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A high-level representation of the contents of a PDB file
The components of a structure can be accessed in several ways ('s' is an instance of this class):
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molecule_constructor Molecule in a PDB file |
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nucleotide_chain_constructor Nucleotide chain in a PDB file |
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peptide_chain_constructor Peptide chain in a PDB file |
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__getitem__(self, item) | |||
__init__(self,
filename,
model=0,
alternate_code='A') Constructor: Structure(|filename|, |model|='0', |alternate_code|='"A"'), |
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__len__(self) | |||
__repr__(self) | |||
_joinChains(self, constructor, chain_list, first, second) | |||
_splitChain(self, constructor, chain_list, number, position) | |||
addMolecule(self, molecule) | |||
deleteHydrogens(self) Remove all hydrogen atoms |
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extractData(self, data) | |||
joinNucleotideChains(self,
first,
second) Join two nucleotide chains into a single one. |
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joinPeptideChains(self,
first,
second) Join two peptide chains into a single one. |
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newChain(self, residue, chain_data) | |||
newResidue(self, residue_data) | |||
parseFile(self, file) | |||
renumberAtoms(self) Renumber all atoms sequentially starting with 1 |
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splitNucleotideChain(self,
number,
position) Split a nucleotide chain into two chains |
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splitPeptideChain(self,
number,
position) Split a peptide chain into two chains |
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writeToFile(self,
file) Write everything to a file |
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Constructor: Structure(|filename|, |model|='0', |alternate_code|='"A"'),
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Remove all hydrogen atoms |
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Join two nucleotide chains into a single one. The new chain occupies the position of the first chain, the second one is removed from the nucleotide chain list.
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Join two peptide chains into a single one. The new chain occupies the position of the first chain, the second one is removed from the peptide chain list.
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Renumber all atoms sequentially starting with 1 |
Split a nucleotide chain into two chains The two chain fragments remain adjacent in the nucleotide chain list, i.e. the numbers of all following chains increase by one.
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Split a peptide chain into two chains The two chain fragments remain adjacent in the peptide chain list, i.e. the numbers of all following chains increase by one.
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Write everything to a file
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