Pml2py
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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]
TODO
comments
'''
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:
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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