is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| place.py (pymol-open-source-2.2.0) | : | place.py (pymol-open-source-2.3.0) |
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| | |
| skipping to change at line 24 | | skipping to change at line 24 |
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| # | | # |
| # | | # |
| # | | # |
| | |
| from __future__ import print_function | | from __future__ import print_function |
| | |
| from . import bond_amber | | from . import bond_amber |
| | |
| from chempy.cpv import * | | from chempy.cpv import * |
| from chempy import feedback | | from chempy import feedback |
|
| | import chempy.models |
| | |
| TET_TAN = 1.41 | | TET_TAN = 1.41 |
| TRI_TAN = 1.732 | | TRI_TAN = 1.732 |
| | |
| #------------------------------------------------------------------------------ | | #------------------------------------------------------------------------------ |
| def find_known_secondary(model,anchor,known_list): | | def find_known_secondary(model,anchor,known_list): |
| at = model.atom[anchor] | | at = model.atom[anchor] |
| h_list = [] | | h_list = [] |
| for id in known_list: | | for id in known_list: |
| for b in model.bond[id]: | | for b in model.bond[id]: |
| | |
| skipping to change at line 54 | | skipping to change at line 55 |
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| if len(h_list): # only return hydrogen as a last resort | | if len(h_list): # only return hydrogen as a last resort |
| return h_list[0] | | return h_list[0] |
| return None | | return None |
| | |
| #------------------------------------------------------------------------------ | | #------------------------------------------------------------------------------ |
| def simple_unknowns(model,bondfield=bond_amber): | | def simple_unknowns(model,bondfield=bond_amber): |
| if feedback['actions']: | | if feedback['actions']: |
| print(" "+str(__name__)+": placing unknowns...") | | print(" "+str(__name__)+": placing unknowns...") |
| # this can be used to build hydrogens and would robably work for | | # this can be used to build hydrogens and would robably work for |
| # acyclic carbons as well | | # acyclic carbons as well |
|
| if str(model.__class__) != 'chempy.models.Connected': | | if not isinstance(model, chempy.models.Connected): |
| raise ValueError('model is not a "Connected" model object') | | raise ValueError('model is not a "Connected" model object') |
| if model.nAtom: | | if model.nAtom: |
| if not model.index: | | if not model.index: |
| model.update_index() | | model.update_index() |
| idx = model.index | | idx = model.index |
| last_count = -1 | | last_count = -1 |
| while 1: | | while 1: |
| need = [ [], [], [], [] ] | | need = [ [], [], [], [] ] |
| bnd_len = bondfield.length | | bnd_len = bondfield.length |
| # find known atoms with missing neighbors, and keep track of the neighbors | | # find known atoms with missing neighbors, and keep track of the neighbors |
| | | |
| End of changes. 2 change blocks. |
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| 1 lines changed or deleted | | 2 lines changed or added |
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