From 4ce52b58fd09505d0917bb9d1616245c6aabcf5c Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 23 Oct 2019 19:14:49 +0200
Subject: [PATCH] Allow to choose remote repository if remote=True in
io.LoadPDB
---
modules/io/pymod/__init__.py | 20 +++++++++++++++-----
1 file changed, 15 insertions(+), 5 deletions(-)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 98d952269..2a8232118 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -65,8 +65,8 @@ def _override(val1, val2):
def LoadPDB(filename, restrict_chains="", no_hetatms=None,
fault_tolerant=None, load_multi=False, quack_mode=None,
join_spread_atom_records=None, calpha_only=None,
- profile='DEFAULT', remote=False, dialect=None,
- seqres=False, bond_feasibility_check=None):
+ profile='DEFAULT', remote=False, remote_repo='pdb',
+ dialect=None, seqres=False, bond_feasibility_check=None):
"""
Load PDB file from disk and return one or more entities. Several options
allow to customize the exact behaviour of the PDB import. For more information
@@ -90,8 +90,16 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
:attr:`IOProfile.join_spread_atom_records`.
:param remote: If set to True, the method tries to load the pdb from the
- remote pdb repository www.pdb.org. The filename is then interpreted as the
- pdb id.
+ remote repository given as *remote_repo*. The filename is then
+ interpreted as the entry id as further specified for the *remote_repo*
+ parameter.
+
+ :param remote_repo: Remote repository to fetch structure if *remote* is True.
+ Must be one in ['pdb', 'smtl', 'pdb_redo']. In case of
+ 'pdb' and 'pdb_redo', the entry must be given as lower
+ case pdb id, which loads the deposited assymetric unit
+ (e.g. '1ake'). In case of 'smtl', the entry must also
+ specify the desired biounit (e.g. '1ake.1').
:rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is
True.
@@ -135,8 +143,10 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
tmp_file = None # avoid getting out of scope
if remote:
+ if remote_repo not in ['pdb', 'smtl', 'pdb_redo']:
+ raise IOError("remote_repo must be in ['pdb', 'smtl', 'pdb_redo']")
from ost.io.remote import RemoteGet
- tmp_file =RemoteGet(filename)
+ tmp_file =RemoteGet(filename, from_repo=remote_repo)
filename = tmp_file.name
conop_inst=conop.Conopology.Instance()
--
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