ample.util.pdb_model module
Created on 7 Aug 2013
@author: jmht
Classes for holding data from PDB files
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class
CrystalInfo(line=None)[source]
Bases: object
Methods
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fromLine(line)[source]
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class
OriginInfo(spaceGroupLabel=None)[source]
Bases: object
Methods
| isFloating |
|
| nonRedundantAlternateOrigins |
|
| redundantAlternateOrigins |
|
| spaceGroup |
|
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isFloating(spaceGroupLabel=None)[source]
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nonRedundantAlternateOrigins(spaceGroupLabel=None)[source]
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redundantAlternateOrigins(spaceGroupLabel=None)[source]
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spaceGroup()[source]
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class
PdbAtom(line=None)[source]
Bases: object
Methods
fromHetatm(hetatm) |
Create Atom from Hetatm |
fromLine(line) |
Initialise from the line from a PDB |
toLine() |
Create a line suitable for printing to a PDB file |
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fromHetatm(hetatm)[source]
Create Atom from Hetatm
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fromLine(line)[source]
Initialise from the line from a PDB
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toLine()[source]
Create a line suitable for printing to a PDB file
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class
PdbHetatm(line=None)[source]
Bases: ample.util.pdb_model.PdbAtom
Identical to PdbAtom but just with a different _atomType
Methods
fromHetatm(hetatm) |
Create Atom from Hetatm |
fromLine(line) |
Initialise from the line from a PDB |
toLine() |
Create a line suitable for printing to a PDB file |
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class
PdbInfo[source]
Bases: object
A class to hold information extracted from a PDB file
Methods
getSequence() |
Return the sequence for the first model/chain |
numAtoms([modelIdx]) |
Return the total number of ATOM atoms in the model |
numCalpha([modelIdx]) |
Return the total number of CA ATOM atoms in the model |
numChains([modelIdx]) |
Return the total number of chains in the model |
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getSequence()[source]
Return the sequence for the first model/chain
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numAtoms(modelIdx=0)[source]
Return the total number of ATOM atoms in the model
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numCalpha(modelIdx=0)[source]
Return the total number of CA ATOM atoms in the model
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numChains(modelIdx=0)[source]
Return the total number of chains in the model
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class
PdbModel[source]
Bases: object
A class to hold information on a single model in a PDB file
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class
PdbModres(line)[source]
Bases: object
Methods
fromLine(line) |
Initialise from the line from a PDB |
toLine() |
Create a line suitable for printing to a PDB file |
-
fromLine(line)[source]
Initialise from the line from a PDB
-
toLine()[source]
Create a line suitable for printing to a PDB file
