
Remove ‘.fasta’ from the fastas file name and use the base for the jobname.
- build_ab(fasta_file, jobname)[source]¶
Given a fasta file containing the sequences of Vh and Vl domains, create an antibody model.
- gen_sim_mat()[source]¶
Compute the pairwise similarity matrix between binding sites using Phase Shape approach. Compare all i,j pairs of MIFs in the mif_dir.