Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
User Manual

Structural_motifs

Authors: F. Cazals and R. Tetley

Introduction

Structural motifs. Structural alignment methods for polypeptide chains aim at identifying conserved structural motifs between structures.

Global structural alignment methods often fail to exploit local properties, i.e. locally conserved distances. Phrased differently, for similarity measures such as $\lrmsd$ (see Molecular_distances and Molecular_distances_flexible), large values between two structures possibly obliterates regions of smaller size and with a much better structural conservation.

This package provides a method identifying locally conserved structural motifs shared by two polypeptide chains whose structure is known. In a nutshell, a structural motif consists in two sets of a.a., one on each structure, such that the $\lrmsd$ of the motif is significantly smaller than that associated with a global alignment between the two structures:

$ \lRMSDRatio \leq \tau $


Applications involving structural motifs. Motifs may be used to compute combined $\rmsd$ as done in Molecular_distances_flexible , and/or investigate the homology between proteins using profile hidden Markov models as done in FunChaT .

Prerequisites

In the sequel, we recall the main concepts and the four steps used to identify motifs, referring the reader to [30] for the details.

For the sake of conciseness, we use structure and polypeptide chain interchangeably; likewise, structural motif and motif are used interchangeably.

Step 1: Computing the seed alignment and its scores

Consider two polypeptide chains $A$ and $B$ of length $n_A$ and $n_B$. Also consider a seed alignment between them; let $N \leq \min(n_A, n_B)$ be its length, namely the number of a.a. matched.

The alignment consists of pairs of a.a. mapped with one another, and can be computed using various methods. In this package, we use the following two aligners:

  • $\text{\apurva}$ is a structural aligner based on contact maps, favoring long and flexible alignments [9]. See the package Apurva .
  • $\text{\kpax}$ is a structural aligner based on a geometric representation of the backbone, favoring a geometric measure known as the G-score [122]. See the package Iterative_alignment .

Denoting $\distaij$ the distance between the $\Calpha$ carbons of indices i and j on chain $A$, and likewise on chain $B$, an assessment of the matching is provided by the distance difference matrix (DDM), a $N \times N$ symmetric matrix whose entries, also called scores, are given by:

$ \scoreij = \fabs{\distaij - \distbij}, i = 1, \dots, N, j=1, \dots, N $


Note that these distances qualify the conservation of distances between $\Calpha$ between the two structures.

Step 2: Building the filtration and its space filling diagram

In mathematics, a filtration is a (finite) sequence of nested spaces [62] . Our method uses a filtration which may be the conserved distances (CD) filtration or the space filling diagram (SFD) filtration.

Conserved distances (CD) filtration. For each molecule, consider a graph whose vertices represent a.a., and edges are associated with all pairs of a.a (complete graph). Each edge is weighted by the score $\scoreij$. Assume that edges have been sorted in ascending order.

To each edge weight–say $w$, corresponds a graph containing only those edges whose weight is $\leq w$. In processing edges by increasing value, these graphs are nested. We call this sequence of graphs the conserved distances (CD) filtration.

Space filling diagram (SFD) filtration. Molecular models defined by union of balls are called space filling diagrams (SFD). Geometric and topological properties of such diagrams are encoded in the so-called $\alpha$-complex (see Alpha_complex_of_molecular_model , as well as Space_filling_model_surface_volume ).

Upon sorting the scores $\scoreij$ by ascending value, define the absolute $\Calpha$ rank of a given a.a. as the smallest index of a score involving that $\Calpha$. Finally, let the $\Calpha$ rank of a given a.a. be the index of its absolute $\Calpha$ rank (see details in [30] ).

For each molecule, to each index–say $i$, corresponds a SFD containing only those a.a. whose index is $\leq i$. In processing indices by increasing value, these SFD are nested. We call this sequence of SFD the SFD filtration.

Persistence diagram. For either filtration, let us focus on connected components, which appear and disappear when inserting edges (CD filtration) or a.a. (SFD filtration). A union-find data structure can be used to maintain these c.c. [46], and track in particular the birth date and the death date of each component.

The collection of all these points ${(\text{birth date}, \text{death date})}$ defines a 2D diagram called the persistence diagram [62] . Note that all points lie above the diagonal $y=x$; moreover, the distance of a point to the diagonal is the lifetime of the c.c. associated to that point.

To compute persistence diagrams, we use the Morse_theory_based_analyzer package.

Step 3: Computing structural motifs

As previously stated, for each structure we compute a persistence diagram, respectively denoted $\persDiagA$ and $\persDiagB$.

Two points located in the same region of their respective PD have comparable birth and death dates. We identify such pairs of points. Denote $a \in \persDiagA$ and $b\in \persDiagB$ two such points. We say that $a$ and $b$ are comparable if the Euclidean distance between the two points (computed by using their respective birth and death dates as coordinates) is below a given threshold $\tau_{PD}$.

When two points are comparable, we identify motifs as follows:

  • First, we compute the connected components associated to the sublevel set of the graph (CD filtration), or SFD (SFD filtration).

  • Second, we perform a structural alignment between all pairs of connected components. We distinguish the cases of homologous proteins and that of conformations:

    • Homologous proteins: the aligner used is that used to compute the seed alignment.
    • Conformations: the sequences being identical, the alignment is trivial. To enlarge the size of motifs, we perform a one step clustering of c.c. using the D-family matching algorithm from D_family_matching. In a nutshell, this method finds a many-to-many correspondence between connected components.

  • Third, we selected the alignments satisfying the $\text{\lrmsd}$ ratio of Eq. eq-lrmsdratio .
Practically, we impose constraints on motifs:
  • comparable points in PD: we impose a distance between points of at most $\tau_{PD} (= 20)$
  • size constraint: a motif should contain at least $s_0 (= 20)$ a.a.
  • $\text{\lrmsd}$ ratio: should be at most $\tau (= 0.7)$


Note that for a given structure, a structural motif is not necessarily connected, neither on the structure, nor on the sequence. This stems from the fact that a motif is defined upon performing a structural alignment on two connected components (from sublevel sets of the CD or SFD filtration). In practice, though, motifs are generally connected on the structure, but not on the sequence. See details in the companion paper [30] .


Step 4: Filtering structural motifs

As detailed in [30] , motifs are filtered in two ways:

  • Motif inclusion. A Hasse diagram is used to detect the nestedness of motifs. The Hasse diagram is defined from the partial order induced by the inclusion between sets of a.a. defining structural motifs.
  • Statistical significance. The statistical significance of motifs is obtained via a two-sample-test p-value calculation (Wilcoxon Mann-Whitney), comparing the motifs obtained against random motifs.

Bonus steps: combined RMSD and seeding iterative alignment

As detailed in [30], motifs can be used to compute the edge-weighted $\text{\rmsdcomb}$ (see Molecular_distances_flexible). Additionally, structural motifs can be used to seed an iterative aligner (see the package Iterative_alignment).

Using structural motif finders

Programs

As explained above, the detection of motifs hinges on two ingredients:

  • An initial seed alignment. To handle two different proteins, we use two seed aligners ( $\text{\apurva}$, $\text{\kpax}$). To handle two conformations of the same protein, the trivial identity alignment is used.
  • A filtration. We use two options: the filtration of conserved distances (CD), and the filtration based on space filling diagrams (SFD).

Combining these yields four methods:

  • Aligners requiring an alignment: $\text{\alignerkpaxcd}$, $\text{\alignerkpaxsfd}$, $\text{\alignerapurvacd}$, $\text{\alignerapurvasfd}$ .
  • Aligners with the identity alignment: $\text{\aligneridcd}$, $\text{\aligneridsfd}$.

These four methods are implemented within the following executables: each giving access to the CD and SFD filtrations:

  • $\text{\sblsmotifsapurva}$: structural motifs for proteins, using the $\text{\apurva}$ aligner
  • $\text{\sblsmotifskpax}$: structural motifs for proteins, using the $\text{\kpax}$ aligner
  • $\text{\sblsmotifsconf}$: structural motifs for conformations
By default, all the executables search for structural motifs which are then used to compute the $\text{\rmsdcomb}$ and seed an iterative alignment. The results of these two bonus calculations are always output.


Main specifications

We illustrate how to run the program on one executable, namely sbl-structural-motifs-conformations.exe . The other executables are used in the same manner.

Input. In a nutshell:

  • A pair of proteins, in PDB file format.
  • Possibly a specification of domains for these proteins. This enables searching for motifs in nested regions of the protein. The specification file is a simpler version of the one described in MolecularSystemLabelsTraits : one line per domain containing in sequential order the domain name, the number of residue ranges and the residue sequence number ranges (examples below).

Main options. The main options are:

–pdb-file string: PDB file passed twice ie once for each structure
–chains string: Chain(s) to load passed twice ie once for each structure
–allow-incomplete-chains: Allow loading incomplete structures
–motif-size: The motif size threshold $s_0$
–lrmsd-threshold: The $\text{\lrmsd}$ threshold $\tau$
–load-domains: The domains spec file. Domains are defined as residue sequence number ranges.


If no domains are specified using the –load-domains option, the executable searches for a file with the same prefix as the PDB file but with the .dom extension in the PDB file directory.


Main output. The output provides statistics for all the structural motifs that were found along with a PyMol script that can be used to visualize them:

  • Run log, txt file, suffix log.txt: main log file
  • Alignment file, txt file, suffix __alignment.txt : the initial alignment, for re-running purposes.
  • Motifs, xml file, suffix __persistent_motifs.xml : XML Archive of all the found structural motifs. Nb: the python module Structural_motifs defines classes to parse this file and retrive the information on motifs. See also the script sbl-structural-motifs-analyzer.py, described below.
  • Motifs diagram, GraphViz file, suffix hasse_diagram_one.dot: Hasse diagram of motifs. Each motif is identified with a unique index.
  • Pymol scripts, python file, suffix .py: one script for each structural motif, as discussed below.

Rigid blocks: Two main blocks found by the executable

Images generated using the outputted pymol scripts.

Using the PyMol scripts

To further investigate each structural motif, the executable outputs PyMol scripts. In order to run the script corresponding to, say motif 8, in the previous run, the user should follow these steps:

  • Open PyMol
  • Load each of the structures. In PyMol:
load data/1URZ.pdb
load data/1SVB.pdb
  • Run the script corresponding to said motif. In PyMol:
    run results/conformations-sf/sbl-structural-motifs-conformations__block_8_script.py
    

A screenshot of the PyMol window after running one of the outputted pymol scripts
PyMol scripts for viewing the final iterative alignment are also outputted (sbl-structural-motifs-conformations__iterative_alignment.py).


Using the VMD script

To be developed.

Using python scripts

The package provides two python scripts:

sbl-structural-motifs-computer.py.

Consider a list of four-tuples, namely {(pdbid1, chain1, pdbid2, chain2)}, listed in a text file. The following call uses $\text{\sblsmotifskpax}$ and/or $\text{\sblsmotifsapurva}$ (see option -a) to perform a motif calculation for each four-tuple:

sbl-structural-motifs-computer.py -i demos/fatcat-2003-pdb-files -f demos/fatcat-2003-pdb-files/list-pairs-of-structures--fatcat-2003.txt -a three

sbl-structural-motifs-analyzer.py.

The scatter plots for motifs indicate motif ids, and the associated Hasse diagram (one for each molecule) also indicates how motifs are nested. The following script processes a directory generated by the previous script, and proposes two analysis:

  • If one motif index is given: the list of resids in this motif is printed.
  • If two motif indices are given, the symmetric difference between the corresponding lists of resids is printed. This analysis eases the interpretation of Hasse diagrams.

The following call lists the resids found in the motif whose id is 5:

dulfer-fcazals> ./sbl-structural-motifs-analyzer.py -d results/apurva/1CID.pdb-A--2RHE.pdb-A -m 5
Motif file is results/apurva/1CID.pdb-A--2RHE.pdb-A/sbl-structural-motifs-chains-apurva__persistent_motifs.xml
Log file is results/apurva/1CID.pdb-A--2RHE.pdb-A/sbl-structural-motifs-chains-apurva__log.txt
Initial alignment size: 103.0
Initial alignment lRMSD: 3.944686
XML: 1 / 1 files were loaded

('Motif indices:', [1, 2, 3, 4, 5, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18])
('Motif lrmsds:', [1.715135302837146, 3.027206911843852, 2.794978851169716, 3.03162145728718, 1.4790716539949267, 1.7351701619296112, 1.695979267778361, 2.9667660204140045, 3.0269885774433014, 2.689248812159066, 3.031806753459111, 2.739264842927472, 1.6532866267424344, 2.871028387233174, 3.031927685048948, 3.0744944632903914])
('Motif sizes:', [34, 77, 47, 63, 12, 17, 19, 40, 68, 52, 75, 50, 32, 44, 66, 61])

List of the 12 resids in molecule 1 for motif index 5:
[9, 10, 13, 16, 26, 31, 73, 83, 95, 96, 97, 98]
12 resids in molecule 2 for motif index 5:
[14, 15, 18, 21, 32, 37, 73, 83, 97, 98, 99, 100]
dulfer-fcazals>

The following call compares the lists of resids associated with two motif ids – which is especially useful to investigate the relationship between motifs of interest identified on the Hasse diagram of motifs:

dulfer-fcazals> ./sbl-structural-motifs-analyzer.py -d results/apurva/1CID.pdb-A--2RHE.pdb-A -m 5 -n 7
Motif file is results/apurva/1CID.pdb-A--2RHE.pdb-A/sbl-structural-motifs-chains-apurva__persistent_motifs.xml
Log file is results/apurva/1CID.pdb-A--2RHE.pdb-A/sbl-structural-motifs-chains-apurva__log.txt
Initial alignment size: 103.0
Initial alignment lRMSD: 3.944686
XML: 1 / 1 files were loaded

('Motif indices:', [1, 2, 3, 4, 5, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18])
('Motif lrmsds:', [1.715135302837146, 3.027206911843852, 2.794978851169716, 3.03162145728718, 1.4790716539949267, 1.7351701619296112, 1.695979267778361, 2.9667660204140045, 3.0269885774433014, 2.689248812159066, 3.031806753459111, 2.739264842927472, 1.6532866267424344, 2.871028387233174, 3.031927685048948, 3.0744944632903914])
('Motif sizes:', [34, 77, 47, 63, 12, 17, 19, 40, 68, 52, 75, 50, 32, 44, 66, 61])

List of the 12 resids in molecule 1 for motif index 5:
[9, 10, 13, 16, 26, 31, 73, 83, 95, 96, 97, 98]
12 resids in molecule 2 for motif index 5:
[14, 15, 18, 21, 32, 37, 73, 83, 97, 98, 99, 100]

List of the 17 resids in molecule 1 for motif index 7:
[9, 10, 13, 16, 25, 26, 28, 31, 60, 67, 73, 83, 84, 95, 96, 97, 98]
17 resids in molecule 2 for motif index 7:
[14, 15, 18, 21, 31, 32, 34, 37, 59, 66, 73, 83, 84, 97, 98, 99, 100]

[molecule1] Symmetric differences, sizes 0 12 5

Symmetric differences, items:
('A minus B:', [])
('A intersection B:', [9, 10, 13, 16, 26, 31, 73, 83, 95, 96, 97, 98])
('B minus A', [25, 28, 60, 67, 84])

[molecule2] Symmetric differences, sizes 0 12 5

Symmetric differences, items:
('A minus B:', [])
('A intersection B:', [14, 15, 18, 21, 32, 37, 73, 83, 97, 98, 99, 100])
('B minus A', [31, 34, 59, 66, 84])

Implementation and functionalities

The implementation is straight-forward: each step described in the previous section is computed in a module, which are all linked together in the following workflow.

Main classes

The package Structural_motifs uses two novel data structures, the filtration graphs. These were implemented in the classes:

  • SBL::CSB::T_Filtration_graph_SFD< Structure , AlphaComplex >. Given an input structure, it builds a vertex weighted graph. This graph corresponds to the history of contacts between residues upon inserting them in a given order. The order is associated with a filtration function, in our case the $\Calpha$ ranks. The first template parameter is the representation of a proteic structure. It should contain residues which provide access to their $\Calpha$ ranks as well as to their usual information. The second parameter is an alpha complex. Practically, we use the class defined in Alpha_complex_of_molecular_model.
  • SBL::CSB::T_Filtration_graph_CD< Structure >. Given an input structure, it builds an edge weighted graph. The vertices are the set of residues, and the edges correspond to all pairs of a.a. (complete graph). The edge weights correspond to the order in which a residue pair appears in the ordering of $s_{ij}$ scores. The template parameter is the representation of a proteic structure. .

These two classes allow to switch between the different types of filtration.

Modules

The package Structural_motifs is centered around two main new modules:

The package also uses the following modules:

SBL::Modules::T_Iterative_alignment_module< ModuleTraits > was created as a new module in this package because it goes beyond the use cases of the module in Iterative_alignment.


T_Structural_motifs_workflow:

Jupyter demo

See the following jupyter notebook:

  • Jupyter notebook file
  • Structural_motifs

    Structural_motifs

    Recall that the SBL provides three executables to mine motifs shared by two structures:

    • sbl-structural-motifs-conformations.exe
    • sbl-structural-motifs-chains-apurva.exe and sbl-structural-motifs-chains-kpax.exe , which use two different methods for seed alignments, namely Apurva and Kpax.

    The main difference is that for conformations of the same molecule, we do not need to compute any alignment.

    In the sequel, we focus on conformations -- using the remaining two executables is similar.

    Useful general functions

    In [1]:
    from SBL import Structural_motifs
    from SBL import SBL_pytools
    from SBL_pytools import SBL_pytools as sblpyt
    help(sblpyt)
    
    Help on class SBL_pytools in module SBL_pytools:
    
    class SBL_pytools(builtins.object)
     |  Static methods defined here:
     |  
     |  convert_eps_to_png(ifname, osize)
     |  
     |  convert_pdf_to_png(ifname, osize)
     |  
     |  find_and_convert(suffix, odir, osize)
     |      # find file with suffix, convert, and return image file
     |  
     |  find_and_show_images(suffix, odir, osize)
     |  
     |  find_file_in_output_directory(suffix, odir)
     |  
     |  show_eps_file(eps_file, osize)
     |  
     |  show_image(img)
     |  
     |  show_log_file(odir)
     |  
     |  show_pdf_file(pdf_file)
     |  
     |  show_row_n_images(images, size)
     |  
     |  ----------------------------------------------------------------------
     |  Data descriptors defined here:
     |  
     |  __dict__
     |      dictionary for instance variables (if defined)
     |  
     |  __weakref__
     |      list of weak references to the object (if defined)
    
    

    We also define some specific functions

    In [2]:
     
    import re  #regular expressions
    import sys #misc system
    import os
    import pdb
    import shutil # python 3 only
    
    import matplotlib.pyplot as plt
    import matplotlib.image as mplimg
    
    from SBL import Structural_motifs
    from SBL import SBL_pytools
    from SBL_pytools import SBL_pytools as sblpyt
    
    from SBL import PALSE
    from PALSE import *
    
    import numpy as np
    import matplotlib.pyplot as plt
    
    exe = "sbl-structural-motifs-conformations.exe"
    aligner_tag = "identity" # since in this demo we compare conformations
    
    # Process two structures
    def process_two_structures(dfname1, dfname2, use_sfd=False):
        pdbid1 = re.sub(".pdb", "", os.path.split(dfname1)[1])
        pdbid2 = re.sub(".pdb", "", os.path.split(dfname2)[1])
        pdbid12 = "%s-%s" % (pdbid1, pdbid2)
    
        odir = "results/conformations-cd"
     
    
        if os.path.exists(odir):
            os.system( ("rm %s" % odir) )
        os.system( ("mkdir -p %s" % odir) )
    
        # check executable exists and is visible
        exe = shutil.which("sbl-structural-motifs-conformations.exe")
        print( ("Using executable %s\n" % exe) )
    
        # run command
        cmd = "sbl-structural-motifs-conformations.exe --dist-threshold 10 --lrmsd-threshold 0.5 --size-diff 5 --allow-incomplete-chains\
            --pdb-file %s --chains A --pdb-file %s --chains A --directory-output %s  --module-uid --log" % (ifname1, ifname2, odir)
        if use_cd:
            cmd += " --use-cd-filtration"
    
        print(cmd)
        os.system(cmd)   
    
        # list output files
        cmd = "ls %s" % odir
        ofnames = os.popen(cmd).readlines()
    
        # find the lof file and display log file
        sblpyt.show_log_file(odir)
        return (pdbid12, odir)
    
    
    
    # Display the result
    def perform_analysis(pdbid12, odir):
        # parse the result of the calculation and retrieve some global stats
        ofn_scatter_plot = "%s/scatter_plot.pdf" % odir
        motifs_collector = Structural_motifs.Motifs_calculation_collector(ofn_scatter_plot)
        motifs_collector.process_alignment(odir)
        
        init_size = motifs_collector.get_motifs()[0].get_initial_alignment_size()
        init_lrmsd = motifs_collector.get_motifs()[0].get_initial_alignment_lrmsd()
        
        stats_lrmsd = motifs_collector.get_motifs()[0].get_motif_lrmsds()
        stats_size = motifs_collector.get_motifs()[0].get_motif_sizes()
        
        # perform the scatter plot
        title = pdbid12
        Structural_motifs.Structural_motifs_plotter.plot(motifs_collector, title,  ofn_scatter_plot)
            
        #(lrmsd_stats, size_stats) = motifs_size_vs_lrmsd_sacetter_plot(odir, seed_size, seed_lrmsd)
        Structural_motifs.Structural_motifs_plotter.score_plot(odir)
        Structural_motifs.Structural_motifs_plotter.CA_distance_plot(odir)
        Structural_motifs.Structural_motifs_plotter.sequence_shift_plot(odir)
    
        hasse1 = Structural_motifs.Structural_motifs_plotter.generate_hasse_pdf(pdbid12, odir, aligner_tag, "hasse_diagram_one.dot", "one", odir)
        hasse2 = Structural_motifs.Structural_motifs_plotter.generate_hasse_pdf(pdbid12, odir, aligner_tag, "hasse_diagram_two.dot", "two", odir)
           
            
        print("Disconnectivity forest and persistence diagram for both structures:")
        images = []
        images.append( sblpyt.find_and_convert("__2__disconnectivity_forest.eps", odir, 100) )
        images.append( sblpyt.find_and_convert("__3__disconnectivity_forest.eps", odir, 100) )
    
        images.append( sblpyt.find_and_convert("-hasse-one.pdf", odir, 100) )
        images.append( sblpyt.find_and_convert("-hasse-two.pdf", odir, 100) )
            
        sblpyt.show_row_n_images(images, 100)
          
        # Intitial alignment: size and lrmsd
        return (stats_size, stats_lrmsd)
     
    
    
     
         
    

    Case study I: extracting motifs using Conserved Distances (CD) filtration

    Run the calculation

    In [3]:
    ifname1 = "data/1SVB.pdb"
    ifname2 = "data/1URZ.pdb"
    
    (pdbid12, odir_sfd) = process_two_structures(ifname1, ifname2)  
    
    Using executable /user/fcazals/home/projects/proj-soft/sbl-install/bin/sbl-structural-motifs-conformations.exe
    
    /user/fcazals/home/projects/proj-soft/sbl-install/bin/sbl-structural-motifs-conformations.exe --dist-threshold 10 --lrmsd-threshold 0.5 --size-diff 5 --allow-incomplete-chains       --pdb-file data/1SVB.pdb --chains A --pdb-file data/1URZ.pdb --chains A --directory-output results/conformations-cd  --module-uid --log
    Log file is: results/conformations-cd/sbl-structural-motifs-conformations__log.txt
    Verbose mode automatically set to 2
    Running:  /user/fcazals/home/projects/proj-soft/sbl-install/bin/sbl-structural-motifs-conformations.exe --dist-threshold 10 --lrmsd-threshold 0.5 --size-diff 5 --allow-incomplete-chains --pdb-file data/1SVB.pdb --chains A --pdb-file data/1URZ.pdb --chains A --directory-output results/conformations-cd --module-uid --log
    
    Annotations Loader
    Statistics:
    
    Molecule File Loader
    Statistics:
    Covalent Structure File Loader statistics:
    Number of loaded proteins: 2
    Details for each protein :
    -- structure 1:
    -- -- Number of loaded chains: 1
    -- -- Number of loaded atoms: 3028
    -- -- Number of particles: 6095
    -- -- Number of embedded particles: 3028
    -- -- Number of bonds: 6152
    -- -- Number of embedded bonds: 3085
    -- -- Number of built disulfide bonds: 6 / 6
    -- structure 2:
    -- -- Number of loaded chains: 1
    -- -- Number of loaded atoms: 2921
    -- -- Number of particles: 5900
    -- -- Number of embedded particles: 2921
    -- -- Number of bonds: 5954
    -- -- Number of embedded bonds: 2975
    -- -- Number of built disulfide bonds: 6 / 6
    
    Alignment
    Statistics:
    Alignment length: 376
    Alignment score : 376
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.328041
    Alignment dRMSD : 10.043994
    
    Report...
    
    CD
    Statistics:
    Number of residues: 376
    Number of contacts: 375
    
    Morse Theory Based Analysis
    Statistics:
    Number of critical vertices of index 0: 376
    Number of regular critical vertices of index 1: 375
    Number of degenerated critical vertices (num, #faces):
    Number of connected components, i.e Betti_0: 1
    Size of connected components (num, size): (1, 376)
    Number of cycles (after simplification), i.e Betti_1: 0
    Number of clusters for stable manifold partition: 376
    Size of stable manifolds, i.e Watershed (num, size): (376, 1)
    
    Report...
    
    CD
    Statistics:
    Number of residues: 376
    Number of contacts: 375
    
    Morse Theory Based Analysis
    Statistics:
    Number of critical vertices of index 0: 376
    Number of regular critical vertices of index 1: 375
    Number of degenerated critical vertices (num, #faces):
    Number of connected components, i.e Betti_0: 1
    Size of connected components (num, size): (1, 376)
    Number of cycles (after simplification), i.e Betti_1: 0
    Number of clusters for stable manifold partition: 376
    Size of stable manifolds, i.e Watershed (num, size): (376, 1)
    
    Report...
    
    D-Family matching
    Statistics:
    Statistics for instance p_one_24-26p_two_24-26
    Statistics for instance p_one_372-374p_two_372-374
    Statistics for instance p_one_77-80p_two_77-80
    Statistics for instance p_one_125-130p_two_125-130
    Statistics for instance p_one_187-192p_two_187-192
    Statistics for instance p_one_48-56p_two_48-56
    Statistics for instance p_one_364-375p_two_364-375
    Statistics for instance p_one_128-143p_two_128-143
    Statistics for instance p_one_41-61p_two_41-61
    Statistics for instance p_one_334-358p_two_334-358
    Statistics for instance p_one_285-314p_two_285-314
    Statistics for instance p_one_230-264p_two_230-264
    Statistics for instance p_one_65-101p_two_65-101
    Statistics for instance p_one_67-103p_two_67-103
    Statistics for instance p_one_98-134p_two_98-134
    Statistics for instance p_one_55-93p_two_55-93
    Statistics for instance p_one_249-287p_two_249-287
    Statistics for instance p_one_207-246p_two_207-246
    Statistics for instance p_one_38-78p_two_38-78
    Statistics for instance p_one_295-342p_two_295-342
    Statistics for instance p_one_34-84p_two_34-84
    Statistics for instance p_one_140-198p_two_140-198
    Statistics for instance p_one_94-153p_two_94-153
    Statistics for instance p_one_126-201p_two_126-201
    Statistics for instance p_one_74-154p_two_74-154
    Statistics for instance p_one_87-168p_two_87-168
    Statistics for instance p_one_167-253p_two_167-253
    Statistics for instance p_one_90-178p_two_90-178
    Statistics for instance p_one_184-272p_two_184-272
    Statistics for instance p_one_76-165p_two_76-165
    Statistics for instance p_one_100-189p_two_100-189
    Statistics for instance p_one_40-131p_two_40-131
    Statistics for instance p_one_200-291p_two_200-291
    Statistics for instance p_one_258-352p_two_258-352
    Statistics for instance p_one_60-157p_two_60-157
    Statistics for instance p_one_146-243p_two_146-243
    Statistics for instance p_one_14-114p_two_14-114
    Statistics for instance p_one_88-190p_two_88-190
    Statistics for instance p_one_9-116p_two_9-116
    Statistics for instance p_one_127-235p_two_127-235
    Statistics for instance p_one_29-142p_two_29-142
    Statistics for instance p_one_152-266p_two_152-266
    Statistics for instance p_one_30-148p_two_30-148
    Statistics for instance p_one_112-234p_two_112-234
    Statistics for instance p_one_39-164p_two_39-164
    Statistics for instance p_one_123-250p_two_123-250
    Statistics for instance p_one_57-186p_two_57-186
    Statistics for instance p_one_70-204p_two_70-204
    Statistics for instance p_one_231-367p_two_231-367
    Statistics for instance p_one_13-151p_two_13-151
    Statistics for instance p_one_6-150p_two_6-150
    Statistics for instance p_one_133-280p_two_133-280
    Statistics for instance p_one_27-176p_two_27-176
    Statistics for instance p_one_8-158p_two_8-158
    Statistics for instance p_one_108-261p_two_108-261
    Statistics for instance p_one_5-160p_two_5-160
    Statistics for instance p_one_18-182p_two_18-182
    Statistics for instance p_one_72-237p_two_72-237
    Statistics for instance p_one_46-215p_two_46-215
    Statistics for instance p_one_4-174p_two_4-174
    Statistics for instance p_one_10-185p_two_10-185
    Statistics for instance p_one_20-195p_two_20-195
    Statistics for instance p_one_96-274p_two_96-274
    Statistics for instance p_one_63-247p_two_63-247
    Statistics for instance p_one_162-346p_two_162-346
    Statistics for instance p_one_66-254p_two_66-254
    Statistics for instance p_one_11-202p_two_11-202
    Statistics for instance p_one_15-214p_two_15-214
    Statistics for instance p_one_107-307p_two_107-307
    Statistics for instance p_one_3-206p_two_3-206
    Statistics for instance p_one_28-233p_two_28-233
    Statistics for instance p_one_50-256p_two_50-256
    Statistics for instance p_one_19-227p_two_19-227
    Statistics for instance p_one_69-279p_two_69-279
    Statistics for instance p_one_156-366p_two_156-366
    Statistics for instance p_one_2-216p_two_2-216
    Statistics for instance p_one_53-269p_two_53-269
    Statistics for instance p_one_85-304p_two_85-304
    Statistics for instance p_one_12-238p_two_12-238
    Statistics for instance p_one_113-357p_two_113-357
    Statistics for instance p_one_31-325p_two_31-325
    Statistics for instance p_one_7-321p_two_7-321
    
    Alignment
    Statistics:
    Statistics for instance p_one_372-374p_two_372-374
    Alignment length: 373
    Alignment score : 373
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.338010
    Alignment dRMSD : 10.088583
    Statistics for instance p_one_125-130p_two_125-130
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_187-192p_two_187-192
    Alignment length: 85
    Alignment score : 85
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 7.959368
    Alignment dRMSD : 8.193299
    Statistics for instance p_one_187-192p_two_187-192
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_187-192p_two_187-192
    Alignment length: 20
    Alignment score : 20
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.476043
    Alignment dRMSD : 0.270498
    Statistics for instance p_one_187-192p_two_187-192
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_364-375p_two_364-375
    Alignment length: 376
    Alignment score : 376
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.328041
    Alignment dRMSD : 10.043994
    Statistics for instance p_one_128-143p_two_128-143
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_128-143p_two_128-143
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.368913
    Alignment dRMSD : 0.242153
    Statistics for instance p_one_334-358p_two_334-358
    Alignment length: 356
    Alignment score : 356
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.128974
    Alignment dRMSD : 10.220018
    Statistics for instance p_one_285-314p_two_285-314
    Alignment length: 304
    Alignment score : 304
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.751958
    Alignment dRMSD : 10.522309
    Statistics for instance p_one_230-264p_two_230-264
    Alignment length: 240
    Alignment score : 240
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.554753
    Alignment dRMSD : 10.896364
    Statistics for instance p_one_65-101p_two_65-101
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.466847
    Alignment dRMSD : 0.272960
    Statistics for instance p_one_67-103p_two_67-103
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.466847
    Alignment dRMSD : 0.272960
    Statistics for instance p_one_98-134p_two_98-134
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_98-134p_two_98-134
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.368913
    Alignment dRMSD : 0.242153
    Statistics for instance p_one_55-93p_two_55-93
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.488883
    Alignment dRMSD : 0.278777
    Statistics for instance p_one_249-287p_two_249-287
    Alignment length: 275
    Alignment score : 275
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.645218
    Alignment dRMSD : 10.441101
    Statistics for instance p_one_207-246p_two_207-246
    Alignment length: 211
    Alignment score : 211
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.414698
    Alignment dRMSD : 10.654769
    Statistics for instance p_one_295-342p_two_295-342
    Alignment length: 334
    Alignment score : 334
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.962673
    Alignment dRMSD : 10.284247
    Statistics for instance p_one_34-84p_two_34-84
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.488883
    Alignment dRMSD : 0.278777
    Statistics for instance p_one_140-198p_two_140-198
    Alignment length: 90
    Alignment score : 90
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 7.800347
    Alignment dRMSD : 8.011979
    Statistics for instance p_one_140-198p_two_140-198
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_140-198p_two_140-198
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_140-198p_two_140-198
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_94-153p_two_94-153
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_94-153p_two_94-153
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_94-153p_two_94-153
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_94-153p_two_94-153
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_126-201p_two_126-201
    Alignment length: 93
    Alignment score : 93
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 7.842994
    Alignment dRMSD : 7.817640
    Statistics for instance p_one_126-201p_two_126-201
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_126-201p_two_126-201
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_126-201p_two_126-201
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_74-154p_two_74-154
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_74-154p_two_74-154
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_74-154p_two_74-154
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_74-154p_two_74-154
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_87-168p_two_87-168
    Alignment length: 15
    Alignment score : 15
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.876126
    Alignment dRMSD : 7.581832
    Statistics for instance p_one_87-168p_two_87-168
    Alignment length: 57
    Alignment score : 57
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.640537
    Alignment dRMSD : 0.380013
    Statistics for instance p_one_87-168p_two_87-168
    Alignment length: 18
    Alignment score : 18
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.492363
    Alignment dRMSD : 0.268861
    Statistics for instance p_one_167-253p_two_167-253
    Alignment length: 222
    Alignment score : 222
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.664477
    Alignment dRMSD : 11.008854
    Statistics for instance p_one_90-178p_two_90-178
    Alignment length: 73
    Alignment score : 73
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.361811
    Alignment dRMSD : 8.862504
    Statistics for instance p_one_90-178p_two_90-178
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_90-178p_two_90-178
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_90-178p_two_90-178
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.219260
    Alignment dRMSD : 0.194134
    Statistics for instance p_one_184-272p_two_184-272
    Alignment length: 251
    Alignment score : 251
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.667603
    Alignment dRMSD : 10.986037
    Statistics for instance p_one_76-165p_two_76-165
    Alignment length: 15
    Alignment score : 15
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.876126
    Alignment dRMSD : 7.581832
    Statistics for instance p_one_76-165p_two_76-165
    Alignment length: 52
    Alignment score : 52
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.614759
    Alignment dRMSD : 0.355367
    Statistics for instance p_one_76-165p_two_76-165
    Alignment length: 18
    Alignment score : 18
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.492363
    Alignment dRMSD : 0.268861
    Statistics for instance p_one_100-189p_two_100-189
    Alignment length: 82
    Alignment score : 82
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.043825
    Alignment dRMSD : 8.337394
    Statistics for instance p_one_100-189p_two_100-189
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_100-189p_two_100-189
    Alignment length: 20
    Alignment score : 20
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.476043
    Alignment dRMSD : 0.270498
    Statistics for instance p_one_100-189p_two_100-189
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_40-131p_two_40-131
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_40-131p_two_40-131
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.368913
    Alignment dRMSD : 0.242153
    Statistics for instance p_one_200-291p_two_200-291
    Alignment length: 280
    Alignment score : 280
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.761623
    Alignment dRMSD : 10.552120
    Statistics for instance p_one_258-352p_two_258-352
    Alignment length: 348
    Alignment score : 348
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.071308
    Alignment dRMSD : 10.340123
    Statistics for instance p_one_60-157p_two_60-157
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_60-157p_two_60-157
    Alignment length: 25
    Alignment score : 25
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.606002
    Alignment dRMSD : 0.365490
    Statistics for instance p_one_60-157p_two_60-157
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_60-157p_two_60-157
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_146-243p_two_146-243
    Alignment length: 207
    Alignment score : 207
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.472538
    Alignment dRMSD : 10.775163
    Statistics for instance p_one_14-114p_two_14-114
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.539083
    Alignment dRMSD : 0.323785
    Statistics for instance p_one_88-190p_two_88-190
    Alignment length: 82
    Alignment score : 82
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.043825
    Alignment dRMSD : 8.337394
    Statistics for instance p_one_88-190p_two_88-190
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_88-190p_two_88-190
    Alignment length: 20
    Alignment score : 20
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.476043
    Alignment dRMSD : 0.270498
    Statistics for instance p_one_88-190p_two_88-190
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_9-116p_two_9-116
    Alignment length: 20
    Alignment score : 20
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.608268
    Alignment dRMSD : 0.357283
    Statistics for instance p_one_127-235p_two_127-235
    Alignment length: 191
    Alignment score : 191
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.388414
    Alignment dRMSD : 10.705111
    Statistics for instance p_one_29-142p_two_29-142
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_29-142p_two_29-142
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.368913
    Alignment dRMSD : 0.242153
    Statistics for instance p_one_152-266p_two_152-266
    Alignment length: 243
    Alignment score : 243
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.514392
    Alignment dRMSD : 10.869570
    Statistics for instance p_one_30-148p_two_30-148
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_30-148p_two_30-148
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_30-148p_two_30-148
    Alignment length: 11
    Alignment score : 11
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.365890
    Alignment dRMSD : 0.254076
    Statistics for instance p_one_112-234p_two_112-234
    Alignment length: 186
    Alignment score : 186
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.288486
    Alignment dRMSD : 10.899319
    Statistics for instance p_one_39-164p_two_39-164
    Alignment length: 15
    Alignment score : 15
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.876126
    Alignment dRMSD : 7.581832
    Statistics for instance p_one_39-164p_two_39-164
    Alignment length: 52
    Alignment score : 52
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.614759
    Alignment dRMSD : 0.355367
    Statistics for instance p_one_39-164p_two_39-164
    Alignment length: 18
    Alignment score : 18
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.492363
    Alignment dRMSD : 0.268861
    Statistics for instance p_one_123-250p_two_123-250
    Alignment length: 218
    Alignment score : 218
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.672054
    Alignment dRMSD : 11.003859
    Statistics for instance p_one_57-186p_two_57-186
    Alignment length: 80
    Alignment score : 80
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.132508
    Alignment dRMSD : 8.461592
    Statistics for instance p_one_57-186p_two_57-186
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_57-186p_two_57-186
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_57-186p_two_57-186
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_70-204p_two_70-204
    Alignment length: 12
    Alignment score : 12
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.665542
    Alignment dRMSD : 0.701024
    Statistics for instance p_one_70-204p_two_70-204
    Alignment length: 111
    Alignment score : 111
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.031333
    Alignment dRMSD : 10.995694
    Statistics for instance p_one_70-204p_two_70-204
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_70-204p_two_70-204
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_231-367p_two_231-367
    Alignment length: 367
    Alignment score : 367
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.304443
    Alignment dRMSD : 10.151296
    Statistics for instance p_one_13-151p_two_13-151
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_13-151p_two_13-151
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_13-151p_two_13-151
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_13-151p_two_13-151
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_6-150p_two_6-150
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_6-150p_two_6-150
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_6-150p_two_6-150
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_133-280p_two_133-280
    Alignment length: 268
    Alignment score : 268
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.640918
    Alignment dRMSD : 10.623370
    Statistics for instance p_one_27-176p_two_27-176
    Alignment length: 72
    Alignment score : 72
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.394075
    Alignment dRMSD : 8.921465
    Statistics for instance p_one_27-176p_two_27-176
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_27-176p_two_27-176
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_27-176p_two_27-176
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.219260
    Alignment dRMSD : 0.194134
    Statistics for instance p_one_8-158p_two_8-158
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_8-158p_two_8-158
    Alignment length: 33
    Alignment score : 33
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.633087
    Alignment dRMSD : 0.380311
    Statistics for instance p_one_8-158p_two_8-158
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_8-158p_two_8-158
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_108-261p_two_108-261
    Alignment length: 235
    Alignment score : 235
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.622062
    Alignment dRMSD : 10.977646
    Statistics for instance p_one_5-160p_two_5-160
    Alignment length: 15
    Alignment score : 15
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.876126
    Alignment dRMSD : 7.581832
    Statistics for instance p_one_5-160p_two_5-160
    Alignment length: 47
    Alignment score : 47
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.595513
    Alignment dRMSD : 0.351797
    Statistics for instance p_one_5-160p_two_5-160
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_18-182p_two_18-182
    Alignment length: 76
    Alignment score : 76
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.285883
    Alignment dRMSD : 8.652274
    Statistics for instance p_one_18-182p_two_18-182
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_18-182p_two_18-182
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_18-182p_two_18-182
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_72-237p_two_72-237
    Alignment length: 194
    Alignment score : 194
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.450883
    Alignment dRMSD : 10.783920
    Statistics for instance p_one_46-215p_two_46-215
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.927583
    Alignment dRMSD : 0.915337
    Statistics for instance p_one_46-215p_two_46-215
    Alignment length: 140
    Alignment score : 140
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.617480
    Alignment dRMSD : 11.817818
    Statistics for instance p_one_46-215p_two_46-215
    Alignment length: 18
    Alignment score : 18
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.966887
    Alignment dRMSD : 1.524618
    Statistics for instance p_one_4-174p_two_4-174
    Alignment length: 72
    Alignment score : 72
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.394075
    Alignment dRMSD : 8.921465
    Statistics for instance p_one_4-174p_two_4-174
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_4-174p_two_4-174
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_10-185p_two_10-185
    Alignment length: 78
    Alignment score : 78
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.213211
    Alignment dRMSD : 8.525551
    Statistics for instance p_one_10-185p_two_10-185
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_10-185p_two_10-185
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_10-185p_two_10-185
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_20-195p_two_20-195
    Alignment length: 87
    Alignment score : 87
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 7.882290
    Alignment dRMSD : 8.108457
    Statistics for instance p_one_20-195p_two_20-195
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_20-195p_two_20-195
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_20-195p_two_20-195
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_96-274p_two_96-274
    Alignment length: 254
    Alignment score : 254
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.616346
    Alignment dRMSD : 10.913340
    Statistics for instance p_one_63-247p_two_63-247
    Alignment length: 215
    Alignment score : 215
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.593305
    Alignment dRMSD : 10.901834
    Statistics for instance p_one_162-346p_two_162-346
    Alignment length: 340
    Alignment score : 340
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.986258
    Alignment dRMSD : 10.219654
    Statistics for instance p_one_66-254p_two_66-254
    Alignment length: 225
    Alignment score : 225
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.653889
    Alignment dRMSD : 10.969844
    Statistics for instance p_one_11-202p_two_11-202
    Alignment length: 110
    Alignment score : 110
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.067405
    Alignment dRMSD : 11.034521
    Statistics for instance p_one_11-202p_two_11-202
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_11-202p_two_11-202
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_15-214p_two_15-214
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.927583
    Alignment dRMSD : 0.915337
    Statistics for instance p_one_15-214p_two_15-214
    Alignment length: 140
    Alignment score : 140
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.617480
    Alignment dRMSD : 11.817818
    Statistics for instance p_one_15-214p_two_15-214
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 3.229689
    Alignment dRMSD : 1.496380
    Statistics for instance p_one_107-307p_two_107-307
    Alignment length: 296
    Alignment score : 296
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.740814
    Alignment dRMSD : 10.521624
    Statistics for instance p_one_3-206p_two_3-206
    Alignment length: 12
    Alignment score : 12
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.665542
    Alignment dRMSD : 0.701024
    Statistics for instance p_one_3-206p_two_3-206
    Alignment length: 135
    Alignment score : 135
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.662223
    Alignment dRMSD : 12.032708
    Statistics for instance p_one_3-206p_two_3-206
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_28-233p_two_28-233
    Alignment length: 186
    Alignment score : 186
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.288486
    Alignment dRMSD : 10.899319
    Statistics for instance p_one_50-256p_two_50-256
    Alignment length: 228
    Alignment score : 228
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.683091
    Alignment dRMSD : 11.048739
    Statistics for instance p_one_19-227p_two_19-227
    Alignment length: 176
    Alignment score : 176
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.379079
    Alignment dRMSD : 10.970236
    Statistics for instance p_one_69-279p_two_69-279
    Alignment length: 266
    Alignment score : 266
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.591281
    Alignment dRMSD : 10.644686
    Statistics for instance p_one_156-366p_two_156-366
    Alignment length: 364
    Alignment score : 364
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.134408
    Alignment dRMSD : 10.123569
    Statistics for instance p_one_2-216p_two_2-216
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.927583
    Alignment dRMSD : 0.915337
    Statistics for instance p_one_2-216p_two_2-216
    Alignment length: 158
    Alignment score : 158
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.558342
    Alignment dRMSD : 11.114469
    Statistics for instance p_one_53-269p_two_53-269
    Alignment length: 247
    Alignment score : 247
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.626868
    Alignment dRMSD : 10.892966
    Statistics for instance p_one_85-304p_two_85-304
    Alignment length: 292
    Alignment score : 292
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.773968
    Alignment dRMSD : 10.569173
    Statistics for instance p_one_12-238p_two_12-238
    Alignment length: 202
    Alignment score : 202
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.356680
    Alignment dRMSD : 10.696009
    Statistics for instance p_one_113-357p_two_113-357
    Alignment length: 354
    Alignment score : 354
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.134047
    Alignment dRMSD : 10.265468
    Statistics for instance p_one_31-325p_two_31-325
    Alignment length: 317
    Alignment score : 317
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.903794
    Alignment dRMSD : 10.502168
    Statistics for instance p_one_7-321p_two_7-321
    Alignment length: 312
    Alignment score : 312
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.714215
    Alignment dRMSD : 10.396964
    
    Report...
    
    Motif distance computer
    Statistics:
    Number of structural motifs: 76
    Number of motif graph components: 5
    Flexible lRMSD: 1.249805
    
    Report...
    
    Iterative alignment
    Statistics:
    Statistics for instance
    Alignment length: 169
    Alignment score : 155.146300
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.839264
    Alignment dRMSD : 0.617799
    Statistics for instance
    Alignment length: 170
    Alignment score : 155.375907
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.852443
    Alignment dRMSD : 0.619454
    Statistics for instance
    Alignment length: 92
    Alignment score : 88.692824
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.544712
    Alignment dRMSD : 0.392899
    Statistics for instance
    Alignment length: 92
    Alignment score : 88.692824
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.544712
    Alignment dRMSD : 0.392899
    Statistics for instance
    Alignment length: 169
    Alignment score : 155.146300
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.839264
    Alignment dRMSD : 0.617799
    
    Report...
    
    End Run
    
    General Statistics:
    
    Times elapsed for computations (in seconds):
    -- Alignment: 0.012111
    -- Alignment: 0.094890
    -- Motif distance computer: 0.002120
    -- Iterative alignment: 0.087149
    -- CD: 0.000748
    -- CD: 0.000520
    -- SFD: 0.000000
    -- SFD: 0.000000
    -- Morse Theory Based Analysis: 0.000000
    -- Morse Theory Based Analysis: 0.000000
    -- Morse Theory Based Analysis: 0.039173
    -- Morse Theory Based Analysis: 0.035181
    -- D-Family matching: 0.115513
    Total: 0.387407
    
    

    Extract statistics from the log file

    The log file produces a number of statistics, the size, score and lRMSD of the seed alignment for example.

    Various statistics and plots

    • Socre plot. Recall that the C-alpha ranks are obtained from a structural distance score, namely the distance difference between two C-alpha carbons. If CA_i and CA_j are aligned to CA_i' and CA_j' respectively, the distance difference is s_ij = |d_ij - d_i'j'| where d_ij = |CA_i - CA_j|. We can plot the s_ij scores against their respective C-alpha ranks.

    • Calpha distance plot. For a given C-alpha rank we can recover the corresponding C-alpha carbons CA_i and CA_j. We can then plot |CA_i - CA_j| (or |CA_i' - CA_j'| for the second structure) against the C-alpha rank. This gives us an indication on how the atoms are selected on the structure. Notice the distinctive sawtooth pattern indicating that atoms can be far apart and we do not necessarily process atoms adjacent to each other on the back-bone.

    • Sequence shift plot. For the same CA carbons (CA_i and CA_j), we assume their residue sequence numbers are i and j. We can then plot |i - j| (|i' - j'| for the second structure) against the C-alpha ranks. This gives us an indication on their proximity in the sequence. Once again we notice a distinctive sawtooth pattern.

    In [4]:
    (stats_size_cd, stats_lrmsd_cd) = perform_analysis(pdbid12, odir_sfd)
    
    Motif file is results/conformations-cd/sbl-structural-motifs-conformations__persistent_motifs.xml
    Log file is results/conformations-cd/sbl-structural-motifs-conformations__log.txt
    Initial alignment size: 376.0
    Initial alignment lRMSD: 11.328041
    XML: 1 / 1 files were loaded
    
    
    Score plot:
    
    CA distance plots:
    
    Sequence shift plots:
    
    Disconnectivity forest and persistence diagram for both structures:
    Figs displayed
    

    Case study II: extracting motifs using the space filling diagram (SFD) filtration

    Sticking to our two original structures (conformations of the Tick-Borne Enciphalitis virus envelope protein), we study the incidence of the filtration on the results. To this end, we re-run the previsous calculations passing with the --use-sfd-filtration option.

    In [5]:
    ifname1 = "data/1SVB.pdb"
    ifname2 = "data/1URZ.pdb"
    (pdbid12, odir_cd) = process_two_structures(ifname1, ifname2, True)
    
    Using executable /user/fcazals/home/projects/proj-soft/sbl-install/bin/sbl-structural-motifs-conformations.exe
    
    /user/fcazals/home/projects/proj-soft/sbl-install/bin/sbl-structural-motifs-conformations.exe --dist-threshold 10 --lrmsd-threshold 0.5 --size-diff 5 --allow-incomplete-chains       --pdb-file data/1SVB.pdb --chains A --pdb-file data/1URZ.pdb --chains A --directory-output results/conformations-cd  --module-uid --log
    Log file is: results/conformations-cd/sbl-structural-motifs-conformations__log.txt
    Verbose mode automatically set to 2
    Running:  /user/fcazals/home/projects/proj-soft/sbl-install/bin/sbl-structural-motifs-conformations.exe --dist-threshold 10 --lrmsd-threshold 0.5 --size-diff 5 --allow-incomplete-chains --pdb-file data/1SVB.pdb --chains A --pdb-file data/1URZ.pdb --chains A --directory-output results/conformations-cd --module-uid --log
    
    Annotations Loader
    Statistics:
    
    Molecule File Loader
    Statistics:
    Covalent Structure File Loader statistics:
    Number of loaded proteins: 2
    Details for each protein :
    -- structure 1:
    -- -- Number of loaded chains: 1
    -- -- Number of loaded atoms: 3028
    -- -- Number of particles: 6095
    -- -- Number of embedded particles: 3028
    -- -- Number of bonds: 6152
    -- -- Number of embedded bonds: 3085
    -- -- Number of built disulfide bonds: 6 / 6
    -- structure 2:
    -- -- Number of loaded chains: 1
    -- -- Number of loaded atoms: 2921
    -- -- Number of particles: 5900
    -- -- Number of embedded particles: 2921
    -- -- Number of bonds: 5954
    -- -- Number of embedded bonds: 2975
    -- -- Number of built disulfide bonds: 6 / 6
    
    Alignment
    Statistics:
    Alignment length: 376
    Alignment score : 376
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.328041
    Alignment dRMSD : 10.043994
    
    Report...
    
    CD
    Statistics:
    Number of residues: 376
    Number of contacts: 375
    
    Morse Theory Based Analysis
    Statistics:
    Number of critical vertices of index 0: 376
    Number of regular critical vertices of index 1: 375
    Number of degenerated critical vertices (num, #faces):
    Number of connected components, i.e Betti_0: 1
    Size of connected components (num, size): (1, 376)
    Number of cycles (after simplification), i.e Betti_1: 0
    Number of clusters for stable manifold partition: 376
    Size of stable manifolds, i.e Watershed (num, size): (376, 1)
    
    Report...
    
    CD
    Statistics:
    Number of residues: 376
    Number of contacts: 375
    
    Morse Theory Based Analysis
    Statistics:
    Number of critical vertices of index 0: 376
    Number of regular critical vertices of index 1: 375
    Number of degenerated critical vertices (num, #faces):
    Number of connected components, i.e Betti_0: 1
    Size of connected components (num, size): (1, 376)
    Number of cycles (after simplification), i.e Betti_1: 0
    Number of clusters for stable manifold partition: 376
    Size of stable manifolds, i.e Watershed (num, size): (376, 1)
    
    Report...
    
    D-Family matching
    Statistics:
    Statistics for instance p_one_24-26p_two_24-26
    Statistics for instance p_one_372-374p_two_372-374
    Statistics for instance p_one_77-80p_two_77-80
    Statistics for instance p_one_125-130p_two_125-130
    Statistics for instance p_one_187-192p_two_187-192
    Statistics for instance p_one_48-56p_two_48-56
    Statistics for instance p_one_364-375p_two_364-375
    Statistics for instance p_one_128-143p_two_128-143
    Statistics for instance p_one_41-61p_two_41-61
    Statistics for instance p_one_334-358p_two_334-358
    Statistics for instance p_one_285-314p_two_285-314
    Statistics for instance p_one_230-264p_two_230-264
    Statistics for instance p_one_65-101p_two_65-101
    Statistics for instance p_one_67-103p_two_67-103
    Statistics for instance p_one_98-134p_two_98-134
    Statistics for instance p_one_55-93p_two_55-93
    Statistics for instance p_one_249-287p_two_249-287
    Statistics for instance p_one_207-246p_two_207-246
    Statistics for instance p_one_38-78p_two_38-78
    Statistics for instance p_one_295-342p_two_295-342
    Statistics for instance p_one_34-84p_two_34-84
    Statistics for instance p_one_140-198p_two_140-198
    Statistics for instance p_one_94-153p_two_94-153
    Statistics for instance p_one_126-201p_two_126-201
    Statistics for instance p_one_74-154p_two_74-154
    Statistics for instance p_one_87-168p_two_87-168
    Statistics for instance p_one_167-253p_two_167-253
    Statistics for instance p_one_90-178p_two_90-178
    Statistics for instance p_one_184-272p_two_184-272
    Statistics for instance p_one_76-165p_two_76-165
    Statistics for instance p_one_100-189p_two_100-189
    Statistics for instance p_one_40-131p_two_40-131
    Statistics for instance p_one_200-291p_two_200-291
    Statistics for instance p_one_258-352p_two_258-352
    Statistics for instance p_one_60-157p_two_60-157
    Statistics for instance p_one_146-243p_two_146-243
    Statistics for instance p_one_14-114p_two_14-114
    Statistics for instance p_one_88-190p_two_88-190
    Statistics for instance p_one_9-116p_two_9-116
    Statistics for instance p_one_127-235p_two_127-235
    Statistics for instance p_one_29-142p_two_29-142
    Statistics for instance p_one_152-266p_two_152-266
    Statistics for instance p_one_30-148p_two_30-148
    Statistics for instance p_one_112-234p_two_112-234
    Statistics for instance p_one_39-164p_two_39-164
    Statistics for instance p_one_123-250p_two_123-250
    Statistics for instance p_one_57-186p_two_57-186
    Statistics for instance p_one_70-204p_two_70-204
    Statistics for instance p_one_231-367p_two_231-367
    Statistics for instance p_one_13-151p_two_13-151
    Statistics for instance p_one_6-150p_two_6-150
    Statistics for instance p_one_133-280p_two_133-280
    Statistics for instance p_one_27-176p_two_27-176
    Statistics for instance p_one_8-158p_two_8-158
    Statistics for instance p_one_108-261p_two_108-261
    Statistics for instance p_one_5-160p_two_5-160
    Statistics for instance p_one_18-182p_two_18-182
    Statistics for instance p_one_72-237p_two_72-237
    Statistics for instance p_one_46-215p_two_46-215
    Statistics for instance p_one_4-174p_two_4-174
    Statistics for instance p_one_10-185p_two_10-185
    Statistics for instance p_one_20-195p_two_20-195
    Statistics for instance p_one_96-274p_two_96-274
    Statistics for instance p_one_63-247p_two_63-247
    Statistics for instance p_one_162-346p_two_162-346
    Statistics for instance p_one_66-254p_two_66-254
    Statistics for instance p_one_11-202p_two_11-202
    Statistics for instance p_one_15-214p_two_15-214
    Statistics for instance p_one_107-307p_two_107-307
    Statistics for instance p_one_3-206p_two_3-206
    Statistics for instance p_one_28-233p_two_28-233
    Statistics for instance p_one_50-256p_two_50-256
    Statistics for instance p_one_19-227p_two_19-227
    Statistics for instance p_one_69-279p_two_69-279
    Statistics for instance p_one_156-366p_two_156-366
    Statistics for instance p_one_2-216p_two_2-216
    Statistics for instance p_one_53-269p_two_53-269
    Statistics for instance p_one_85-304p_two_85-304
    Statistics for instance p_one_12-238p_two_12-238
    Statistics for instance p_one_113-357p_two_113-357
    Statistics for instance p_one_31-325p_two_31-325
    Statistics for instance p_one_7-321p_two_7-321
    
    Alignment
    Statistics:
    Statistics for instance p_one_372-374p_two_372-374
    Alignment length: 373
    Alignment score : 373
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.338010
    Alignment dRMSD : 10.088583
    Statistics for instance p_one_125-130p_two_125-130
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_187-192p_two_187-192
    Alignment length: 85
    Alignment score : 85
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 7.959368
    Alignment dRMSD : 8.193299
    Statistics for instance p_one_187-192p_two_187-192
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_187-192p_two_187-192
    Alignment length: 20
    Alignment score : 20
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.476043
    Alignment dRMSD : 0.270498
    Statistics for instance p_one_187-192p_two_187-192
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_364-375p_two_364-375
    Alignment length: 376
    Alignment score : 376
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.328041
    Alignment dRMSD : 10.043994
    Statistics for instance p_one_128-143p_two_128-143
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_128-143p_two_128-143
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.368913
    Alignment dRMSD : 0.242153
    Statistics for instance p_one_334-358p_two_334-358
    Alignment length: 356
    Alignment score : 356
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.128974
    Alignment dRMSD : 10.220018
    Statistics for instance p_one_285-314p_two_285-314
    Alignment length: 304
    Alignment score : 304
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.751958
    Alignment dRMSD : 10.522309
    Statistics for instance p_one_230-264p_two_230-264
    Alignment length: 240
    Alignment score : 240
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.554753
    Alignment dRMSD : 10.896364
    Statistics for instance p_one_65-101p_two_65-101
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.466847
    Alignment dRMSD : 0.272960
    Statistics for instance p_one_67-103p_two_67-103
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.466847
    Alignment dRMSD : 0.272960
    Statistics for instance p_one_98-134p_two_98-134
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_98-134p_two_98-134
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.368913
    Alignment dRMSD : 0.242153
    Statistics for instance p_one_55-93p_two_55-93
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.488883
    Alignment dRMSD : 0.278777
    Statistics for instance p_one_249-287p_two_249-287
    Alignment length: 275
    Alignment score : 275
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.645218
    Alignment dRMSD : 10.441101
    Statistics for instance p_one_207-246p_two_207-246
    Alignment length: 211
    Alignment score : 211
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.414698
    Alignment dRMSD : 10.654769
    Statistics for instance p_one_295-342p_two_295-342
    Alignment length: 334
    Alignment score : 334
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.962673
    Alignment dRMSD : 10.284247
    Statistics for instance p_one_34-84p_two_34-84
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.488883
    Alignment dRMSD : 0.278777
    Statistics for instance p_one_140-198p_two_140-198
    Alignment length: 90
    Alignment score : 90
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 7.800347
    Alignment dRMSD : 8.011979
    Statistics for instance p_one_140-198p_two_140-198
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_140-198p_two_140-198
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_140-198p_two_140-198
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_94-153p_two_94-153
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_94-153p_two_94-153
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_94-153p_two_94-153
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_94-153p_two_94-153
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_126-201p_two_126-201
    Alignment length: 93
    Alignment score : 93
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 7.842994
    Alignment dRMSD : 7.817640
    Statistics for instance p_one_126-201p_two_126-201
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_126-201p_two_126-201
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_126-201p_two_126-201
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_74-154p_two_74-154
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_74-154p_two_74-154
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_74-154p_two_74-154
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_74-154p_two_74-154
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_87-168p_two_87-168
    Alignment length: 15
    Alignment score : 15
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.876126
    Alignment dRMSD : 7.581832
    Statistics for instance p_one_87-168p_two_87-168
    Alignment length: 57
    Alignment score : 57
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.640537
    Alignment dRMSD : 0.380013
    Statistics for instance p_one_87-168p_two_87-168
    Alignment length: 18
    Alignment score : 18
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.492363
    Alignment dRMSD : 0.268861
    Statistics for instance p_one_167-253p_two_167-253
    Alignment length: 222
    Alignment score : 222
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.664477
    Alignment dRMSD : 11.008854
    Statistics for instance p_one_90-178p_two_90-178
    Alignment length: 73
    Alignment score : 73
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.361811
    Alignment dRMSD : 8.862504
    Statistics for instance p_one_90-178p_two_90-178
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_90-178p_two_90-178
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_90-178p_two_90-178
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.219260
    Alignment dRMSD : 0.194134
    Statistics for instance p_one_184-272p_two_184-272
    Alignment length: 251
    Alignment score : 251
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.667603
    Alignment dRMSD : 10.986037
    Statistics for instance p_one_76-165p_two_76-165
    Alignment length: 15
    Alignment score : 15
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.876126
    Alignment dRMSD : 7.581832
    Statistics for instance p_one_76-165p_two_76-165
    Alignment length: 52
    Alignment score : 52
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.614759
    Alignment dRMSD : 0.355367
    Statistics for instance p_one_76-165p_two_76-165
    Alignment length: 18
    Alignment score : 18
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.492363
    Alignment dRMSD : 0.268861
    Statistics for instance p_one_100-189p_two_100-189
    Alignment length: 82
    Alignment score : 82
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.043825
    Alignment dRMSD : 8.337394
    Statistics for instance p_one_100-189p_two_100-189
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_100-189p_two_100-189
    Alignment length: 20
    Alignment score : 20
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.476043
    Alignment dRMSD : 0.270498
    Statistics for instance p_one_100-189p_two_100-189
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_40-131p_two_40-131
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_40-131p_two_40-131
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.368913
    Alignment dRMSD : 0.242153
    Statistics for instance p_one_200-291p_two_200-291
    Alignment length: 280
    Alignment score : 280
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.761623
    Alignment dRMSD : 10.552120
    Statistics for instance p_one_258-352p_two_258-352
    Alignment length: 348
    Alignment score : 348
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.071308
    Alignment dRMSD : 10.340123
    Statistics for instance p_one_60-157p_two_60-157
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_60-157p_two_60-157
    Alignment length: 25
    Alignment score : 25
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.606002
    Alignment dRMSD : 0.365490
    Statistics for instance p_one_60-157p_two_60-157
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_60-157p_two_60-157
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_146-243p_two_146-243
    Alignment length: 207
    Alignment score : 207
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.472538
    Alignment dRMSD : 10.775163
    Statistics for instance p_one_14-114p_two_14-114
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.539083
    Alignment dRMSD : 0.323785
    Statistics for instance p_one_88-190p_two_88-190
    Alignment length: 82
    Alignment score : 82
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.043825
    Alignment dRMSD : 8.337394
    Statistics for instance p_one_88-190p_two_88-190
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_88-190p_two_88-190
    Alignment length: 20
    Alignment score : 20
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.476043
    Alignment dRMSD : 0.270498
    Statistics for instance p_one_88-190p_two_88-190
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_9-116p_two_9-116
    Alignment length: 20
    Alignment score : 20
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.608268
    Alignment dRMSD : 0.357283
    Statistics for instance p_one_127-235p_two_127-235
    Alignment length: 191
    Alignment score : 191
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.388414
    Alignment dRMSD : 10.705111
    Statistics for instance p_one_29-142p_two_29-142
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_29-142p_two_29-142
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.368913
    Alignment dRMSD : 0.242153
    Statistics for instance p_one_152-266p_two_152-266
    Alignment length: 243
    Alignment score : 243
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.514392
    Alignment dRMSD : 10.869570
    Statistics for instance p_one_30-148p_two_30-148
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_30-148p_two_30-148
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_30-148p_two_30-148
    Alignment length: 11
    Alignment score : 11
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.365890
    Alignment dRMSD : 0.254076
    Statistics for instance p_one_112-234p_two_112-234
    Alignment length: 186
    Alignment score : 186
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.288486
    Alignment dRMSD : 10.899319
    Statistics for instance p_one_39-164p_two_39-164
    Alignment length: 15
    Alignment score : 15
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.876126
    Alignment dRMSD : 7.581832
    Statistics for instance p_one_39-164p_two_39-164
    Alignment length: 52
    Alignment score : 52
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.614759
    Alignment dRMSD : 0.355367
    Statistics for instance p_one_39-164p_two_39-164
    Alignment length: 18
    Alignment score : 18
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.492363
    Alignment dRMSD : 0.268861
    Statistics for instance p_one_123-250p_two_123-250
    Alignment length: 218
    Alignment score : 218
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.672054
    Alignment dRMSD : 11.003859
    Statistics for instance p_one_57-186p_two_57-186
    Alignment length: 80
    Alignment score : 80
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.132508
    Alignment dRMSD : 8.461592
    Statistics for instance p_one_57-186p_two_57-186
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_57-186p_two_57-186
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_57-186p_two_57-186
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_70-204p_two_70-204
    Alignment length: 12
    Alignment score : 12
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.665542
    Alignment dRMSD : 0.701024
    Statistics for instance p_one_70-204p_two_70-204
    Alignment length: 111
    Alignment score : 111
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.031333
    Alignment dRMSD : 10.995694
    Statistics for instance p_one_70-204p_two_70-204
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_70-204p_two_70-204
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_231-367p_two_231-367
    Alignment length: 367
    Alignment score : 367
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.304443
    Alignment dRMSD : 10.151296
    Statistics for instance p_one_13-151p_two_13-151
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_13-151p_two_13-151
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_13-151p_two_13-151
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_13-151p_two_13-151
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_6-150p_two_6-150
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_6-150p_two_6-150
    Alignment length: 21
    Alignment score : 21
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.607665
    Alignment dRMSD : 0.362079
    Statistics for instance p_one_6-150p_two_6-150
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_133-280p_two_133-280
    Alignment length: 268
    Alignment score : 268
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.640918
    Alignment dRMSD : 10.623370
    Statistics for instance p_one_27-176p_two_27-176
    Alignment length: 72
    Alignment score : 72
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.394075
    Alignment dRMSD : 8.921465
    Statistics for instance p_one_27-176p_two_27-176
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_27-176p_two_27-176
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_27-176p_two_27-176
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.219260
    Alignment dRMSD : 0.194134
    Statistics for instance p_one_8-158p_two_8-158
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.378175
    Alignment dRMSD : 7.549258
    Statistics for instance p_one_8-158p_two_8-158
    Alignment length: 33
    Alignment score : 33
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.633087
    Alignment dRMSD : 0.380311
    Statistics for instance p_one_8-158p_two_8-158
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_8-158p_two_8-158
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.404322
    Alignment dRMSD : 0.230685
    Statistics for instance p_one_108-261p_two_108-261
    Alignment length: 235
    Alignment score : 235
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.622062
    Alignment dRMSD : 10.977646
    Statistics for instance p_one_5-160p_two_5-160
    Alignment length: 15
    Alignment score : 15
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.876126
    Alignment dRMSD : 7.581832
    Statistics for instance p_one_5-160p_two_5-160
    Alignment length: 47
    Alignment score : 47
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.595513
    Alignment dRMSD : 0.351797
    Statistics for instance p_one_5-160p_two_5-160
    Alignment length: 16
    Alignment score : 16
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.356497
    Alignment dRMSD : 0.226139
    Statistics for instance p_one_18-182p_two_18-182
    Alignment length: 76
    Alignment score : 76
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.285883
    Alignment dRMSD : 8.652274
    Statistics for instance p_one_18-182p_two_18-182
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_18-182p_two_18-182
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_18-182p_two_18-182
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_72-237p_two_72-237
    Alignment length: 194
    Alignment score : 194
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.450883
    Alignment dRMSD : 10.783920
    Statistics for instance p_one_46-215p_two_46-215
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.927583
    Alignment dRMSD : 0.915337
    Statistics for instance p_one_46-215p_two_46-215
    Alignment length: 140
    Alignment score : 140
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.617480
    Alignment dRMSD : 11.817818
    Statistics for instance p_one_46-215p_two_46-215
    Alignment length: 18
    Alignment score : 18
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.966887
    Alignment dRMSD : 1.524618
    Statistics for instance p_one_4-174p_two_4-174
    Alignment length: 72
    Alignment score : 72
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.394075
    Alignment dRMSD : 8.921465
    Statistics for instance p_one_4-174p_two_4-174
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_4-174p_two_4-174
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_10-185p_two_10-185
    Alignment length: 78
    Alignment score : 78
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 8.213211
    Alignment dRMSD : 8.525551
    Statistics for instance p_one_10-185p_two_10-185
    Alignment length: 10
    Alignment score : 10
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.891476
    Alignment dRMSD : 1.721263
    Statistics for instance p_one_10-185p_two_10-185
    Alignment length: 19
    Alignment score : 19
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.484162
    Alignment dRMSD : 0.265091
    Statistics for instance p_one_10-185p_two_10-185
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_20-195p_two_20-195
    Alignment length: 87
    Alignment score : 87
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 7.882290
    Alignment dRMSD : 8.108457
    Statistics for instance p_one_20-195p_two_20-195
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_20-195p_two_20-195
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_20-195p_two_20-195
    Alignment length: 17
    Alignment score : 17
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.342722
    Alignment dRMSD : 0.251546
    Statistics for instance p_one_96-274p_two_96-274
    Alignment length: 254
    Alignment score : 254
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.616346
    Alignment dRMSD : 10.913340
    Statistics for instance p_one_63-247p_two_63-247
    Alignment length: 215
    Alignment score : 215
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.593305
    Alignment dRMSD : 10.901834
    Statistics for instance p_one_162-346p_two_162-346
    Alignment length: 340
    Alignment score : 340
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.986258
    Alignment dRMSD : 10.219654
    Statistics for instance p_one_66-254p_two_66-254
    Alignment length: 225
    Alignment score : 225
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.653889
    Alignment dRMSD : 10.969844
    Statistics for instance p_one_11-202p_two_11-202
    Alignment length: 110
    Alignment score : 110
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.067405
    Alignment dRMSD : 11.034521
    Statistics for instance p_one_11-202p_two_11-202
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_11-202p_two_11-202
    Alignment length: 23
    Alignment score : 23
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.462770
    Alignment dRMSD : 0.265504
    Statistics for instance p_one_15-214p_two_15-214
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.927583
    Alignment dRMSD : 0.915337
    Statistics for instance p_one_15-214p_two_15-214
    Alignment length: 140
    Alignment score : 140
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.617480
    Alignment dRMSD : 11.817818
    Statistics for instance p_one_15-214p_two_15-214
    Alignment length: 14
    Alignment score : 14
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 3.229689
    Alignment dRMSD : 1.496380
    Statistics for instance p_one_107-307p_two_107-307
    Alignment length: 296
    Alignment score : 296
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.740814
    Alignment dRMSD : 10.521624
    Statistics for instance p_one_3-206p_two_3-206
    Alignment length: 12
    Alignment score : 12
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.665542
    Alignment dRMSD : 0.701024
    Statistics for instance p_one_3-206p_two_3-206
    Alignment length: 135
    Alignment score : 135
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.662223
    Alignment dRMSD : 12.032708
    Statistics for instance p_one_3-206p_two_3-206
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 2.799039
    Alignment dRMSD : 1.433493
    Statistics for instance p_one_28-233p_two_28-233
    Alignment length: 186
    Alignment score : 186
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.288486
    Alignment dRMSD : 10.899319
    Statistics for instance p_one_50-256p_two_50-256
    Alignment length: 228
    Alignment score : 228
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.683091
    Alignment dRMSD : 11.048739
    Statistics for instance p_one_19-227p_two_19-227
    Alignment length: 176
    Alignment score : 176
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.379079
    Alignment dRMSD : 10.970236
    Statistics for instance p_one_69-279p_two_69-279
    Alignment length: 266
    Alignment score : 266
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.591281
    Alignment dRMSD : 10.644686
    Statistics for instance p_one_156-366p_two_156-366
    Alignment length: 364
    Alignment score : 364
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.134408
    Alignment dRMSD : 10.123569
    Statistics for instance p_one_2-216p_two_2-216
    Alignment length: 13
    Alignment score : 13
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.927583
    Alignment dRMSD : 0.915337
    Statistics for instance p_one_2-216p_two_2-216
    Alignment length: 158
    Alignment score : 158
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.558342
    Alignment dRMSD : 11.114469
    Statistics for instance p_one_53-269p_two_53-269
    Alignment length: 247
    Alignment score : 247
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.626868
    Alignment dRMSD : 10.892966
    Statistics for instance p_one_85-304p_two_85-304
    Alignment length: 292
    Alignment score : 292
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.773968
    Alignment dRMSD : 10.569173
    Statistics for instance p_one_12-238p_two_12-238
    Alignment length: 202
    Alignment score : 202
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.356680
    Alignment dRMSD : 10.696009
    Statistics for instance p_one_113-357p_two_113-357
    Alignment length: 354
    Alignment score : 354
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 11.134047
    Alignment dRMSD : 10.265468
    Statistics for instance p_one_31-325p_two_31-325
    Alignment length: 317
    Alignment score : 317
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.903794
    Alignment dRMSD : 10.502168
    Statistics for instance p_one_7-321p_two_7-321
    Alignment length: 312
    Alignment score : 312
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 10.714215
    Alignment dRMSD : 10.396964
    
    Report...
    
    Motif distance computer
    Statistics:
    Number of structural motifs: 76
    Number of motif graph components: 5
    Flexible lRMSD: 1.249805
    
    Report...
    
    Iterative alignment
    Statistics:
    Statistics for instance
    Alignment length: 169
    Alignment score : 155.146300
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.839264
    Alignment dRMSD : 0.617799
    Statistics for instance
    Alignment length: 170
    Alignment score : 155.375907
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.852443
    Alignment dRMSD : 0.619454
    Statistics for instance
    Alignment length: 92
    Alignment score : 88.692824
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.544712
    Alignment dRMSD : 0.392899
    Statistics for instance
    Alignment length: 92
    Alignment score : 88.692824
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.544712
    Alignment dRMSD : 0.392899
    Statistics for instance
    Alignment length: 169
    Alignment score : 155.146300
    Alignment identity percentage: 1.000000
    Alignment similarity percentage: 1.000000
    Alignment lRMSD : 0.839264
    Alignment dRMSD : 0.617799
    
    Report...
    
    End Run
    
    General Statistics:
    
    Times elapsed for computations (in seconds):
    -- Alignment: 0.015082
    -- Alignment: 0.095764
    -- Motif distance computer: 0.001976
    -- Iterative alignment: 0.078327
    -- CD: 0.000000
    -- CD: 0.000542
    -- SFD: 0.000000
    -- SFD: 0.000000
    -- Morse Theory Based Analysis: 0.000000
    -- Morse Theory Based Analysis: 0.000000
    -- Morse Theory Based Analysis: 0.042970
    -- Morse Theory Based Analysis: 0.027647
    -- D-Family matching: 0.114733
    Total: 0.377042
    
    
    In [6]:
    (stats_size_sfd, stats_lrmsd_sfd) = perform_analysis(pdbid12, odir_cd)
    
    Motif file is results/conformations-cd/sbl-structural-motifs-conformations__persistent_motifs.xml
    Log file is results/conformations-cd/sbl-structural-motifs-conformations__log.txt
    Initial alignment size: 376.0
    Initial alignment lRMSD: 11.328041
    XML: 1 / 1 files were loaded
    
    
    Score plot:
    
    CA distance plots:
    
    Sequence shift plots:
    
    Disconnectivity forest and persistence diagram for both structures:
    Figs displayed
    

    Comparing the SFD and CD filtration with Pareto envelopes

    We can then proceed to compute pareto envelopes and plot the stats for both methods on the same figure.

    In [7]:
     
    def compute_pareto_envelope(lrmsd_stats, size_stats):
        #create motif points
        motif_points = [[lrmsd_stats[i], size_stats[i]] for i in range(0, len(lrmsd_stats))]
    
        #sort motifs by increasing lRMSD
        motif_points = sorted(motif_points, key=lambda motifs: motifs[0])
    
        #find dominated points
        dominated_points = []
        for i in range(0, len(motif_points)):
            for j in range(i+1, len(motif_points)):
                if(motif_points[i][1] >= motif_points[j][1]):
                    dominated_points.append(motif_points[j])
    
        #exclude them from the pareto envelope
        pareto_envelope = list(zip(*[motif for motif in motif_points if (motif not in dominated_points)]))
        motif_points = list(zip(*motif_points))
    
        # just for plotting purposes  (so the limits are will defined)
        min_lrmsd = min(pareto_envelope[0])
        pareto_envelope[0] = [min_lrmsd] + list(pareto_envelope[0])
        pareto_envelope[1] = [0] + list(pareto_envelope[1])
    
        return motif_points, pareto_envelope
    
    def pareto(cd_lrmsd_stats, cd_size_stats, sfd_lrmsd_stats, sfd_size_stats):
        #just to define the bounds of the pareto envelope (for esthetic purposes)
        max_lrmsd = max(max(cd_lrmsd_stats), max(sfd_lrmsd_stats))
        max_size = max(max(cd_size_stats), max(sfd_size_stats))
    
        cd_motif_points, cd_pareto_env = compute_pareto_envelope(cd_lrmsd_stats, cd_size_stats)
        sfd_motif_points, sfd_pareto_env = compute_pareto_envelope(sfd_lrmsd_stats, sfd_size_stats)
    
        cd_pareto_env[0].append(max_lrmsd+5)
        cd_pareto_env[1].append(max(cd_pareto_env[1]))
        sfd_pareto_env[0].append(max_lrmsd+5)
        sfd_pareto_env[1].append(max(sfd_pareto_env[1]))
    
        plt.plot(cd_pareto_env[0], cd_pareto_env[1])
        plt.scatter(cd_motif_points[0], cd_motif_points[1])
    
        plt.plot(sfd_pareto_env[0], sfd_pareto_env[1], color='red')
        plt.scatter(sfd_motif_points[0], sfd_motif_points[1], color='red')
    
        plt.xlabel('lRMSD')
        plt.ylabel('Size')
    
        plt.show()
    
    In [8]:
    pareto(stats_lrmsd_cd, stats_size_cd, stats_lrmsd_sfd, stats_size_sfd)
    

    Visual inspection of motifs

    The executable also outputs a number of PyMol script to view motifs directly. Each motifs has a unique identifier and the scripts follow the same nomenclature: to view motif 31 look for the '_block_31_script.py' file.

    To run the script from PyMol simply load the two structures and type 'run name_of_the_script.py' Below is the image of two motifs yielded from the previous comparisons. As you can see our method allows to recover the blocks which are invariant in the conformational changes.

    In [9]:
    from IPython.display import Image
    
    display(Image(filename ="fig/motif_51.png", width=500, height=500));
    display(Image(filename ="fig/motif_54.png", width=500, height=500));