6. Molecular File Formats

QuacPac can read and write a variety of molecular file formats. The file format is automatically interpreted from the filename suffix.

File type	Extension
SMILES	`.smi .ism .can .smi.gz .ism.gz .can.gz`
SDF	`.sdf .mol .sdf.gz .mol.gz`
SKC	`.skc .skc.gz`
CDK	`.cdk .cdk.gz`
MOL2	`.mol2 .mol2.gz`
PDB	`.pdb .ent .pdb.gz .ent.gz`
MacroModel	`.mmod .mmod.gz`
OEBinary v2	`.oeb .oeb.gz`
Old OEBinary	`.bin`

Old OEBinary format can be read but not written by QuacPac. Gzipped OEBinary version 2 (.oeb.gz) is the recommended output format.

QuacPac is also capable of piping formatted input and output. The simple "-" can be used in place of a file name to indicate std::cin or std::cout with the default SMILES format.

prompt> (quacpac application) -in - -out -

This execution will run QuacPac with std::cin as the input with SMILES format. It will also open std::cout with SMILES format as output. However, the use of "-" does not allow control of the file format.

To control the format of std::cin and std::cout one may use the file extensions without a preceeding filename.

prompt> (quacpac application) -in .ism -out .oeb.gz

This executes QuacPac with the input from std::cin formated in isomeric SMILES and the output sent to std::cout in gzipped OEBinary version 2 format.

				QuacPac Quality Atomic Charges, Proton Assignment and Canonicalization