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 | |||

# | # | |||

# | # | |||

# | # | |||

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 | |||

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. | ||||

1 lines changed or deleted | | 2 lines changed or added |