PTR format

Specification

PTR (or pointer) format is a compact representation for molecules which does not actually contain coordinates. Instead, it contains the transformations to the coordinates and "points" back to a source file where the untransformed coordinates reside.

All information about a molecule is packed into one line. Each item of data is identified by a field name. Some fields are required, like the molecule source information. Some are optional, like the coordinate transformation information. All others are considered comments and are ignored, like the molecule name and score information.

Table 6. PTR Format Data Fields

6A: Required PTR Fields 

These fields must be present in every PTR record.

Field

Type

Description

<FILE>

String

Directory path and name of file which contains molecule.

<FPOS>

Integer

Byte position in file of molecule.

<END>

 

End of record flag.

 

6B: Optional PTR Fields1 of 2

If these fields are present, they will be read and used to update the molecule. The transformation fields will modify the position or conformation of the molecule.

Field

Type

Description

<TRANS>

Real[3]

XYZ translation vector in Angstroms.

<ROT>

Real[3]

Quaternion rotation vector (unitless, range 0-1).

<TORS>

Integer

Number of rotatable torsions.

<REFL>

Integer

Flag for chiral reflection (0 or 1).

<T1>,<T2>, ...

Integer, Real

Bond identifier and torsion angle.

<KEY> c

Integer

Number of chemical keys.

<KFOLD> c

Integer

Flag for folded chemical keys.

<KI1>,<KI2>, ... c

Integer

Chemical key label and distance fingerprint
  1. This field is only read during a chemical screening run.

 

6C: Comment PTR Fields 

These fields are generated for output only. They are completely ignored during input.

Field

Type

Description

<ID>

Integer

Line position in ptr file.

<SRC_ID>

Integer

Line position in input ptr file.

<NAME>

String

Molecule name.

<DESCR>

String

Molecule description.

<BMP>

Integer

Number of bumps.

<CNT>

Real

Contact score.

<CHM>

Real

Chemical score.

<NRG>

Real

Total energy score.

<INTRA>

Real

Intramolecular component of score.

<INTER>

Real

Intermolecular component of score.

<VDW>

Real

VDW component of score.

<ELE>

Real

Electrostatic component of score.

<RMSD>

Real

RMS deviation of current orientation from input.

Example

Database Entry

<ID> 10 <NAME> CAMYLOFIN_C00000105 <DESCR> **** <FILE> /marco/db/mol2.95.1/cmc/cmc.2.mol2 <FPOS> 46204 <END>
Flexible Docking Output

<ID> 5 <SRCID> 5 <NAME> DANAZOL_C00002993 <DESCR> **** <FILE> db/db3.mol2 <FPOS> 14144 <TRANS> 5.00991 29.9234 16.2096 <ROT> 0.270641 1.05337 0.0158567 <TORS> 2 <TANCHOR> 1 <T1> 20 153.624 <T2> 21 -28.0673 <REFL> 0 <BMP> 2 <NRG> -32.43 <INTRA> -0.48 <INTER> -31.95 <VDW> -32.53 <ELECTRO> 0.09 <RMSD> 34.95 <END>
Chemical Screen Database Entry

<ID> 1 <NAME> DAZOQUINAST_C00005118 <DESCR> **** <FILE> /marco/db/mol2.95.1/cmc/cmc.1.mol2 <FPOS> 9689688 <KEY> 5 <KFOLD> 1 <KI1> 0 <KJ1> 10 2d7 <KJ2> 35 3fff <KJ3> 0 0 <KJ4> 20 f65 <KJ5> 0 0 <KI2> 1 <KJ2> 21 fd <KJ3> 0 0 <KJ4> 28 ab7e <KJ5> 0 0 <KI3> 2 <KJ3> 0 0 <KJ4> 0 0 <KJ5> 0 0 <KI4> 3 <KJ4> 6 c1a <KJ5> 0 0 <KI5> 4 <KJ5> 0 0 <END>

Usage

Check out the ptrentry and ptrfield utilities to help manipulate PTR files.

The <FILE> field can contain the relative path or absolute path of a filename. If you use the absolute path, then the ptr file can be used in any other directory. Otherwise, the ptr file is only useful in the idrectory in which it was originally made.

© UC Regents 1998
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