pyCABS Copyright (C) 2013 Michal Jamroz <jamroz@chem.uw.edu.pl>
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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CABS main class.
Warning
Manually update self.FF variable here (path to the FF directory with CABS files)
Parameters: 


This is only simple wrapper to CatDCD software (http://www.ks.uiuc.edu/Development/MDTools/catdcd/), could be usable since *.dcd binary format is few times lighter than pdb, and many python libraries (ProDy, MDAnalysis) use *.dcd as trajectory input format. Before use, download CatDCD from http://www.ks.uiuc.edu/Development/MDTools/catdcd/ and modify catdcd_path.
Create protein models projected onto CABS lattice, which will be used as replicas.
Parameters: 


Note
If number of replicas is smaller than number of templates  program will create replicas using first replicas templates. If there is less templates than replicas, they are creating sequentially using template models.
Calculate distance constraints using templates 3D models. Constraint will be a square well of size dstd_dev1.0,d+std_dev+1.0, where d is mean distance among templates between Cα atoms (if constraint will be exceeded, there is penalty, scaled by weight.
Weight is defined as a fraction of particular average distance among templates i.e. if pair of residues exist in 2 of 3 templates, weight will be 0.66. Using multiple sequence alignments it should provide stronger constraints on consistently aligned parts.
Parameters: 


Calculate distance constraints using templates 3D models. Constraint will be a square well of size min(d), max(d) where d is mean distance among templates between Cα atoms (if constraint will be exceeded, there is penalty, scaled by weight.
Weight is defined as a fraction of particular average distance among templates i.e. if pair of residues exist in 2 of 3 templates, weight will be 0.66. Using multiple sequence alignments it should provide stronger constraints on consistently aligned parts.
Parameters: 


Read CABS energy values into list
Returns:  list of models energy 

Read trajectory file into 2D list of coordinates
Returns:  2D list of trajectory coordinates ( list[1][6] is sixth coordinate of second trajectory model = z coordinate of second atom of second model) 

Read center of mass of sidegroups from TRASG file
Returns:  2D list of sidechains coordinates 

Start CABS modeling
param Ltemp: Low temperature for Replica Exchange Monte Carlo type Ltemp: float param Htemp: High temperature for Replica Exchange Monte Carlo type Htemp: float param cycles: number of Replica Exchange cycles type cycles: integer param iphot: number of microcycles (inside REMC loop) type iphot: integer param constraints_force: Slope of constraints force potential type constraints_force: float
Parameters:  dynamics – Use of special CABS version for dynamics pathway studies :type dynamics: boolean 

seed for random generator
Save trajectory model into pdb file
Parameters: 


Convert TRASG (sidechains pseudoatoms) into multimodel pdb. Default filename TRASG.pdb
Convert TRAF CABS pseudotrajectory file format into multimodel pdb (default filename TRAF.pdb)
Inherit if you want to process data used with Monitor class.
Parameters:  output (array/list) – output array with calculated results 

Use it in calculate method if you parsing TRAF file, and want to calculate something on structure
Returns:  array of model coordinates 

Simple error messages
Simple message system
Class for monitoring of CABS output data. You can run it and dynamically update output arrays with calculated results.
Parameters:  calculate (Calculate) – what to do with gathered data ? 

if True, it will terminate when script terminates
Run monitor in background
Terminate monitor
Class used for storage of templates atom positions and distance calculation
Parameters:  filename – path to file with template (in PDB format) 

Returns:  Nx3 list of coordinates 
Parameters: 


Returns:  euclidean distance between Cα(i) and Cα(j) 
Compute fraction of contacts in a trajectory, where trajectory is 2D list of coordinates (trajectory[2][5] is the zth coordinate of second atom of third model)
Parameters: 


Returns:  2D array of fraction of contacts (number of contacts divided by trajectory length) for each pair of residue. 
Save heat map using pylab
Parameters:  data (float) – 2D list of values 

Read center of mass of sidegroups from TRASG file
Parameters:  filename – path to the TRASG file 

Returns:  2D list of sidechains coordinates 
Read trajectory file into 2D list of coordinates
Returns:  2D list of trajectory coordinates ( list[1][6] is sixth coordinate of second trajectory model = z coordinate of second atom of second model) 

Helper function for extracting sequence and secondary structure assignments from the DSSP output. Useful for dynamics studies or other where we know protein structure.
You can download DSSP files directly from PDB server: http://www.pdb.org/pdb/files/PDBID.dssp
Function for parsing of Cα coordinates from PDB file.
Parameters:  pdb_filename (string) – path to PDB file 

Returns:  1D list of Cα coordinates (for example: list[4] is yth coordinate of second atom) 
Porter (protein secondary stucture prediction, http://distill.ucd.ie/porter/) output parser. Porter emailed output looks like:
IDVLLGADDGSLAFVPSEFSISPGEKIVFKNNAGFPHNIVFDEDSIPSGVDASKISMSEE
CEEEECCCCCCCCEECCEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCHHHHCCCCC
DLLNAKGETFEVALSNKGEYSFYCSPHQGAGMVGKVTVN
CCECCCCCEEEEECCCCEEEEEECCHHHHCCCEEEEEEC
Parameters:  porter_output_fn (string) – path to the porter output file 

Returns:  tuple (sequence, secondary_structure) 
Psipred (protein secondary structure prediction, http://bioinf.cs.ucl.ac.uk/psipred/) output parser. Psipred output looks like:
> head psipred.ss
1 P C 1.000 0.000 0.000
2 K C 0.665 0.000 0.459
3 A E 0.018 0.000 0.991
4 L E 0.008 0.000 0.997
5 I E 0.002 0.000 0.998
6 V E 0.003 0.000 0.999
7 Y E 0.033 0.000 0.981
Parameters:  psipred_output_fn (string) – path to the psipred output file 

Returns:  tuple (sequence, secondary_structure) 
Calculate coordinate Root Mean Square Deviation between two sets of coordinates.
Parameters: 


Returns:  RMSD value after optimal superimposition of two structures 
Save cluster medoids in PDB file format.
Parameters: 

