Pml2py: Difference between revisions
Jump to navigation
Jump to search
(use pymol.parsing module) |
(aliases, multiple commands in one line) |
||
Line 19: | Line 19: | ||
TODO | TODO | ||
comments | comments | ||
''' | ''' | ||
def quote(args): | def quote(args): | ||
Line 31: | Line 31: | ||
arg = arg.lstrip() | arg = arg.lstrip() | ||
yield prefix + repr(arg) | 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): | if isinstance(out, basestring): | ||
Line 41: | Line 54: | ||
''' % (filename) | ''' % (filename) | ||
handle = | handle = stackiter(open(filename, 'rU')) | ||
for line in handle: | for line in handle: | ||
while line.endswith('\\\n'): | while line.endswith('\\\n'): | ||
Line 90: | Line 103: | ||
split_mx = kw[4] - parsing.LITERAL | split_mx = kw[4] - parsing.LITERAL | ||
if len(a) > 1: | 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: | if split_mx == 0: | ||
args = [a[1]] | args = [a[1]] | ||
Line 100: | Line 118: | ||
if kw[4] == parsing.LEGACY and '=' in args[0]: | if kw[4] == parsing.LEGACY and '=' in args[0]: | ||
args = [i.strip() for i in args[0].split('=', 1)] + args[1:] | 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 | # use 'cmd' module if possible |
Revision as of 06:54, 25 May 2011
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)
# vi:expandtab:smarttab