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Biskit :: PDBDope :: PDBDope :: Class PDBDope
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Class PDBDope

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Decorate a PDBModel with calculated properties (profiles)

Instance Methods [hide private]
  __init__(self, model)
str version(self)
Returns version of class
PDBModel model(self)
Returns model
  addASA(self)
Add profiles of Accessible Surface Area: 'relASA', 'ASA_total', 'ASA_sc', 'ASA_bb'.
  addSurfaceMask(self, pname='relAS')
Adds a surface mask profie that contains atoms with > 40% exposure compared to a random coil state.
  addSecondaryStructure(self)
Adds a residue profile with the secondary structure as calculated by the DSSP program.
  addConservation(self, pfamEntries=None)
Adds a conservation profile.
  addDensity(self, radius=6, minasa=None, profName='density')
Count the number of heavy atoms within the given radius.
  addFoldX(self)
Adds dict with fold-X energies to PDBModel's info dict.
  addSurfaceRacer(self, probe=1.4, vdw_set=1, probe_suffix=0)
Always adds three different profiles as calculated by fastSurf:

Method Details [hide private]

__init__(self, model)
(Constructor)

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Parameters:
  • model (PDBModel) - model to dope

version(self)

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Returns: str
version of class

model(self)

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Returns: PDBModel
model

addASA(self)

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Add profiles of Accessible Surface Area: 'relASA', 'ASA_total', 'ASA_sc', 'ASA_bb'. See Biskit.WhatIf
Raises:
  • ProfileError - if WhatIf-returned atom/residue lists don't match. Usually that means, WhatIf didn't recognize some residue name

Note: Using WhatIf to calculate relative accessabilities is not nessesary any more. SurfaceRacer now also adds a profile 'relAS' (conataining relative solvent accessible surf) and 'relMS' (relative molecular surface).

addSurfaceMask(self, pname='relAS')

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Adds a surface mask profie that contains atoms with > 40% exposure compared to a random coil state.
Parameters:
  • pname (str) - name of relative profile to use (Whatif-relASA OR SurfaceRacer - relAS) (default: relAS)

addSecondaryStructure(self)

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Adds a residue profile with the secondary structure as calculated by the DSSP program.

Profile code: 
 B = residue in isolated beta-bridge
 E = extended strand, participates in beta ladder
 G = 3-helix (3/10 helix)
 I = 5 helix (pi helix)
 T = hydrogen bonded turn
 S = bend
 . = loop or irregular

addConservation(self, pfamEntries=None)

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Adds a conservation profile. See Biskit.Hmmer
Parameters:
  • pfamEntries ({dict}]) - External hmmSearch result, list of (non-overlapping) profile hits. (default: None, do the search) Example: 
     [{'ribonuclease': [[1, 108]]},..]
 [{profileName : [ [startPos, endPos],
                   [start2, end2]]}]
- startPos, endPos as reported by hmmPfam
  for PDB sequence generated from this model

addDensity(self, radius=6, minasa=None, profName='density')

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Count the number of heavy atoms within the given radius. Values are only collected for atoms with |minasa| accessible surface area.
Parameters:
  • minasa (float) - relative exposed surface - 0 to 100%
  • radius (float) - in Angstrom

addFoldX(self)

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Adds dict with fold-X energies to PDBModel's info dict. See Biskit.Fold_X

addSurfaceRacer(self, probe=1.4, vdw_set=1, probe_suffix=0)

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Always adds three different profiles as calculated by fastSurf: 
  curvature - average curvature (or curvature_1.4 if probe_suffix=1)
  MS - molecular surface area   (or MS_1.4 if probe_suffix=1)
  AS - accessible surface area  (or AS_1.4 if probe_suffix=1)
If the probe radii is 1.4 Angstrom and the Richards vdw radii set is used the following two profiles are also added: 
  relAS - Relative solvent accessible surface
  relMS - Relative molecular surface
{Bikit.SurfaceRacer}
Parameters:
  • probe (float) - probe radius
  • vdw_set (1|2) - defines what wdv-set to use (1-Richards, 2-Chothia)
  • probe_suffix (1|0) - append probe radius to profile names

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