def read_chem_comp_bond_atom_ids(self, fields, field_dict, values):
try:
label_1 = field_dict['_chem_comp_bond_atom_id_1']
label_2 = field_dict['_chem_comp_bond_atom_id_2']
except KeyError:
return False
order_table = {'sing': 1, 'doub': 2, 'trip': 3, 'delo': 4}
# create index of atom name
cnt = 0
name_dict = {}
for atom in self.model.atom:
if hasattr(atom, 'name'):
name_dict[atom.name] = cnt
cnt = cnt + 1
order = field_dict.get('_chem_comp_bond_value_order', None)
for value in values:
try:
index = [
name_dict[self.index_to_str(label_1, value)],
name_dict[self.index_to_str(label_2, value)]
]
except KeyError:
print(" CIF _chem_comp_bond_atom_id, invalid keys:", value)
continue
bond = Bond()
bond.index = index
if order is not None:
order_string = self.index_to_str(order, value).lower()
bond.order = order_table.get(order_string[0:4], 1)
else:
bond.order = 1
self.model.bond.append(bond)
# don't do distance-based bonding
self.model.connect_mode = 1
return True
def read_chem_comp_bond_atom_ids(self,fields,field_dict,values):
try:
label_1 = field_dict['_chem_comp_bond_atom_id_1']
label_2 = field_dict['_chem_comp_bond_atom_id_2']
except KeyError:
return False
order_table = { 'sing' : 1, 'doub' : 2, 'trip' :3, 'delo': 4 }
# create index of atom name
cnt = 0
name_dict = {}
for atom in self.model.atom:
if hasattr(atom,'name'):
name_dict[atom.name] = cnt
cnt = cnt + 1
order = field_dict.get('_chem_comp_bond_value_order',None)
for value in values:
try:
index = [name_dict[self.index_to_str(label_1, value)],
name_dict[self.index_to_str(label_2, value)]]
except KeyError:
print " CIF _chem_comp_bond_atom_id, invalid keys:", value
continue
bond = Bond()
bond.index = index
if order != None:
order_string = self.index_to_str(order,value).lower()
bond.order = order_table.get(order_string[0:4],1)
else:
bond.order = 1
self.model.bond.append(bond)
# don't do distance-based bonding
self.model.connect_mode = 1
return True
def cap(object):
from pymol import cmd
model = cmd.get_model(object)
# guarantee identical ordering
cmd.delete(object)
cmd.load_model(model,object)
n_list = cmd.identify("(n;n &!(n;c a;2.0))")
c_list = cmd.identify("(n;c &!(n;n a;2.0))")
print n_list
print c_list
for a in n_list:
newat = copy.deepcopy(model.atom[a])
newat.coord = [
newat.coord[0] + random.random(),
newat.coord[1] + random.random(),
newat.coord[2] + random.random(),
]
newat.symbol = 'H'
newat.name = 'HN'
newat.numeric_type = 43
bond = Bond()
bond.order = 1
bond.stereo = 0
bond.index = [ a, model.nAtom ]
print "adding",newat.name,bond.index
model.add_atom(newat)
model.add_bond(bond)
for a in c_list:
newat = copy.deepcopy(model.atom[a])
newat.coord = [
newat.coord[0] + random.random(),
newat.coord[1] + random.random(),
newat.coord[2] + random.random(),
]
newat.symbol = 'H'
newat.name = 'HC'
newat.numeric_type = 41
bond = Bond()
bond.order = 1
bond.stereo = 0
bond.index = [ a, model.nAtom ]
print "adding",newat.name,bond.index
model.add_atom(newat)
model.add_bond(bond)
# reload
cmd.delete(object)
cmd.load_model(model,object)
cmd.sort(object)
def bondseeker(model, nbr, excludeH=True, ceil=BONDNOHMAX):
pairs = []
for i, at in enumerate(model.atom):
if at.symbol == "H" and excludeH:
continue
if at.symbol != "H" and not excludeH:
continue
lst = nbr.get_neighbors(at.coord)
for b in lst:
at2 = model.atom[b]
if at2.symbol == 'H': #we can always exclude these, since we don't expect to find H-H bonds. If you want to add H2 molecules, you are not in luck, I guess
continue
if excludeH and [
b, i
] in pairs: #we can save some comparisons because if we are not excluding H, we are sure that at is an H, and at2 isn't, so the pair [at2,at1] can never be added.
continue
dst = chempy.cpv.distance(at.coord, at2.coord)
if dst > ceil:
if not (at.symbol == "S" and at2.symbol == "S"
and dst < SSBONDMAX): #allow for SS bonds.
continue
pairs.append([i, b])
bnd = Bond()
bnd.index = [i, b]
bnd.order = 1 #yeah, not going to do the proper bond order.
model.bond.append(bnd)
def read_chem_comp_bond_atom_ids(self,fields,field_dict,values):
order_table = { 'sing' : 1, 'doub' : 2, 'trip' :3, 'delo': 4 }
# create index of atom name
cnt = 0
name_dict = {}
for atom in self.model.atom:
if hasattr(atom,'name'):
name_dict[atom.name] = cnt
cnt = cnt + 1
label_1 = field_dict['_chem_comp_bond_atom_id_1']
label_2 = field_dict['_chem_comp_bond_atom_id_2']
order = field_dict.get('_chem_comp_bond_value_order',None)
for value in values:
bond = Bond()
bond.index = [
name_dict[self.index_to_str(label_1,value)],
name_dict[self.index_to_str(label_2,value)]]
if order != None:
order_string = string.lower(self.index_to_str(order,value))
bond.order = order_table.get(order_string[0:4],1)
else:
bond.order = 1
self.model.bond.append(bond)
def read_chem_comp_bond_atom_ids(self, fields, field_dict, values):
order_table = {'sing': 1, 'doub': 2, 'trip': 3, 'delo': 4}
# create index of atom name
cnt = 0
name_dict = {}
for atom in self.model.atom:
if hasattr(atom, 'name'):
name_dict[atom.name] = cnt
cnt = cnt + 1
label_1 = field_dict['_chem_comp_bond_atom_id_1']
label_2 = field_dict['_chem_comp_bond_atom_id_2']
order = field_dict.get('_chem_comp_bond_value_order', None)
for value in values:
bond = Bond()
bond.index = [
name_dict[self.index_to_str(label_1, value)],
name_dict[self.index_to_str(label_2, value)]
]
if order != None:
order_string = string.lower(self.index_to_str(order, value))
bond.order = order_table.get(order_string[0:4], 1)
else:
bond.order = 1
self.model.bond.append(bond)
def read_geom_bond_atom_site_labels(self,fields,field_dict,values):
# create index of atom name
cnt = 0
name_dict = {}
for atom in self.model.atom:
if hasattr(atom,'name'):
name_dict[atom.name] = cnt
cnt = cnt + 1
label_1 = field_dict['_geom_bond_atom_site_label_1']
label_2 = field_dict['_geom_bond_atom_site_label_2']
for value in values:
bond = Bond()
bond.index = [
name_dict[self.index_to_str(label_1,value)],
name_dict[self.index_to_str(label_2,value)]]
bond.order = 1
self.model.bond.append(bond)
def read_geom_bond_atom_site_labels(self, fields, field_dict, values):
# create index of atom name
cnt = 0
name_dict = {}
for atom in self.model.atom:
if hasattr(atom, 'name'):
name_dict[atom.name] = cnt
cnt = cnt + 1
label_1 = field_dict['_geom_bond_atom_site_label_1']
label_2 = field_dict['_geom_bond_atom_site_label_2']
for value in values:
bond = Bond()
bond.index = [
name_dict[self.index_to_str(label_1, value)],
name_dict[self.index_to_str(label_2, value)]
]
bond.order = 1
self.model.bond.append(bond)
def test(self):
from chempy import Atom, Bond, models
m = models.Indexed()
for i in range(2):
a = Atom()
a.coord = [float(i), 0., 0.]
m.add_atom(a)
b = Bond()
b.index = [0, 1]
b.order = 0
m.add_bond(b)
cmd.load_model(m, 'foo')
cmd.set('valence')
cmd.show('sticks')
def add_bonds(model, topology=None, forcefield=None):
if not isinstance(model, chempy.models.Indexed):
raise ValueError('model is not an "Indexed" model object')
nAtom = model.nAtom
if nAtom:
tmpl = topology.normal
ffld = forcefield.normal
res_list = model.get_residues()
if len(res_list):
for a in res_list:
base = model.atom[a[0]]
resn = base.resn
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)
def read_geom_bond_atom_site_labels(self, fields, field_dict, values):
try:
label_1 = field_dict.get('_geom_bond_atom_site_id_1', None)
if label_1 is not None:
label_2 = field_dict['_geom_bond_atom_site_id_2']
else:
label_1 = field_dict['_geom_bond_atom_site_label_1']
label_2 = field_dict['_geom_bond_atom_site_label_2']
except KeyError:
return False
symm_1 = field_dict.get('_geom_bond_site_symmetry_1', -1)
symm_2 = field_dict.get('_geom_bond_site_symmetry_2', -1)
# create index of atom name
cnt = 0
name_dict = {}
for atom in self.model.atom:
if hasattr(atom, 'name'):
name_dict[atom.name] = cnt
cnt = cnt + 1
for value in values:
if self.index_to_str(symm_1, value) != self.index_to_str(
symm_2, value):
# don't bond to symmetry mates
continue
try:
index = [
name_dict[self.index_to_str(label_1, value)],
name_dict[self.index_to_str(label_2, value)]
]
except KeyError:
print(" CIF _geom_bond_atom_site_label, invalid keys:", value)
continue
bond = Bond()
bond.index = index
bond.order = 1
self.model.bond.append(bond)
return True
def add_bonds(model, topology = None, forcefield = None ):
if str(model.__class__) != 'chempy.models.Indexed':
raise ValueError('model is not an "Indexed" model object')
nAtom = model.nAtom
if nAtom:
tmpl = topology.normal
ffld = forcefield.normal
res_list = model.get_residues()
if len(res_list):
for a in res_list:
base = model.atom[a[0]]
resn = base.resn
if not tmpl.has_key(resn):
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 aliases.has_key(at.name):
at.name = aliases[at.name]
dict[at.name] = b
if forcefield:
k = (resn,at.name)
if ffld.has_key(k):
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 bonds.keys():
if dict.has_key(b[0]) and dict.has_key(b[1]):
bnd = Bond()
bnd.index = [ dict[b[0]], dict[b[1]] ]
bnd.order = bonds[b]['order']
mbond.append(bnd)
def _read_m_bond(self,m_bond,model):
bd_ent = m_bond[1]
bd_dat = m_bond[2]
nBond = m_bond[0]
if len(bd_dat[0]): # not empty right?
if 'i_m_from' in bd_ent and \
'i_m_to' in bd_ent and \
'i_m_order' in bd_ent:
a1 = bd_dat[bd_ent['i_m_from']]
a2 = bd_dat[bd_ent['i_m_to']]
a3 = bd_dat[bd_ent['i_m_order']]
for b in range(nBond):
bd1 = a1[b] - 1
bd2 = a2[b] - 1
bd3 = a3[b]
if bd1<bd2:
bnd = Bond()
bnd.index = [ bd1,bd2 ]
bnd.order = bd3
model.bond.append(bnd)
def read_geom_bond_atom_site_labels(self,fields,field_dict,values):
try:
label_1 = field_dict.get('_geom_bond_atom_site_id_1', None)
if label_1 is not None:
label_2 = field_dict['_geom_bond_atom_site_id_2']
else:
label_1 = field_dict['_geom_bond_atom_site_label_1']
label_2 = field_dict['_geom_bond_atom_site_label_2']
except KeyError:
return False
symm_1 = field_dict.get('_geom_bond_site_symmetry_1', -1)
symm_2 = field_dict.get('_geom_bond_site_symmetry_2', -1)
# create index of atom name
cnt = 0
name_dict = {}
for atom in self.model.atom:
if hasattr(atom,'name'):
name_dict[atom.name] = cnt
cnt = cnt + 1
for value in values:
if self.index_to_str(symm_1, value) != self.index_to_str(symm_2, value):
# don't bond to symmetry mates
continue
try:
index = [name_dict[self.index_to_str(label_1, value)],
name_dict[self.index_to_str(label_2, value)]]
except KeyError:
print " CIF _geom_bond_atom_site_label, invalid keys:", value
continue
bond = Bond()
bond.index = index
bond.order = 1
self.model.bond.append(bond)
return True
def fromList(self, MMODList):
model = Connected()
# get header information
nAtom = int(MMODList[0][1:6])
model.molecule.title = string.strip(MMODList[0][8:])
irec = 1
# loop through atoms
cnt = 0
for a in range(nAtom):
model.bond.append([])
for a in range(nAtom):
at = Atom()
at.numeric_type = int(MMODList[irec][1:4])
# extract connectivity information
tokens = string.splitfields(MMODList[irec][5:52])
at.neighbor = []
at.bondorder = []
for i in range(6):
if tokens[2 * i] != "0":
a2 = int(tokens[2 * i]) - 1
if (a2 > cnt):
b = Bond()
b.index = [cnt, a2]
b.order = int(tokens[2 * i + 1])
model.bond[b.index[0]].append(
b) # note two refs to same object
model.bond[b.index[1]].append(
b) # note two refs to same object
else:
break
# extract other information
at.coord = [
float(MMODList[irec][53:64]),
float(MMODList[irec][65:76]),
float(MMODList[irec][77:88])
]
at.resi = string.strip(MMODList[irec][89:94])
at.resi_number = int(at.resi)
resn_code = string.strip(MMODList[irec][94:95])
if len(resn_code): at.resn_code = resn_code
color_code = string.strip(MMODList[irec][96:100])
if color_code != '':
at.color_code = int(color_code)
else:
at.color_code = 0
chain = string.strip(MMODList[irec][95:96])
if len(chain): at.chain = chain
at.partial_charge = float(MMODList[irec][100:109])
at.resn = MMODList[irec][119:123]
name = string.strip(MMODList[irec][124:128])
if len(name): at.name = name
model.atom.append(at)
irec = irec + 1
cnt = cnt + 1
# fill in remaining datatypes
cnt = 1
for a in model.atom:
a.text_type = MMOD_atom_data[a.numeric_type][0]
a.symbol = MMOD_atom_data[a.numeric_type][1]
a.formal_charge = MMOD_atom_data[a.numeric_type][4]
cnt = cnt + 1
return (model.convert_to_indexed())
def add_hydrogens(model, forcefield=protein_amber, skip_sort=None):
# assumes no bonds between non-hetatms
if feedback['actions']:
print(" " + str(__name__) + ": adding hydrogens...")
if not isinstance(model, chempy.models.Connected):
raise ValueError('model is not a "Connected" model object')
if model.nAtom:
if not model.index:
model.update_index()
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
# 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:
# build dictionary
dict = {}
for b in range(a[0], a[1]):
at = model.atom[b]
dict[at.name] = b
# find missing bonds with hydrogens
bonds = tmpl[resn]['bonds']
mbond = model.bond
for b in list(bonds.keys()):
if b[0] in dict and (b[1] not in dict):
at = model.atom[dict[b[0]]]
if at.symbol != 'H':
name = b[1]
symbol = tmpl[resn]['atoms'][name][
'symbol']
if symbol == 'H':
newat = at.new_in_residue()
newat.name = name
newat.symbol = symbol
k = (resn, newat.name)
newat.text_type = ffld[k]['type']
newat.partial_charge = ffld[k][
'charge']
idx1 = model.index[id(at)]
idx2 = model.add_atom(newat)
bnd = Bond()
bnd.index = [idx1, idx2]
bnd.order = bonds[b]['order']
mbond[idx1].append(bnd)
mbond[idx2].append(bnd)
if (b[0] not in dict) and b[1] in dict:
at = model.atom[dict[b[1]]]
if at.symbol != 'H':
name = b[0]
symbol = tmpl[resn]['atoms'][name][
'symbol']
if symbol == 'H':
newat = at.new_in_residue()
newat.name = name
newat.symbol = symbol
k = (resn, newat.name)
newat.text_type = ffld[k]['type']
newat.partial_charge = ffld[k][
'charge']
idx1 = model.index[id(at)]
idx2 = model.add_atom(newat)
bnd = Bond()
bnd.index = [idx1, idx2]
bnd.order = bonds[b]['order']
mbond[idx1].append(bnd)
mbond[idx2].append(bnd)
if not skip_sort:
model.sort()
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
def convert_to_chempy_model(atom_array):
"""
Convert an :class:`AtomArray` into a :class:`chempy.models.Indexed`
object.
Returns
-------
chempy_model : Indexed
The converted structure.
"""
model = IndexedModel()
annot_cat = atom_array.get_annotation_categories()
for i in range(atom_array.array_length()):
atom = Atom()
atom.segi = atom_array.chain_id[i]
atom.chain = atom_array.chain_id[i]
atom.resi_number = atom_array.res_id[i]
atom.ins_code = atom_array.ins_code[i]
res_name = atom_array.res_name[i]
atom.resn = res_name
if len(res_name) == 1:
atom.resn_code = res_name
else:
try:
atom.resn_code = ProteinSequence.convert_letter_3to1(res_name)
except KeyError:
atom.resn_code = "X"
atom.hetatm = 1 if atom_array.hetero[i] else 0
atom.name = atom_array.atom_name[i]
atom.symbol = atom_array.element[i]
if "b_factor" in annot_cat:
atom.b = atom_array.b_factor[i]
if "occupancy" in annot_cat:
atom.q = atom_array.occupancy[i]
if "charge" in annot_cat:
atom.formal_charge = atom_array.charge[i]
atom.coord = tuple(atom_array.coord[..., i, :])
atom.index = i + 1
model.add_atom(atom)
if atom_array.bonds is not None:
for i, j, bond_type in atom_array.bonds.as_array():
bond = Bond()
bond.order = BOND_ORDER[bond_type]
bond.index = [i, j]
model.add_bond(bond)
else:
warnings.warn(
"The given atom array (stack) has no associated bond information")
return model
def MakeBond(self, at1, at2, bo):
bnd = Bond()
bnd.index = [at1.index, at2.index]
bnd.order = bo
self.model.bond.append(bnd)
def add_hydrogens(model, topology=None, forcefield=None):
if not isinstance(model, chempy.models.Connected):
raise ValueError('model is not a "Connected" model object')
nAtom = model.nAtom
if nAtom:
if not model.index:
model.update_index()
ffld = forcefield.normal
tmpl = topology.normal
res_list = model.get_residues()
if len(res_list):
for a in res_list:
base = model.atom[a[0]]
resn = base.resn
if resn not in tmpl:
raise RuntimeError("unknown residue type '" + resn + "'")
else:
# build dictionary
dict = {}
for b in range(a[0], a[1]):
at = model.atom[b]
dict[at.name] = b
# find missing bonds with hydrogens
bonds = tmpl[resn]['bonds']
mbond = model.bond
for b in list(bonds.keys()):
if b[0] in dict and (b[1] not in dict):
at = model.atom[dict[b[0]]]
if at.symbol != 'H':
name = b[1]
symbol = tmpl[resn]['atoms'][name]['symbol']
if symbol == 'H':
newat = at.new_in_residue()
newat.name = name
newat.symbol = symbol
k = (resn, newat.name)
newat.text_type = ffld[k]['type']
newat.partial_charge = ffld[k]['charge']
idx1 = model.index[id(at)]
idx2 = model.add_atom(newat)
bnd = Bond()
bnd.index = [idx1, idx2]
bnd.order = bonds[b]['order']
mbond[idx1].append(bnd)
mbond[idx2].append(bnd)
if (b[0] not in dict) and b[1] in dict:
at = model.atom[dict[b[1]]]
if at.symbol != 'H':
name = b[0]
symbol = tmpl[resn]['atoms'][name]['symbol']
if symbol == 'H':
newat = at.new_in_residue()
newat.name = name
newat.symbol = symbol
k = (resn, newat.name)
newat.text_type = ffld[k]['type']
newat.partial_charge = ffld[k]['charge']
idx1 = model.index[id(at)]
idx2 = model.add_atom(newat)
bnd = Bond()
bnd.index = [idx1, idx2]
bnd.order = bonds[b]['order']
mbond[idx1].append(bnd)
mbond[idx2].append(bnd)
for a in atoms: new_atom = Atom() new_atom.symbol = a[0] # elemental symbol new_atom.name = a[1] # atom name new_atom.resi = a[2] # residue identifier new_atom.resn = a[3] # residue name model.atom.append(new_atom) # (note that there are a bunch of other fields we're not using -- and none are required) # add coordinates onto the atoms for a in model.atom: # now assign coordinates a.coord = coords.pop(0) # now specify the bonds for a in bonds: new_bond = Bond() new_bond.index = [a[0],a[1]] # atom indices (zero-based) new_bond.order = a[2] # bond order model.bond.append(new_bond) # finally, load the model into PyMOL cmd.load_model(model,"example")
def fromList(self,molList):
model = Indexed()
# read header information
model.molecule.title = string.strip(molList[0])
model.molecule.dim_code = string.strip(molList[1][20:22])
model.molecule.comments = string.strip(molList[2])
try:
model.molecule.chiral = int(molList[3][12:15])
except:
model.molecule.chiral = 0
nAtom = int(molList[3][0:3])
nBond = int(molList[3][3:6])
# read atoms
nameDict = {}
irec = 4
cnt = 0
for a in range(nAtom):
at = Atom()
at.index = cnt
at.coord = [float(molList[irec][0:10]),
float(molList[irec][10:20]),float(molList[irec][20:30])]
at.symbol = string.strip(molList[irec][31:33])
try:
at.stereo = int(molList[irec][39:42])
except:
at.stereo = 0
chg=int(molList[irec][36:39])
if chg>0: chg=4-chg
at.formal_charge = chg
model.atom.append(at)
irec = irec + 1
cnt = cnt + 1
# read bonds
for a in range(nBond):
bnd = Bond()
bnd.index = [ int(molList[irec][0:3])-1,int(molList[irec][3:6])-1 ]
bnd.order = int(molList[irec][6:9])
try:
bnd.stereo = int(molList[irec][9:12])
except:
bnd.stereo = 0
model.bond.append(bnd)
irec = irec+1
# obtain formal charges from M CHG record
while molList[irec][0:6]!='M END':
if molList[irec][0:6]=='M CHG':
cl = string.split(string.strip(molList[irec][6:]))
cll = int(cl[0])*2
a=1
while a<=cll:
model.atom[int(cl[a])-1].formal_charge=int(cl[a+1])
a=a+2
irec =irec+1
if irec >= len(molList): break
return model
def add_hydrogens(model,forcefield=protein_amber,skip_sort=None):
# assumes no bonds between non-hetatms
if feedback['actions']:
print(" "+str(__name__)+": adding hydrogens...")
if not isinstance(model, chempy.models.Connected):
raise ValueError('model is not a "Connected" model object')
if model.nAtom:
if not model.index:
model.update_index()
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
# 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:
# build dictionary
dict = {}
for b in range(a[0],a[1]):
at = model.atom[b]
dict[at.name] = b
# find missing bonds with hydrogens
bonds = tmpl[resn]['bonds']
mbond = model.bond
for b in list(bonds.keys()):
if b[0] in dict and (b[1] not in dict):
at = model.atom[dict[b[0]]]
if at.symbol != 'H':
name = b[1]
symbol = tmpl[resn]['atoms'][name]['symbol']
if symbol == 'H':
newat = at.new_in_residue()
newat.name = name
newat.symbol = symbol
k = (resn,newat.name)
newat.text_type = ffld[k]['type']
newat.partial_charge = ffld[k]['charge']
idx1 = model.index[id(at)]
idx2 = model.add_atom(newat)
bnd = Bond()
bnd.index = [ idx1, idx2 ]
bnd.order = bonds[b]['order']
mbond[idx1].append(bnd)
mbond[idx2].append(bnd)
if (b[0] not in dict) and b[1] in dict:
at = model.atom[dict[b[1]]]
if at.symbol != 'H':
name = b[0]
symbol = tmpl[resn]['atoms'][name]['symbol']
if symbol == 'H':
newat = at.new_in_residue()
newat.name = name
newat.symbol = symbol
k = (resn,newat.name)
newat.text_type = ffld[k]['type']
newat.partial_charge = ffld[k]['charge']
idx1 = model.index[id(at)]
idx2 = model.add_atom(newat)
bnd = Bond()
bnd.index = [ idx1, idx2 ]
bnd.order = bonds[b]['order']
mbond[idx1].append(bnd)
mbond[idx2].append(bnd)
if not skip_sort:
model.sort()
def MakeBond(self,at1, at2, bo):
bnd = Bond()
bnd.index = [ at1.index, at2.index ]
bnd.order = bo
self.model.bond.append(bnd)
def add_bond(i1, i2, order, offset=0):
bond = Bond()
bond.order = order
bond.index = [i1 + offset, i2 + offset]
model.add_bond(bond)
def add_hydrogens(model,topology=None,forcefield=None):
if str(model.__class__) != 'chempy.models.Connected':
raise ValueError('model is not a "Connected" model object')
nAtom = model.nAtom
if nAtom:
if not model.index:
model.update_index()
ffld = forcefield.normal
tmpl = topology.normal
res_list = model.get_residues()
if len(res_list):
for a in res_list:
base = model.atom[a[0]]
resn = base.resn
if not tmpl.has_key(resn):
raise RuntimeError("unknown residue type '"+resn+"'")
else:
# build dictionary
dict = {}
for b in range(a[0],a[1]):
at = model.atom[b]
dict[at.name] = b
# find missing bonds with hydrogens
bonds = tmpl[resn]['bonds']
mbond = model.bond
for b in bonds.keys():
if dict.has_key(b[0]) and (not dict.has_key(b[1])):
at = model.atom[dict[b[0]]]
if at.symbol != 'H':
name = b[1]
symbol = tmpl[resn]['atoms'][name]['symbol']
if symbol == 'H':
newat = at.new_in_residue()
newat.name = name
newat.symbol = symbol
k = (resn,newat.name)
newat.text_type = ffld[k]['type']
newat.partial_charge = ffld[k]['charge']
idx1 = model.index[id(at)]
idx2 = model.add_atom(newat)
bnd = Bond()
bnd.index = [ idx1, idx2 ]
bnd.order = bonds[b]['order']
mbond[idx1].append(bnd)
mbond[idx2].append(bnd)
if (not dict.has_key(b[0])) and dict.has_key(b[1]):
at = model.atom[dict[b[1]]]
if at.symbol != 'H':
name = b[0]
symbol = tmpl[resn]['atoms'][name]['symbol']
if symbol == 'H':
newat = at.new_in_residue()
newat.name = name
newat.symbol = symbol
k = (resn,newat.name)
newat.text_type = ffld[k]['type']
newat.partial_charge = ffld[k]['charge']
idx1 = model.index[id(at)]
idx2 = model.add_atom(newat)
bnd = Bond()
bnd.index = [ idx1, idx2 ]
bnd.order = bonds[b]['order']
mbond[idx1].append(bnd)
mbond[idx2].append(bnd)
def load_cml(filename, object='', discrete=0, multiplex=1, zoom=-1,
quiet=1, _self=cmd):
'''
DESCRIPTION
Load a CML formatted structure file
'''
from chempy import Atom, Bond, models
multiplex, discrete = int(multiplex), int(discrete)
try:
root = etree.fromstring(_self.file_read(filename))
except etree.XMLSyntaxError:
raise CmdException("File doesn't look like XML")
if root.tag != 'cml':
raise CmdException('not a CML file')
molecule_list = root.findall('./molecule')
if len(molecule_list) < 2:
multiplex = 0
elif not multiplex:
discrete = 1
for model_num, molecule_node in enumerate(molecule_list, 1):
model = models.Indexed()
atom_idx = {}
for atom_node in molecule_node.findall('./atomArray/atom'):
atom = Atom()
atom.name = atom_node.get('id', '')
if 'x3' in atom_node.attrib:
atom.coord = [float(atom_node.get(a))
for a in ['x3', 'y3', 'z3']]
elif 'x2' in atom_node.attrib:
atom.coord = [float(atom_node.get(a))
for a in ['x2', 'y2']] + [0.0]
else:
print(' Warning: no coordinates for atom', atom.name)
continue
atom.symbol = atom_node.get('elementType', '')
atom.formal_charge = int(atom_node.get('formalCharge', 0))
atom_idx[atom.name] = len(model.atom)
model.add_atom(atom)
for bond_node in molecule_node.findall('./bondArray/bond'):
refs = bond_node.get('atomsRefs2', '').split()
if len(refs) == 2:
bnd = Bond()
bnd.index = [int(atom_idx[ref]) for ref in refs]
bnd.order = int(bond_node.get('order', 1))
model.add_bond(bnd)
# object name
if not object:
object = os.path.basename(filename).split('.', 1)[0]
# load models as objects or states
if multiplex:
oname = molecule_node.get('id') or _self.get_unused_name('unnamed')
model_num = 1
else:
oname = object
_self.load_model(model, oname,
state=model_num, zoom=zoom, discrete=discrete)
def fromList(self,MMODList):
model = Connected()
# get header information
nAtom = int(MMODList[0][1:6])
model.molecule.title = string.strip(MMODList[0][8:])
irec = 1
# loop through atoms
cnt = 0
for a in range(nAtom):
model.bond.append([])
for a in range(nAtom):
at = Atom()
at.numeric_type = int(MMODList[irec][1:4])
# extract connectivity information
tokens = string.splitfields(MMODList[irec][5:52])
at.neighbor = []
at.bondorder = []
for i in range(6):
if tokens[2*i] != "0":
a2 = int(tokens[2*i])-1
if (a2>cnt):
b = Bond()
b.index = [cnt,a2]
b.order = int(tokens[2*i+1])
model.bond[b.index[0]].append(b) # note two refs to same object
model.bond[b.index[1]].append(b) # note two refs to same object
else:
break
# extract other information
at.coord = [float(MMODList[irec][53:64]),
float(MMODList[irec][65:76]), float(MMODList[irec][77:88])]
at.resi = string.strip(MMODList[irec][89:94])
at.resi_number = int(at.resi)
resn_code = string.strip(MMODList[irec][94:95])
if len(resn_code): at.resn_code = resn_code
color_code = string.strip(MMODList[irec][96:100])
if color_code!='':
at.color_code = int(color_code)
else:
at.color_code = 0
chain = string.strip(MMODList[irec][95:96])
if len(chain): at.chain = chain
at.partial_charge = float(MMODList[irec][100:109])
at.resn = MMODList[irec][119:123]
name = string.strip(MMODList[irec][124:128])
if len(name): at.name = name
model.atom.append(at)
irec = irec + 1
cnt = cnt + 1
# fill in remaining datatypes
cnt = 1
for a in model.atom:
a.text_type = MMOD_atom_data[a.numeric_type][0]
a.symbol = MMOD_atom_data[a.numeric_type][1]
a.formal_charge = MMOD_atom_data[a.numeric_type][4]
cnt = cnt + 1
return(model.convert_to_indexed())
def load_cml(filename, object='', discrete=0, multiplex=1, zoom=-1,
quiet=1, _self=cmd):
'''
DESCRIPTION
Load a CML formatted structure file
'''
from chempy import Atom, Bond, models
multiplex, discrete = int(multiplex), int(discrete)
try:
root = etree.fromstring(_self.file_read(filename))
except etree.XMLSyntaxError:
raise CmdException("File doesn't look like XML")
if root.tag != 'cml':
raise CmdException('not a CML file')
molecule_list = root.findall('./molecule')
if len(molecule_list) < 2:
multiplex = 0
elif not multiplex:
discrete = 1
for model_num, molecule_node in enumerate(molecule_list, 1):
model = models.Indexed()
atom_idx = {}
for atom_node in molecule_node.findall('./atomArray/atom'):
atom = Atom()
atom.name = atom_node.get('id', '')
if 'x3' in atom_node.attrib:
atom.coord = [float(atom_node.get(a))
for a in ['x3', 'y3', 'z3']]
elif 'x2' in atom_node.attrib:
atom.coord = [float(atom_node.get(a))
for a in ['x2', 'y2']] + [0.0]
else:
print(' Warning: no coordinates for atom', atom.name)
continue
atom.symbol = atom_node.get('elementType', '')
atom.formal_charge = int(atom_node.get('formalCharge', 0))
atom_idx[atom.name] = len(model.atom)
model.add_atom(atom)
for bond_node in molecule_node.findall('./bondArray/bond'):
refs = bond_node.get('atomsRefs2', '').split()
if len(refs) == 2:
bnd = Bond()
bnd.index = [int(atom_idx[ref]) for ref in refs]
bnd.order = int(bond_node.get('order', 1))
model.add_bond(bnd)
# object name
if not object:
object = os.path.basename(filename).split('.', 1)[0]
# load models as objects or states
if multiplex:
oname = molecule_node.get('id') or _self.get_unused_name('unnamed')
model_num = 1
else:
oname = object
_self.load_model(model, oname,
state=model_num, zoom=zoom, discrete=discrete)
model = Indexed()
# append the atoms onto it
for a in atoms:
new_atom = Atom()
new_atom.symbol = a[0] # elemental symbol
new_atom.name = a[1] # atom name
new_atom.resi = a[2] # residue identifier
new_atom.resn = a[3] # residue name
model.atom.append(new_atom)
# (note that there are a bunch of other fields we're not using -- and none are required)
# add coordinates onto the atoms
for a in model.atom: # now assign coordinates
a.coord = coords.pop(0)
# now specify the bonds
for a in bonds:
new_bond = Bond()
new_bond.index = [a[0], a[1]] # atom indices (zero-based)
new_bond.order = a[2] # bond order
model.bond.append(new_bond)
# finally, load the model into PyMOL
cmd.load_model(model, "example")
def fromList(self, molList):
model = Indexed()
# read header information
model.molecule.title = string.strip(molList[0])
model.molecule.dim_code = string.strip(molList[1][20:22])
model.molecule.comments = string.strip(molList[2])
try:
model.molecule.chiral = int(molList[3][12:15])
except:
model.molecule.chiral = 0
nAtom = int(molList[3][0:3])
nBond = int(molList[3][3:6])
# read atoms
nameDict = {}
irec = 4
cnt = 0
for a in range(nAtom):
at = Atom()
at.index = cnt
at.coord = [
float(molList[irec][0:10]),
float(molList[irec][10:20]),
float(molList[irec][20:30])
]
at.symbol = string.strip(molList[irec][31:33])
try:
at.stereo = int(molList[irec][39:42])
except:
at.stereo = 0
chg = int(molList[irec][36:39])
if chg > 0: chg = 4 - chg
at.formal_charge = chg
model.atom.append(at)
irec = irec + 1
cnt = cnt + 1
# read bonds
for a in range(nBond):
bnd = Bond()
bnd.index = [
int(molList[irec][0:3]) - 1,
int(molList[irec][3:6]) - 1
]
bnd.order = int(molList[irec][6:9])
try:
bnd.stereo = int(molList[irec][9:12])
except:
bnd.stereo = 0
model.bond.append(bnd)
irec = irec + 1
# obtain formal charges from M CHG record
while molList[irec][0:6] != 'M END':
if molList[irec][0:6] == 'M CHG':
cl = string.split(string.strip(molList[irec][6:]))
cll = int(cl[0]) * 2
a = 1
while a <= cll:
model.atom[int(cl[a]) - 1].formal_charge = int(cl[a + 1])
a = a + 2
irec = irec + 1
if irec >= len(molList): break
return model
def read_moestr(contents,
object,
state=0,
finish=1,
discrete=1,
quiet=1,
zoom=-1,
_self=cmd):
moestr = contents
name = object
import sys
if sys.version_info[0] > 2 and isinstance(moestr, bytes):
moestr = moestr.decode()
cmd = _self
mr = MOEReader()
mr.appendFromStr(moestr)
split_chains = cmd.get_setting_int("moe_separate_chains")
cmd.group(name)
if hasattr(mr, 'system'):
have_valences = 0
chain_count = 0
cmd.set_color("_aseg0", [1.0, 1.0, 1.0])
aseg_color = cmd.get_color_index("_aseg0")
aseg_flag = 0
aseg_rep = {}
model = Indexed()
molecule = mr.system['molecule']
if 'atoms' in molecule:
n_atom = molecule['atoms']
model.atom = [Atom() for x in range(n_atom)]
residues = {}
chains = {}
for columns, data in molecule['attr']:
for row in data:
cur_atom = None
for key, value in zip(columns, row):
key = key[0]
if key == 'ID':
ID = value
else:
aProp = _atom_prop_map.get(key, None)
if aProp != None:
setattr(model.atom[ID - 1], aProp, value)
else:
xyz = _atom_coord_map.get(key, None)
if xyz != None:
coord = list(model.atom[ID - 1].coord)
coord[xyz] = value
model.atom[ID - 1].coord = coord
elif key in _atom_vis_map:
atom = model.atom[ID - 1]
if hasattr(atom, 'visible'):
visible = atom.visible
else:
visible = _default_visible
if key == 'aBondLook':
if value == 'cylinder':
atom.visible = 0x00000001 | visible
elif value == 'line':
atom.visible = 0x00000080 | visible
elif value == 'none':
atom.visible = -129 & Visible # 0xFFFFFF7F
elif key == 'aNucleusLook':
if value == 'sphere':
atom.visible = 0x00000002 | visible
elif value == 'small-sphere': # need to set sphere_scale=0.2 for these atoms
atom.visible = 0x00000002 | visible
atom.sphere_scale = 0.2
elif value == 'point': # nonbonded
atom.visible = 0x00000800 | visible
elif value == 'none':
atom.visible = -2067 & visible # 0xFFFFF7ED
elif key == 'aHidden':
atom.visible = 0
atom.hidden = 1
if hasattr(
atom, 'hidden'
): # be sure that hidden atoms aren't shown
atom.visible = 0
elif key in _atom_color_map:
if key == 'aRGB':
model.atom[ID - 1].trgb = value
elif key == 'aColorBy':
model.atom[ID - 1].aColorBy = value
elif key in _atom_label_map:
atom = model.atom[ID - 1]
if hasattr(atom, 'label_dict'):
atom.label_dict[key] = None
else:
atom.label_dict = {key: None}
elif key in _residue_prop_map:
resi_dict = residues.get(ID, {})
resi_dict[key] = value
residues[ID] = resi_dict
elif key in _chain_prop_map:
chain_dict = chains.get(ID, {})
if ID not in chains:
chain_count = chain_count + 1
chain_dict['count'] = chain_count
chain_dict[key] = value
chains[ID] = chain_dict
chn_keys = list(chains.keys())
chn_keys.sort()
res_keys = list(residues.keys())
res_keys.sort()
# map chain properties onto residues
chn_resi = 0
ch_colors = copy.deepcopy(_ch_colors)
unique_chain_names = {}
for chn_idx in chn_keys:
chain_dict = chains[chn_idx]
cName = make_valid_name(chain_dict.get('cName', ''))
segi = cName[0:4]
chain = cName[-1:]
if not len(cName):
if 'count' in chain_dict:
cName = "chain_" + str(chain_dict['count'])
else:
cName = str(chn_idx)
if cName not in unique_chain_names:
unique_chain_names[cName] = cName
else:
cnt = 2
while (cName + "_" + str(cnt)) in unique_chain_names:
cnt = cnt + 1
newCName = cName + "_" + str(cnt)
unique_chain_names[newCName] = cName
cName = newCName
chain_dict['chain_color'] = ch_colors[0]
ch_colors = ch_colors[1:] + [ch_colors[0]]
cResCount = chain_dict.get('cResidueCount', 0)
for res_idx in range(chn_resi, chn_resi + cResCount):
resi_dict = residues[res_keys[res_idx]]
resi_dict['chain'] = chain
resi_dict['segi'] = segi
resi_dict['cName'] = cName
resi_dict['chain_dict'] = chain_dict
chn_resi = chn_resi + cResCount
# map residue properties onto atoms
res_atom = 0
for res_idx in res_keys:
resi_dict = residues[res_idx]
rRibbonMode = resi_dict.get('rRibbonMode', 'none')
rAtomCount = resi_dict['rAtomCount']
rType = resi_dict.get('rType', '')
if rAtomCount > 0:
for at_idx in range(res_atom, res_atom + rAtomCount):
atom = model.atom[at_idx]
setattr(
atom, 'resi',
string.strip(
str(resi_dict.get('rUID', '')) +
resi_dict.get('rINS', '')))
setattr(atom, 'resn', resi_dict.get('rName', ''))
setattr(atom, 'chain', resi_dict.get('chain', ''))
setattr(atom, 'segi', resi_dict.get('segi', ''))
setattr(atom, 'custom', resi_dict.get('cName', ''))
# add labels
if hasattr(atom, 'label_dict'):
label = ''
label_dict = atom.label_dict
if 'aLabelElement' in label_dict:
label = atom.symbol
if 'aLabelRes' in label_dict:
if len(label):
label = label + ","
label = label + atom.resn + "_" + atom.resi
if 'aLabelName' in label_dict:
if len(label):
label = label + "."
label = label + atom.name
atom.label = label
if rType not in ['none', 'heme']:
atom.hetatm = 0 # all normal atoms
else:
atom.flags = 0x02000000 # hetatom or ligand -- ignore when surfacing
if rRibbonMode != 'none':
if hasattr(atom, 'visible'):
visible = atom.visible
else:
visible = _default_visible
rRibbonColorBy = resi_dict['rRibbonColorBy']
repeat = 1
while repeat:
repeat = 0
if rRibbonColorBy in ['rgb', 'r:rgb'
]: # handled automatically
pass
elif rRibbonColorBy == 'chain':
chain_dict = resi_dict['chain_dict']
cColorBy = chain_dict['cColorBy']
if cColorBy == 'rgb':
cColorBy = 'c:rgb'
rRibbonColorBy = cColorBy
repeat = 1
rRibbon_color = 0
rRibbon_trgb = 0xFFFFFF # default -- white
# now color ribbon
if rRibbonColorBy == 'r:rgb':
rRibbon_trgb = resi_dict.get('rRGB', 0xFFFFFF)
elif rRibbonColorBy == 'rgb':
rRibbon_trgb = resi_dict.get(
'rRibbonRGB', 0xFFFFFF)
elif rRibbonColorBy == 'c:rgb':
chain_dict = resi_dict['chain_dict']
rRibbon_trgb = chain_dict.get('cRGB', 0xFFFFFF)
elif rRibbonColorBy == 'r:aseg':
rRibbon_trgb = None
rRibbon_color = aseg_color
aseg_flag = 1
elif rRibbonColorBy == 'tempfactor':
pass # TO DO
elif rRibbonColorBy == 'c:number': # per chain colors
rRibbon_trgb = chain_dict['chain_color']
if rRibbonMode in ['line', 'trace']:
atom.visible = 0x00000040 | visible # PyMOL ribbon
if rRibbon_trgb != None:
atom.ribbon_trgb = rRibbon_trgb
else:
atom.ribbon_color = rRibbon_color
aseg_rep['ribbon'] = 1
else:
atom.visible = 0x00000020 | visible # PyMOL cartoon
if rRibbon_trgb != None:
atom.cartoon_trgb = rRibbon_trgb
else:
atom.cartoon_color = rRibbon_color
aseg_rep['cartoon'] = 1
if hasattr(atom, 'label'):
if hasattr(atom, 'visible'):
visible = atom.visible
else:
visible = _default_visible
atom.visible = 0x00000028 | visible # labels
if not hasattr(atom, 'aColorBy'):
atom.aColorBy = 'element'
if hasattr(atom, 'aColorBy'):
aColorBy = atom.aColorBy
repeat = 1
while repeat:
repeat = 0
if aColorBy == 'ribbon':
aColorBy = resi_dict.get('rRibbonColorBy')
if aColorBy == 'rgb':
aColorBy = 'rib:rgb'
else:
repeat = 1
# TO DO still need to handle "cartoon_color", "ribbon_color"
elif aColorBy == 'element':
if hasattr(atom, 'trgb'):
del atom.trgb
elif aColorBy in ['rgb', 'a:rgb'
]: # handled automatically
pass
elif aColorBy == 'residue':
rColorBy = resi_dict.get('rColorBy')
if rColorBy == 'rgb':
rColorBy = 'r:rgb'
aColorBy = rColorBy
repeat = 1
elif aColorBy == 'chain':
chain_dict = resi_dict['chain_dict']
cColorBy = chain_dict['cColorBy']
if cColorBy == 'rgb':
cColorBy = 'c:rgb'
aColorBy = cColorBy
repeat = 1
# now color atom...
if aColorBy == 'r:rgb':
atom.trgb = resi_dict.get('rRGB', 0xFFFFFF)
elif aColorBy == 'rib:rgb':
atom.trgb = resi_dict.get('rRibbonRGB', 0xFFFFFF)
elif aColorBy == 'c:rgb':
chain_dict = resi_dict['chain_dict']
atom.trgb = chain_dict.get('cRGB', 0xFFFFFF)
elif aColorBy == 'r:aseg':
pass # TO DO
elif aColorBy == 'tempfactor':
pass # TO DO
elif aColorBy == 'c:number': # per chain colors
atom.trgb = chain_dict['chain_color']
res_atom = res_atom + rAtomCount
bond_list = molecule.get('bond', [])
for bond in bond_list:
new_bond = Bond()
new_bond.index = [bond[0] - 1, bond[1] - 1]
if len(bond) > 2:
new_bond.order = bond[2]
if bond[2] == 2: # work around .MOE bug with triple bonds
if model.atom[new_bond.index[0]].hybridization == 'sp':
if model.atom[new_bond.index[1]].hybridization == 'sp':
new_bond.order = 3
have_valences = 1
model.bond.append(new_bond)
if 'ViewOrientationY' in mr.system:
vy = mr.system['ViewOrientationY']
vz = mr.system['ViewOrientationZ']
pos = mr.system['ViewLookAt']
scale = mr.system['ViewScale']
vx = cpv.cross_product(vy, vz)
m = [cpv.normalize(vx), cpv.normalize(vy), cpv.normalize(vz)]
m = cpv.transpose(m)
asp_rat = 0.8 # MOE default (versus 0.75 for PyMOL)
cmd.set("field_of_view", 25.0)
fov = float(cmd.get("field_of_view"))
window_height = scale * asp_rat
dist = (0.5 * window_height) / math.atan(3.1415 *
(0.5 * fov) / 180.0)
new_view = tuple(m[0] + m[1] + m[2] + [0.0, 0.0, -dist] + pos +
[dist * 0.5, dist * 1.5, 0.0])
cmd.set_view(new_view)
zoom = 0
cmd.set("auto_color", 0)
cmd.set_color("carbon", [0.5, 0.5, 0.5]) # default MOE grey
obj_name = name + ".system"
if split_chains < 0: # by default, don't split chains if over 50 objects would be created
if len(unique_chain_names) > 50:
split_chains = 0
if not split_chains:
cmd.load_model(model,
obj_name,
state=state,
finish=finish,
discrete=discrete,
quiet=quiet,
zoom=zoom)
obj_name_list = [obj_name]
else:
cmd.load_model(model,
obj_name,
state=state,
finish=finish,
discrete=discrete,
quiet=1,
zoom=zoom)
obj_name_list = []
system_name = obj_name
for chain in unique_chain_names.keys():
obj_name = name + "." + chain
obj_name_list.append(obj_name)
cmd.select("_moe_ext_tmp",
"custom %s" % chain,
domain=system_name)
cmd.extract(obj_name, "_moe_ext_tmp", quiet=quiet, zoom=0)
# cmd.extract(obj_name,system_name+" and text_type %s"%chain,quiet=quiet)
cmd.delete("_moe_ext_tmp")
if not cmd.count_atoms(system_name):
cmd.delete(system_name)
else:
obj_name_list.append(system_name)
cmd.order(name + ".*", sort=1)
for obj_name in obj_name_list:
cmd.set("stick_radius", 0.1, obj_name)
cmd.set("line_width", 2.0, obj_name)
cmd.set("label_color", "white", obj_name)
cmd.set("nonbonded_size", 0.05,
obj_name) # temporary workaround...
if have_valences: # if this MOE file has valences, then show em!
cmd.set("valence", 1, obj_name)
cmd.set("stick_valence_scale", 1.25, obj_name)
if aseg_flag:
cmd.dss(obj_name)
if 'cartoon' in aseg_rep:
cmd.set("cartoon_color", "red",
obj_name + " and cartoon_color _aseg0 and ss h")
cmd.set("cartoon_color", "yellow",
obj_name + " and cartoon_color _aseg0 and ss s")
cmd.set(
"cartoon_color", "cyan",
obj_name + " and cartoon_color _aseg0 and not ss h+s")
if 'ribbon' in aseg_rep:
cmd.set("ribbon_color", "red",
obj_name + " and ribbon_color _aseg0 and ss h"
) # need selection op ribbon_color
cmd.set("ribbon_color", "yellow",
obj_name + " and ribbon_color _aseg0 and ss s")
cmd.set(
"ribbon_color", "cyan",
obj_name + " and ribbon_color _aseg0 and not ss h+s")
if 'ViewZFront' in mr.system:
moe_front = mr.system['ViewZFront']
moe_width = mr.system['ViewZWidth']
extent = cmd.get_extent(
name) # will this work with groups? TO DO: check!
dx = (extent[0][0] - extent[1][0])
dy = (extent[0][1] - extent[1][1])
dz = (extent[0][2] - extent[1][2])
half_width = 0.5 * math.sqrt(dx * dx + dy * dy + dz * dz)
cmd.clip("atoms", 0.0, name)
cur_view = cmd.get_view()
center = (cur_view[-3] +
cur_view[-2]) * 0.5 # center of clipping slab
front = center - half_width
back = center + half_width
width = half_width * 2
new_view = tuple(
list(cur_view[0:15]) + [
front + width * moe_front, front + width *
(moe_front + moe_width), 0.0
])
cmd.set_view(new_view)
if 'graphics' in mr.system:
cgo_cnt = 1
lab_cnt = 1
unique_cgo_names = {}
for graphics in mr.system['graphics']:
cgo = []
for gvertex in graphics.get('gvertex', []):
vrt = gvertex[0]
seg_list = gvertex[1]['seg']
idx = gvertex[1]['idx']
len_idx = len(idx)
if not cmd.is_list(seg_list):
seg_list = [seg_list] * (len_idx / seg_list)
last_seg = None
ix_start = 0
for seg in seg_list:
if seg != last_seg:
if last_seg != None:
cgo.append(END)
if seg == 3:
cgo.extend([BEGIN, TRIANGLES])
elif seg == 2:
cgo.extend([BEGIN, LINES])
elif seg == 1:
cgo.extend([BEGIN, POINTS])
ix_stop = seg + ix_start
if seg == 3:
for s in idx[ix_start:ix_stop]:
v = vrt[s - 1]
cgo.extend([
COLOR, (0xFF & (v[0] >> 16)) / 255.0,
(0xFF & (v[0] >> 8)) / 255.0,
(0xFF & (v[0])) / 255.0
])
if len(v) > 4:
cgo.extend([NORMAL, v[4], v[5], v[6]])
cgo.extend([VERTEX, v[1], v[2], v[3]])
elif seg == 2:
for s in idx[ix_start:ix_stop]:
v = vrt[s - 1]
cgo.extend([
COLOR, (0xFF & (v[0] >> 16)) / 255.0,
(0xFF & (v[0] >> 8)) / 255.0,
(0xFF & (v[0])) / 255.0
])
if len(v) > 4:
cgo.extend([NORMAL, v[4], v[5], v[6]])
cgo.extend([VERTEX, v[1], v[2], v[3]])
elif seg == 1:
for s in idx[ix_start:ix_stop]:
v = vrt[s - 1]
cgo.extend([
COLOR, (0xFF & (v[0] >> 16)) / 255.0,
(0xFF & (v[0] >> 8)) / 255.0,
(0xFF & (v[0])) / 255.0
])
if len(v) > 4:
cgo.extend([NORMAL, v[4], v[5], v[6]])
cgo.extend([VERTEX, v[1], v[2], v[3]])
ix_start = ix_stop
last_seg = seg
if last_seg != None:
cgo.append(END)
for gtext in graphics.get('gtext', []):
lab_name = name + ".label_%02d" % lab_cnt
exists = 0
for entry in gtext:
exists = 1
cmd.pseudoatom(lab_name,
pos=[
float(entry[1]),
float(entry[2]),
float(entry[3])
],
color="0x%06x" % entry[0],
label=entry[4])
if exists:
cmd.set('label_color', -1, lab_name)
lab_cnt = lab_cnt + 1
# TO DO -- via CGO's?
if len(cgo):
cgo_name = name + "." + make_valid_name(
graphics.get('GTitle', 'graphics'))
if cgo_name not in unique_cgo_names:
unique_cgo_names[cgo_name] = cgo_name
else:
cnt = 2
while cgo_name + "_" + str(cnt) in unique_cgo_names:
cnt = cnt + 1
new_name = cgo_name + "_" + str(cnt)
unique_cgo_names[new_name] = new_name
cgo_name = new_name
cmd.load_cgo(cgo,
cgo_name,
state=state,
quiet=quiet,
zoom=0)
cgo_cnt = cgo_cnt + 1
cmd.set("two_sided_lighting", 1) # global setting...
cmd.set("cgo_line_width", 2, cgo_name)
if 'GTransparency' in graphics:
g_trans = graphics['GTransparency']
if len(g_trans) >= 2:
if g_trans[0] != 0:
cmd.set('cgo_transparency',
'%1.6f' % (g_trans[0] / 255.0),
cgo_name)
cmd.set('transparency_global_sort')
if 'meter' in mr.system:
meter_name = name + ".meter"
exists = 0
for meter_block in mr.system['meter']:
if meter_block[0][0:2] == ['type', 'atoms']:
for meter in meter_block[1]:
(type, atoms) = meter[0:2]
arg = tuple([meter_name] + list(
map(lambda x, o=name: o + " and id " + str(x - 1),
atoms)))
getattr(cmd, type)(*arg)
exists = 1
if exists:
cmd.color("green", meter_name)
# print mr.system['meter']
elif hasattr(mr, 'feature'):
model = Indexed()
cols = mr.feature[0]
rows = mr.feature[1]
col = {}
cnt = 0
for a in cols:
col[a] = cnt
cnt = cnt + 1
for row in rows:
atom = Atom()
atom.coord = [row[col['x']], row[col['y']], row[col['z']]]
atom.vdw = row[col['r']]
atom.custom = row[col['expr']]
model.atom.append(atom)
obj_name = name + ".feature"
cmd.load_model(model,
obj_name,
state=state,
finish=finish,
discrete=discrete,
quiet=quiet,
zoom=zoom)
rank = 1
for row in rows:
cmd.color("0x%06x" % row[col['color']],
obj_name + " & id %d" % (rank - 1))
rank = rank + 1
cmd.show("mesh", obj_name)
cmd.set("min_mesh_spacing", 0.55, obj_name)
cmd.label(obj_name, "' '+custom")
cmd.set("label_color", "yellow", obj_name)
else:
print(dir(mr))