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Returns: | The result of the tmscore superposition |
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TMScore
(model1, model2, tmscore=None)¶Performs a sequence dependent superposition of model1 onto model2, the reference.
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Returns: | The result of the tmscore superposition |
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TMScoreResult
(rmsd_common, tm_score, max_sub, gdt_ts, gdt_ha, rmsd_below_five, transform)¶Holds the result of running TMscore
rmsd_common
¶The RMSD of the common Calpha atoms of both structures
rmsd_below_five
¶The RMSD of all Calpha atoms that can be superposed below five Angstroem
tm_score
¶The TM-score of the structural superposition
gdt_ha
¶The GDT_HA of the model to the reference structure.
gdt_ts
¶The GDT_TS of the model to the reference structure.
Instead of calling the TMalign executable, ost also provides a wrapper around its C++ implementation. The advantage is that no intermediate files need to be generated in order to call the executable.
from ost import bindings
pdb1=io.LoadPDB('1ake.pdb').Select("peptide=true")
pdb2=io.LoadPDB('4ake.pdb').Select("peptide=true")
result = bindings.WrappedTMAlign(pdb1.chains[0], pdb2.chains[0],
fast=True)
print(result.tm_score)
print(result.alignment.ToString(80))
TMAlignResult
(rmsd, tm_score, aligned_length, transform, alignment)¶All parameters of the constructor are available as attributes of the class
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WrappedTMAlign
(chain1, chain2[, fast=False])¶Takes two chain views and runs TMalign with chain2 as reference. The positions and sequences are directly extracted from the chain residues for every residue that fulfills:
- peptide linking
- valid one letter code(no ‘?’)
- valid CA atom
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WrappedTMAlign
(pos1, pos2, seq1, seq2 [fast=False])Similar as described above, but directly feeding in raw data.
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Enter search terms or a module, class or function name.
msms
– Calculating Molecular Surfaces
clustalw
- Perform multiple sequence alignment
bindings
– Interfacing external programs
tmtools
- Structural superposition