Hello pyMol Users,
I have recently started working with pyMol. Here is my script, which one of the
users (I am not sure whether it is right or not to write the name) has helped
me to fix:
import os
from pymol import cmd
cmd.reinitialize()
myDir = '/Users/User/myFolder'
#print(myDir)
for filename in os.listdir(myDir):
print('HERE FILENAME is' , filename)
if os.access(filename, os.R_OK):
#check whether file exists and readable
if ‘cif' in filename:
#only cif format is needed
cmd.load (filename)
obj_name = os.path.splitext(filename)[0]
filenameN = obj_name + '.mol'
cmd.save(filenameN, obj_name)
cmd.delete(obj_name)
Here is the mistake log:
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/importing.py",
line 819, in load
_processCIF(cif,oname,state,quiet,discrete,_self)
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/importing.py",
line 409, in _processCIF
for i, rec in enumerate(cif):
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py",
line 671, in next
rec = CIFRec(self.datablocks_it.next())
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py",
line 226, in __init__
self.read_chem_comp_bond()
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py",
line 575, in read_chem_comp_bond
if self.read_chem_comp_bond_atom_ids(None, loop.keys, loop.rows):
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py",
line 557, in read_chem_comp_bond_atom_ids
name_dict[self.index_to_str(label_2,value)]]
KeyError: ‘AtomName’
#atom name, e.g. ‘O’, ‘H2'
Selector-Error: Invalid selection name «obj_name".
(obj_name)<--
Traceback (most recent call last):
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/parsing.py",
line 452, in run_file
execfile(file,global_ns,local_ns)
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/parsing.py",
line 447, in execfile
b.execfile(filename, global_ns, local_ns)
File "/Users/User/pyMolScript.py", line 13, in <module>
cmd.save(filenameN, obj_name)
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/exporting.py",
line 626, in save
io.mol.toFile(_self.get_model(selection,state,ref,ref_state),filename)
File
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/querying.py",
line 1064, in get_model
if _raising(r,_self): raise pymol.CmdException
CmdException: Error: None
Can you, please, tell how to fix this? And, if possible, what caused the
mistake?
Thank you,
Best Regards,
Alsa
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