def assign_types(model, forcefield=protein_amber, histidine='HIE'):
'''
assigns types: takes HIS -> HID,HIE,HIP and CYS->CYX where appropriate
but does not add any bonds!
'''
if feedback['actions']:
print(" " + str(__name__) + ": assigning types...")
if not isinstance(model, chempy.models.Indexed):
raise ValueError('model is not an "Indexed" model object')
if model.nAtom:
crd = model.get_coord_list()
nbr = Neighbor(crd, MAX_BOND_LEN)
res_list = model.get_residues()
if len(res_list):
for a in res_list:
base = model.atom[a[0]]
if not base.hetatm:
resn = base.resn
if resn == 'HIS':
for c in range(a[0], a[1]): # this residue
model.atom[c].resn = histidine
resn = histidine
if resn == 'N-M': # N-methyl from Insight II,
for c in range(a[0], a[1]): # this residue
model.atom[c].resn = 'NME'
resn = 'NME'
# find out if this is n or c terminal residue
names = []
for b in range(a[0], a[1]):
names.append(model.atom[b].name)
tmpl = protein_residues.normal
if forcefield:
ffld = forcefield.normal
for b in N_TERMINAL_ATOMS:
if b in names:
tmpl = protein_residues.n_terminal
if forcefield:
ffld = forcefield.n_terminal
break
for b in C_TERMINAL_ATOMS:
if b in names:
tmpl = protein_residues.c_terminal
if forcefield:
ffld = forcefield.c_terminal
break
if resn not in tmpl:
raise RuntimeError("unknown residue type '" + resn +
"'")
else:
# reassign atom names and build dictionary
dict = {}
aliases = tmpl[resn]['aliases']
for b in range(a[0], a[1]):
at = model.atom[b]
if at.name in aliases:
at.name = aliases[at.name]
dict[at.name] = b
if forcefield:
k = (resn, at.name)
if k in ffld:
at.text_type = ffld[k]['type']
at.partial_charge = ffld[k]['charge']
else:
raise RuntimeError("no parameters for '" +
str(k) + "'")
if 'SG' in dict: # cysteine
cur = dict['SG']
at = model.atom[cur]
lst = nbr.get_neighbors(at.coord)
for b in lst:
if b > cur: # only do this once (only when b>cur - i.e. this is 1st CYS)
at2 = model.atom[b]
if at2.name == 'SG':
if not at2.in_same_residue(at):
dst = distance(at.coord, at2.coord)
if dst <= MAX_BOND_LEN:
if forcefield:
for c in range(
a[0], a[1]
): # this residue
atx = model.atom[c]
atx.resn = 'CYX'
resn = atx.resn
if (c <= b):
k = ('CYX',
atx.name)
if k in ffld:
atx.text_type = ffld[
k]['type']
atx.partial_charge = ffld[
k]['charge']
else:
raise RuntimeError(
"no parameters for '"
+ str(k) +
"'")
for d in res_list: # other residue
if (b >= d[0]) and (
b < d[1]):
for c in range(
d[0],
d[1]):
atx = model.atom[
c]
atx.resn = 'CYX'
# since b>cur, assume assignment later on
break
def assign_types(model, forcefield = protein_amber, histidine = 'HIE' ):
'''
assigns types: takes HIS -> HID,HIE,HIP and CYS->CYX where appropriate
but does not add any bonds!
'''
if feedback['actions']:
print(" "+str(__name__)+": assigning types...")
if not isinstance(model, chempy.models.Indexed):
raise ValueError('model is not an "Indexed" model object')
if model.nAtom:
crd = model.get_coord_list()
nbr = Neighbor(crd,MAX_BOND_LEN)
res_list = model.get_residues()
if len(res_list):
for a in res_list:
base = model.atom[a[0]]
if not base.hetatm:
resn = base.resn
if resn == 'HIS':
for c in range(a[0],a[1]): # this residue
model.atom[c].resn = histidine
resn = histidine
if resn == 'N-M': # N-methyl from Insight II,
for c in range(a[0],a[1]): # this residue
model.atom[c].resn = 'NME'
resn = 'NME'
# find out if this is n or c terminal residue
names = []
for b in range(a[0],a[1]):
names.append(model.atom[b].name)
tmpl = protein_residues.normal
if forcefield:
ffld = forcefield.normal
for b in N_TERMINAL_ATOMS:
if b in names:
tmpl = protein_residues.n_terminal
if forcefield:
ffld = forcefield.n_terminal
break
for b in C_TERMINAL_ATOMS:
if b in names:
tmpl = protein_residues.c_terminal
if forcefield:
ffld = forcefield.c_terminal
break
if resn not in tmpl:
raise RuntimeError("unknown residue type '"+resn+"'")
else:
# reassign atom names and build dictionary
dict = {}
aliases = tmpl[resn]['aliases']
for b in range(a[0],a[1]):
at = model.atom[b]
if at.name in aliases:
at.name = aliases[at.name]
dict[at.name] = b
if forcefield:
k = (resn,at.name)
if k in ffld:
at.text_type = ffld[k]['type']
at.partial_charge = ffld[k]['charge']
else:
raise RuntimeError("no parameters for '"+str(k)+"'")
if 'SG' in dict: # cysteine
cur = dict['SG']
at = model.atom[cur]
lst = nbr.get_neighbors(at.coord)
for b in lst:
if b>cur: # only do this once (only when b>cur - i.e. this is 1st CYS)
at2 = model.atom[b]
if at2.name=='SG':
if not at2.in_same_residue(at):
dst = distance(at.coord,at2.coord)
if dst<=MAX_BOND_LEN:
if forcefield:
for c in range(a[0],a[1]): # this residue
atx = model.atom[c]
atx.resn = 'CYX'
resn = atx.resn
if (c<=b):
k = ('CYX',atx.name)
if k in ffld:
atx.text_type = ffld[k]['type']
atx.partial_charge = ffld[k]['charge']
else:
raise RuntimeError("no parameters for '"+str(k)+"'")
for d in res_list: # other residue
if (b>=d[0]) and (b<d[1]):
for c in range(d[0],d[1]):
atx = model.atom[c]
atx.resn = 'CYX'
# since b>cur, assume assignment later on
break
def add_bonds(model, forcefield=protein_amber, histidine='HIE'):
'''
add_bonds(model, forcefield = protein_amber, histidine = 'HIE' )
(1) fixes aliases, assigns types, makes HIS into HIE,HID, or HIP
and changes cystine to CYX
(2) adds bonds between existing atoms
'''
if feedback['actions']:
print(" " + str(__name__) + ": assigning types and bonds...")
if not isinstance(model, chempy.models.Indexed):
raise ValueError('model is not an "Indexed" model object')
if model.nAtom:
crd = model.get_coord_list()
nbr = Neighbor(crd, MAX_BOND_LEN)
res_list = model.get_residues()
if len(res_list):
for a in res_list:
base = model.atom[a[0]]
if not base.hetatm:
resn = base.resn
if resn == 'HIS':
for c in range(a[0], a[1]): # this residue
model.atom[c].resn = histidine
resn = histidine
if resn == 'N-M': # N-methyl from Insight II,
for c in range(a[0], a[1]): # this residue
model.atom[c].resn = 'NME'
resn = 'NME'
# find out if this is n or c terminal residue
names = []
for b in range(a[0], a[1]):
names.append(model.atom[b].name)
tmpl = protein_residues.normal
if forcefield:
ffld = forcefield.normal
for b in N_TERMINAL_ATOMS:
if b in names:
tmpl = protein_residues.n_terminal
if forcefield:
ffld = forcefield.n_terminal
break
for b in C_TERMINAL_ATOMS:
if b in names:
tmpl = protein_residues.c_terminal
if forcefield:
ffld = forcefield.c_terminal
break
if resn not in tmpl:
raise RuntimeError("unknown residue type '" + resn +
"'")
else:
# reassign atom names and build dictionary
dict = {}
aliases = tmpl[resn]['aliases']
for b in range(a[0], a[1]):
at = model.atom[b]
if at.name in aliases:
at.name = aliases[at.name]
dict[at.name] = b
if forcefield:
k = (resn, at.name)
if k in ffld:
at.text_type = ffld[k]['type']
at.partial_charge = ffld[k]['charge']
else:
raise RuntimeError("no parameters for '" +
str(k) + "'")
# now add bonds for atoms which are present
bonds = tmpl[resn]['bonds']
mbond = model.bond
for b in list(bonds.keys()):
if b[0] in dict and b[1] in dict:
bnd = Bond()
bnd.index = [dict[b[0]], dict[b[1]]]
bnd.order = bonds[b]['order']
mbond.append(bnd)
if 'N' in dict: # connect residues N-C based on distance
cur_n = dict['N']
at = model.atom[cur_n]
lst = nbr.get_neighbors(at.coord)
for b in lst:
at2 = model.atom[b]
if at2.name == 'C':
if not at2.in_same_residue(at):
dst = distance(at.coord, at2.coord)
if dst <= PEPT_CUTOFF:
bnd = Bond()
bnd.index = [cur_n, b]
bnd.order = 1
mbond.append(bnd)
break
if 'SG' in dict: # cysteine
cur = dict['SG']
at = model.atom[cur]
lst = nbr.get_neighbors(at.coord)
for b in lst:
if b > cur: # only do this once (only when b>cur - i.e. this is 1st CYS)
at2 = model.atom[b]
if at2.name == 'SG':
if not at2.in_same_residue(at):
dst = distance(at.coord, at2.coord)
if dst <= MAX_BOND_LEN:
bnd = Bond()
bnd.index = [cur, b]
bnd.order = 1
mbond.append(bnd)
if forcefield:
for c in range(
a[0], a[1]
): # this residue
atx = model.atom[c]
atx.resn = 'CYX'
resn = atx.resn
k = ('CYX', atx.name)
if k in ffld:
atx.text_type = ffld[
k]['type']
atx.partial_charge = ffld[
k]['charge']
else:
raise RuntimeError(
"no parameters for '"
+ str(k) + "'")
for d in res_list:
if (b >= d[0]) and (
b < d[1]
): # find other residue
for c in range(
d[0],
d[1]):
atx = model.atom[
c]
atx.resn = 'CYX'
# since b>cur, assume assignment later on
break
def add_bonds(model, forcefield = protein_amber, histidine = 'HIE' ):
'''
add_bonds(model, forcefield = protein_amber, histidine = 'HIE' )
(1) fixes aliases, assigns types, makes HIS into HIE,HID, or HIP
and changes cystine to CYX
(2) adds bonds between existing atoms
'''
if feedback['actions']:
print(" "+str(__name__)+": assigning types and bonds...")
if not isinstance(model, chempy.models.Indexed):
raise ValueError('model is not an "Indexed" model object')
if model.nAtom:
crd = model.get_coord_list()
nbr = Neighbor(crd,MAX_BOND_LEN)
res_list = model.get_residues()
if len(res_list):
for a in res_list:
base = model.atom[a[0]]
if not base.hetatm:
resn = base.resn
if resn == 'HIS':
for c in range(a[0],a[1]): # this residue
model.atom[c].resn = histidine
resn = histidine
if resn == 'N-M': # N-methyl from Insight II,
for c in range(a[0],a[1]): # this residue
model.atom[c].resn = 'NME'
resn = 'NME'
# find out if this is n or c terminal residue
names = []
for b in range(a[0],a[1]):
names.append(model.atom[b].name)
tmpl = protein_residues.normal
if forcefield:
ffld = forcefield.normal
for b in N_TERMINAL_ATOMS:
if b in names:
tmpl = protein_residues.n_terminal
if forcefield:
ffld = forcefield.n_terminal
break
for b in C_TERMINAL_ATOMS:
if b in names:
tmpl = protein_residues.c_terminal
if forcefield:
ffld = forcefield.c_terminal
break
if resn not in tmpl:
raise RuntimeError("unknown residue type '"+resn+"'")
else:
# reassign atom names and build dictionary
dict = {}
aliases = tmpl[resn]['aliases']
for b in range(a[0],a[1]):
at = model.atom[b]
if at.name in aliases:
at.name = aliases[at.name]
dict[at.name] = b
if forcefield:
k = (resn,at.name)
if k in ffld:
at.text_type = ffld[k]['type']
at.partial_charge = ffld[k]['charge']
else:
raise RuntimeError("no parameters for '"+str(k)+"'")
# now add bonds for atoms which are present
bonds = tmpl[resn]['bonds']
mbond = model.bond
for b in list(bonds.keys()):
if b[0] in dict and b[1] in dict:
bnd = Bond()
bnd.index = [ dict[b[0]], dict[b[1]] ]
bnd.order = bonds[b]['order']
mbond.append(bnd)
if 'N' in dict: # connect residues N-C based on distance
cur_n = dict['N']
at = model.atom[cur_n]
lst = nbr.get_neighbors(at.coord)
for b in lst:
at2 = model.atom[b]
if at2.name=='C':
if not at2.in_same_residue(at):
dst = distance(at.coord,at2.coord)
if dst<=PEPT_CUTOFF:
bnd=Bond()
bnd.index = [cur_n,b]
bnd.order = 1
mbond.append(bnd)
break
if 'SG' in dict: # cysteine
cur = dict['SG']
at = model.atom[cur]
lst = nbr.get_neighbors(at.coord)
for b in lst:
if b>cur: # only do this once (only when b>cur - i.e. this is 1st CYS)
at2 = model.atom[b]
if at2.name=='SG':
if not at2.in_same_residue(at):
dst = distance(at.coord,at2.coord)
if dst<=MAX_BOND_LEN:
bnd=Bond()
bnd.index = [cur,b]
bnd.order = 1
mbond.append(bnd)
if forcefield:
for c in range(a[0],a[1]): # this residue
atx = model.atom[c]
atx.resn = 'CYX'
resn = atx.resn
k = ('CYX',atx.name)
if k in ffld:
atx.text_type = ffld[k]['type']
atx.partial_charge = ffld[k]['charge']
else:
raise RuntimeError("no parameters for '"+str(k)+"'")
for d in res_list:
if (b>=d[0]) and (b<d[1]): # find other residue
for c in range(d[0],d[1]):
atx = model.atom[c]
atx.resn = 'CYX'
# since b>cur, assume assignment later on
break