Editing User:Mglerner (section)

= My ~/.pymolrc runs this .py script=
<source lang="python">
#!/usr/bin/env python
from pymol import cmd,stored
cmd.set('pdb_retain_ids',1)
cmd.set('retain_order',1)
import os
def gro(fnm,name=None):
    os.system("/usr/local/bin/editconf -f %s -o /tmp/tmp.pdb" % fnm)
    print "Just did","/usr/local/bin/editconf -f %s -o /tmp/tmp.pdb" % fnm
    if name is None:
        name = fnm[:-4]
    cmd.load("/tmp/tmp.pdb",name)
cmd.extend("gro",gro)

def splitseq(seq,size):
    """ Split up seq in pieces of size """
    return [seq[i:i+size] for i in range(0, len(seq), size)]

def getIDsInSel(sel, sorted=True, reversed=False):
    """
    PARAMETERS
        sel,
            The selection, object or group to iterate over
        sorted (boolean),
            Should the list be sorted?
        reversed (boolean)
            Should the list be reversed before returned?  (Combined
            with the above, you can return a decreasing-sorted list
            of names
 
    RETURNS
        list[] of strings, representing the object IDs desired.

    CREDITS
        This is a very slightly modified version of getNamesInSel 
        from http://pymolwiki.org/index.php/GetNamesInSel
    """
    stored.tempNames = set()
    cmd.iterate(sel, "stored.tempNames.add(ID)")
    rList = list(stored.tempNames)
 
    # if you want the list reversed or sorted,
    # uncomment the following lines
    if sorted:
        rList.sort()
    if reversed:
        rList.reverse()
    return rList
 
cmd.extend("getIDsInSel", getIDsInSel)
def togrp(selname,fname):
    '''Make a GROMACS index group from a selection'''
    f = file(fname,'w')
    f.write('[ %s ]\n'%selname)
    #   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
    #7267 7268 7269 7270 7271 7272 7273 7274 7275 7276 7277 7278 7279 7280 7281 
    idxs = getIDsInSel(selname)
    for g in splitseq(idxs,15):
        line = ' '.join(['%4s'%i for i in g])
        line = line + '\n'
        f.write(line)
    f.write('\n')
    f.close()
cmd.extend('togrp',togrp)

def rayy(width=-1,height=-1,units='in',dpi=-1,**kwargs):
    """
    Slightly better version of the ray command.
    You can specify width and height in the units of your choice, e.g.

    rayy 3,2,units=in,dpi=300
    rayy 3in,2in
    rayy 1in, 2 cm, dpi=600

    Extra keyword arguments get passed on to the normal ray command.

    Units can be 'in' or 'cm'.

    For backwards compatibility, the conversion to dpi (or dots per
    centimeter) is only performed when dpi is specified.
    """
    if type(dpi) in [type('')]: dpi = int(dpi)
    in_per_cm = 0.393700787
    def todots(x,units,dpi):
        if type(x) in [type('')]:
            x = x.lower()
            if 'in' in x:   units = 'in'
            elif 'cm' in x: units = 'cm'
            x = float(x.replace(units,'').strip())
        if (dpi == -1):
            return x
        if units ==   'cm': x = x * in_per_cm
        elif units == 'in': pass
        else:               raise ValueError('Unknown units (%s)'%units)
        print '%s%s at %sdpi'%(x,units,dpi)
        return int(x * dpi)
    # How do we get current width/height of viewport? MainSceneGetSize perhaps
    # But it doesn't matter, as PyMOL will autoscale internally for us when given -1.
    try:
        width,height = todots(width,units,dpi),todots(height,units,dpi)
    except ValueError:
        print "Unknown units"
        return
    print 'width',width,'height',height
    cmd.ray(width=width,height=height,**kwargs)
cmd.extend('rayy',rayy)


</source>