build.rna_tools.tools.PyMOL4RNA.PyMOL4RNA.align_all2() - Code Metrics - Inspection of "Merge branch 'master' of github.com:mmagnus/rna-to..." - mmagnus/rna-tools - Measure and Improve Code Quality continuously with Scrutinizer

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Push — master ( 94ade9...f9d2c1 )

by Marcin
created 2020-06-30 09:36 UTC
build.rna_tools.tools.PyMOL4RNA.PyMOL4RNA.align_all2() B

↳ Parent: Project
Complexity

Conditions
Size

Total Lines	31
Code Lines	15
Duplication

Lines	0
Ratio	0 %
Importance

Changes
Metric	Value
cc	8
eloc	15
nop	1
dl	0
loc	31
rs	7.3333
c	0
b	0
f	0
#!/usr/bin/env python
"""
Quick reference:

- clarna: show contacts classification of the selected fragment based on ClaRNA
- ss: show secondary structure of the selection based on py3dna.py (3DNA (Lu, Olson 2003))
- ss_all: the same as ss() but for all objects
- pdbsrc: show PDB content (source) of selection.
- seq: show sequence of the selection
- ino: represent ions as sphare and yellow inorganic, such us Mg
- p: shortcut for putting a seq at the bottom. Pretty cool for screenshots with names of objects
- spli: color snRNA of the spliceosome and bases according to identity U(blue), A(orange), G(red), C(forest)
- rp: @todo
- rs: @todo
- rib: @todo
- select br. all within 12 of resi 574
-
If you want more, read for interesting functions https://daslab.stanford.edu/site_data/docs_pymol_rhiju.pdf
"""
# imports
import tempfile
import math
import subprocess
import os
import sys

import getpass
user = getpass.getuser()

try:
    from pymol import cmd
except ImportError:
    print("PyMOL Python lib is missing")
    # sys.exit(0)

import imp
try:
    from rna_tools.rna_tools_lib import RNAStructure
    from rna_tools.tools.PyMOL4RNA import code_for_spl
    imp.reload(code_for_spl)
    from rna_tools.tools.PyMOL4RNA import code_for_color_spl
    imp.reload(code_for_color_spl)
    from rna_tools.tools.PyMOL4RNA import code_for_color_spl_objects
    imp.reload(code_for_color_spl_objects)
    import rna_tools
    RNA_TOOLS_PATH = rna_tools.rna_tools_lib.get_rna_tools_path()
except ImportError:
    print("rna_tools lib is missing")
    RNA_TOOLS_PATH = ''
    
try:
    RNA_TOOLS_PATH
    EXECUTABLE

except NameError:
    EXECUTABLE="/bin/zsh"
    SOURCE=""

try:
    cmd.set('cartoon_gap_cutoff', 0)
except:
    pass

def exe(cmd, verbose=False):
    """Helper function to run cmd. Using in this Python module."""
    if verbose: print('cmd:' + cmd)
    o = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
                         executable=EXECUTABLE)
    out = o.stdout.read().strip().decode()
    err = o.stderr.read().strip().decode()
    return out, err

def color_protein():
    cmd.do("color blue, resn ARG+LYS+HIS")
    cmd.do("color red, resn ASP+GLU")
    cmd.do("color green, resn GLY+ALA+VAL+LEU+ILE+MET+PHE")
    cmd.do("color yellow, resn TYR+TRP")
    cmd.do("color forest, resn SER+THR+CYS+ASN+GLN")
    cmd.do("color pink, resn PRO")

cmd.extend('cp', color_protein)

def save_transformed(object, file):
    """Saves the molecule with coordinates from the current orientation.

     Args:
        object (string): PyMOL name
        file (string): a file name to output file

    Example::

         PyMOL>save_transformed 6bk8_RNA_only_Oriented, 6bk8_RNA_only_Oriented.pdb

    Source: <https://pymolwiki.org/index.php/Modeling_and_Editing_Structures>
    """
    m = cmd.get_view(0)
    ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
    cmd.transform_object(object,ttt,transpose=1)
    cmd.save(file,object)


def color_by_text(txt):
    """Helper function used for color-coding based on residue indexes ranges."""
    for t in txt.strip().split('\n'):
        print(t)
        color, resi = t.replace('color ', '').split(',')
        print((color, resi))
        cmd.color(color.strip(), resi.strip())


def rp():
    """Represent your RNA."""
    cmd.hide("sticks", "all")
    cmd.hide("lines", "all")
    cmd.show("cartoon", "all")
    cmd.set("cartoon_ring_mode", 3)
    cmd.set("cartoon_ring_finder", 2)
    cmd.set("cartoon_ladder_mode", 1)

def show_all_at_once():
    cmd.set('states', 'on')


def rp06():
  txt = """color black, all
  color pink, resi 2-10+163-170
  color grey, resi 12-33
  color green, resi 40-41
  color green, resi 161-162
  color orange, resi 45-61
  color green, resi 64-73
  color blue, resi 74-155
  color cyan, resn B1Z"""
  for t in txt.split('\n'):
    color, resi = t.replace('color ', '').split(',')
    print(color, resi)
    cmd.color(color.strip(), resi.strip())


def grid_on():
    cmd.set('grid_mode', 1)


def grid_off():
    cmd.set('grid_mode', 0)


def rp14():
  """color black; # everything
 color blue, resi 1-5+55-59; # p1
 color green, resi 7-11+16-20; # p2
 color magenta, resi 23+60; # pk
 color yellow, resi 29-34+45-50; # p3
 color grey, resi 24-28+51-54; # e-loop
 color red, resi 6+21+22+24+25+28+52+54; # higly conserved"""
 #color blue, resi 5+55


  txt ="""color black, all
 color red, resi 1-5+55-59
 color blue, resi 1-5+55-59; # p1
 color green, resi 7-11+16-20
 color magenta, resi 23+60
 color yellow, resi 29-34+45-50
 color grey, resi 24-28+51-54
 color red, resi 6+21+22"""
  for t in txt.split('\n'):
    color, resi = t.replace('color ', '').split(',')
    print(color, resi)
    cmd.color(color.strip(), resi.strip())

def rp14s():
  """color with Baker's SHAPE data for rp14!"""
  txt = """
   color yellow, resi 12-15+25-29+35-44
   color red, resi 21-24+53+54+60
  """
  color_by_text(txt)

def rs():
    """    The function creates super-cool cartoon-like RNA and colors each structure as a rainbow.
    Good to view aligned structures in a grid.

    .. image:: ../../rna_tools/utils/PyMOL4RNA/doc/rs.png
    """
    cmd.hide("sticks", "all")
    cmd.hide("lines", "all")
    cmd.show("cartoon", "all")
    cmd.set("cartoon_ring_mode", 3)
    cmd.set("cartoon_ring_finder", 2)
    cmd.set("cartoon_ladder_mode", 2)
    cmd.set("cartoon_ring_transparency", 0.30)
    cmd.spectrum()

    obj_list = cmd.get_names('objects')

    colours = ['rainbow']
    ncolours = len(colours)
    # Loop over objects
    i = 0
    for obj in obj_list:
        print("  ", obj, colours[i])
        cmd.spectrum('count', colours[i], obj)
        i = i+1
        if(i == ncolours):
           i = 0



def align_all():
    """
    This returns a list with 7 items:
 
    RMSD after refinement
    Number of aligned atoms after refinement
    Number of refinement cycles
    RMSD before refinement
    Number of aligned atoms before refinement
    Raw alignment score
    Number of residues aligned 

    old version:

          1_solution_0_rpr 1_santalucia_1_rpr 5.60600471496582 958 4 5.763411521911621 974 416.0 46 -- RMSD 5.76  of  46 residues

"""
    molecules = cmd.get_names_of_type("object:molecule")
    ref = molecules.pop(0)
    report = []
    print('Ref                  Model                RaR  #AA  CoR  RbR  #AbR RS   AR')
    for molecule in molecules:
        values = cmd.align(molecule, ref)
        print(ref[:20].ljust(20), molecule[:20].ljust(20),
              str(round(values[0], 2)).ljust(4),
              str(round(values[1], 2)).ljust(4),
              str(round(values[2], 2)).ljust(4),
              str(round(values[3], 2)).ljust(4),
              str(round(values[4], 2)).ljust(4),
              str(round(values[5])).ljust(4),
              str(round(values[6], 2)).ljust(4),
              )
              #' '.join([str(v) for v in values]), '-- RMSD', round(values[3], 2), ' of ', values[6], 'residues')
        #print(ref, molecule, 'RMSD: ', round(values[3], 2), ' of ', values[6], 'residues')
        report.append([ref, molecule, values[3], values[6]])

    for l in report:
       if not l[1].startswith('_align'):
         # rp14_5ddp_bound_clean_ligand rp14_farna_eloop_nol2fixed_cst.out.1 RMSD:  4.49360132217 of 52 residues
         if l[1] not in ['sele', 'rov_pc']: # skip them
              #print(l[0], l[1], 'RMSD:', round(l[2],2), str(l[3]) + 'nt')
              pass
              #f.write(i[0] + '-' + i[1] + ' ' + str(i[2]) + '\n')

cmd.extend('align_all', align_all)

def save_each_object(folder='', prefix=''):
    """

    Usage::

        save_each_object /Users/magnus/work/spliceosome/PyMOL4Spliceosome/chains/yB_5zwo, yB_5zwo_

        p = 'yP_6exn' # yP_5ylz' #yI_5y88' # yE_6n7r'
        pth = '/Users/magnus/work/spliceosome/PyMOL4Spliceosome/chains/'
        save_each_object(pth + p, p + '_')

    See the application here <https://github.com/mmagnus/PyMOL4Spliceosome/releases/tag/v0.32>

    .. todo:: add some way to select which objects to use
    """
    obj_list = cmd.get_names('objects')
    for o in obj_list:
        if folder:
            folder += '/'
        fn = folder + prefix.strip() + o.strip() + '.pdb'
        cmd.save(fn, o)

cmd.extend('save_each_object', save_each_object)

def rcomp():
    """RNA like in papers ;-)

    Similar to rc() but this time it colors each (and every) structure in different colour.
    Great on viewing-comparing superimposed structures.

    """
    cmd.hide("sticks", "all")
    cmd.hide("lines", "all")
    cmd.show("cartoon", "all")
    cmd.set("cartoon_ring_mode", 3)
    cmd.set("cartoon_ring_finder", 2)
    cmd.set("cartoon_ladder_mode", 2)
    cmd.set("cartoon_ring_transparency", 0.30)

    obj_list = cmd.get_names('objects')

    colours = ['red', 'green', 'blue', 'yellow', 'violet', 'cyan',    \
           'salmon', 'lime', 'pink', 'slate', 'magenta', 'orange', 'marine', \
           'olive', 'purple', 'teal', 'forest', 'firebrick', 'chocolate',    \
           'wheat', 'white', 'grey' ]
    ncolours = len(colours)

           # Loop over objects
    i = 0
    for obj in obj_list:
        print("  ", obj, colours[i])
        cmd.color(colours[i], obj)
        i = i+1
        if(i == ncolours):
           i = 0


def align_all2( subset = [] ):
  """
  Superimpose all open models onto the first one.
  This may not work well with selections.

  This function is probably taken from https://daslab.stanford.edu/site_data/docs_pymol_rhiju.pdf
  """
  print("""This returns a list with 7 items:

    RMSD after refinement
    Number of aligned atoms after refinement
    Number of refinement cycles
    RMSD before refinement
    Number of aligned atoms before refinement
    Raw alignment score
    Number of residues aligned """)

  AllObj=cmd.get_names("all")
  for x in AllObj[1:]:
    #print(AllObj[0],x)
    subset_tag = ''
    if isinstance( subset, int ):
      subset_tag = ' and resi %d' % subset
    elif isinstance( subset, list ) and len( subset ) > 0:
      subset_tag = ' and resi %d' % (subset[0])
      for m in range( 1,len(subset)): subset_tag += '+%d' % subset[m]
    elif isinstance( subset, str ) and len( subset ) > 0:
      subset_tag = ' and %s' % subset
    values = cmd.align(x+subset_tag,AllObj[0]+subset_tag)
    print(AllObj[0], x, ' '.join([str(v) for v in values]), '-- RMSD', values[3], ' of ', values[6], 'residues')
    cmd.zoom()


def pdb():
    """Get PDB content of selection.

    .. image:: ../../rna_tools/utils/PyMOL4RNA/doc/pdb.png"""
    tmpfn = '/tmp/pymol_get_pdb.pdb'
    cmd.save(tmpfn, '(sele)')
    s = RNAStructure(tmpfn)
    for l in s.lines:
        print(l)


def x3dna():
    f = tempfile.NamedTemporaryFile(delete=False) # True)
    #cmd.save(f.name + '.pdb', '(backbone_)')
    cmd.save(f.name + '.pdb', '(sele)')
    out, err = exe("rna_x3dna.py --show-log " + f.name + ".pdb ")
    print('\n'.join(out.split('\n')[1:]))  # to remove first line of py3dna /tmp/xxx
    if err:
        print(err)
    f.close()

def clarna():
    """Get contacts classification of the selected fragment based on ClaRNA.

    .. image:: ../../rna_tools/tools/PyMOL4RNA/doc/clarna.png
    """
    AllObj = cmd.get_names("objects")
    # print AllObj
    for name in AllObj[:]:
        print(name + ' ' + '-' * (70 - len(name)))
        f = tempfile.NamedTemporaryFile(delete=False) # True)
        #cmd.save(f.name + '.pdb', '(backbone_)')
        cmd.save(f.name + '.pdb', '(sele) and "' + name + '"')
        CLARNA_RUN = 'rna_clarna_run.py'
        out, err = exe(SOURCE + " && " + CLARNA_RUN + " -ipdb " + f.name + '.pdb -bp+stack')
        print('\n'.join(out.split('\n')[1:]))  # to remove first line of py3dna /tmp/xxx
        if err:
            print(err)
        f.close()


def seq():
    """Get sequence of the selected fragment using ``rna_pdb_toolsx.py --get_seq ``.

    .. image:: ../../rna_tools/utils/PyMOL4RNA/doc/ss.png
    """
    f = tempfile.NamedTemporaryFile(delete=False) # True)
    cmd.save(f.name, '(sele)')
    out, err = exe('source ~/.zshrc && ' + RNA_TOOLS_PATH + '/bin/rna_pdb_toolsx.py --get_seq ' + f.name)
    print(out)
    if err:
        print(err)
    f.close()

def ss():
    """Get Secondary Structure of (sele) based on py3dna.py.

    .. image:: ../../rna_tools/utils/PyMOL4RNA/doc/ss.png
    """
    f = tempfile.NamedTemporaryFile(delete=False) # True)
    cmd.save(f.name, '(sele)')
    out, err = exe(RNA_TOOLS_PATH + '/bin/rna_x3dna.py ' + f.name)
    print('\n'.join(out.split('\n')[2:]))  # to remove first line of py3dna /tmp/xxx
    if err:
        print(err)
    f.close()


def ss_all():
    """The same as ss() but for all objects."""
    subset = "*"
    AllObj = cmd.get_names("all")
    # print AllObj
    for name in AllObj[:]:
        if not name.startswith('_align'):
            print('> ' + name)
            f = tempfile.NamedTemporaryFile(delete=False) # True)
            cmd.save(f.name, name)
            out, err = exe(RNA_TOOLS_PATH + '/bin/rna_x3dna.py ' + f.name)
            print('\n'.join(out.split('\n')[2:]))  # to remove first line of py3dna /tmp/xxx
            # hide this line: is >tmpGCszi7 nts=4 [tmpGCszi7] -- secondary structure derived by DSSR
            if err:
                print(err)
            f.close()
    print('-- secondary structure derived by DSSR')


def p():
    """A shortcut for putting a seq at the bottom. Pretty cool for screenshots with names of objects.

    .. image:: ../../rna_tools/utils/PyMOL4RNA/doc/p.png
    """
    cmd.set("seq_view_format", 4)
    cmd.set("seq_view", 1)
    cmd.set("seq_view_location", 1)
    cmd.set("seq_view_overlay", 1)


def rna_cartoon():
    """http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol

    .. image:: ../pngs/rna_cartoon.png
    """
    cmd.set("cartoon_ring_mode", 3)
    cmd.set("cartoon_ring_finder", 1)
    cmd.set("cartoon_ladder_mode", 1)
    cmd.set("cartoon_nucleic_acid_mode", 4)
    cmd.set("cartoon_ring_transparency", 0.5)


def rp17():
    """Color-coding for secondary structure elements for the RNA Puzzle 17.

    For the variant::

         CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAAAUAUCAGGUGCAA
         ((((.[[[[[[.))))........((((.....]]]]]]...(((((....)))))..))))
         # len 62-nt

    .. image:: ../../rna_tools/tools/PyMOL4RNA/doc/rna.png
    """
    txt = """color forest, resi 1-5+12-16; # p1
 color magenta, resi 6-11+34-39;
 color grey, resi 17-24;
 color marine, resi 25-28+59-62;
 color deepblue, resi 29-33+40-42;
 color orange, resi 44-47+48-56;
 color yellow, resi 57-58;
 color red, resi 19+20+21;
"""
    color_by_text(txt)

def rp17csrv():
    """Color-coding for secondary structure elements for the RNA Puzzle 17.

    For the variant::

         CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAAAUAUCAGGUGCAA
         ((((.[[[[[[.))))........((((.....]]]]]]...(((((....)))))..))))
         # len 62-nt

    .. image:: ../../rna_tools/utils/PyMOL4RNA/doc/rna.png
    """
    txt = """color forest, resi 1-5+12-16; # p1
 color magenta, resi 6-11+34-39;
 color grey, resi 17-24;
 color marine, resi 25-28+59-62;
 color deepblue, resi 29-33+40-42;
 color orange, resi 44-47+48-56;
 color yellow, resi 57-58;
 color red, resi 5+19+20+21+31+32+33+40+41+42
"""
    color_by_text(txt)



def rp172():
    """Color-coding for secondary structure elements for the RNA Puzzle 17.

    For the variant::

         CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAUCAGGUGCAA
         ((((.[[[[[[.))))........((((.....]]]]]]...((((()))))..))))
         # len 58-nt

    See rp17()
    """

    txt = """color forest, resi 1-5+12-16; # p1
 color magenta, resi 6-11+34-39
 color grey, resi 17-24
 color marine, resi 25-28+55-58
 color deepblue, resi 29-33+40-42;
 color orange, resi 43-47+48-52;
 color yellow, resi 53-54;
 color red, resi 19+20+21;
"""
    color_by_text(txt)

def color_aa_types():
    """Color aminoacides types like in Cider (http://pappulab.wustl.edu/CIDER/)"""
    txt = """
color gray70, resn Ala+Ile+Leu+Met+Phe+Trp+Val #hydrophobic
color yellow, resn Tyr+Trp #aromatic
color blue, resn Arg+Lys+His # positive
color forest, resn GLN+SER+GLY+thr
color pink, resn PRO # pro
color red, resn GLU+asp # """
    print("""color (according to) amino-acids types)
hydrohobic (gray)  Ala+Ile+Leu+Met+Phe+Trp+Val
aromatic (yellow) Tyr+Trp
positive (blue)  Arg+Lys+His
polar (forest) Gln+Ser+Glu+Thr
negative (red) Glu+Asp
prolina ;) (pink) Pro""")
    color_by_text(txt)


def color_obj(rainbow=0):


        """
        stolen from :)
AUTHOR
        Gareth Stockwell

USAGE
        color_obj(rainbow=0)

        This function colours each object currently in the PyMOL heirarchy
        with a different colour.  Colours used are either the 22 named
        colours used by PyMOL (in which case the 23rd object, if it exists,
        gets the same colour as the first), or are the colours of the rainbow

        """

        # Process arguments
        rainbow = int(rainbow)

        # Get names of all PyMOL objects
        obj_list = cmd.get_names('objects')

        if rainbow:

           print("\nColouring objects as rainbow\n")

           nobj = len(obj_list)

           # Create colours starting at blue(240) to red(0), using intervals
           # of 240/(nobj-1)
           for j in range(nobj):
              hsv = (240-j*240/(nobj-1), 1, 1)
              # Convert to RGB
              rgb = hsv_to_rgb(hsv)

              # Define the new colour
              cmd.set_color("col" + str(j), rgb)
              print(obj_list[j], rgb)
              # Colour the object
              cmd.color("col" + str(j), obj_list[j])

        else:
           # List of available colours
           colours = ['red', 'green', 'blue', 'yellow', 'violet', 'cyan',    \
           'salmon', 'lime', 'pink', 'slate', 'magenta', 'orange', 'marine', \
           'olive', 'purple', 'teal', 'forest', 'firebrick', 'chocolate',    \
           'wheat', 'white', 'grey' ]
           ncolours = len(colours)

           # Loop over objects
           i = 0
           for obj in obj_list:
              print("  ", obj, colours[i])
              cmd.color(colours[i], obj)
              i = i+1
              if(i == ncolours):
                 i = 0


def names():
    # Get names of all PyMOL objects
    obj_list = cmd.get_names('objects')
    for o in obj_list:
        print(o)


def color_rbw(rainbow=0):

        """
        similar to color_obj() but this time colors every obect as rainbow
        """
        rainbow = int(rainbow)

        # Get names of all PyMOL objects
        obj_list = cmd.get_names('objects')

        if rainbow:

           print("\nColouring objects as rainbow\n")

           nobj = len(obj_list)

           # Create colours starting at blue(240) to red(0), using intervals
           # of 240/(nobj-1)
           for j in range(nobj):
              hsv = (240-j*240/(nobj-1), 1, 1)
              # Convert to RGB
              rgb = hsv_to_rgb(hsv)

              # Define the new colour
              cmd.set_color("col" + str(j), rgb)
              print(obj_list[j], rgb)
              # Colour the object
              cmd.color("col" + str(j), obj_list[j])
        else:
           colours = ['rainbow']
           ncolours = len(colours)

           # Loop over objects
           i = 0
           for obj in obj_list:
              print("  ", obj, colours[i])
              cmd.spectrum('count', colours[i], obj)
#              cmd.color(colours[i], obj)
              i = i+1
              if(i == ncolours):
                 i = 0

def ino():
    """Sphare and yellow inorganic, such us Mg.

    .. image:: ../../rna_tools/utils/PyMOL4RNA/doc/ion.png"""
    cmd.show("spheres", "inorganic")
    #cmd.set('sphere_scale', '0.25', '(all)')
    cmd.set('sphere_scale', '1', '(all)')
    cmd.color("yellow", "inorganic")

mapping = [[u'PRP8', 'A', u'skyblue'], [u'BRR2', 'B', u'grey60'], [u'BUD31', 'C', u'dirtyviolet'], [u'CEF1', 'D', u'raspberry'], [u'CLF1', 'E', u'raspberry'], [u'CWC15', 'F', u'dirtyviolet'], [u'CWC16/YJU2', 'G', u'lightteal'], [u'CWC2', 'H', u'ruby'], [u'CWC21', 'I', u'violetpurple'], [u'CWC22', 'J', u'bluewhite'], [u'CWC25', 'K', u'deepteal'], [u'Intron', 'L', u'black'], [u'ISY1', 'M', u'dirtyviolet'], [u'LEA1', 'N', u'palegreen'], [u'Msl1', 'O', u'palegreen'], [u'PRP45', 'P', u'lightpink'], [u'PRP16', 'Q', u'smudge'], [u'CDC40\xa0(PRP17, SLU4, XRS2)', 'R', u'dirtyviolet'], [u'PRP19 (PSO4)', 'S', u'grey70'], [u'PRP46', 'T', u'lightblue'], [u'SLT11/ECM2', 'U', u'chocolate'], [u'SNT309', 'V', u'grey70'], [u'SNU114', 'W', u'slate'], [u'SYF2', 'X', u'brightorange'], [u'SYF1', 'Y', u'brightorange'], [u'U2', 'Z', u'forest'], [u'U5', 'a', u'density'], [u'U5_SmRNP', 'b', u'deepblue'], [u'U6', 'c', u'firebrick'], [u'Intron', 'r', u'grey50'], [u'Exon', 'z', u'yellow'], [u'exon-3', 'y', u'yellow'], [u'exon-5', 'z', u'yellow'], [u'PRP4 ', 'd', u'grey50'], [u'PRP31', 'e', u'grey50'], [u'PRP6', 'f', u'grey50'], [u'PRP3', 'g', u'grey50'], [u'DIB1', 'h', u'grey50'], [u'SNU13', 'i', u'grey50'], [u'LSM8', 'j', u'grey50'], [u'LSM2', 'k', u'grey50'], [u'LSM3', 'l', u'grey50'], [u'LSM6', 'm', u'grey50'], [u'LSM5', 'n', u'grey50'], [u'LSM7', 'o', u'grey50'], [u'LSM4', 'p', u'grey50'], [u'SNU66', 'q', u'grey50'], [u'RNA (intron or U6 snRNA)', 'r', u'grey50'], [u'5EXON', 's', u'grey50'], [u'BUD13', 't', u'grey60'], [u'CLF2', 'u', u'rasberry'], [u'Cus1', 'v', u'palegreen'], [u'CWC24', 'w', u'grey60'], [u'CWC27', 'x', u'grey60'], [u'HSH155', '1', u'smudge'], [u'HSH49', '2', u'sand'], [u'PML1', '3', u'grey60'], [u'PRP11', '4', u'palegreen'], [u'PRP2', '5', u'palegreen'], [u'RDS3', '6', u'palegreen'], [u'RSE1', '7', u'smudge'], [u'SNU17', '8', u'grey60'], [u'Ysf3', '9', u'palegreen'], [u'cwc23', 'd', u'grey50'], [u'SPP382\xa0(CCF8, NTR1)', 'e', u'grey50'], [u'NTR2', 'f', u'grey50'], [u'PRP43', 'g', u'grey50'], [u'SMB1', 'h', u'grey50'], [u'SME1', 'i', u'grey50'], [u'SMX3', 'j', u'grey50'], [u'SMX2\xa0(SNP2)', 'k', u'grey50'], [u'SMD3', 'l', u'grey50'], [u'SMD1', 'm', u'grey50'], [u'SMD2', 'n', u'grey50'], [u'PRP22', 'o', u'grey50'], [u'PRP18', 'p', u'grey50'], [u'SLU7', 'q', u'grey50'], [u'SMF', 'd', u'grey50'], [u'SMG', 'e', u'grey50'], [u'PRP9', 'f', u'grey50'], [u'PRP21', 'g', u'grey50'], [u'SNU23', 'r', u'grey50'], [u'PRP38', 's', u'grey50'], [u'SPP381', 'w', u'grey50']]

def spl(arg=''):
    """
    action='', name=''
    """
    if ' ' in arg:
        action, name = arg.split()
        name = name.lower()
    else:
        action = arg
        name = ''
    #import pandas as pd
    #df = pd.read_excel("/home/magnus/Desktop/pyMoL_colors-EMX.xlsx")
    if not action or action == 'help':
        spl_help()
    elif action == 'color' or arg=='c':
        code_for_color_spl.spl_color()

        code_for_color_spl_objects.spl_color()
    elif arg == 'extract all' or arg == 'e':
        code_for_spl.spl_extract()
    elif arg == 'align' or arg=='a':
        cmd.do("""
    align /5gm6//6, /5lj3//V;
    align /5mps//6, /5lj3//V;
    align /6exn//6, /5lj3//V;
    align /5y88//D, /5lj3//V;
    align /5ylz//D, /5lj3//V;
    """)
    else:
        spl_help()

cmd.extend('spl', spl)

def spl_help():
    print("""################ SPL #################
extract all (ea)  - show
colors            - list all colors
######################################
""")

spl_help()


def __spl_color():
    for m in mapping:
        protein = m[0]
        chain = m[1]
        color = m[2]
        print('\_' + ' '.join([protein, chain, color]))
        cmd.do('color ' + color + ', chain ' + chain)
        # cmd.do('color firebrick, chain V') # U6

def _spl_color():
    """Color spl RNAs (for only color spl RNA and use 4-color code for residues see `spl2`)
    """
    AllObj = cmd.get_names("all")
    for name in AllObj:
        if 'Exon' in name or 'exon' in name:
            cmd.color('yellow', name)
        if 'Intron' in name or 'intron' in name or '5splicing-site' in name:
            cmd.color('gray40', name)
        if '3exon-intron' in name.lower():
            cmd.color('gray20', name)
        if name.startswith("U2_snRNA"):
            cmd.color('forest', name)
        if name.startswith("U5_snRNA"):
            cmd.color('blue', name)
        if name.startswith("U4_snRNA"):
            cmd.color('orange', name)
        if name.startswith("U6_snRNA"):
            cmd.color('red', name)

    cmd.do('color gray')

    # trisnrp
    cmd.do('color orange, chain V') # conflict
    cmd.do('color red, chain W')
    cmd.do('color blue, chain U')
    #
    cmd.do('color blue, chain 5')
    cmd.do('color forest, chain 2')
    cmd.do('color red, chain 6')
    cmd.do('color orange, chain 4')
    cmd.do('color yellow, chain Y')
    # shi
    cmd.do('color blue, chain D') # u5
    cmd.do('color forest, chain L') # u2
    cmd.do('color red, chain E') # u6
    cmd.do('color yellow, chain M')
    cmd.do('color yellow, chain N')
    # afte branch
    cmd.do('color blue, chain U') # u5
    cmd.do('color forest, chain Z') # u2
    cmd.do('color red, chain V') # u6
    cmd.do('color yellow, chain E')
    cmd.do('color black, chain I')
    # 5WSG
    # Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution
    cmd.do('color blue, chain D') # u5
    #cmd.do('color forest, chain L') # u2
    cmd.do('color yellow, chain B')
    cmd.do('color yellow, chain b')
    cmd.do('color black, chain N')
    cmd.do('color black, chain M')

    cmd.do('color black, chain 3') # orange
    cmd.do('color black, chain E') # yellow
    cmd.do('color black, chain i')
    cmd.do('color black, chain e')

    cmd.do('color black, chain e')

    cmd.do('color dirtyviolet, chain L') # bud31
    cmd.do('color rasberry, chain L') # CERF1

    cmd.do('color skyblue, chain A') # PRP8
    cmd.do('color grey60, chain B') # BRR2
    cmd.do('color dirtyiolet, chain L') # BUD31
    cmd.do('color rasberry, chain O') # CEF1
    cmd.do('color rasberry, chain S') # CLF1
    cmd.do('color dirtyviolet, chain P') # CWC15
    cmd.do('color lightteal, chain D') # CWC16/YJU2
    cmd.do('color ruby, chain M') # CWC2
    cmd.do('color violetpurple, chain R') # CWC21
    cmd.do('color bluewhite, chain H') # CWC22
    cmd.do('color deepteal, chain F') # CWC25
    cmd.do('color black, chain I') # Intron
    cmd.do('color dirtyviolet, chain G') # ISY1
    cmd.do('color palegreen, chain W') # LEA1
    cmd.do('color palegreen, chain Y') # Msl1
    cmd.do('color lightpink, chain K') # PRP45
    cmd.do('color smudge, chain Q') # Prp16
    cmd.do('color grey70, chain t') # Prp19
    cmd.do('color lightblue, chain J') # PRP46
    cmd.do('color chocolate, chain N') # SLT11/ECM2
    cmd.do('color grey70, chain s') # Snt309
    cmd.do('color slate, chain C') # SNU114
    cmd.do('color brightorange, chain T') # SYF1
    cmd.do('color forest, chain Z') # U2
    cmd.do('color density, chain U') # U5
    cmd.do('color deepblue, chain b') # U5_Sm

    cmd.do('bg gray')
    # cmd.do('remove (polymer.protein)')

    cmd.set("cartoon_tube_radius", 1.0)
    ino()

def spl2():
    """Color spl RNAs and use 4-color code for residues (for only color spl RNA see `spl`)
    """

    AllObj = cmd.get_names("all")
    for name in AllObj:
        if 'Exon' in name or 'exon' in name:
            cmd.color('yellow', name)
        if 'Intron' in name or 'intron' in name or '5splicing-site' in name:
            cmd.color('gray40', name)
        if '3exon-intron' in name.lower():
            cmd.color('gray20', name)
        if name.startswith("U2_snRNA"):
            cmd.color('forest', name)
        if name.startswith("U5_snRNA"):
            cmd.color('blue', name)
        if name.startswith("U4_snRNA"):
            cmd.color('orange', name)
        if name.startswith("U6_snRNA"):
            cmd.color('red', name)

    cmd.do('color gray')

    # trisnrp
    cmd.do('color orange, chain V') # conflict
    cmd.do('color red, chain W')
    cmd.do('color blue, chain U')
    #
    cmd.do('color blue, chain 5')
    cmd.do('color forest, chain 2')
    cmd.do('color red, chain 6')
    cmd.do('color orange, chain 4')
    cmd.do('color yellow, chain Y')
    # shi
    cmd.do('color blue, chain D') # u5
    cmd.do('color forest, chain L') # u2
    cmd.do('color red, chain E') # u6
    cmd.do('color yellow, chain M')
    cmd.do('color yellow, chain N')
    # afte branch
    cmd.do('color blue, chain U') # u5
    cmd.do('color forest, chain Z') # u2
    cmd.do('color red, chain V') # u6
    cmd.do('color yellow, chain E')
    cmd.do('color black, chain I')
    # 5WSG
    # Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution
    cmd.do('color blue, chain D') # u5
    #cmd.do('color forest, chain L') # u2
    cmd.do('color yellow, chain B')
    cmd.do('color yellow, chain b')
    cmd.do('color black, chain N')
    cmd.do('color black, chain M')

    cmd.do('color black, chain 3') # orange
    cmd.do('color black, chain E') # yellow
    cmd.do('color black, chain i')
    cmd.do('color black, chain e')

    cmd.do('bg gray')
    cmd.do('remove (polymer.protein)')

    cmd.color("red",'resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2')
    cmd.color("forest",'resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6')
    cmd.color("orange",'resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2')
    cmd.color("blue",'resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2')
    cmd.set("cartoon_tube_radius", 1.0)
    ino()


def _spli():
    """
    # this trick is taken from Rhiju's Das code
    color red,resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2
    color forest,resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6
    color orange, resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2
    color blue, resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2

    #
    #cmd.color("yellow", "*intron*")
    #cmd.color("yellow", "*exon*")

    #cmd.show("spheres", "inorganic")
    #cmd.color("yellow", "inorganic")
    """
    cmd.color("orange", "U4_snRNA*")
    cmd.color("red", "U6_snRNA*")
    cmd.color("blue", "U5_snRNA*")
    cmd.color("green", "U2_snRNA*")
    cmd.color("red",'resn rG+G and name n1+c6+o6+c5+c4+n7+c8+n9+n3+c2+n1+n2')
    cmd.color("forest",'resn rC+C and name n1+c2+o2+n3+c4+n4+c5+c6')
    cmd.color("orange",'resn rA+A and name n1+c6+n6+c5+n7+c8+n9+c4+n3+c2')
    cmd.color("blue",'resn rU+U and name n3+c4+o4+c5+c6+n1+c2+o2')


def g2():
    txt = """color gray, all;
    color yellow, chain B;
    color red, resi 788-824;
    color yellow, resi 828-866;
    color forest, resi 476-490;
    """
    color_by_text(txt)
    cmd.color('pink', 'resi 120')
    cmd.color('pink', 'resi 2')


def rgyration(selection='(all)', quiet=1):
    '''

[PyMOL] RES: radius of gyration
From: Tsjerk Wassenaar <tsjerkw@gm...> - 2011-03-31 14:07:03
https://sourceforge.net/p/pymol/mailman/message/27288491/
DESCRIPTION

    Calculate radius of gyration

USAGE

    rgyrate [ selection ]
 :::warning:::
 if nothing is selected  function is calculating radius of gyration for all pdbs in current Pymol session
    '''
    from itertools import izip
    quiet = int(quiet)
    model = cmd.get_model(selection).atom
    x = [i.coord for i in model]
    mass = [i.get_mass() for i in model]
    xm = [(m*i,m*j,m*k) for (i,j,k),m in izip(x,mass)]
    tmass = sum(mass)
    rr = sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in izip(x,xm))
    mm = sum((sum(i)/tmass)**2 for i in izip(*xm))
    rg = math.sqrt(rr/tmass - mm)
    if not quiet:
        print("Radius of gyration: %.2f" % (rg))
    return rg


def qrnass():
    cmd.save('sele.pdb', '(sele)')
    mini('sele.pdb')


def qrnas():
    subset = "*"
    AllObj=cmd.get_names("all")
    #print AllObj
    for x in AllObj[:]:
      print(x, 'qrnas...')
      #print(AllObj[0],x)
      f = tempfile.NamedTemporaryFile(delete=True)
      #print f.name
      #f.write(XX)
      cmd.save(f.name, x)
      #p = Process(target=mini)
      #p.start()
      mini()
      #cmd.load('out.pdb', 'ref')
      #p.join()
      #print x
      #print '\n'.join(out.split('\n')[1:]) # to remove first line of py3dna /tmp/xxx
      f.close()
      break
    align_all()
    rr()

    cmd.set('grid_mode', 1)


def mini(f):
    #os.system('/home/magnus/opt/qrnas/QRNA02/QRNA -i ' + f + ' -c /home/magnus/opt/qrnas/QRNA02/configfile.txt -o out.pdb')
    os.system('~/opt/qrnas/QRNA02/QRNA -i ' + f + ' -c ~/opt/qrnas/QRNA02/configfile.txt -o out.pdb')
    cmd.delete('mini')
    cmd.load('out.pdb', 'mini')
    print('end')


def reload():
    """Reload ~/.pymolrc and all included there packages (e.g. with run <foo.py>)"""
    cmd.do('@ ~/.pymolrc')

def clr():
  """clr - make white bg and structure black"""
  cmd.bg_color( "white" )
  color_by_text('color black, all')


def rlabel():
    cmd = "n. C1'", '"%s %s" % (resn, resi)'
    print('label ' + cmd)
    cmd.label(cmd)


def sav(name):
    cmd.bg_color( "white" )
    cmd.save('/home/magnus/Desktop/' + name + '.png')
    cmd.save('/home/magnus/Desktop/' + name + '.pse')

def hide_rna():
    cmd.hide('(polymer.nucleic)')
cmd.extend('rna-hide', hide_rna)

def show_rna():
    cmd.show('(polymer.nucleic)')
cmd.extend('rna-show', show_rna)

def select_rna():
    cmd.select('polymer.nucleic')
cmd.extend('select-rna', select_rna)

def hide_protein():
    cmd.hide('(polymer.protein)')
cmd.extend('protein-hide', hide_protein)
cmd.extend('rprotein-hide', hide_protein)

def select_protein():
    cmd.select('polymer.protein')
cmd.extend('protein-select', select_protein)

def tmp():
    cmd.save('/home/' + user + '/Desktop/' + tmp + '.png')
    cmd.save('/home/' + user + '/Desktop/' + tmp + '.pse')


################################################################################
def sav_tmp():
    from shutil import copyfile
    import datetime
    try:
        TMP_FOLDER + ' '

    except:
        print("Error: Set up TMP_FOLDER in your ~/.pymolrc, e.g. TMP_FOLDER = '/home/magnus/Desktop/PyMOL/'")
        return

    try:
        os.mkdir(TMP_FOLDER)
    except:
        pass

    date = datetime.datetime.today().strftime('%Y-%m-%d.%S')
    try:
        fn = TMP_FOLDER +  os.sep + id + '_' + date + '.pse'
    except TypeError:
        fn = TMP_FOLDER +  os.sep + '_' + date + '.pse'
    cmd.save(fn)
    print('Save...' + fn)
    cmd.save(fn.replace('.pse', '.png'))
    copyfile(fn, TMP_FOLDER + '/last.pse')

def load_tmp():
    print('Load...')
    cmd.load(TMP_FOLDER + '/last.pse')


def quickref():
    print('   PyMOL4RNA (rna-tools)  ')
    print('~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~')
    print('Quickref `qr`: ')
    print('  alter (sele), chain="B" ')
    print('  alter (sele), resv -= 4')
    print('  alter (chain B), resv -= 44 ')
    print("  select br. all within 15 of (sele)")
    print("  select br. all within 15 of resi 574")
    print("  select br. all within 15 of resi 377 # O. ihheyensis")
    print('  select br. all within 15 of U6_snRNA and resi 80')
    print('  set dash_color, red; set dash_width, 4')
    print('  p - prepare seq for printing')
    print('  rp - rna present, object names only click to get compact legend')
    print('  rp17')
    print('  rna_cartoon')
    print('  rs')
    print('  rcomp')
    print('  color_obj')
    print('  color_rbw')
    print('  aa')
    print('  savt - save_transformed <object>, <file>')
    #print('  spl - color snRNAs of the spliceosome:'
    #    green: U2,  blue: U5, red:U6, orange:U2""")
    print('\_ RNA_TOOLS_PATH env variable used: ' + RNA_TOOLS_PATH)

try:
    from pymol import cmd
except ImportError:
    print("PyMOL Python lib is missing")
else:
    quickref()
    #cmd.set_key('CTRL-S', cmd.save, ['/home/magnus/Desktop/tmp.pse'])
    cmd.set_key('CTRL-S', sav_tmp)
    cmd.set_key('CTRL-Z', load_tmp)  # ostatni wrzucam tutaj
    #cmd.load, ['/home/magnus/Desktop/tmp.pse'])
    # main code #

    cmd.extend('quickref', quickref)
    cmd.extend('qr', quickref)
    cmd.extend('rp17', rp17)
    cmd.extend('rp17csrv', rp17csrv)
    cmd.extend('rg2', g2)
    cmd.extend('x', g2)

    cmd.extend('rp', rp)
    cmd.extend('p', p)
    cmd.extend('pdb', pdb)
    cmd.extend('seq', seq)
    cmd.extend('rseq', seq)
    cmd.extend('rna_cartoon', rna_cartoon)
    cmd.extend('rs', rs)
    cmd.extend('ino', ino)
    cmd.extend('rcomp', rcomp)
    cmd.extend('color_obj', color_obj)
    cmd.extend('color_rbw', color_rbw)
    cmd.extend('aa', align_all)
    cmd.extend('ss', ss)
    cmd.extend('ss_all', ss_all)
    cmd.extend('clarna', clarna)
    cmd.extend('x3dna', x3dna)
    cmd.extend("rgyration", rgyration)
    #cmd.extend("spl", spl)
    cmd.extend("spl2", spl2)
    cmd.extend('rlabel', 'rlabel')

    cmd.extend('grid_on', grid_on)
    cmd.extend('grid_off', grid_off)
    cmd.extend('reload', reload)

    cmd.extend('color_aa_types', color_aa_types)

    cmd.extend('names', names)

    # set dash lines
    cmd.set('dash_color', 'red')
    cmd.set('dash_width', 4)

    cmd.extend('sav', sav)
    cmd.extend('save_transformed', save_transformed)
    cmd.extend('savt', save_transformed)
    cmd.extend('show_all_at_once', show_all_at_once)

    cmd.set('ignore_case', 'off')
    #cmd.set('cartoon_ring_mode', '3')
    #cmd.set('cartoon_ring_finder', '2')
    #cmd.extend('spl_select', spl_select)
    #    print('ignore_case made off')
    print('\_ PYMOL4RNA loading .... [ok]')

mmagnus / rna-tools

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