Data Inputs and Outputs

The current version of I.S.A.A.C.S. can import 3D structure models in five different formats [Tab. 3.1]:

Table 3.1: Model structure files read by I.S.A.A.C.S..

XYZ [3]

Chem3D [4]

PDB (Protein Data Bank)

CPMD trajectory [5]^*

VASP trajectory [6]^**

^* atomic units are assumed in the case of CPMD trajectories.
^* and ^** require to enter extra parameters through interactive dialog boxes:

• Total number of atoms
• Number of chemical species
• Label and number of each atomic species

the input order, label and number of each atomic species will be the one assumed when reading the coordinates from the trajectory file.

The coordinates of atoms from a 3D model can be in any of the widely used formats listed in table [Tab. 3.2]:

Table 3.2: Formats of atomic coordinates imported and exported by I.S.A.A.C.S..

Cartesian

Atomic units (in input for CPMD trajectory files only)

Fractional with center of the model box for origin (0,0,0)

Fractional with a corner of the model box for origin (0,0,0)

I.S.A.A.C.S. can output an already imported 3D model in XYZ structure format [3] in either of the atomic coordinates formats presented in table [Tab. 3.2].