The MSC Molecule Format

Introduction

The MSC Molecule Format (MMF) is a flexible format for molecular modeling. It is currently in revision 0.1. We plan to keep the format backwards compatible provided that version numbers are included in the first line.

Line One: Version Number

If line one contains the string: #MMF 0.1 then it is assumed that the file version is 0.1. If this line is absent, it is assumed that the version is the most up-to-date version. Currently, this is 0.1, so the line isn't particularly meaningful. However, it will be used in future versions to insure backwards compatibility.

Comment Lines

With the exception of the first line, any line that begins with a '#' will be ignored. Moreover, any totally blank line will be ignored.

Keywords for the MSC Molecule Format

atom atno x y z
Add an atom to the molecule. The user must specify the atomic number atno, and the cartesian coordinates x, y, and z. The coordinates are specified in Angstroms.
orb lab en occ nterms
Add an orbital to the molecule. The user must specify a label lab (which can be arbitrary), an energy en, and an occupation occ. If a nonzero number of terms nterms is specified the subsequent nterms lines will contain the basis function number ibf and the coefficient coeff. If no terms are specified, the data is saved for display purposes.
bfn iat l nterms
Add a (contracted) basis function to the molecule, specifying the atom number atom of the origin (this many atoms must already be specified) and the angular quantum number l of the function (s=0, p=1, d=2, etc.). If a nonzero number of terms nterms is specified, the following nterms lines will contain the contraction coefficient icontr and the exponent exp for this function.
bond iat jat itype
Add a bond to the molecule. If no bonds are specified, the bond information will be generated from distances. The user must specify the atoms iat and jat that comprise the bond, and, optionally, the bond type itype.
uc a b c alpha beta gamma.
Specify unit cell information as a, b, c, alpha, beta, gamma.
charge chg
Set the charge of the molecule to chg.
spin sp
Set the spin of the molecule to sp.
frag i j k l m n
Specify atoms i,j,k,... as belonging to a fragment.
fragbuff size
Specify the buffer zone as extending over size Angstoms.