Maestro User Manual

Appendix A: The Maestro File Format

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Blocks can be nested within other blocks, and if a block contains a list of data values, the block

may be indexed. That is, the number of data values contained in the block can be appended to

the name. Indexed blocks are identified by having names of the form: 'name[

items>]'

. For example, the file shown in 

Section A.5

 contains an indexed block of the name

m_atom[18]

. In this block name, 'm' means that the data originated in Maestro, 'atom'

means that the data values included in the block belong to atoms, and '18' indicates that are

18 sets of data in the indexed block (representing 18 atoms). 

Within each block there are two sections: a list of the names corresponding to the data fields

included in each data item, and the actual data items. In the example file, the first three data

field names in the m_atom[18] block are:

The end of the first section is denoted by a separator ':::', and followed by the actual data items.

In the example file, the first three data items are:

There must be the same number of data values as there are data names, and the fields within the

data items must appear in the same order as the data names are listed. In the above example, for

instance, the first field in the first line of data ('1') is the index number. The second number

('3') is the MacroModel atom type, indicated by the data name i_m_mmod_type. Index

numbers are required in an indexed block and do not count against data names.

The end of the data item section is indicated by a second ':::' separator. A file may contain any

number of structures (CT blocks), and each structure block may contain any number of atom

and bond data items. 

    i_m_mmod_type

    r_m_x_coord

    r_m_y_coord

    1    3   0.547623    1.262401   -0.990300    1 " " X " "    2   

0.00000   0.00000 CHEX "    " "    "      6   0   0  1   ""

    2   3   -0.930177    1.296701   -1.411700    1 " " X " "    2   

0.00000   0.00000 CHEX "    " "    "     6   0   0  1   ""

    3   3   -1.821477    1.772701   -0.253300    1 " " X " "    2   

0.00000   0.00000 CHEX "    " "  c1"   6   0   0  1   ""

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Appendix A: The Maestro File Format

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A.3

Compressed Format

Files may use a compressed format, most commonly when storing information for a set of

conformers. In a compressed file, the first CT block must be a “full” block containing all the

information described above. The name of this block is 'f_m_ct'. This full block can be

followed by any number of “partial” CT blocks with the name 'p_m_ct'. The partial blocks

contain only information which is different from that in the last preceding full CT block. For

example, a file of conformers will have only one copy of the bond table (the m_bond[36]

block in the example file), and it will be stored in the full CT. Subsequent partial CT blocks

will read bond information from the preceding full CT block.

A.4

Data Item Names

The names of data items in a Maestro format file follow a convention which allows the type of

the data item and the “owner” of the data to be identified. Names have the form 't_o_d',

where t is the type descriptor, o is the “owner” and d is the actual data name. For instance, the

first data name in the m_bond[36] block is 'i_m_mmod_type'. The first character of the name

represents the data type. The acceptable types are:

Owner values indicate the application from which the data item most likely originated.

Including this field in the data name allows multiple applications to store identically titled

quantities. For instance, two applications could store data fields named “energy.” Currently,

basic geometrical and connectivity information, which is shared by most Schrödinger applica-

tions, have 'm' (for Maestro) owner fields. Data introduced by MacroModel have 'mmod'

owner fields, data introduced by QikProp have 'qp' owner fields.

In the 'i_m_mmod_type' example, 'i' indicates the value in the corresponding data field is an

integer. The letter 'm' in the owner field means that the data originated from Maestro, and

'mmod_type'

 is an abbreviation for “MacroModel atom type,” which is what the data field

represents.

A.5

Example Maestro File

Below is extract from a Maestro format file. The complete file is not shown. Where data has

been exempted, it has been noted with an ellipse (...). The text in italic type is provided as

annotation and is not a part of the file.

i – integer 

s – string value

r – real number

b – Boolean value

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Appendix A: The Maestro File Format

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The first block in the file is unnamed. This contains required information that is relevant to

the whole file.

{ 

  s_m_m2io_version

  :::

  1.0.0

}

f_m_ct {

The “CT” block. Each structure in the file is contained in such 

a block. This is a full block.

  s_m_title

The only CT-level data name. A string value 

representing the title of this structure.

  :::

The separator between the data names and data values.

 "Cyclohexane"

The value of the “title” data item.

 m_atom[18] {

The start of the atom block for this CT block. There are 18 

atoms in this block.

    i_m_mmod_type

The MacroModel atom type.

    r_m_x_coord

The X-coordinate.

    r_m_y_coord

The Y-coordinate.

    r_m_z_coord

The Z-coordinate.

    i_m_residue_number

The residue number.

    s_m_insertion_code

The PDB insertion code.

    s_m_mmod_res

The one-letter MacroModel residue code.

    s_m_chain_name

The PDB chain name.

    i_m_color 

The color for this atom.

    r_m_charge1

The partial atomic charge.

    r_m_charge2

The partial atomic charge.

 s_m_pdb_residue_name

The PDB residue name.

    s_m_pdb_atom_name

The PDB atom name.

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