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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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<BODY LANG="en-US" DIR="LTR">
<H1>mmp file format (Alpha)</H1>
<P>An mmp file consists of a <EM>molecular machine part</EM> (MMP)
with a sequence of molecules. The simulator will check for van der
Waals interactions between atoms of different molecules, but not
within a given molecule. If such interactions are expected within the
same molecule, the "waals" record can be used.
</P>
<P>The file is a nested tree structure where each node begins with a
<B>group </B>record and ends with an <B>egroup</B> record.</P>
<P>Each molecule is a <STRONG>mol</STRONG> record followed by <STRONG>atom</STRONG>
and <STRONG>bond</STRONG> records. The bonds must be back-references,
i.e. if <EM>atom1</EM> and <EM>atom2</EM> are bonded, <EM>atom1</EM>
will have no bond record, while <EM>atom2</EM> will have a record
pointing back to <EM>atom1</EM>.</P>
<P>MMP files begin with a group containing a <strong>csys</strong>
record, followed by standard <strong>datum</strong> plane objects
(XY, YZ and XZ). Then is a group containing the rest of the
part. This is followed by an <STRONG>end1</STRONG> record. The final
section of the MMP file is a group that can include cut/paste objects. The intent of this section of the file is to support cut/paste when the user cuts a selection, then immediately saves the file. The final record in the MMP file is the <strong>end</strong> record. </P>
<H2>Record types</H2>
<P>Note parentheses and commas are required. Braces are metacomments.
</P>
<HR>
<P><EM><FONT SIZE=4><STRONG>mol</STRONG> (name</FONT></EM>) <EM><FONT SIZE=4>mode
</FONT></EM>
</P>
<P>Begins a new molecule. Applies to all atoms until the next <STRONG>mol</STRONG>
record, where:</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM><STRONG>name</STRONG></EM>
- </STRONG>name of the molecule that appears in the model tree
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>mode</EM></STRONG> -
the default display mode for this molecule equals one of:
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">vdw" - van der Waals
</P>
<LI><P STYLE="margin-bottom: 0in">"cpk" - ball and stick
</P>
<LI><P STYLE="margin-bottom: 0in">"tub" - tube
</P>
<LI><P STYLE="margin-bottom: 0in">"lin" - lines
</P>
<LI><P STYLE="margin-bottom: 0in">"inv"- invisible
</P>
<LI><P>"def" - default (this display mode is determined
by the software)
</P>
</UL>
</UL>
<HR>
<P><FONT SIZE=4><STRONG>atom </STRONG><EM>n (e) (x, y, z) mode</EM></FONT></P>
<P>Creates a new atom, where:
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><EM><B>mode</B> – the
display mode for the atom, same list as above</EM></P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>n</EM></STRONG> - atom
number, a unique atom ID
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>e</EM></STRONG> -
element number, e.g. carbon = 6
</P>
<LI><P><EM><STRONG>x, y, z</STRONG></EM> - the position in 1e-13m
</P>
</UL>
<HR>
<P><FONT SIZE=4><STRONG>bond1 </STRONG><EM>atom1 atom2 ... atom25 {up
to 25}</EM></FONT>
</P>
<P>Bonds the last-definted atom to the indicated atoms.
</P>
<P>Note: The intent in calling this bond record <STRONG>bond1</STRONG>
is that we intend to support <STRONG>bond2</STRONG>, <STRONG>bond3</STRONG>,
and <STRONG>bond4</STRONG> for <EM>double</EM>, <EM>triple</EM>, and
<EM>aromatic</EM> bonds.</P>
<HR>
<P><FONT SIZE=4><STRONG>waals </STRONG><EM>atom1 atom2 ... atom25 {up
to 25}</EM></FONT></P>
<P><FONT SIZE=4>I</FONT>ndicates van der Waals interaction to be
simulated between indicated and last-defined atoms (NB vdW
interactions are automatically simulated between atoms of different
molecules)
</P>
<HR>
<P><FONT SIZE=4><STRONG>ground </STRONG><EM>(name) (r, g, b) atom1
atom2 ... atom25 {up to 25}</EM></FONT>
</P>
<P>Creates a ground object in which atoms are anchored in space,
where:</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>name</EM></STRONG> -
name of the ground
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>r, g, b</EM></STRONG>
- red, green, and blue color components, between 0-255 (int)
</P>
<LI><P><STRONG><EM>atoms</EM></STRONG> - atoms of mol that are
anchored in space
</P>
</UL>
<HR>
<P><FONT SIZE=4><STRONG>lmotor</STRONG> <EM>(name) (r, g, b) force
stiffness (cx, cy, cz) (ax, ay, az)</EM> </FONT>
</P>
<P>Creates a linear motor, where:
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>name</EM></STRONG> -
name of the linear motor
</P>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>r, g, b</STRONG></EM>
- red, green, and blue color components, between 0-255 (int)
</P>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>force</STRONG></EM> -
force of motor in nN*nm (float)
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>stiffness</EM></STRONG>
- stiffness of motor in N/m (float)
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>cx, cy, cz</EM></STRONG>
- center of rotation (same format as atom positions)
</P>
<LI><P><STRONG><EM>ax, xy, az</EM></STRONG> - axis of rotation (same
format as atom positions)
</P>
</UL>
<P><FONT SIZE=4><STRONG>shaft </STRONG><EM>atom1 atom2 ... atom25 {up
to 25}</EM></FONT>
</P>
<P>Atoms to which the linear motor is connected (<STRONG>shaft</STRONG>
must follow <STRONG>lmotor</STRONG> immediately)</P>
<HR>
<P><FONT SIZE=4><STRONG>rmotor</STRONG> <EM>(name) (r, g, b) torque
speed (cx, cy, cz) (ax, ay, az)</EM></FONT></P>
<P>Creates a rotary motor, where:
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>name</STRONG></EM> -
name of the linear motor
</P>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>r, g, b</STRONG></EM>
- red, green, and blue color components, between 0-255 (int)
</P>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>torque</STRONG></EM> -
torque of motor in nN*nm (float)
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>speed</EM></STRONG> -
speed of motor in gHz (float)
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>cx, cy, cz</EM></STRONG>
- center of rotation (same format as atom positions)
</P>
<LI><P><STRONG><EM>ax, xy, az</EM></STRONG> - axis of rotation (same
format as atom positions)
</P>
</UL>
<P><FONT SIZE=4><STRONG>shaft </STRONG><EM>atom1 atom2 ... atom25 {up
to 25}</EM></FONT>
</P>
<P>Atoms to which the rotary motor is connected (<STRONG>shaft</STRONG>
must follow <STRONG>rmotor</STRONG> immediately)</P>
<HR>
<P><FONT SIZE=4><STRONG>kelvin </STRONG><EM>n</EM></FONT></P>
<P>The temperature of the part, where:</P>
<UL>
<LI><P><STRONG><EM>n</EM></STRONG> - the temperature in kelvins
(int)
</P>
</UL>
<HR>
<P><FONT SIZE=4><STRONG>csys</STRONG> <EM>(name) (w, x, y, z) (zoom)</EM></FONT></P>
<P>The coordsystem record, which contains default property settings
for the part, where:</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>name</STRONG></EM> -
the name of the csys object that appears in the model tree
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>w, x, y, z </EM></STRONG>-
quaternion for the default orientation for home view (float). (No
rotation = 1.0, 0.0, 0.0, 0.0)
</P>
<LI><P><EM><STRONG>zoom</STRONG></EM> - default zoom for home view
(float).
</P>
</UL>
<P>There can only be one csys record per part (file).</P>
<HR>
<P><FONT SIZE=4><STRONG>datum</STRONG> <EM>(name) <EM><FONT SIZE=4>(r,
g, b)
</FONT></EM>type (x1, y1, z1) (x2, y2, z2) (x3, y3, z3)</EM></FONT></P>
<P><EM>Creates a datum (point, line or plane) object, where:</EM></P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>name</EM></STRONG> -
the name of the datum object that appears in the model tree
</P>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>type - </STRONG></EM>one
of "point", "line" or "plane"
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>x1, y1, z1 –</EM></STRONG>
center point for object
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG><EM>x2, y2, z2 –</EM></STRONG>
direction vector for line and normal for plane
</P>
<LI><P><STRONG><EM>x3, y3, z3</EM></STRONG> – orientation
vector for lines and planes
</P>
</UL>
<P><EM>All three points are given for each datum type.</EM></P>
<HR>
<P><FONT SIZE=4><STRONG>group</STRONG> <EM>(name)</EM></FONT></P>
<P><B><FONT SIZE=4>egroup</FONT></B> <I><FONT SIZE=4>(name)</FONT></I></P>
<P>Creates/begins (group) and ends (egroup) a group object, where:
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>name</STRONG></EM> -
the group name that appears in the model tree
</P>
</UL>
<P STYLE="margin-bottom: 0in">These records enclose a list of other
objects or groups. The names should match for checking purposes but
do not have to be unique.</P>
<HR>
<P><FONT SIZE=4><STRONG>stat </STRONG><EM>(name) (r, g, b) temp atom1
atom2 ... atom25 {up to 25}</EM></FONT>
</P>
<P>Creates a thermostat jig that specifies the temperature of the
listed atoms, where:</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><EM><STRONG>name</STRONG></EM> -
name of the thermostat
</P>
<LI><P STYLE="margin-bottom: 0in"><STRONG>r, g, b</STRONG> - red,
green, and blue color components, between 0-255 (int)
</P>
<LI><P STYLE="margin-bottom: 0in"><EM>t<B>emp</B> –
temperature the thermostat maintains, integer, in kelvins</EM>
</P>
<LI><P><EM><STRONG>atoms</STRONG></EM> - atoms of mol that are
associated with this thermostat
</P>
</UL>
<HR>
<P><STRONG><FONT SIZE=4>end1</FONT></STRONG></P>
<P>Logical end of file for simulator; objects that follow are for
cut/paste</P>
<HR>
<P><STRONG><FONT SIZE=4>end </FONT></STRONG>
</P>
<P>Logical end of file
</P>
<HR>
<P><STRONG><FONT SIZE=5>Planned for Beta </FONT></STRONG>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>bearing
</STRONG><EM>(name)</EM> <EM>(r, g, b) (cx, cy, cz) (ax, ay, az) </EM></FONT>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">shaft ...
</P>
<LI><P STYLE="margin-bottom: 0in">shaft ... or ground
</P>
</UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>dyno </STRONG><EM>(name)</EM>
<EM>(r, g, b) </EM>??? </FONT>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">???
</P>
</UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>handle</STRONG>
<EM>(name) (r, g, b) torque, speed, (cx, cy, cz) (ax, ay, az)</EM></FONT>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">shaft ...
</P>
<LI><P STYLE="margin-bottom: 0in">shaft ... or ground
</P>
</UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>heatsink</STRONG>
<EM>(name) </EM></FONT><EM><FONT SIZE=4>(r, g, b) </FONT></EM>???
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">???
</P>
</UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>spring</STRONG>
</FONT><EM><FONT SIZE=4>(name) (r, g, b) force, stiffness, (cx, cy,
cz) (ax, ay, az)</FONT></EM>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">shaft ...
</P>
<LI><P>shaft ... or ground
</P>
</UL>
</UL>
<HR>
<P><STRONG><FONT SIZE=5>Planned for Gamma or Future releases </FONT></STRONG>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>ball </STRONG><EM>(name)</EM>
<EM>(r, g, b) (cx, cy, cz)</EM></FONT>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">shaft ...
</P>
<LI><P STYLE="margin-bottom: 0in">shaft ... or ground
</P>
</UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>hooke </STRONG><EM>(name)</EM>
<EM>(r, g, b) (cx, cy, cz) (a1x, a1y, a1z) (a2x, a2y, a2z) </EM></FONT>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">shaft ...
</P>
<LI><P STYLE="margin-bottom: 0in">shaft ... or ground
</P>
</UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>link </STRONG><EM>(name)
(r, g, b) (x1, y1, z1) (x2, y2, z2)</EM></FONT>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">shaft ...
</P>
<LI><P STYLE="margin-bottom: 0in">shaft ... or ground
</P>
</UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>planar </STRONG><EM>(name)</EM>
<EM>(r, g, b) (nx, ny, nz) </EM></FONT>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">shaft ...
</P>
<LI><P STYLE="margin-bottom: 0in">shaft ... or ground
</P>
</UL>
<LI><P STYLE="margin-bottom: 0in"><FONT SIZE=4><STRONG>prism </STRONG><EM>(name)</EM>
<EM>(r, g, b) (ax, ay, az)</EM></FONT>
</P>
<UL>
<LI><P STYLE="margin-bottom: 0in">shaft ...
</P>
<LI><P>shaft ... or ground
</P>
</UL>
</UL>
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