swamp.wrappers.mapalign module

class MapAlign(workdir, map_a, map_b, format_a='mapalign', format_b='mapalign', gap_o=-1, gap_e=-0.01, sep_cut=0, pdb_a=None, pdb_b=None, logger=None)

Bases: swamp.wrappers.wrapper.Wrapper

Wrapper around map_align

Parameters:

• workdir (str) – working directory
• map_a (str) – file name of the map A to be used in the alignment
• pdb_a (str) – file name of the pdb A to be used for benchmarking of the alignment
• format_a (str) – contact prediction file format of map A (default ‘mapalign’)
• map_b (str) – file name of the map B to be used in the alignment
• pdb_b (str) – file name of the pdb B to be used for benchmarking of the alignment
• format_b (str) – contact prediction file format of map B (default ‘mapalign’)
• gap_o (int) – gap opening penalty (default -1)
• gap_e (float) – gap extension penalty (default -0.01)
• sep_cut (int) – separation cutoff to compute contacts (default 0)
• logger (SwampLogger) – logging interface for the wrapper (default None)

Variables:

• error (bool) – if True an error has occurred along the process
• con_sco (str) – the contact score obtained after alignment of the input maps
• gap_sco (str) – the gap score obtained in the alignment
• total_sco (str) – the gap score obtained after alignment of the input maps
• alignment_length (int) – the length of the alignment obtained between the two input maps
• qscore (float) – qscore as reported by Gesamt
• rmsd (float) – the obtained rmsd as reported by Gesamt
• seq_id (float) – seq identity between the input structures obtained with Gesamt
• n_align (int) – number of aligned residues with Gesamt

Example:

>>> from swamp.wrappers import MapAlign
>>> mapalign = MapAlign('<workdir>', '<map_a>', '<map_b>')
>>> mapalign.run()

benchmark()

Use Gesamt to perform a structural alignment between the input structures for benchmarking purposes

cmd

Command to be executed in the shell

get_scores(logfile=None)

Method to extract the figures of merit out the stdout

Parameters:logfile (str) – Not in use

input_a

File name of the map file A to use in the alignment

input_b

File name of the map file B to use in the alignment

keywords

Keywords passed through the command line to map_align

map_a_id

Basename of map_a file without extension

map_b_id

Basename of map_b file without extension

summary_results

A list with the figures of merit obtained

wrapper_name

The name of this ~swamp.wrapper.wrapper.Wrapper child class (aleigen)