Pml2py

This script converts a pml script to a python script.

See pymol-users mailing list (Subject: Convert pml script to Pymol Python script, Fri, 8 Apr 2011).

import sys
from pymol import cmd, parsing

def pml2py(filename, out=sys.stdout):
    '''
DESCRIPTION

    Convert a pml script to python syntax.

USAGE

    pml2py infile [, outfile]
    '''
    def quote(args):
        args = iter(args)
        for arg in args:
            if '=' not in arg:
                prefix = ''
            else:
                prefix, arg = arg.split('=', 1)
                prefix += '='
                arg = arg.lstrip()
            yield prefix + repr(arg)

    class stackiter:
        def __init__(self, collection):
            self.iterator = iter(collection)
            self.stack = []
        def __iter__(self):
            return self
        def next(self):
            if len(self.stack):
                return self.stack.pop()
            return self.iterator.next()
        def push(self, v):
            self.stack.append(v)

    if isinstance(out, basestring):
        out = open(out, 'w')

    print >> out, '''
# automatically converted from "%s"
import pymol
from pymol import *
''' % (filename)

    handle = stackiter(open(filename, 'rU'))
    for line in handle:
        while line.endswith('\\\n'):
            line = line[:-2] + handle.next()

        a = line.split(None, 1)
        if len(a) > 1 and a[0] == '_':
            line = a[1]
            a = line.split(None, 1)

        try:
            name = a[0]
            if name.startswith('/'):
                line = line.lstrip()[1:]
                raise
            name = cmd.kwhash.shortcut.get(name, name)
            kw = cmd.keyword[name]
            assert kw[4] != parsing.PYTHON
            func = kw[0]
        except:
            out.write(line)
            continue
        
        # PyMOL stuff without named python function
        if func.__name__ == '<lambda>' or name.startswith('@'):
            print >> out, 'cmd.do(%s)' % (repr(line.strip()))
            continue

        # code blocks
        if name == 'python':
            for line in handle:
                if line.split() == ['python', 'end']:
                    break
                out.write(line)
            continue
        if name == 'skip':
            for line in handle:
                if line.split() == ['skip', 'end']:
                    break
            continue

        # split args
        tok = ','
        if kw[4] == parsing.MOVIE:
            tok = kw[3]
            split_mx = 1
        else:
            split_mx = kw[4] - parsing.LITERAL
        if len(a) > 1:
            a[1] = parsing.split(a[1], '#', 1)[0] # strip of comment
            if split_mx < 0:
                # strip of additional commands
                a[1:] = parsing.split(a[1], ';', 1)
                if len(a) > 2:
                    handle.push(a[2])
            if split_mx == 0:
                args = [a[1]]
            else:
                args = [i.strip() for i in parsing.split(a[1], tok, max(0, split_mx))]
        else:
            args = []

        # old syntax: set property=value
        if kw[4] == parsing.LEGACY and '=' in args[0]:
            args = [i.strip() for i in args[0].split('=', 1)] + args[1:]

        # register alias
        if name == 'alias':
            cmd.alias(*args)

        # use 'cmd' module if possible
        try:
            test = getattr(cmd, func.__name__)
            assert func == test
            module = 'cmd'
        except:
            module = func.__module__

        print >> out, '%s.%s(%s)' % (module, func.__name__, ', '.join(quote(args)))

cmd.extend('pml2py', pml2py)

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