schrodinger.application.fragment_virtual_screening.frag_vs_utils module

class schrodinger.application.fragment_virtual_screening.frag_vs_utils.StageStatus(value)

Bases: enum.Enum

An enumeration.

NOT_STARTED = 0
STARTED = 1
FINISHED = 2
schrodinger.application.fragment_virtual_screening.frag_vs_utils.get_runtime_relpath(file_path, jobdir_path)

Get the relative path of file’s runtime path to job directory’s path.

Parameters

  • file_path (str) – path of the file of interest

  • jobdir_path (str) – path of the job directory

Returns

the relative path of the file to the job directory

Return type

str

schrodinger.application.fragment_virtual_screening.frag_vs_utils.get_top_poses_from_sorted_ligands(input_ligand_file, output_ligand_file, max_ligands, poses_per_lig=1)

Write the top poses of the top ligands from the input file to output file. Ligands are distinguished by SMILES. This function always returns max_ligands unique SMILES. For each unique SMILES, it includes the top poses_per_lig poses of each selected SMILES.

Parameters

  • input_ligand_file (str) – file tha contains sorted input ligands.

  • output_ligand_file (str) – file that contains picked output ligands.

  • max_ligands (int) – number of unique ligands to be returned.

  • poses_per_lig (int) – maximum number of poses per ligands to be returned.

schrodinger.application.fragment_virtual_screening.frag_vs_utils.merge_ligand_files(ligand_file_list, output_file, smi_index=1, name_index=2)

Merge ligands in multiple file to a single file. It supports .mae, .csv, .smi and their corresponding zipped formats. Returns an error message if file format is not correct.

Parameters

  • ligand_file_list (list(str)) – list of input ligand files

  • output_file (str) – output ligand file

  • smi_index (int) – 1-based index of SMILES column for .csv input file.

  • name_index (int) – 1-based index of title column for .csv input file.

Returns

error message if file format is not correct

Return type

None or str

schrodinger.application.fragment_virtual_screening.frag_vs_utils.read_input_file(input_file)

Read the input argument file with inputconfig. Convert the generated InputConfig instance to dictionary.

schrodinger.application.fragment_virtual_screening.frag_vs_utils.to_yaml(data, yaml_file)

Dump the data to a yaml file

schrodinger.application.fragment_virtual_screening.frag_vs_utils.from_yaml(yaml_file)

Load data from a yaml file. Return the data.