Input formats in CPSign

Numerical file format

CPSign loads and stores numerical data in LibSVM/Liblinear file format:

<value> <index>:<occurrances> <index>:<occurrances> ..
<value> <index>:<occurrances> <index>:<occurrances> ..
..

Also note that the <index> must start at 1 and not 0, to conform with LibLinear and LibSVM requirements.

CSV file format

CPSign supports CSV files in a fairly flexible manner, allowing to specify the separator characters and other parameters that might differ between formats. Molecules should be encoded as SMILES strings and there is a requirement that the CSV must contain a header row - so the SMILES field can be located. There must exist a header containing “smiles” (case insensitive), the first header containing “smiles” will be taken as SMILES column. Example of a supported CSV file, using tab as delimiter:

SMILES   Sample_ID   Activity Additional_Notes
OC(=O)\C=C/C(O)=O.C[C@]12CC=C3[C@@H](CCC4=CC(=O)C=C[C@]34C)[C@@H]1CC[C@@H]2C(=O)CN1CCN(CC1)C1=NC(=NC(=C1)N1CCCC1)N1CCCC1   NCGC00261900-01   POS   Here's some additional information
[Na+].NC1=NC=NC2=C1N=C(Br)N2C1OC2CO[P@]([O-])(=O)O[C@@H]2C1O   NCGC00260869-01   NEG   More notes
O=C1N2CCC3=C(NC4=C3C=CC=C4)C2=NC2=C1C=CC=C2  NCGC00261776-01   NEG
Cl.FC1=CC=C(C=C1)C(OCCCC1=CNC=N1)C1=CC=C(F)C=C1 NCGC00261380-01   POS
CC1=CC=C(C=C1)S(=O)(=O)N[C@@H](CC1=CC=CC=C1)C(=O)CCl  NCGC00261842-01   NEG   Not all lines need to contain the additional notes
...

SDF

SDFiles are supported in both v2000 and v3000.

SMILES as single molecule

The predict command can predict single molecules using the --smiles flag, this flag takes a string of texts where the string must start with a valid SMILES and can then optionally include a blank space character (tab, space) and an identifier.

JSON file format

CPSign supports a JSON input format, the format require that the top level starts as a JSON array (meaning that the first character must be a hard bracket “[“). Each index of the array is one record and each record must include a key-value for SMILES for the molecule. This SMILES key-value pair must have the key “SMILES”, “smiles” or “Smiles”. Here are some examples for the file fromat (it is not required that the file is properly indented).

Example classification JSON file:

[
   {
      "cdk:Title" : "1728-95-6",
      "Ames test categorisation" : "mutagen",
      "smiles" : "C1(=C(C=2C=CC=CC2)N=C(N1)C3=CC=C(OC)C=C3)C=4C=CC=CC4"
   },

   {
      "cdk:Title" : "91-08-7",
      "Ames test categorisation" : "mutagen",
      "smiles" : "C=1(C(=C(C=CC1)N=C=O)C)N=C=O"
   },

   ..
]

Example regression JSON file:

[
   {
      "BIO" : "0.43",
      "comment" : "This is a comment",
      "smiles" : "SC1=C(C(F)(F)F)C=CC=C1"
   },

   {
      "BIO" : "1.60",
      "comment" : "Comment for second molecule",
      "smiles" : "SC1=C(C(F)(F)F)C=C([N+]([O-])=O)C=C1"
   },

   ..
]

Compression

CPSign automatically reads files compressed in GZIP format, there is no need to unzip these files.