Pml2py - Revision history

Cchem: 1 revision

2020-03-03T04:30:39Z

1 revision

Speleo3: py3

2020-02-17T13:32:34Z

py3

Bell: 5 revisions

2014-03-28T03:08:45Z

5 revisions

Speleo3: strip of comment

2011-06-07T13:36:22Z

strip of comment

Speleo3: aliases, multiple commands in one line

2011-05-25T10:54:08Z

aliases, multiple commands in one line

Speleo3: use pymol.parsing module

2011-05-20T14:29:51Z

use pymol.parsing module

Speleo3: parse list arguments

2011-04-09T18:22:11Z

parse list arguments

Speleo3: created

2011-04-09T17:10:24Z

created

New page

This script converts a pml script to a python script.

See [http://sourceforge.net/mailarchive/message.php?msg_id=27331786 pymol-users mailing list] (Subject: Convert pml script to Pymol Python script, Fri, 8 Apr 2011).

<source lang="python">
import sys
from pymol import cmd

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

Convert a pml script to python syntax.

USAGE

pml2py infile [, outfile]

TODO

comments, aliases, list arguments
'''
def quote(args):
for arg in args:
if '=' not in arg:
yield repr(arg)
else:
a = arg.split('=', 1)
yield a[0] + '=' + repr(a[1])
if isinstance(out, basestring):
out = open(out, 'w')
print >> out, '''
# automatically converted from "%s"
import pymol
from pymol import *
''' % (filename)
handle = iter(open(filename))
for line in handle:
while line.endswith('\\\n'):
line = line[:-2] + handle.next()

a = line.split(None, 1)
try:
name = a[0]
if name.startswith('/'):
line = line.lstrip()[1:]
raise
name = cmd.kwhash.shortcut.get(name, name)
func = cmd.keyword[name][0]
assert func.func_name != 'python_help'
except:
out.write(line)
continue

if func.func_name == '<lambda>':
print >> out, 'cmd.do(%s)' % (repr(line.strip()))
continue

# FIXME hack for set_view list argument
if name == 'set_view':
print >> out, 'cmd.set_view(' + a[1] + ')'
continue

if len(a) > 1:
args = [i.strip() for i in a[1].split(',')]
else:
args = []

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

print >> out, '%s.%s(%s)' % (func.__module__, func.func_name, ', '.join(quote(args)))

cmd.extend('pml2py', pml2py)

# vi:expandtab:smarttab
</source>

@@ Line 4: / Line 4: @@
 <source lang="python">
 import sys
 from pymol import cmd, parsing
@@ Line 37: / Line 39: @@
              if len(self.stack):
                  return self.stack.pop()
-             return self.iterator.next()
+             return next(self.iterator)
          def push(self, v):
              self.stack.append(v)
      if isinstance(out, basestring):
          out = open(out, 'w')
-     print >> out, '''
+     print('''
 # automatically converted from "%s"
 import pymol
 from pymol import *
-''' % (filename)
+''' % (filename), file=out)
      handle = stackiter(open(filename, 'rU'))
      for line in handle:
          while line.endswith('\\\n'):
-             line = line[:-2] + handle.next()
+             line = line[:-2] + next(handle)
          a = line.split(None, 1)
@@ Line 75: / Line 79: @@
          # PyMOL stuff without named python function
          if func.__name__ == '<lambda>' or name.startswith('@'):
-             print >> out, 'cmd.do(%s)' % (repr(line.strip()))
+             print('cmd.do(%s)' % (repr(line.strip())), file=out)
              continue
@@ Line 128: / Line 132: @@
              module = func.__module__
-         print >> out, '%s.%s(%s)' % (module, func.__name__, ', '.join(quote(args)))
+         print('%s.%s(%s)' % (module, func.__name__, ', '.join(quote(args))), file=out)
 cmd.extend('pml2py', pml2py)

@@ Line 16: / Line 16: @@
      pml2py infile [, outfile]
      '''
      def quote(args):
@@ Line 103: / Line 99: @@
              split_mx = kw[4] - parsing.LITERAL
          if len(a) > 1:
              if split_mx < 0:
                  # strip of additional commands

@@ Line 19: / Line 19: @@
 TODO
-     comments, aliases, multiple commands in one line
+     comments
      '''
      def quote(args):
@@ Line 31: / Line 31: @@
                  arg = arg.lstrip()
              yield prefix + repr(arg)
      if isinstance(out, basestring):
@@ Line 41: / Line 54: @@
 ''' % (filename)
-     handle = iter(open(filename, 'rU'))
+     handle = stackiter(open(filename, 'rU'))
      for line in handle:
          while line.endswith('\\\n'):
@@ Line 90: / Line 103: @@
              split_mx = kw[4] - parsing.LITERAL
          if len(a) > 1:
              if split_mx == 0:
                  args = [a[1]]
@@ Line 100: / Line 118: @@
          if kw[4] == parsing.LEGACY and '=' in args[0]:
              args = [i.strip() for i in args[0].split('=', 1)] + args[1:]
          # use 'cmd' module if possible

← Older revision	Revision as of 04:30, 3 March 2020
(No difference)

← Older revision	Revision as of 03:08, 28 March 2014
(No difference)

@@ Line 19: / Line 19: @@
 TODO
-     comments, aliases, list arguments
+     comments, aliases
      '''
      def quote(args):
          for arg in args:
              if '=' not in arg:
-                 yield repr(arg)
+                 prefix = ''
              else:
-                 a = arg.split('=', 1)
+                 prefix, arg = arg.split('=', 1)
-                 yield a[0] + '=' + repr(a[1])
+                 prefix += '='
      if isinstance(out, basestring):
          out = open(out, 'w')
      print >> out, '''
 # automatically converted from "%s"
@@ Line 35: / Line 46: @@
 from pymol import *
 ''' % (filename)
      handle = iter(open(filename))
      for line in handle:
@@ Line 48: / Line 60: @@
              name = cmd.kwhash.shortcut.get(name, name)
              func = cmd.keyword[name][0]
-             assert func.func_name != 'python_help'
+             assert func.__name__ != 'python_help'
          except:
              out.write(line)
              continue
-         if func.func_name == '<lambda>':
+         if func.__name__ == '<lambda>':
              print >> out, 'cmd.do(%s)' % (repr(line.strip()))
              continue
@@ Line 66: / Line 73: @@
          else:
              args = []
          if name == 'python':
@@ Line 74: / Line 85: @@
              continue
-         print >> out, '%s.%s(%s)' % (func.__module__, func.func_name, ', '.join(quote(args)))
+        # use 'cmd' module if possible
 cmd.extend('pml2py', pml2py)
 # vi:expandtab:smarttab
 </source>