From 8fd7c2a5131f2eaecc31e7f47c36cea3c4551d04 Mon Sep 17 00:00:00 2001
From: Berk Onat <b.onat@warwick.ac.uk>
Date: Tue, 13 Mar 2018 10:57:01 +0000
Subject: [PATCH] Correction for arrays in topology extraction through ParmEd
in MDDataAccess
---
.../nomadcore/md_data_access/MDDataAccess.py | 27 +++++++++++++------
1 file changed, 19 insertions(+), 8 deletions(-)
diff --git a/common/python/nomadcore/md_data_access/MDDataAccess.py b/common/python/nomadcore/md_data_access/MDDataAccess.py
index 806a692..cde30a7 100644
--- a/common/python/nomadcore/md_data_access/MDDataAccess.py
+++ b/common/python/nomadcore/md_data_access/MDDataAccess.py
@@ -422,6 +422,16 @@ def pmdConvertTopoDict(topoStor, topoPMD):
def atompairids(atom1,atom2):
return [atom1[0],atom2[0]]
+
+ def getX(x, attr, attr2=None):
+ try:
+ if attr2 is not None:
+ xa = getattr(x, attr)
+ return getX(xa, attr2)
+ else:
+ return getattr(x, attr)
+ except AttributeError:
+ return None
structure=None
segmentList = None
@@ -435,14 +445,15 @@ def pmdConvertTopoDict(topoStor, topoPMD):
# If topo is a PsfFile, the parameter files were not supplied.
# Hence, we can only extract topo info from Psf class in topo.
if isinstance(topoPMD, pmd.charmm.CharmmPsfFile):
- structure = [[x.name, x.type, x.residue.name,
- x.residue._idx, x.residue.segid,
- x.residue.chain, x.altloc,
- x.irotat, x.occupancy, x.bfactor, x.mass,
- x._charge, x.solvent_radius, x.atomic_number,
- x.tree, x.atom_type.name, x.atom_type.epsilon,
- x.atom_type.rmin, x.atom_type.epsilon_14,
- x.atom_type.rmin_14, x.atom_type.nbfix] for x in topoPMD.atoms]
+ structure = [[getX(x,'name'), getX(x,'type'), getX(x,'residue','name'),
+ getX(x,'residue','_idx'), getX(x,'residue','segid'),
+ getX(x,'residue','chain'), getX(x,'altloc'),
+ getX(x,'irotat'), getX(x,'occupancy'), getX(x,'bfactor'),
+ getX(x,'mass'), getX(x,'_charge'), getX(x,'solvent_radius'),
+ getX(x,'atomic_number'), getX(x,'tree'), getX(x,'atom_type','name'),
+ getX(x,'atom_type','epsilon'), getX(x,'atom_type','rmin'),
+ getX(x,'atom_type','epsilon_14'), getX(x,'atom_type','rmin_14'),
+ getX(x,'atom_type','nbfix')] for x in topoPMD.atoms]
chainList = [a[5] for a in structure]
segmentList = [a[4] for a in structure]
residList = [a[3] for a in structure]
--
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