psico.importing

3. 2011 Thomas Holder, MPI for Developmental Biology

License: BSD-2-Clause

Functions

cath_parse_domall([filename, _self])	Download "CathDomall.seqreschopping" to fetch_path (once), parse it and store results in global dict "cath_domains".
fetch(code[, name, type, quiet, _self])	Psico Notes
fetch_cath(code[, name, _self])
fetch_chain(code[, name, _self])
fetch_scop(code[, name, _self])
load_3d(filename[, object, _self])	Load a survex 3d cave survey as "molecule"
load_aln(filename[, object, mobile, target, ...])	Load a pairwise alignment from file and apply it to two loaded structures.
load_coords(coords, object, state[, quiet, ...])	API only.
load_gro(filename[, object, state, quiet, ...])	Load a gro file (molecular structure in Gromos87 format).
load_mtz(filename[, prefix, maptypes, ...])	Deprecated.
load_smi(filename[, oname, discrete, quiet, ...])	Load a SMILES file with an openbabel backend
load_traj_crd(filename[, object, state, ...])	Load Amber CRD trajectory file.
load_traj_dcd(filename[, object, state, ...])	Load DCD trajectory.
loadall(pattern[, group, quiet, _self])	Load all files matching given globbing pattern
loadall_traj(pattern[, object, state, sort, ...])	Load all trajectory files matching given globbing pattern
local_mirror_pdb(code)	API only.
set_raw_alignment(name, aln[, transform, ...])	API only.

psico.importing.cath_parse_domall(filename='', *, _self=...)

Download “CathDomall.seqreschopping” to fetch_path (once), parse it and store results in global dict “cath_domains”.

psico.importing.fetch(code, name='', type='pdb', quiet=1, *, _self=..., **kwargs)

Psico Notes

This is an enhanced version of the “fetch” command that also handles SCOP and CATH identifiers.

You can also fetch from a local filesystem mirror by setting up a function “psico.importing.local_mirror_pdb(code)” that returns a full path to a pdb file.

MagicMock is a subclass of Mock with default implementations of most of the magic methods. You can use MagicMock without having to configure the magic methods yourself.

If you use the spec or spec_set arguments then only magic methods that exist in the spec will be created.

Attributes and the return value of a MagicMock will also be MagicMocks.

psico.importing.fetch_cath(code, name='', *, _self=..., **kwargs)

psico.importing.fetch_chain(code, name='', *, _self=..., **kwargs)

psico.importing.fetch_scop(code, name='', *, _self=..., **kwargs)

psico.importing.load_3d(filename, object='', *, _self=...)

Load a survex 3d cave survey as “molecule”

http://survex.com http://trac.survex.com/browser/trunk/doc/3dformat.htm

psico.importing.load_aln(filename, object=None, mobile=None, target=None, mobile_id=None, target_id=None, format='', transform=0, quiet=1, *, _self=...)

Load a pairwise alignment from file and apply it to two loaded structures.

Usage

load_aln filename [, object [, mobile [, target [, mobile_id [, target_id [, format ]]]]]]

Arguments

filename = string: alignment file

object = string: name of the object {default: filename prefix}

mobile, target = string: atom selections {default: ids from alignment file}

mobile_id, target_id = string: ids from alignment file {default: first two}

format = string: file format, see http://biopython.org/wiki/AlignIO {default: guess from first line in file}

Example

fetch 1bz4 1cpr, async=0 super 1bz4 and guide, 1cpr and guide, object=aln1, window=5 save /tmp/super.aln, aln1 delete aln1 load_aln /tmp/super.aln, aln2, format=clustal

psico.importing.load_coords(coords, object, state, quiet=1, *, _self=...)

API only. Load object coordinates.

TODO: How to handle the object matrix?

See Also

cmd.load_coordset (new in 1.7.3.0)

psico.importing.load_gro(filename, object='', state=-1, quiet=1, zoom=-1, *, _self=...)

Load a gro file (molecular structure in Gromos87 format).

http://manual.gromacs.org/online/gro.html

This command can handle larger ID and resi values than PDB files and thus is better (but slower) than converting a gro file to PDB format using editconf.

Based on a script from Tsjerk Wassenaar, posted on pymol-users mailing list. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09394.html

psico.importing.load_mtz(filename, prefix='', maptypes='FoFc 2FoFc', multistate=0, quiet=1, *, _self=...)

Deprecated. Use PyMOL’s cmd.load_mtz() instead, or psico.load_mtz_cctbx.load_mtz_cctbx()

psico.importing.load_smi(filename, oname='', discrete=-1, quiet=1, multiplex=None, zoom=-1, _self=...)

Load a SMILES file with an openbabel backend

psico.importing.load_traj_crd(filename, object='', state=0, box=0, start=1, stop=-1, quiet=1, *, _self=...)

Load Amber CRD trajectory file.

http://ambermd.org/formats.html#trajectory

For some (unkown to me) reason, this does not work with load_traj (but it should!).

See Also

load_traj

psico.importing.load_traj_dcd(filename, object='', state=0, start=1, stop=-1, quiet=1, *, _self=...)

Load DCD trajectory.

http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html

See Also

save_traj, load_traj_crd, load_traj

psico.importing.loadall(pattern, group='', quiet=1, *, _self=..., **kwargs)

Load all files matching given globbing pattern

psico.importing.loadall_traj(pattern: str, object: str = '', state: int = 1, *, sort: int = 1, quiet: int = 1, _self=..., **kwargs)

Load all trajectory files matching given globbing pattern

Usage

loadall_traj pattern [, object [, state ]]

Arguments

pattern = str: File globbing pattern

object = str: Object name {default: <auto>}

state = int: First state to populate {default: 1}

sort = 0/1: Sort the globbed file names {default: 1}

Example

loadall_traj *.dcd

psico.importing.local_mirror_pdb(code)

API only. Returns the filename for given PDB code. If you have a local PDB mirror, you probably want to overwrite this function.

psico.importing.set_raw_alignment(name, aln, transform=0, guide='', *, _self=...)

API only. Load an alignment object from a list like the one obtained with cmd.get_raw_alignment

See Also

cmd.set_raw_alignment in PyMOL 2.3