Importing
flat.importing
Module that allows to load files in additional formats.
- flat.importing.load_all(pattern, group='', quiet=1, *, _self=cmd, **kwargs)
- DESCRIPTION
Load all files matching given globbing pattern
- USAGE
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- ARGUMENTS
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Warning
Not yet implemented.
- flat.importing.load_aln(filename, object=None, mobile=None, target=None, mobile_id=None, target_id=None, format=None, transform=0, quiet=1, *, _self=cmd)
- DESCRIPTION
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
- filenamestr
Path to alignment file.
- objectstr, optional
Name of the object. Defaults to the filename prefix.
- mobile, targetstr, optional
Atom selections to align. By default uses IDs from alignment file.
- mobile_id, target_idstr, optional
IDs from alignment file. Use first two by default.
- formatstr, default = None
File format. By default try to guess from first line in file. See http://biopython.org/wiki/AlignIO
- 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
- SOURCE
From PSICO (c) 2011 Thomas Holder, MPI for Developmental Biology
- flat.importing.load_csv(filename, selection='all', prop=None, var='b', vis=True, *, _self=cmd)
- DESCRIPTION
Load property from CSV file to selection. Atom selector is automatically generated from CSV header.
- USAGE
load_csv filename [, selection [, prop [, var [, vis ]]]]
- ARGUMENTS
- filenamestr
Input file name.
- selectionstr, default = ‘all’
Atom selection.
- propstr, optional
Property name to import (first by default).
- varstr, default = ‘b’
Variable where property is saved.
- visint, default = True
Visualize output.
- RETURNS
- : Dict
Dictionary of atom identifiers and corresponding values.
- flat.importing.load_ndx(filename, quiet=0, *, _self=cmd)
- DESCRIPTION
Read a GROMACS index (.ndx) file as a selection.
- USAGE
read_ndx filename
- ARGUMENTS
- filenamestr
Input file name.
- flat.importing.load_smi(filename, object=None, discrete=-1, multiplex=None, zoom=-1, quiet=0, *, _self=cmd)
- DESCRIPTION
Load a SMILES file using OpenBabel as backend.
- USAGE
load_smi filename [, name [, discrete [, multiplex [, zoom ]]]]
- ARGUMENTS
- filenamestr
Path or URL to the file to load.
- objectstr, default = None
Name of Pymol object to store the structure in. Defaults to the filename prefix.
- discreteint
For multi-model structures, a value of 0 indicates that models have the same set of atoms (e.g. trajectory files or NMR structures), allowing memory savings, while a value of 1 forces the creation of independent atom sets for each model.
- multiplexinteger, default = None
Load a multi-model file as separate objects instead of states.
- zoomint, default = -1
Use auto_zoom setting.
- SOURCE
From PSICO (c) 2011 Thomas Holder, MPI for Developmental Biology
- flat.importing.load_topol(filename, selection='all', *, _self=cmd)
- DESCRIPTION
Load GROMACS topology (.top) file to selection.
Note
Experimental, currently supports only limited number of properties.
- USAGE
load_topol filename [, selection ]
- ARGUMENTS
- filenamestr
Input file name.
- selectionstr, default = ‘all’
Atom selection.