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Separate finish and parse functionality #41

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merged 44 commits into from
Dec 12, 2024
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313875b
Separate NWChem "finish" and "parse" functionality
smcolby Apr 12, 2024
a2d065f
Improve NWChem parsing
smcolby Apr 12, 2024
07f14ea
Merge branch 'master' into develop
smcolby Apr 15, 2024
660a14d
Load geometry during `finish` call
smcolby Apr 15, 2024
2a84f72
Add charge/spin multiplicity params to ORCA, improve multiple geometr…
smcolby Apr 15, 2024
b49c201
Return final geometry when parsing
smcolby Apr 19, 2024
8b0757f
Begin overhaul of charge propagation
smcolby Apr 19, 2024
ce4b00d
Separate wrapper from result during return
smcolby Apr 22, 2024
a0ea3f8
Remove try/except blocks for geometry parsing
smcolby Apr 22, 2024
3d22c1e
Remove attribute update from atom count method
smcolby Apr 22, 2024
7613c5c
Remove charge kwarg
smcolby Apr 22, 2024
1f3e63b
Improve `finish` method for XTB parser
smcolby Apr 22, 2024
6dc1c3a
Remove extra blank line
smcolby Apr 23, 2024
5f45cd2
Overhaul XTB parser
smcolby Apr 23, 2024
e2a8255
Remove charge attribute in init
smcolby May 1, 2024
2b99d74
Decrease verbosity of if checks
smcolby May 1, 2024
44937f1
Simplify return for XTB when only single geometry type present
smcolby May 1, 2024
f6d0c38
Improve edge case handling when finishing a run
smcolby May 1, 2024
ad395b1
Fix bad attribute reference, return logic for XTB parser
smcolby May 1, 2024
c39a5b5
Add missing import
smcolby May 1, 2024
e4a6bd2
Fix parsing bugs for XTB
smcolby May 1, 2024
2a539e8
Remove charge as kwarg
smcolby May 1, 2024
b90ee9f
Merge pull request #36 from pnnl/charge
smcolby May 1, 2024
f8d4b2a
Merge pull request #37 from pnnl/md-refactor
smcolby May 1, 2024
d159d99
Merge branch 'develop' into separate-parsers
smcolby May 1, 2024
0dc0f7f
Return dictionary of results instead of wrapper instance
smcolby May 22, 2024
1b06c86
Add todo
smcolby May 31, 2024
5daec4a
Add view method
smcolby Jul 12, 2024
020b3b4
Add conformers and rotamers to finish method
smcolby Jul 12, 2024
d7b7f67
Merge branch 'develop' into separate-parsers
smcolby Jul 23, 2024
0699a62
Merge pull request #33 from pnnl/separate-parsers
smcolby Jul 23, 2024
43906cb
Remove TINKER functionality until stable
smcolby Jul 23, 2024
5c3c9d0
Remove unnecessary imports, reorder imports
smcolby Jul 23, 2024
e11efc5
Merge pull request #40 from pnnl/remove-openbabel
smcolby Jul 23, 2024
af284f2
Add parse module
smcolby Jul 29, 2024
3d76540
Remove tinker from program selector
smcolby Jul 30, 2024
3d48677
Remove determine bonds step for XYZ
smcolby Jul 30, 2024
f39c6c6
Remove charge kwarg from `load_xyz` function calls
smcolby Oct 18, 2024
a144c6d
Allow more recent versions of python
smcolby Dec 12, 2024
2ec213e
Update miniforge version to latest
smcolby Dec 12, 2024
dc9c131
Comment out rdkit and nwchem versions to test CI
smcolby Dec 12, 2024
32f6fc5
Disable flag to only use tar-bz2
smcolby Dec 12, 2024
ddab36c
Respecify nwchem and rdkit version minimums
smcolby Dec 12, 2024
cc34dc8
Specify python minimum
smcolby Dec 12, 2024
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Decrease verbosity of if checks
  • Loading branch information
smcolby committed May 1, 2024
commit 2b99d74c8786a7296813687bf95fae5dedebf0e7
4 changes: 2 additions & 2 deletions isicle/md.py
Original file line number Diff line number Diff line change
@@ -396,7 +396,7 @@ def finish(self):
contents = f.readlines()

# Single-structure outputs
if (basename == "struc") or (basename == "best") or (basename == "xtbopt"):
if basename in ["struc", "best", "xtbopt"]:
xyzblock = "".join(contents)

raw_mol = Chem.MolFromXYZBlock(xyzblock)
@@ -444,7 +444,7 @@ def finish(self):
ext = None

# Key management
if (ext is None) or (ext == "tmp"):
if ext in [None, "tmp"]:
key = basename
else:
key = ext