Refactor: Modularize mol3D class into a package with I/O, geometry, and vectorized methods#538
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sniderg wants to merge 3 commits into
Open
Refactor: Modularize mol3D class into a package with I/O, geometry, and vectorized methods#538sniderg wants to merge 3 commits into
sniderg wants to merge 3 commits into
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| import re | ||
| import sys | ||
| import time | ||
| import tempfile |
| s = xyzstring.split('\n') | ||
| try: | ||
| s.remove('') | ||
| except ValueError: |
| s = filename.split('\n') | ||
| try: | ||
| s.remove('') | ||
| except ValueError: |
| with open(filename, 'w') as f: | ||
| f.write(mol_contents) | ||
|
|
||
| def writemol2(self, filename, writestring=False, ignoreX=False, force=False): |
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| def writemol2_bodict( | ||
| self, | ||
| ignore_dummy_atoms=True, | ||
| write_bond_orders=True, | ||
| return_string=True, | ||
| output_file=None | ||
| ): |
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| def writexyz(self, filename, symbsonly=True, ignoreX=False, | ||
| ordering=False, writestring=False, withgraph=False, | ||
| specialheader=False, no_tabs=False): |
Contributor
|
Hi, this is a good idea. I am a bit swamped so I am unsure when I can get around to fixing it for the tests, if you get time let me know. In the meantime I will let the pull stand as I don't want to close it yet since I think this is a good approach for a class as dense as mol3D. Best,
|
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Converts
mol3D.py→ mol3D/package with
core.py, io.py, geometry.py
Extracts 20+ I/O methods and geometric transforms into mixin classes
Vectorizes centermass, centersym, adds get_coords_matrix()/ get_mass_vector()
Fixes writemol2 bug: missing bond_count increment when bond orders present
Full backward compatibility — zero import changes needed