psico.modelling
2010-2012 Thomas Holder, MPI for Developmental Biology
License: BSD-2-Clause
Functions
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Mutate those residues to themselves which have missing atoms |
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Add ACE and NME caps to all open peptide termini. |
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Gets the one-letter sequence, including residues without coordinates |
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Mutate a single residue. |
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Mutate all residues in selection. |
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Rebuild the peptide from selection. |
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Remodel the given selection using modeller. |
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Sculpt mobile towards target, based on sequence alignment. |
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Relax the given selection. |
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Update (and optionally fix) coordinates based on sequence alignment. |
- psico.modelling.add_missing_atoms(selection='all', cycles=200, quiet=1, *, _self=...)[source]
Mutate those residues to themselves which have missing atoms
See Also
stub2ala
- psico.modelling.cap_termini(selection: str = 'polymer', *, _self=...)[source]
Add ACE and NME caps to all open peptide termini.
Residue number 1 is considered the actual N-terminus (no cap) Residue with atom OXT is considered the actual C-terminus (no cap).
- psico.modelling.get_seq(selection, chainbreak='/', unknown='A', *, _self=...)[source]
Gets the one-letter sequence, including residues without coordinates
- psico.modelling.mutate(selection, new_resn, inplace=0, sculpt=0, hydrogens='auto', mode=3, quiet=1, *, _self=...)[source]
Mutate a single residue. Does call the mutagenesis wizard non-interactively and tries to select the best rotamer. Can do some sculpting in the end to the best rotamer.
Usage
mutate selection, new_resn [, inplace [, sculpt [, hydrogens]]]
Arguments
selection = string: atom selection of single residue
new_resn = string: new residue name (3-letter or 1-letter)
inplace = 0 or 1: work on copy of input object if 0 {default: 0}
sculpt = 0: no sculpting {default} sculpt = 1: do sculpting on best rotamer sculpt = 2: do sculpting with neighbors
hydrogens = string: keep, auto or none {default: auto}
mode = 0: select rotamer with best clash score mode = 1: take chi angles from original residue mode = 2: first rotamer mode = 3: wizard default {default}
Example
fetch 2x19, async=0 select x, A/CYS`122/ zoom x mutate x, LYS
- psico.modelling.mutate_all(selection, new_resn, inplace=1, sculpt=0, *args, _self=..., **kwargs)[source]
Mutate all residues in selection. By default do mutation in-place (unlike the ‘mutate’ command which by default works on a copy).
FOR SCULPTING ONLY SUPPORTS SELECTIONS WITHIN THE SAME MODEL!
See Also
mutate
- psico.modelling.peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1, *, _self=...)[source]
Rebuild the peptide from selection. All atoms which are present in selection will be kept fixed, while atoms missing in selection are placed by sculpting.
Usage
peptide_rebuild name [, selection [, cycles [, state ]]]
See Also
stub2ala, add_missing_atoms, peptide_rebuild_modeller
- psico.modelling.peptide_rebuild_modeller(name, selection='all', hetatm=0, sequence=None, nmodels=1, hydro=0, quiet=1, *, _self=...)[source]
Remodel the given selection using modeller. This is useful for example to build incomplete sidechains. More complicated modelling tasks are not the intention of this simple interface.
Side effects: Alters “type” property for MSE residues in selection (workaround for bug #3512313).
Usage
peptide_rebuild_modeller name [, selection [, hetatm [, sequence ]]]
Arguments
name = string: new object name
selection = string: atom selection
hetatm = 0/1: read and model HETATMs (ligands) {default: 0}
sequence = string: if provided, use this sequence instead of the template sequence {default: None}
nmodels = int: number of models (states) to generate {default: 1}
- psico.modelling.sculpt_homolog(mobile: str, target: str, state: int = 1, cycles: int = 1000, *, fix: str = 'restrain', quiet: int = 1, _self=...)[source]
Sculpt mobile towards target, based on sequence alignment.
Arguments
cycles: Number of sculpt iterations
fix = restrain | fix | protect | none: Method for fixing updated atoms
- psico.modelling.sculpt_relax(selection, backbone=1, neighbors=0, model=None, cycles=100, state=0, quiet=1, *, _self=...)[source]
Relax the given selection.
SO FAR ONLY SUPPORTS SELECTIONS WITHIN THE SAME MODEL!
Do 100 iterations, 75 of them with all terms but low VDW weights, and 25 with only local geometry terms. With default VDW weights and atom clashes, the structure gets distorted very easily!
Usage
sculpt_relax selection [, backbone [, neighbors [, model [, cycles ]]]]