mmp file format

An mmp file consists of a sequence of parts. Each is typically a connected molecule. The simulator will check for van der Waals interactions between atoms of different parts, but not within a given part. If such interactions are expected, the "waals" record can be used.

Each part is a "part" record followed by atom and bond records. The bonds must be back-references, i.e. if atom 1 and atom 2 are bonded, atom 1 will have no bond record, and atom 2 will have a record pointing back to atom 1.

The intent in calling the bond records "bond1" was that there are intended to be bond2, bond3, and bond4 for double, triple, and aromatic bonds.

record types

• part xxx comment
  • xxx is "vdw", "bns", or "nil" (see show)
• atom n (e) (x, y, z)
  • n is atom number -- intended to rise sequentially from 1
  • e is element number, e.g. carbon = 6
  • x, y, z, the position in 1e-13m
• bond1 atom# atom# ... {up to 25}
  • bonds the last-defined atom to the indicated ones
• waals atom# atom# ... {up to 25}
  • indicates vanderwaals interaction to be simulated between indicated and last-defined atoms (NB vdW interactions are automatically simulated between atoms of different parts)
• show xxx
  • xxx is "vdw" (van der Waals), "bns" (ball and stick), or "nil" (don't show). Applies to all atoms until the next show or part record.
• ground atom# atom# ... {up to 25}
  • given atoms are "welded to space"
• motor torque, speed, (cx, cy, cz) (ax, ay, az)
  • torque in nN*nm (float)
  • speed in gHz (float)
  • cx, cy, cz is center of rotation (same format as atom posns)
  • ax, xy, az is axis of rotation (ditto)
• shaft atom# atom# ...

  (up to 25) (must follow motor immediately)

  • atoms to which the motor is connected
• kelvin n
  • n is temperature in kelvins (int)
• end
  • logical end of file

unimplemented:

• link (x1, y1, z1) (x2, y2, z2)
  • shaft ...
  • shaft ... or ground
• bearing (cx, cy, cz) (ax, ay, az)
  • shaft ...
  • shaft ... or ground
• ball (cx, cy, cz)
  • shaft ...
  • shaft ... or ground
• linear (ax, ay, az)
  • shaft ...
  • shaft ... or ground
• planar (nx, ny, nz)
  • shaft ...
  • shaft ... or ground
• hooke (cx, cy, cz) (a1x, a1y, a1z) (a2x, a2y, a2z)
  • shaft ...
  • shaft ... or ground
• prism (ax, ay, az)
  • shaft ...
  • shaft ... or ground