Module hexTools

source code

Various common functions used by the docking modeles.

Classes

[hide private]

Test
Test case

Functions

[hide private]

str createHexPdb_single(model, fout=None)
Write PDB of one structure for hex.

str createHexPdb(modelDic, fout=None)
Write pdb for hex with models separated by MODEL%i/ENDMODEL

float, float centerSurfDist(model, surf_mask, mask=None)
Calculate the longest and shortest distance from the center of the molecule to the surface.

str, str, boolean createHexInp(recPdb, recModel, ligPdb, ligModel, comPdb=None, outFile=None, macDock=None, silent=0, sol=512)
Prepare a Hex macro file for the docking of the receptor(s) against ligand(s).

Function Details

[hide private]

createHexPdb_single(model, fout=None)

source code

Write PDB of one structure for hex.

Parameters:

model (PDBModel) - model
fout (str) - out file name (default: pdbCode + _hex.pdb)

Returns: str: file name of result PDB

createHexPdb(modelDic, fout=None)

source code

Write pdb for hex with models separated by MODEL%i/ENDMODEL

Parameters:

modelDic ({int:PCRModel}) - dictionary mapping an integer to each model
fout (str) - output name, default is pdbCode + _hex.pdb

Returns: str: file name of result PDB

centerSurfDist(model, surf_mask, mask=None)

source code

Calculate the longest and shortest distance from the center of the molecule to the surface.

Parameters:

mask ([1|0]) - atoms not to be considerd (default: None)
surf_mask ([1|0]) - atom surface mask, needed for minimum surface distance

Returns: float, float: max distance, min distance

createHexInp(recPdb, recModel, ligPdb, ligModel, comPdb=None, outFile=None, macDock=None, silent=0, sol=512)

source code

Prepare a Hex macro file for the docking of the receptor(s) against ligand(s).

Parameters:

recPdb (str) - hex-formatted PDB
recModel (str) - hex-formatted PDB
ligPdb (PDBModel) - PDBModel, get distances from this one
ligModel (PDBModel) - PDBModel, getdistances from this one
comPdb (str) - reference PDB
outFile (str) - base of file name for mac and out
macDock (None|1|0) - None -> hex decides (from the size of the molecule), 1 -> force macroDock, 0-> force off (default: None)
silent (0|1) - don't print distances and macro warnings (default: 0)
sol (int) - number of solutions that HEx should save (default: 512)

Returns: str, str, boolean: HEX macro file name, HEX out generated bu the macro, macro docking status