# File formats¶

## .prm file format¶

The .prm file format is an RxDock-specific text format and is used for:

• system definition files (known previously as receptor .prm files)

• scoring function definition files

• search protocol definition files

The format is simple and allows for an arbitrary number of named parameter/value pairs to be defined, optionally divided into named sections. Sections provide a namespace for parameter names, to allow parameter names to be duplicated within different sections. The key features of the format are:

• The first line of the file must be RBT_PARAMETER_FILE_V1.00 with no preceeding whitespace.

• Subsequent lines may contain either:

1. comment lines

2. reserved keywords TITLE, SECTION, or END_SECTION

3. parameter name/value pairs

• Comment lines should start with a # character in the first column with no preceeding whitespace, and are ignored.

• The reserved words must start in the first column with no preceeding whitespace.

• The TITLE record should occur only once in the file and is used to provide a title string for display by various scripts such as run rbscreen.pl. The keyword should be followed by a single space character and then the title string, which may contain spaces. If the TITLE line occurs more than once, the last occurence is used.

• SECTION records can occur more than once, and should always be paired with a closing END_SECTION record. The keyword should be followed by a single space character and then the section name, which may NOT itself contain spaces. All section names must be unique within a .prm file. All parameter name/value pairs within the SECTION / END_SECTION block belong to that section.

• Parameter name/value pairs are read as free-format tokenised text and can have preceeding, trailing, and be separated by arbitrary whitespace. This implies that the parameter name and value strings themselves are not allowed to contain any spaces. The value strings are interpreted as numeric, string, or boolean values as appropriate for that parameter. Boolean values should be entered as TRUE or FALSE uppercase strings.

Caution

The current implementation of the .prm file reader does not tolerate a tab character immediately following the TITLE and SECTION keywords. It is very important that the first character after the SECTION keyword in particular is a true space character, otherwise the reserved word will not be detected and the parameters for that section will be ignored.

Example .prm file In the following example, RECEPTOR_FILE is defined in the top level namespace. The remaining parameters are defined in the MAPPER and CAVITY namespaces. The indentation is for readability, and has no significance in the format.

RBT_PARAMETER_FILE_V1.00
TITLE 4dfr oxido-reductase

RECEPTOR_FILE 4dfr.mol2

SECTION MAPPER
SITE_MAPPER RbtLigandSiteMapper
REF_MOL 4dfr_c.sd
SMALL_SPHERE 1.0
MIN_VOLUME 100
MAX_CAVITIES 1
VOL_INCR 0.0
GRIDSTEP 0.5
END_SECTION

SECTION CAVITY
SCORING_FUNCTION RbtCavityGridSF
WEIGHT 1.0
END_SECTION


## Water PDB file format¶

RxDock requires explicit water PDB files to be in the style as output by the Dowser program. In particular:

• Records can be HETATM or ATOM

• The atom names must be OW, H1 and H2

• The atom records for each water molecule must belong to the same subunit ID

• The subunit IDs for different waters must be distinct, but do not have to be consecutive

• The atom IDs are not used and do not have to be consecutive (they can even be duplicated)

• The order of the atom records within a subunit is unimportant

• The temperature factor field of the water oxygens can be used to define the per-solvent flexibility modes. The temperature factors of the water hydrogens are not used.

Table 17 Conversion of temperature values to solvent flexibility modes

PDB temperature factor

Solvent translational flexibility

Solvent rotational flexibility

0

FIXED

FIXED

1

FIXED

TETHERED

2

FIXED

FREE

3

TETHERED

FIXED

4

TETHERED

TETHERED

5

TETHERED

FREE

6

FREE

FIXED

7

FREE

TETHERED

8

FREE

FREE

Example Valid RxDock PDB file for explicit, flexible waters:

REMARK tmp 1YET.pdb xtal_hoh.pdb
HETATM 3540 OW HOH W 106 28.929 12.684 20.864 1.00 1.0
HETATM 3540 H1 HOH W 106 28.034 12.390 21.200 1.00
HETATM 3540 H2 HOH W 106 29.139 12.204 20.012 1.00
HETATM 3542 OW HOH W 108 27.127 14.068 22.571 1.00 2.0
HETATM 3542 H1 HOH W 108 26.632 13.344 23.052 1.00
HETATM 3542 H2 HOH W 108 27.636 13.673 21.806 1.00
HETATM 3679 OW HOH W 245 27.208 10.345 27.250 1.00 3.0
HETATM 3679 H1 HOH W 245 27.657 10.045 26.409 1.00
HETATM 3679 H2 HOH W 245 26.296 10.693 27.036 1.00
HETATM 3680 OW HOH W 246 31.737 12.425 21.110 1.00 4.0
HETATM 3680 H1 HOH W 246 31.831 12.448 22.106 1.00
HETATM 3680 H2 HOH W 246 30.775 12.535 20.863 1.00


## Pharmacophore restraints file format¶

Pharmacophore restraints are defined in a simple text file, with one restraint per line. Each line should contain the following values, separated by commas or whitespace:

x y z coords of restraint centre, tolerance (in Angstroms), restraint type string


The supported restraint types are:

Table 18 Pharmacophore restraint types

String

Description

Matches

Any

Any atom

Any non-hydrogen atom

Don

H-bond donor

Any neutral donor hydrogen

Acc

H-bond acceptor

Any neutral acceptor

Aro

Aromatic

Any aromatic ring centre (pseudo atom)

Hyd

Hydrophobic

Any non-polar hydrogens (if present), any C sp3 or S sp3, any C or S not bonded to O sp2, any Cl, Br, I

Hal

Hydrophobic, aliphatic

Subset of Hyd, sp3 atoms only

Har

Hydrophobic, aromatic

Subset of Hyd, aromatic atoms only

Ani

Anionic

Any atom with negative distributed formal charge

Cat

Cationic

Any atom with positive distributed formal charge