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APPENDIX E. LEGACY APPLICATIONS: PREPARING A MAESTRO
STRUCTURE FILE
156
r_chorus_box_ay
r_chorus_box_az
:::
"this is the title"
25.0
0.0
0.0
m_atom[2] {
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
:::
1 0.326 0.704 0.726
2 1 -0.431 1.245 1.295
:::
}
}
The ct block in the previous Example shows four attributes, plus an array block called
m atom. The attributes are m title, chorus box ax, chorus box ay, and chorus box az.
The array block called m atom has three attributes and two records. The attribute
names are prepended by s , r , or i , depending on whether the corresponding value is
a string (text), real number, or integer, respectively.
Note: In the discussion below, these prefixes are ordinarily excluded.
Attributes names also encode the owner of the attribute—that is, the name of the
application responsible for managing that quantity. For example, the attribute name
prefix m indicates that Maestro is responsible for managing that attribute. In an array,
each record has a one-based index, followed by values for the attributes of the block, one
for each record. The size of the array block is given by the number in square brackets
after the name. In the Example above, the value corresponding to chorus box ax is
25.0, and the m x coord attribute takes on the values of 0.326 and -0.431 in the first and
second m atom records, respectively.
Note: Two kinds of ct blocks exist: full or partial, indicated by the respective name
components f and p . Partial blocks contain only attributes and values that override
the corresponding values in the preceding full block. Desmond makes no use of this
feature.
You can think of each ct block as containing a complete description of a chemical
system and the interaction between its particles. Desmond reads all the ct blocks in a
structure file and simulates them together in one chemical system, with two exceptions:
• ct blocks with the attribute ffio ct type equal to full system are not included
in the simulation. Such ct blocks are used by Maestro for visualization.