structconvert Command Help

Command: $SCHRODINGER/utilities/structconvert

usage: structconvert [-h] [-a] [-stereo {none,3d,annotation}]
                        [-smi SMILESCol] [-name nameCol]
                        [-split-nstructures STRUCTURES_PER_OUTPUTFILE | -split-nfiles OUTPUTFILE_COUNT]
                        [-n selectStr] [-no_color] [-no_dup_conect]
                        [-no_geometry] [-no_renum] [-no_reorder]
                        [-reorder_by_resnum] [-reorder_by_sequence]
                        [-no_fixelem] [-first_occ] [-all_occ] [-hybrid36]
                        [-psp] [-use_component_dict] [-no_component_dict]
                        [-model MODEL] [-num_models NUM_MODELS]
                        [-histidine HISTIDINE] [-occ OCC] [-2D] [-u]
                        [-coreCif | -PDBx]
                        inputfile outputfile

Universal chemical structure conversion program able to interconvert between
the following formats:

  Maestro format (.mae)
  SD format (.sdf)
  PDB format (.pdb)
  CIF format (.cif)
  SYBYL MOL2 format (.mol2)
  SMILES format (.smi)
  CSV file, SMILES with properties (.csv)

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  inputfile
  outputfile

options:
  -h, --help            show this help message and exit
  -a                    Append to output file instead of overwriting (not supported for all conversions)
  -stereo {none,3d,annotation}
                        Stereochemistry source when writing to SMILES (default 3d)
  -smi SMILESCol        User specified field of SMILES strings, either by name or by column index starting at 1. By default, SMILES column is the first column (CSV format only).
  -name nameCol         User specified field to use as molecule name, either by name or by column index. By default, it is the second column (CSV format only).
  -split-nstructures STRUCTURES_PER_OUTPUTFILE
                        Split the output files in N structures per file (Only mae -> mae or sdf -> sdf conversions)
  -split-nfiles OUTPUTFILE_COUNT
                        Split the output into N files. (Only mae -> mae or sdf -> sdf conversions)
  -n selectStr          The set of input structures to process:
                        1,4       - structures 1 and 4
                        1:10,14   - structures 1 through 10 and 14
                        2:        - structures 2 through the end of file
                        :5,13:18  - structures 1 through 5 and 13 through 18
                        
                        All structures are processed by default.
                        (This option is not supported by all conversions)

For conversion to/from PDB format, the following options are also supported:
  -no_color
  -no_dup_conect
  -no_geometry
  -no_renum
  -no_reorder
  -reorder_by_resnum
  -reorder_by_sequence
  -no_fixelem
  -first_occ
  -all_occ
  -hybrid36
  -psp
  -use_component_dict
  -no_component_dict
  -model MODEL
  -num_models NUM_MODELS
  -histidine HISTIDINE
  -occ OCC

For conversion between SD and MAE format, the following options are also supported:
  -2D

For conversion to SMILES format, the following options are also supported:
  -u

For conversion *to* CIF format, one the following format flags *must* be specified:
  -coreCif              Small-molecule Crystallographic Information File (UICr core CIF)
  -PDBx                 Macromolecular Crystallographic Information File (RCSB PDBx/mmCIF)

Limitations:
  * PDB and SMILES format can not be interconverted.
  * Only first structure is written when writing to PDB format.
  * The obsolete MM format is not supported.
  * When SMILES are converted to Maestro format, the output structures
      are 2D (not valid for many programs). Use LigPrep to
      generate 3D Maestro structures from SMILES.
  * SMILES to mol2 format conversion is not supported.