Seam YAML Transform Index

AlignLigands

Align ligands.

Example usage

type: AlignLigands
config:
  arg_string: "TODO"
  method_type: FLEX/TUG/DEFAULT
  input_field: "structure"
  output_field: "aligned_structure"

Configuration

• label ? (Optional)

Usage

type: AlignLigands
input: ...
config:
  label: label

CreateMols

Create a collection of rdkit Mols from a collection of SMILES strings or dictionaries containing SMILES strings.

Example usage

type: CreateMols
config:
  mol_field: "mol"
  elements:
  - "CC(=O)C1=CC=C(C=C1)C(=O)O"
  - "Cn1cnc2c1c(=O)n(C)c(=O)n2C"
  - "CC(C)[C@H]1CCC(C)CC1O"

or

type: CreateMols
config:
  smiles_field: "smiles"
  mol_field: "mol"
  elements:
    - smiles: "CC(=O)C1=CC=C(C=C1)C(=O)O"
      name: "Aspirin"
    - smiles: "Cn1cnc2c1c(=O)n(C)c(=O)n2C"
      name: "Caffeine"

Configuration

• mol_field string

• smiles_field string

• elements Array[?]

Usage

type: CreateMols
config:
  mol_field: "mol_field"
  smiles_field: "smiles_field"
  elements:
  - element
  - element
  - ...

CreateStructures

Create a collection of schrodinger Structure objects from a collection of SMILES strings or dictionaries containing SMILES strings.

Example usage

type: CreateStructures
config:
  structure_field: "structure"
  elements:
  - "CC(=O)C1=CC=C(C=C1)C(=O)O"
  - "Cn1cnc2c1c(=O)n(C)c(=O)n2C"
  - "CC(C)[C@H]1CCC(C)CC1O"

or

type: CreateStructures
config:
  smiles_field: "smiles"
  structure_field: "structure"
  elements:
    - smiles: "CC(=O)C1=CC=C(C=C1)C(=O)O"
      name: "Aspirin"
    - smiles: "Cn1cnc2c1c(=O)n(C)c(=O)n2C"
      name: "Caffeine"

Configuration

• structure_field string

• smiles_field string

• elements Array[?]

Usage

type: CreateStructures
config:
  structure_field: "structure_field"
  smiles_field: "smiles_field"
  elements:
  - element
  - element
  - ...

CreateStructuresFromSmiles

Create Structure objects from a list of SMILES strings.

This is a source transform that creates structures from SMILES.

Example usage in YAML

pipeline:
  - type: CreateStructuresFromSmiles
    config:
      elements:
        - "c1ccccc1"
        - "CCO"

:param elements: List of SMILES strings to convert to structures.

Configuration

• elements Array[string]

Usage

type: CreateStructuresFromSmiles
config:
  elements:
  - "element"
  - "element"
  - ...

EpikClassicProtonateLigands

Enumerate protonation states of ligands using Epik classic.

Example usage

type: EpikClassicProtonateLigands
config:
  arg_string: "TODO"
  epik_classic_infile: "epik_classic.in"
  input_field: "structure"
  output_field: "protonated_structure"

Configuration

• label ? (Optional)

Usage

type: EpikClassicProtonateLigands
input: ...
config:
  label: label

EpikProtonateLigands

Enumerate protonation states of ligands using Epik.

Example usage

type: EpikProtonateLigands
config:
  arg_string: "--query -lowest_pka 1"
  input_field: "structure"

Configuration

• arg_string string

• input_field string

Usage

type: EpikProtonateLigands
input: ...
config:
  arg_string: "arg_string"
  input_field: "input_field"

FlexAlignLigands

Flex align ligands.

Example usage

type: FlexAlignLigands
config:
  arg_string: "TODO"
  input_field: "structure"
  output_field: "aligned_structure"

Configuration

• label ? (Optional)

Usage

type: FlexAlignLigands
input: ...
config:
  label: label

GlideDock

Generate 3d docked poses from a collection of structures using Glide.

Example usage

type: GlideDock
config:
  structure_field: "structure"
  grid_file: "foo.grid"
  reference_ligand_file: "reference_ligand.maegz"
  glide_in_file: "settings.in"
  poses_per_lig: 1

Configuration

• grid_file string

• reference_ligand_file string

• glide_in_file string

• structure_field string

• poses_per_lig int64

Usage

type: GlideDock
input: ...
config:
  grid_file: "grid_file"
  reference_ligand_file: "reference_ligand_file"
  glide_in_file: "glide_in_file"
  structure_field: "structure_field"
  poses_per_lig: poses_per_lig

LigFilter

A PTransform that filters molecules based on LigFilter criteria.

This is a wrapper transform that uses RunLigFilter internally and returns only the structures that pass the filter.

Example usage with standard args

>>> from schrodinger import adapter
>>> st1 = adapter.to_structure('c1ccccc1')
>>> st1.title = "benzene_fail"
>>> st2 = adapter.to_structure('CCO')
>>> st2.title = "ethanol_pass"
>>> with beam.Pipeline() as p:
...     filtered_structures = (p
...         | beam.Create([st1, st2])
...         | FilterLigands(criteria=['Num_heavy_atoms==3'])
...         | beam.Map(lambda st: st.title)
...         | beam.LogElements())
ethanol_pass

Example usage with legacy arg string

>>> from schrodinger import adapter
>>> st1 = adapter.to_structure('c1ccccc1')
>>> st1.title = "benzene_pass"
>>> st2 = adapter.to_structure('CCO')
>>> st2.title = "ethanol_fail"
>>> with beam.Pipeline() as p:
...     filtered_structures = (p
...         | beam.Create([st1, st2])
...         | FilterLigands(legacy_arg_string='-e Num_heavy_atoms>3')
...         | beam.Map(lambda st: st.title)
...         | beam.LogElements())
Filtering criteria:
  Num_heavy_atoms>3
benzene_pass

:param match_any: If True, matches any of the criteria instead of all. :param invert_criteria: If True, inverts the filter (removes matching structures). :param criteria: A list of compiled LigFilter criteria. :param add_props: If True, adds properties to structures (not currently supported). :param legacy_arg_string: Legacy CLI argument string (mutually exclusive with other fields).

Configuration

• kwargs ? (Optional)

Usage

type: LigFilter
input: ...
config:
  kwargs: kwargs

LigPrep

Perform LigPrep on a collection of molecules.

LigPrep works by expanding tautomeric and ionization states, ring conformations, and stereoisomers consistent with the input information to fully capture the relevant states of the molecule in 3D.

Example usage

type: LigPrep
config:
  arg_string: "-nt -epik -s 32"

Configuration

• arg_string string : (optional) The ligprep argstring to use. Defaults to "-nt -epik -s 32".

  LigPrep Args

  Ionization: -epik Use Epik Classic for ionization and tautomerization (Recommended, overrides -i). -epikx Use Epik for ionization and tautomerization (Recommended, overrides -i). -emb, -epik_metal_binding Run Epik with the metal_binding option so that states appropriate for interactions with metal ions in protein binding pockets are also generated. -i {0,1,2} Ionization treatment: 0 - do not neutralize or ionize, 1 - neutralize only, 2 - neutralize and ionize (Default: 1). Note that -epik option overrides -i and always implies ionization and tautomerization. -mg Ionizer will skip over structures containing more than this number of ionizable groups (Default: 10). -no_refine Disable the final refinement in EpikX. -ph Effective/target pH. (default = 7.0 for Ionizer/Epik Classic, 7.4 for Epik) -pht pH tolerance for generated structures. Tautomerization: -nt Disable tautomerizer (Default: enabled). -t # Run tautomerizer and set the maximum number of tautomers to generate to # (Default: 8). -tp # Run tautomerizer and set the minimum probability for retaining tautomers to # (Default: 0.01). Stereoisomers: -ac Do not respect existing chirality properties and do not respect chiralities from the input geometry. Generate stereoisomers for all chiral centers up to the number permitted (specified using the -s option). This is equivalent to "Generate all combinations" in the Ligand Preparation user interface. Default behavior is to respect only explicitly indicated chiralities. -g Respect chiralities from input geometry when generating stereoisomers. -ns Do not use the stereoizer. -s # Generate up to this many (#) stereoisomers per input structure. (Default: 32). -strict_v2000_stereo For SD V2000 input, generate enantiomers if the chiral flag is 0. Filtering: -ng Disable filtering out of exotic structures. -lp Pass -addprops to LigFilter. -lab Add an internal tracking label to the processed structures. -lab_filter Use tracking labels to filter derived structures (this option turns on -lab). Currently supported: ionizer:# - select at most # output structures for each ionizer input structure such that the formal charge on each ionizable groups is minimized. Force-field based geometry optimization: -bff {14,16} Force-field to be used for the final geometry optimization. Default: 14 (OPLS_2005). For S-OPLS specify 16. -bvac Set dielectric constant to 1.0 for the final force- field based geometry optimization. -cgx_noopt Skip final force-field based geometry optimization. -no_cm1a Skip CM1A charge assignment for S-OPLS. -L CGX fragment library path. Overrides default location in the appdata directory if specified. Meta options: (turn on a number of actual options) -unt : Only run stereoizer and cgx to untangle structures. -adjust : Adjust to a suitable state. -vary : Generate different states. -expand : Aggressively generate different states. -retain : Retain characteristics of the input structures (specifying 'i' also turns on retention of tautomers). specify one or more of: c chiralities i ionization and neutralization t tautomerization

• input_field string : (optional) The field to use as input. Must be a Structure field. Defaults to structure.

• output_field string : (optional) The field to save the ligprepped structure to. If it's the same as input_field, the input field will be replaced. Defaults to structure.

Usage

type: LigPrep
input: ...
config:
  arg_string: "arg_string"
  input_field: "input_field"
  output_field: "output_field"

MolToSmiles

Convert a collection of rdkit Mols to SMILES strings

Example usage

type: MolToSmiles
config:
  input_field: "mol"
  output_field: "smiles"

Configuration

• input_field string

• output_field string

Usage

type: MolToSmiles
input: ...
config:
  input_field: "input_field"
  output_field: "output_field"

MolToStructure

Convert a collection of rdkit Mols to schrodinger Structure objects

Example usage

type: MolToStructure
config:
  input_field: "mol"
  output_field: "structure"

Configuration

• input_field string

• output_field string

Usage

type: MolToStructure
input: ...
config:
  input_field: "input_field"
  output_field: "output_field"

PrettyPrint

Pretty-print Beam Rows as JSON strings.

The expand configuration option controls the formatting: - If expand is True, the JSON output is printed with indentation across multiple lines. - If expand is False (default), the JSON output is compact and printed on a single line.

Example usage

type: PrettyPrint
config:
  expand: true

Configuration

• expand boolean

Usage

type: PrettyPrint
input: ...
config:
  expand: true|false

QikProp

Perform QikProp.

Example usage

type: QikProp
config:
  arg_string: "TODO"
  input_field: "structure"

Configuration

• arg_string string : (optional) The qikprop argstring to use.

Usage

type: QikProp
input: ...
config:
  arg_string: "arg_string"

ReadFileToStructures

Read Structure objects from a file.

This is a source transform that reads structures from a file.

Example usage in YAML

pipeline:
  - type: ReadFileToStructures
    config:
      input_file: "ligands.maegz"

:param input_file: Path to the structure file to read.

Configuration

• input_file string

Usage

type: ReadFileToStructures
config:
  input_file: "input_file"

ReadMolsFromFile

Read a collection of rdkit Mols from a file (or files) containing a newline separated list of SMILES strings.

Invalid SMILES strings are skipped. A warning is printed if silent is set to False.

Example usage

type: ReadMolsFromFile
config:
  input_file: "ligands.smi"

Configuration

• input_file string

• silent boolean

Usage

type: ReadMolsFromFile
config:
  input_file: "input_file"
  silent: true|false

ReadStructuresFromFile

Read a collection of schrodinger Structure objects from a file (or files).

Example usage

type: ReadStructuresFromFile
config:
  input_file: "ligands.maegz"

Configuration

• input_file string

Usage

type: ReadStructuresFromFile
config:
  input_file: "input_file"

SmilesToMol

Convert a collection of SMILES strings to rdkit Mols

Example usage

type: SmilesToMol
config:
  input_field: "smiles"
  output_field: "mol"

Configuration

• input_field string

• output_field string

Usage

type: SmilesToMol
input: ...
config:
  input_field: "input_field"
  output_field: "output_field"

SmilesToStructure

Convert a collection of SMILES strings to schrodinger Structure objects

Example usage

type: SmilesToStructure
config:
  input_field: "smiles"
  output_field: "structure"

Configuration

• input_field string

• output_field string

Usage

type: SmilesToStructure
input: ...
config:
  input_field: "input_field"
  output_field: "output_field"

StructureToMol

Convert a collection of schrodinger Structure objects to rdkit Mols

Example usage

type: StructureToMol
config:
  input_field: "structure"
  output_field: "mol"

Configuration

• input_field string

• output_field string

Usage

type: StructureToMol
input: ...
config:
  input_field: "input_field"
  output_field: "output_field"

StructureToRow

Convert Structure objects to Beam Rows.

This transform wraps each Structure in a Row with a 'structure' field, enabling use of Row-based transforms like MapToFields.

Example usage in YAML

pipeline:
  - type: CreateStructuresFromSmiles
    config:
      elements:
        - "c1ccccc1"
  - type: LigFilter
    config:
      criteria: ["Num_heavy_atoms > 3"]
  - type: StructureToRow
  - type: MapToFields
    config:
      fields:
        title:
          callable: "lambda row: row.structure.title"

Configuration

• label ? (Optional)

Usage

type: StructureToRow
input: ...
config:
  label: label

TugAlignLigands

Tug align ligands.

Example usage

type: TugAlignLigands
config:
  arg_string: "--nconfs 5 --max_tries 20000"
  reference_file: "reference.maegz"
  receptor_file: "receptor.maegz"
  input_field: "structure"

Configuration

• reference_file string

• receptor_file string

• arg_string string

• input_field string

Usage

type: TugAlignLigands
input: ...
config:
  reference_file: "reference_file"
  receptor_file: "receptor_file"
  arg_string: "arg_string"
  input_field: "input_field"

WriteMolsToFile

Write a collection of rdkit Mols to a file.

The transform expects input pcollection to contain schemad rows with field named mol containing rdkit Mol objects.

Example usage

type: WriteMolsToFile
config:
  output_file: "ligands.smi"

Configuration

• output_file string

Usage

type: WriteMolsToFile
input: ...
config:
  output_file: "output_file"

WriteStructures

Write Structure objects to a file.

This is a sink transform that writes structures to a file. It passes through the input structures unchanged for chaining.

Example usage in YAML

pipeline:
  - type: ReadFileToStructures
    config:
      input_file: "ligands.maegz"
  - type: LigFilter
    config:
      criteria: ["Num_heavy_atoms > 5"]
  - type: WriteStructures
    config:
      output_file: "filtered.maegz"

:param output_file: Path to the output structure file.

Configuration

• output_file string

Usage

type: WriteStructures
input: ...
config:
  output_file: "output_file"

WriteStructuresToFile

Write a collection of schrodinger Structure objects to a file.

The transform expects input pcollection to contain schemad rows with field named structure containing schrodinger.Structure objects.

Example usage

type: WriteStructuresToFile
config:
  output_file: "ligands.maegz"

Configuration

• output_file string

Usage

type: WriteStructuresToFile
input: ...
config:
  output_file: "output_file"

ReadFromChembl

Read a collection of molecules from the Chembl database. Returns a Beam PCollection of Rows with mol and chembl_id fields.

Configuration

• sample_size int64 (Optional) : (optional) Specifies the maximum number of molecules to fetch from Chembl. If not provided, all available molecules will be fetched.

Usage

type: ReadFromChembl
config:
  sample_size: sample_size

ReadFromPDB

Read a collection of PDB structures from a list of PDB codes. Returns a Beam PCollection of Rows with the PDB code and its structure.

Example usage

type: ReadFromPDB
config:
    pdb_codes:
        - "1A2B"
        - "3C4D"
    preserve_caps: false

Configuration

• pdb_codes Array[string]

• preserve_caps boolean

Usage

type: ReadFromPDB
config:
  pdb_codes:
  - "pdb_codes"
  - "pdb_codes"
  - ...
  preserve_caps: true|false

WriteToRowSink

Configuration

• label ? (Optional)

Usage

type: WriteToRowSink
input: ...
config:
  label: label

ReadFromRowSource

Configuration

• label ? (Optional)

Usage

type: ReadFromRowSource
config:
  label: label