Cerius²·Ludi

4       Ludi_Genlib

Generating and adding to Ludi libraries

The ADD button on the Ludi Add Library Entry card, run once for each molecule, is useful when only a few molecules are to be added to the library. This command is discussed in detail in the The Ludi interface chapter.

The Unix-level command Ludi_Genlib will process an entire sd file into a Ludi library, automatically generating Ludi labels for each entry. Ludi_Genlib can also be used to add to a library that was created earlier with genfra.

The command syntax is:

Ludi_Genlib <-p parameters_file> <-s output_structures> <-t output_targets> input_structures

$C2DIR/res/LUDI/bin/Ludi_Genlib

Runtime parameters for Ludi_Genlib

Indicates that the input file is in PDB format. A single header line must be prepended to the input molecule file giving a 4 character library label and the atom count.

IREAD 3

Indicates that the input file is in MDL MOL format. A single header line must be prepended to the input molecule file giving a 4 character library label.

IREAD 4

Indicates that the input file is in MDL SD format. Labels are created automatically for the input molecules starting with AAAA unless the LABEL parameter is set. This is the default.

ILINK 0

Do not create link sites at methyl groups. This is the default.

ILINK 1

Create link sites at methyl groups.

SLINK X Y

Create a link site at a specific atom. X is the index number of the link atom and Y is the index number of the link antecedent in the input structure file.

The index number is the record number within the atom coordinate section of the input structure file. For example in the following PDB file, C1 has index 1, 2H has index 2, 3H has index 3 and so on:

REMARK   4 benz COMPLIES WITH FORMAT V. 2.0
HETATM    1  C1  UNK     0      -1.468  16.289   0.000  1.00  0.00           C
HETATM    2 2H   UNK     0      -0.518  16.289   0.000  1.00  0.00           H
HETATM    3 3H   UNK     0      -1.785  17.185   0.000  1.00  0.00           H
HETATM    4 4H   UNK     0      -1.785  15.841  -0.776  1.00  0.00           H
HETATM    5 5H   UNK     0      -1.785  15.841   0.776  1.00  0.00           H
END

Consider link sites at all atoms with element type EL. The element type does not have to be a real element but it is case specific.

REMAP EL

May follow a TLINK specification to indicate that the element type in the TLINK should be converted to the element type specified by EL in the REMAP after the link sites are found. The REMAP element type is used in determining whether the atom is in a non-link target site.

ILINK, TLINK and SLINK specifications are cumulative.

APPEND 1

Append to an existing library.

LABEL XXXX

Start automatic label generation at the label that would follow XXXX.

START X

Start library conversion with entry number X in the SD file.

STOP Y

Stop library conversion with entry number Y in the SD file.

IPROT 0

Do not alter protonation states. This is the default.

IPROT 1

Set protonation states.

COOH COO^-
PO₄H₂ PO₄^2-
PO₄H₁ PO₄^2-
NH-C-NH₂ C(NH₂)₂⁺
NH₂ NH₃⁺
SO₃H₁ SO₃^-

Write ASCII library. The library will be in PDB or MOL format depending on the type of the input format. This is the default.

IWRITE 1

Write unformatted library. Only available for MOL or SD input.

Example

IREAD 3
SLINK 1 5
SLINK 4 3
TLINK Y
REMAP H