Hi Arthur & Jerome,
I wrote a basic PDBML importer for PyMOL, see attached script which adds a
"load_pdbml" command. I meant to assess the complexity of such a project and
ended up writing the entire thing. So far, this only reads atoms and symmetry
information. If you find this useful we can include that in the next PyMOL
release.
Cheers,
Thomas
'''
Adds a "load_pdbml" command to PyMOL.
(c) Thomas Holder, Schrodinger, LLC
'''
import os
from pymol import cmd
@cmd.extend
def load_pdbml(filename, object='', discrete=0, multiplex=1, zoom=-1, quiet=1, _self=cmd):
'''
DESCRIPTION
Load a PDBML formatted structure file
'''
from lxml import etree
from chempy import Atom, models
from collections import defaultdict
multiplex, discrete = int(multiplex), int(discrete)
try:
root = etree.parse(filename).getroot()
atom_site_list = root.xpath('./PDBx:atom_siteCategory/PDBx:atom_site', namespaces=root.nsmap)
except etree.XMLSyntaxError:
print " Error: File doesn't look like XML"
return
except etree.XPathEvalError:
print " Error: XML file doesn't look like a PDBML file"
return
if not atom_site_list:
print ' Error: no PDBx:atom_site nodes found in XML file'
return
# state -> model dictionary
model_dict = defaultdict(models.Indexed)
# atoms
for atom_site in atom_site_list:
atom = Atom()
atom.coord = [None, None, None]
model_num = 1
for child in atom_site:
tag = etree.QName(child).localname
if tag == 'Cartn_x':
atom.coord[0] = float(child.text)
elif tag == 'Cartn_y':
atom.coord[1] = float(child.text)
elif tag == 'Cartn_z':
atom.coord[2] = float(child.text)
elif tag == 'B_iso_or_equiv':
atom.b = float(child.text)
elif tag == 'auth_asym_id':
atom.chain = child.text or ''
elif tag == 'auth_atom_id':
atom.name = child.text or ''
elif tag == 'auth_comp_id':
atom.resn = child.text or ''
elif tag == 'auth_seq_id':
atom.resi = child.text or ''
elif tag == 'label_alt_id':
atom.resi = child.text or ''
elif tag == 'label_asym_id':
atom.segi = child.text or ''
elif tag == 'label_atom_id':
if not atom.name:
atom.name = child.text or ''
elif tag == 'label_comp_id':
if not atom.resn:
atom.resn = child.text or ''
elif tag == 'label_seq_id':
if not atom.resi:
atom.resi = child.text or ''
elif tag == 'label_entity_id':
atom.properties['entity_id'] = child.text or ''
elif tag == 'occupancy':
atom.q = float(child.text)
elif tag == 'pdbx_PDB_model_num':
model_num = int(child.text)
elif tag == 'type_symbol':
atom.symbol = child.text or ''
elif tag == 'group_PDB':
atom.hetatm = (child.text == 'HETATM')
if None not in atom.coord:
model_dict[model_num].add_atom(atom)
# symmetry and cell
try:
node = root.xpath('./PDBx:cellCategory/PDBx:cell', namespaces=root.nsmap)[0]
cell = [float(node.xpath('./PDBx:' + a + '/text()', namespaces=root.nsmap)[0])
for a in ['length_a', 'length_b', 'length_c',
'angle_alpha', 'angle_beta', 'angle_gamma']]
spacegroup = root.xpath(
'./PDBx:symmetryCategory/PDBx:symmetry/PDBx:space_group_name_H-M/text()',
namespaces=root.nsmap)[0]
except IndexError:
cell = None
spacegroup = ''
# object name
if not object:
object = os.path.basename(filename).split('.', 1)[0]
# only multiplex if more than one model/state
multiplex = multiplex and len(model_dict) > 1
# load models as objects or states
for model_num in sorted(model_dict):
if model_num < 1:
print " Error: model_num < 1 not supported"
continue
model = model_dict[model_num]
model.connect_mode = 3
if cell:
model.cell = cell
model.spacegroup = spacegroup
if multiplex:
oname = '%s_%04d' % (object , model_num)
model_num = 1
else:
oname = object
_self.load_model(model, oname,
state=model_num, zoom=zoom,
discrete=discrete)
On 23 Sep 2015, at 03:27, Arthur Zalevsky <aozalev...@fbb.msu.ru> wrote:
> Sorry for bumping old thread, but is support for pdbml still
> unimplemented? In such case i think it's a good project for our
> students.
>
> Regards,
> Arthur
>
>> From: Thomas Holder <speleo3@us...> - 2013-12-02 19:23:18
>> Hi Jerome,
>>
>> I think the simple reason is that nobody ever wrote a PDBML parser for
>> PyMOL. Is that a good reason?
>>
>> Cheers,
>> Thomas
>>
>>> On 28 Nov 2013, at 13:21, Jerome BENOIT <g6299304p@...> wrote:
>>> Hello List,
>>>
>>> is there any good reason why PyMOL can not read PDBML data files ?
>>>
>>> Cheers,
>>> Jerome
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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