def fix_carbonyl(residue_id, cg, at, cross_vector):
chiral = {}
carbonyl = {}
for atom in at:
if at[atom]['atom'] in ['N', 'CA', 'C', 'O']:
carbonyl[at[atom]['atom']] = atom
if at[atom]['atom'] in g_var.res_top[at[atom]
['res_type']]['CHIRAL']['atoms']:
chiral[at[atom]['atom']] = atom
if not np.any(cross_vector):
ca = []
res_off = 0
for x in range(2):
for bead in cg[residue_id + res_off]:
resname = cg[residue_id + res_off][next(
iter(cg[residue_id + res_off]))]['residue_name']
if bead in g_var.res_top[resname]['CONNECT']:
if x == 0:
ca.append(cg[residue_id + res_off][bead]['coord'])
for con_val, con_dir in enumerate(
g_var.res_top[resname]['CONNECT'][bead]['dir']):
if con_dir > 0:
ca.append(cg[residue_id + con_dir + res_off]
[g_var.res_top[resname]['CONNECT'][bead]
['Con_Bd'][con_val]]['coord'])
res_off = con_dir
cross_vector = at_mod.find_cross_vector(ca)
rotation = at_mod.align_to_vector(
at_mod.noramlised_vector(at[carbonyl['O']]['coord'],
at[carbonyl['C']]['coord']), cross_vector)
at[carbonyl['O']]['coord'] = (
at[carbonyl['O']]['coord'] -
at[carbonyl['C']]['coord']).dot(rotation) + at[carbonyl['C']]['coord']
at[carbonyl['C']]['coord'] = at[
carbonyl['C']]['coord'] + cross_vector * 0.2
at[carbonyl['N']]['coord'] = at[
carbonyl['N']]['coord'] - cross_vector * 0.5
if len(g_var.res_top[at[1]['res_type']]['CHIRAL']) >= 2:
for chiral_group in g_var.res_top[at[1]['res_type']]['CHIRAL']:
if chiral_group != 'atoms':
p1 = chiral[chiral_group]
c1 = chiral[g_var.res_top[at[1]['res_type']]['CHIRAL']
[chiral_group]['c1']]
c2 = chiral[g_var.res_top[at[1]['res_type']]['CHIRAL']
[chiral_group]['c2']]
c3 = chiral[g_var.res_top[at[1]['res_type']]['CHIRAL']
[chiral_group]['c3']]
cross_vector_chiral = at_mod.find_cross_vector(
[at[c3]['coord'], at[c2]['coord'], at[c1]['coord']])
at[p1]['coord'] = at[p1]['coord'] + cross_vector_chiral * 0.5
if g_var.res_top[at[1]['res_type']]['CHIRAL'][chiral_group][
'm'] in chiral:
m = chiral[g_var.res_top[at[1]['res_type']]['CHIRAL']
[chiral_group]['m']]
at[m]['coord'] = at[m]['coord'] + cross_vector_chiral * 1
return at, cross_vector
def fix_carbonyl_chiral(residue_id, cg, at, cross_vector):
chiral, carbonyl = get_chiral_carbonyl(at)
if not np.any(cross_vector):
ca = get_crossvector(cg, residue_id)
cross_vector = at_mod.find_cross_vector(ca)
at = correct_carbonyl_alignment(at, cross_vector, carbonyl)
if len(g_var.res_top[at[1]['res_type']]['CHIRAL']) >= 2:
at = correct_protein_chiral(at, chiral)
return at, cross_vector
def correct_protein_chiral(at, chiral):
for chiral_group in g_var.res_top[at[1]['res_type']]['CHIRAL']:
if chiral_group != 'atoms':
atom_list = [chiral[chiral_group]]
for chiral_atoms in ['c1','c2','c3']:
atom_list.append(chiral[g_var.res_top[at[1]['res_type']]['CHIRAL'][chiral_group][chiral_atoms]])
cross_vector_chiral = at_mod.find_cross_vector( [at[atom_list[3]]['coord'], at[atom_list[2]]['coord'], at[atom_list[1]]['coord']])
at[atom_list[0]]['coord'] = at[atom_list[0]]['coord'] + cross_vector_chiral*0.5
if g_var.res_top[at[1]['res_type']]['CHIRAL'][chiral_group]['m'] in chiral:
m = chiral[g_var.res_top[at[1]['res_type']]['CHIRAL'][chiral_group]['m']]
at[m]['coord'] = at[m]['coord'] + cross_vector_chiral*1
return at
def fix_carbonyl(residue_id, cg, at):
ca=[]
for index in range(3):
ca.append(cg[residue_id+index]['BB']['coord'])
for atom in at:
if at[atom]['atom'] == 'C':
C = atom
if at[atom]['atom'] in 'O':
O = atom
initial_vector, cross_vector = at_mod.find_cross_vector( ca, at[C]['coord'], at[O]['coord'])
rotation = at_mod.align_to_vector(initial_vector, cross_vector)
center = ca[0]+(ca[1]-ca[0])/3
at[C]['coord'] = (at[C]['coord']-center).dot(rotation)+center
at[O]['coord'] = (at[O]['coord']-center).dot(rotation)+center
return at