psico.creating
2010-2012 Thomas Holder
License: BSD-2-Clause
Functions
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Conformer generation with RDKit |
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Run corina on selection and load as new object |
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Run X3DNA's "fiber" tool. |
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The reverse of split_states |
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Creates a new molecule object from a selection and adds missing atoms, assignes charges and radii using PDB2PQR. |
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Run the SCHRODINGER Protein Preparation Wizard. |
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Deprecated: Use cmd.ramp_update() instead. |
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Creates an object with sidechain representing pseudoatoms for each residue in selection. |
- psico.creating.confgen_rdkit(name: str, selection: str, state: int = -1, numconf: int = 10, ff='none', prune: float = 0.1, *, quiet=1, _self=...)[source]
Conformer generation with RDKit
Based on https://github.com/iwatobipen/rdk_confgen
Arguments
name = str: Name of new object
selection = str: atom selection
state = int: object state of selection {default: -1}
numconf = int: Number of conformations to generate {default: 10}
ff = MMFF94s|MMFF94|UFF|none: force field {default: none}
prune = float: RMSD threshold for pruning {default: 0.1}
- psico.creating.corina(name, selection, exe='corina', state=-1, preserve=0, quiet=1, *, _self=...)[source]
Run corina on selection and load as new object
- psico.creating.fiber(seq, num=4, name='', rna=0, single=0, repeats=0, preserve=0, exe='$X3DNA/bin/fiber', quiet=1, *, _self=...)[source]
Run X3DNA’s “fiber” tool.
For the list of structure identification numbers, see for example: http://xiang-jun.blogspot.com/2009/10/fiber-models-in-3dna.html
Usage
fiber seq [, num [, name [, rna [, single ]]]]
Arguments
seq = str: single letter code sequence or number of repeats for repeat models.
num = int: structure identification number {default: 4}
name = str: name of object to create {default: random unused name}
rna = 0/1: 0=DNA, 1=RNA {default: 0}
single = 0/1: 0=double stranded, 1=single stranded {default: 0}
Examples
# environment (this could go into ~/.pymolrc or ~/.bashrc) os.environ[“X3DNA”] = “/opt/x3dna-v2.3”
# B or A DNA from sequence fiber CTAGCG fiber CTAGCG, 1, ADNA
# double or single stranded RNA from sequence fiber AAAGGU, name=dsRNA, rna=1 fiber AAAGGU, name=ssRNA, rna=1, single=1
# poly-GC Z-DNA repeat model with 10 repeats fiber 10, 15
- psico.creating.join_states(name, selection='all', discrete=-1, zoom=0, quiet=1, *, _self=...)[source]
The reverse of split_states
Arguments
name = string: name of object to create or modify
selection = string: atoms to include in the new object
discrete = -2: match atoms by sequence alignment discrete = -1: Assume identical input objects (matching all atom
identifiers) but also check for missing atoms and only include atoms that are present in all input objects {default}
discrete = 0: Assume identical input objects discrete = 1: Input object may be (totally) different
- psico.creating.pdb2pqr(name, selection='all', ff='AMBER', debump=1, opt=1, assignonly=0, ffout='', ph=None, neutraln=0, neutralc=0, state=-1, preserve=0, exe='pdb2pqr30', quiet=1, *, keep_chain=1, _self=...)[source]
Creates a new molecule object from a selection and adds missing atoms, assignes charges and radii using PDB2PQR.
http://www.poissonboltzmann.org/pdb2pqr/
Usage
- pdb2pqr name [, selection [, ff [, debump [, opt [, assignonly [, ffout [,
ph [, neutraln [, neutralc [, state [, preserve ]]]]]]]]]]]
Arguments
name = string: name of object to create or modify
selection = string: atoms to include in the new object {default: all}
ff = string: forcefield {default: AMBER}
- psico.creating.prepwizard(name, selection='all', options='', state=-1, preserve=0, exe='$SCHRODINGER/utilities/prepwizard', quiet=1, *, _self=...)[source]
Run the SCHRODINGER Protein Preparation Wizard. Builds missing side chains and converts MSE to MET. Other non-default options need to be passed with the “options=” argument.
Usage
prepwizard name [, selection [, options [, state ]]]
Arguments
name = str: name of object to create
selection = str: atoms to send to the wizard {default: all}
options = str: additional command line options for prepwizard
state = int: object state {default: -1 (current)}
- psico.creating.ramp_levels(name, levels, quiet=1, *, _self=...)[source]
Deprecated: Use cmd.ramp_update() instead.
Changes the slot levels of a ramp.
See Also
ramp_new, isolevel
- psico.creating.sidechaincenters(object='scc', selection='all', method='bahar1996', name='PS1', *, _self=...)[source]
Creates an object with sidechain representing pseudoatoms for each residue in selection.
Two methods are available: (1) Sidechain interaction centers as defined by Bahar and Jernigan 1996
Sidechain centroids, the pseudoatom is the centroid of all atoms except hydrogens and backbone atoms (N, C and O).
Note
With method “bahar1996”, if a residue has all relevant sidechain center atoms missing (for example a MET without SD), it will be missing in the created pseudoatom object.
With method “centroid”, if you want to exclude C-alpha atoms from sidechains, modify the selection like in this example:
sidechaincenters newobject, all and (not name CA or resn GLY), method=2
Usage
sidechaincenters object [, selection [, method ]]
Arguments
object = string: name of object to create
selection = string: atoms to consider {default: (all)}
method = string: bahar1996 or centroid {default: bahar1996}
name = string: atom name of pseudoatoms {default: PS1}
See Also
pseudoatom