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Difference between revisions of "User:Speleo3"

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m (rlc download)
(remove pastebin script which are in psico, update build script)
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Some random scripts with no dedicated PyMOLWiki page.
 
Some random scripts with no dedicated PyMOLWiki page.
−
 
−
<source lang="python">
 
−
def mse2met(selection='all', quiet=1):
 
−
    '''
 
−
DESCRIPTION
 
−
 
−
    Mutate selenomethionine to methionine
 
−
    '''
 
−
    quiet = int(quiet)
 
−
    x = cmd.alter('(%s) and MSE/SE' % selection, 'name="SD";elem="S"')
 
−
    cmd.alter('(%s) and MSE/' % selection, 'resn="MET";type="ATOM"')
 
−
    if not quiet:
 
−
        print 'Altered %d MSE residues to MET' % (x)
 
−
    cmd.sort()
 
−
cmd.extend('mse2met', mse2met)
 
−
 
−
def remove_alt(selection='all', keep='A', quiet=1):
 
−
    '''
 
−
DESCRIPTION
 
−
 
−
    Remove alternative location atoms.
 
−
 
−
ARGUMENTS
 
−
 
−
    selection = string: atom selection
 
−
 
−
    keep = string: AltLoc to keep {default: A}
 
−
    '''
 
−
    cmd.remove('(%s) and not alt +%s' % (selection, keep), quiet=int(quiet))
 
−
    cmd.alter(selection, 'alt=""')
 
−
    cmd.sort()
 
−
cmd.extend('remove_alt', remove_alt)
 
−
</source>
 
−
 
−
<source lang="python">
 
−
def cbm(selection='(all)'):
 
−
    '''
 
−
DESCRIPTION
 
−
 
−
    Color by molecule
 
−
    '''
 
−
    col = 2
 
−
    for model in cmd.get_object_list(selection):
 
−
        cmd.color(col, '%s and (%s)' % (model, selection))
 
−
        col += 1
 
−
cmd.extend('cbm', cbm)
 
−
</source>
 
−
 
−
<source lang="python">
 
−
def dev2b(selection='name CA'):
 
−
    '''
 
−
DESCRIPTION
 
−
 
−
    Determine the RMSD per residue for a multi-state object and assign b-factor
 
−
    '''
 
−
    import numpy
 
−
    stored.x = dict()
 
−
    stored.b = dict()
 
−
    for state in range(1, cmd.count_states()+1):
 
−
        cmd.iterate_state(state, selection, 'stored.x.setdefault((model,segi,chain,resi,name), []).append([x,y,z])')
 
−
    for key, coord_list in stored.x.iteritems():
 
−
        b_sq = numpy.array(coord_list).var(0).mean() # var over states, mean over x,y,z
 
−
        stored.b[key] = numpy.sqrt(b_sq) * 10.0
 
−
    cmd.alter(selection, 'b = stored.b[model,segi,chain,resi,name]')
 
−
cmd.extend('dev2b', dev2b)
 
−
</source>
 
−
 
−
<source lang="python">
 
−
def select_extendbyss(selection, name=None, quiet=0):
 
−
    '''
 
−
DESCRIPTION
 
−
 
−
    Extend selection by connected secondary structure elements.
 
−
 
−
ARGUMENTS
 
−
 
−
    selection = string: selection-expression
 
−
 
−
    name = string: create a named atom selection if not None {default: None}
 
−
    '''
 
−
    def in_intervals(i, intervals):
 
−
        for interval in intervals:
 
−
            if interval[0] <= i and i <= interval[1]:
 
−
                return True
 
−
        return False
 
−
    quiet = int(quiet)
 
−
    stored.x = set()
 
−
    # only iterate over CAs since for example PyMOL's dss command just
 
−
    # assignes ss to CAs.
 
−
    cmd.iterate('bycalpha (%s)' % (selection),
 
−
            'stored.x.add((model,segi,chain,resv,ss))')
 
−
    elements = dict()
 
−
    for model,segi,chain,resv,ss in stored.x:
 
−
        key = (model,segi,chain,ss)
 
−
        elements.setdefault(key, [])
 
−
        if in_intervals(resv, elements[key]):
 
−
            continue
 
−
        stored.b = set()
 
−
        cmd.iterate('/%s/%s/%s//CA and ss "%s"' % key, 'stored.b.add(resv)')
 
−
        resv_min = resv
 
−
        resv_max = resv
 
−
        while (resv_min - 1) in stored.b:
 
−
            resv_min -= 1
 
−
        while (resv_max + 1) in stored.b:
 
−
            resv_max += 1
 
−
        elements[key].append((resv_min, resv_max))
 
−
    sele_list = []
 
−
    ss_names = {'S': 'Strand', 'H': 'Helix', '': 'Loop'}
 
−
    for key in elements:
 
−
        model,segi,chain,ss = key
 
−
        for resv_min,resv_max in elements[key]:
 
−
            sele = '/%s/%s/%s/%d-%d' % (model, segi, chain, resv_min, resv_max)
 
−
            sele_list.append(sele)
 
−
            if not quiet:
 
−
                print ss_names.get(ss, ss), sele
 
−
    sele = ' or '.join(sele_list)
 
−
    if name is not None:
 
−
        cmd.select(name, sele)
 
−
    if not quiet:
 
−
        print 'Selection:', sele
 
−
    return sele
 
−
cmd.extend('select_extendbyss', select_extendbyss)
 
−
</source>
 
−
 
−
<source lang="python">
 
−
def diff(sele1, sele2, byres=1, name=None, operator='in', quiet=0):
 
−
    '''
 
−
DESCRIPTION
 
−
 
−
    Difference between two molecules
 
−
 
−
ARGUMENTS
 
−
 
−
    sele1 = string: atom selection
 
−
 
−
    sele2 = string: atom selection
 
−
 
−
    byres = 0/1: report residues, not atoms (does not affect selection)
 
−
    {default: 1}
 
−
 
−
    operator = in/like/align: operator to match atoms {default: in}
 
−
 
−
SEE ALSO
 
−
 
−
    symdiff
 
−
    '''
 
−
    byres, quiet = int(byres), int(quiet)
 
−
    if name is None:
 
−
        name = cmd.get_unused_name('diff')
 
−
    if operator == 'align':
 
−
        alnobj = cmd.get_unused_name('__aln')
 
−
        cmd.align(sele1, sele2, cycles=0, transform=0, object=alnobj)
 
−
        sele = '(%s) and not %s' % (sele1, alnobj)
 
−
        cmd.select(name, sele)
 
−
        cmd.delete(alnobj)
 
−
    else:
 
−
        sele = '(%s) and not ((%s) %s (%s))' % (sele1, sele1, operator, sele2)
 
−
        cmd.select(name, sele)
 
−
    if not quiet:
 
−
        if byres:
 
−
            seleiter = 'byca ' + name
 
−
            expr = 'print "/%s/%s/%s/%s`%s" % (model,segi,chain,resn,resi)'
 
−
        else:
 
−
            seleiter = name
 
−
            expr = 'print "/%s/%s/%s/%s`%s/%s" % (model,segi,chain,resn,resi,name)'
 
−
        cmd.iterate(seleiter, expr)
 
−
    return name
 
−
 
−
def symdiff(sele1, sele2, byres=1, name=None, operator='in', quiet=0):
 
−
    '''
 
−
DESCRIPTION
 
−
 
−
    Symmetric difference between two molecules
 
−
 
−
SEE ALSO
 
−
 
−
    diff
 
−
    '''
 
−
    byres, quiet = int(byres), int(quiet)
 
−
    if name is None:
 
−
        name = cmd.get_unused_name('symdiff')
 
−
    tmpname = cmd.get_unused_name('__tmp')
 
−
    diff(sele1, sele2, byres, name, operator, quiet)
 
−
    diff(sele2, sele1, byres, tmpname, operator, quiet)
 
−
    cmd.select(name, tmpname, merge=1)
 
−
    cmd.delete(tmpname)
 
−
    return name
 
−
 
−
cmd.extend('symdiff', symdiff)
 
−
cmd.extend('diff', diff)
 
−
</source>
 
  
 
Launch interactive python terminal with PyMOL process:
 
Launch interactive python terminal with PyMOL process:
Line 249: Line 58:
 
#!/bin/bash -e
 
#!/bin/bash -e
  
−
prefix=/opt/pymol-svn
+
src=/tmp
−
modules=$prefix/modules
+
prefix=/opt/pymol-git
 +
 
 +
pyinstall() {
 +
    cd $src
 +
    name=$(basename $2)
 +
   
 +
    if [[ -e $name ]]; then
 +
        cd $name && $1 pull
 +
    else
 +
        $1 clone $2 && cd $name
 +
    fi
  
−
python setup.py build install \
+
    python setup.py build install \
−
    --home=$prefix \
+
        --home=$prefix \
−
    --install-purelib=$modules \
+
        --install-lib=$prefix/modules \
−
    --install-platlib=$modules
+
        --install-scripts=$prefix
 +
}
  
−
export PYTHONPATH=$modules:$PYTHONPATH
+
pyinstall git git@github.com:speleo3/pymol
−
python setup2.py install
+
pyinstall git git@github.com:speleo3/pymol-psico
−
install pymol $prefix/
+
pyinstall hg https://hg.codeplex.com/csb
 
</source>
 
</source>
  

Revision as of 09:05, 30 August 2012

My name is Thomas Holder and I am a bioinformatician at the MPI for Developmental Biology in Tübingen, Germany.

I was awarded the Warren L. DeLano Memorial PyMOL Open-Source Fellowship for 2011-2012.

Contact

  • speleo3/users.sourceforge.net
  • thomas.holder/tuebingen.mpg.de

Scripts written by me

Scripts Pastebin

Some random scripts with no dedicated PyMOLWiki page.

Launch interactive python terminal with PyMOL process: (see also Launching From a Script) 

#!/usr/bin/python2.6 -i

import sys, os

# autocompletion
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')

# pymol environment
moddir='/opt/pymol-svn/modules'
sys.path.insert(0, moddir)
os.putenv('PYMOL_PATH', os.path.join(moddir, 'pymol/pymol_path'))

# pymol launching
import pymol
pymol.pymol_argv = ['pymol','-qc'] + sys.argv[1:]
pymol.finish_launching()
cmd = pymol.cmd

Build PyMOL: (see also Linux Install) 

#!/bin/bash -e

src=/tmp
prefix=/opt/pymol-git

pyinstall() {
    cd $src
    name=$(basename $2)
    
    if [[ -e $name ]]; then
        cd $name && $1 pull
    else
        $1 clone $2 && cd $name
    fi

    python setup.py build install \
        --home=$prefix \
        --install-lib=$prefix/modules \
        --install-scripts=$prefix
}

pyinstall git git@github.com:speleo3/pymol
pyinstall git git@github.com:speleo3/pymol-psico
pyinstall hg https://hg.codeplex.com/csb

Download all PyMOL scripts from Robert L. Campbell's website: 

wget -r -np -nd --level=1 -A .py \
    http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
Retrieved from "http://wiki.pymol.org/index.php?title=User:Speleo3&oldid=3208"