def data_to_molecule(data: data_lammps):
"""
Creates a molecule provided a data_lammps object.
Note that the the data_lammps must only contain
one species. In the case of an atom the function
will return an error.
"""
if (not data.NBonds > 1):
sys.exit(
'data_to_molecule : ERROR - This function only works for data with bonds'
)
Atoms = []
iSpc = data.At[0].iSpc
for iAt in range(0, data.NAtoms):
At = data.At[iAt]
if (At.iSpc != iSpc):
sys.exit(
'data_to_molecule : ERROR - This function only works for data with atoms belonging to a single molecule'
)
Atoms.append(At)
Bonds = deepcopy(data.Bnd)
Angles = deepcopy(data.Ang)
return molecule(iSpc, Atoms, Bonds, Angles)
def read_cdml(text):
"""returns the last molecule for now"""
doc = dom.parseString(text)
#if doc.childNodes()[0].nodeName == 'svg':
# path = "/svg/cdml/molecule"
#else:
# path = "/cdml/molecule"
path = "//molecule"
do_not_continue_this_mol = 0
for mol_el in dom_ext.simpleXPathSearch(doc, path):
atom_id_remap = {}
mol = molecule()
groups = []
for atom_el in dom_ext.simpleXPathSearch(mol_el, "atom"):
name = atom_el.getAttribute('name')
if not name:
#print "this molecule has an invalid symbol"
do_not_continue_this_mol = 1
break
pos = dom_ext.simpleXPathSearch(atom_el, 'point')[0]
x = cm_to_float_coord(pos.getAttribute('x'))
y = cm_to_float_coord(pos.getAttribute('y'))
z = cm_to_float_coord(pos.getAttribute('z'))
if name in PT:
# its really an atom
a = atom(symbol=name,
charge=atom_el.getAttribute('charge')
and int(atom_el.getAttribute('charge')) or 0,
coords=(x, y, z))
mol.add_vertex(v=a)
elif name in cdml_to_smiles:
# its a known group
group = smiles.text_to_mol(cdml_to_smiles[name], calc_coords=0)
a = group.vertices[0]
a.x = x
a.y = y
a.z = z
mol.insert_a_graph(group)
atom_id_remap[atom_el.getAttribute('id')] = a
if do_not_continue_this_mol:
break
for bond_el in dom_ext.simpleXPathSearch(mol_el, "bond"):
type = bond_el.getAttribute('type')
if type[1] == u'0':
# we ignore bonds with order 0
continue
v1 = atom_id_remap[bond_el.getAttribute('start')]
v2 = atom_id_remap[bond_el.getAttribute('end')]
e = bond(order=int(type[1]), type=type[0])
mol.add_edge(v1, v2, e=e)
if mol.is_connected():
# this is here to handle diborane and similar weird things
yield mol
else:
for comp in mol.get_disconnected_subgraphs():
yield comp
def get_transformed_template(self, n, coords, type="empty", paper=None):
"""type is type of connection - 'bond', 'atom1'(for single atom), 'atom2'(for atom with more than 1 bond), 'empty'"""
pap = paper or Store.app.paper
pap.onread_id_sandbox_activate() # must be here to mangle the ids
current = molecule(pap, package=self.templates[n])
pap.onread_id_sandbox_finish(apply_to=[current]) # id mangling
current.name = ""
self._scale_ratio = 1
trans = transform()
# type empty - just draws the template - no conection
if type == "empty":
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1 = coords
bond_length = Screen.any_to_px(Store.app.paper.standard.bond_length)
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
trans.set_move(-xt2, -yt2)
trans.set_scaling(bond_length / math.sqrt((xt1 - xt2) ** 2 + (yt1 - yt2) ** 2))
trans.set_move(x1, y1)
# type atom
elif type == "atom1" or type == "atom2":
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1, x2, y2 = coords
trans.set_move(-xt2, -yt2)
trans.set_scaling(
math.sqrt((x1 - x2) ** 2 + (y1 - y2) ** 2) / math.sqrt((xt1 - xt2) ** 2 + (yt1 - yt2) ** 2)
)
trans.set_rotation(math.atan2(xt1 - xt2, yt1 - yt2) - math.atan2(x1 - x2, y1 - y2))
trans.set_move(x2, y2)
# type bond
elif type == "bond":
if not (current.t_bond_first and current.t_bond_second):
warn("this template is not capable to be added to bond - sorry.")
return None
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
xt1, yt1 = current.t_bond_first.get_xy()
xt2, yt2 = current.t_bond_second.get_xy()
x1, y1, x2, y2 = coords
self._scale_ratio = math.sqrt((x1 - x2) ** 2 + (y1 - y2) ** 2) / math.sqrt(
(xt1 - xt2) ** 2 + (yt1 - yt2) ** 2
) # further needed for bond.bond_width transformation
trans.set_move(-xt1, -yt1)
trans.set_rotation(math.atan2(xt1 - xt2, yt1 - yt2) - math.atan2(x1 - x2, y1 - y2))
trans.set_scaling(self._scale_ratio)
trans.set_move(x1, y1)
self.transform_template(current, trans)
# remove obsolete info from template
if type == "atom1":
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
elif type == "atom2":
current.t_atom.x = x1
current.t_atom.y = y1
current.t_atom = None
current.t_bond_first = None
current.t_bond_second = None
# return ready template
return current
def read_cdml( text):
"""returns the last molecule for now"""
doc = dom.parseString( text)
#if doc.childNodes()[0].nodeName == 'svg':
# path = "/svg/cdml/molecule"
#else:
# path = "/cdml/molecule"
path = "//molecule"
do_not_continue_this_mol = 0
for mol_el in dom_ext.simpleXPathSearch( doc, path):
atom_id_remap = {}
mol = molecule()
groups = []
for atom_el in dom_ext.simpleXPathSearch( mol_el, "atom"):
name = atom_el.getAttribute( 'name')
if not name:
#print "this molecule has an invalid symbol"
do_not_continue_this_mol = 1
break
pos = dom_ext.simpleXPathSearch( atom_el, 'point')[0]
x = cm_to_float_coord( pos.getAttribute('x'))
y = cm_to_float_coord( pos.getAttribute('y'))
z = cm_to_float_coord( pos.getAttribute('z'))
if name in PT:
# its really an atom
a = atom( symbol=name,
charge=atom_el.getAttribute( 'charge') and int( atom_el.getAttribute( 'charge')) or 0,
coords=( x, y, z))
mol.add_vertex( v=a)
elif name in cdml_to_smiles:
# its a known group
group = smiles.text_to_mol( cdml_to_smiles[ name], calc_coords=0)
a = group.vertices[0]
a.x = x
a.y = y
a.z = z
mol.insert_a_graph( group)
atom_id_remap[ atom_el.getAttribute( 'id')] = a
if do_not_continue_this_mol:
break
for bond_el in dom_ext.simpleXPathSearch( mol_el, "bond"):
type = bond_el.getAttribute( 'type')
if type[1] == u'0':
# we ignore bonds with order 0
continue
v1 = atom_id_remap[ bond_el.getAttribute( 'start')]
v2 = atom_id_remap[ bond_el.getAttribute( 'end')]
e = bond( order=int( type[1]), type=type[0])
mol.add_edge( v1, v2, e=e)
if mol.is_connected():
# this is here to handle diborane and similar weird things
yield mol
else:
for comp in mol.get_disconnected_subgraphs():
yield comp
def generate_random_universe():
u = universe()
mols = []
attractors = []
for i in range(0, 100):
mols.append(molecule(random_atom()))
u.molecules = mols
u.attractors = attractors
return u
def oasa_mol_to_bkchem_mol(mol, paper):
m = molecule.molecule(paper)
if None in reduce(operator.add, [[a.x, a.y] for a in mol.atoms], []):
calc_position = 0
else:
calc_position = 1
minx = None
maxx = None
miny = None
maxy = None
# atoms
for a in mol.vertices:
a2 = oasa_atom_to_bkchem_atom(a, paper, m)
m.insert_atom(a2)
if calc_position:
# data for rescaling
if not maxx or a2.x > maxx:
maxx = a2.x
if not minx or a2.x < minx:
minx = a2.x
if not miny or a2.y < miny:
miny = a2.y
if not maxy or a2.y > maxy:
maxy = a2.y
# bonds
bond_lengths = []
for b in mol.edges:
b2 = oasa_bond_to_bkchem_bond(b, paper)
aa1, aa2 = b.vertices
atom1 = m.atoms[mol.vertices.index(aa1)]
atom2 = m.atoms[mol.vertices.index(aa2)]
m.add_edge(atom1, atom2, b2)
b2.molecule = m
if calc_position:
bond_lengths.append(
math.sqrt((b2.atom1.x - b2.atom2.x)**2 +
(b2.atom1.y - b2.atom2.y)**2))
# rescale
if calc_position:
bl = sum(bond_lengths) / len(bond_lengths)
scale = Screen.any_to_px(paper.standard.bond_length) / bl
movex = (maxx + minx) / 2
movey = (maxy + miny) / 2
trans = transform3d.transform3d()
trans.set_move(-movex, -movey, 0)
trans.set_scaling(scale)
trans.set_move(320, 240, 0)
for a in m.atoms:
a.x, a.y, a.z = trans.transform_xyz(a.x, a.y, a.z)
return m
def _read_molecule(self, el):
m = molecule(self.paper)
for v in xpath.Evaluate("vertex", el):
a2 = self._read_atom(v, m)
m.insert_atom(a2)
# bonds
bond_lengths = []
for b in xpath.Evaluate("edge", el):
b2 = self._read_bond(b)
b2.molecule = m
m.add_edge(b2.atom1, b2.atom2, b2)
self._mol_ids[el.getAttribute('id')] = m
return m
def _read_molecule(self, el):
m = molecule(self.paper)
for v in xpath.Evaluate("vertex", el):
a2 = self._read_atom(v, m)
m.insert_atom(a2)
# bonds
bond_lengths = []
for b in xpath.Evaluate("edge", el):
b2 = self._read_bond(b)
b2.molecule = m
m.add_edge(b2.atom1, b2.atom2, b2)
self._mol_ids[el.getAttribute("id")] = m
return m
def oasa_mol_to_bkchem_mol( mol, paper):
m = molecule.molecule( paper)
if None in reduce( operator.add, [[a.x, a.y] for a in mol.atoms], []):
calc_position = 0
else:
calc_position = 1
minx = None
maxx = None
miny = None
maxy = None
# atoms
for a in mol.vertices:
a2 = oasa_atom_to_bkchem_atom( a, paper, m)
m.insert_atom( a2)
if calc_position:
# data for rescaling
if not maxx or a2.x > maxx:
maxx = a2.x
if not minx or a2.x < minx:
minx = a2.x
if not miny or a2.y < miny:
miny = a2.y
if not maxy or a2.y > maxy:
maxy = a2.y
# bonds
bond_lengths = []
for b in mol.edges:
b2 = oasa_bond_to_bkchem_bond( b, paper)
aa1, aa2 = b.vertices
atom1 = m.atoms[ mol.vertices.index( aa1)]
atom2 = m.atoms[ mol.vertices.index( aa2)]
m.add_edge( atom1, atom2, b2)
b2.molecule = m
if calc_position:
bond_lengths.append( math.sqrt( (b2.atom1.x-b2.atom2.x)**2 + (b2.atom1.y-b2.atom2.y)**2))
# rescale
if calc_position:
bl = sum( bond_lengths) / len( bond_lengths)
scale = Screen.any_to_px( paper.standard.bond_length) / bl
movex = (maxx+minx)/2
movey = (maxy+miny)/2
trans = transform3d.transform3d()
trans.set_move( -movex, -movey, 0)
trans.set_scaling( scale)
trans.set_move( 320, 240, 0)
for a in m.atoms:
a.x, a.y, a.z = trans.transform_xyz( a.x, a.y, a.z)
return m
def smiles_files_to_molecules(self, file_name, smile_pos, class_pos=None):
compounds = []
f = open(file_name, "r")
while 1:
txt = rf.read_line(f.readline())
if txt == []: break
mol_loc = self.smile_to_nodes_and_edges(txt[smile_pos])
if mol_loc["nodes"] != [] and mol_loc["edges"] != []:
clas = txt[class_pos]
if clas:
clas = int(clas)
if clas == 0: clas = -1
compounds.append([
molecule.molecule(mol_loc["nodes"], mol_loc["edges"],
mol_loc["covalences"], self.p_q),
clas
])
else:
compounds.append([
molecule.molecule(mol_loc["nodes"], mol_loc["edges"],
mol_loc["covalences"], self.p_q), '?'
])
self.my_set = compounds
return compounds
def pybel_to_oasa_molecule_with_atom_map(self, pmol):
omol = molecule()
patom_idx2oatom = {}
for pa in pmol.atoms:
oa = self.pybel_to_oasa_atom(pa)
omol.add_vertex(oa)
patom_idx2oatom[pa.idx] = oa
for pb in openbabel.OBMolBondIter(pmol.OBMol):
ob = self.pybel_to_oasa_bond(pb)
i1 = pb.GetBeginAtomIdx()
i2 = pb.GetEndAtomIdx()
oa1 = patom_idx2oatom[i1]
oa2 = patom_idx2oatom[i2]
omol.add_edge(oa1, oa2, ob)
return omol, patom_idx2oatom
def pybel_to_oasa_molecule_with_atom_map( self, pmol):
omol = molecule()
patom_idx2oatom = {}
for pa in pmol.atoms:
oa = self.pybel_to_oasa_atom( pa)
omol.add_vertex( oa)
patom_idx2oatom[ pa.idx] = oa
for pb in openbabel.OBMolBondIter( pmol.OBMol):
ob = self.pybel_to_oasa_bond( pb)
i1 = pb.GetBeginAtomIdx()
i2 = pb.GetEndAtomIdx()
oa1 = patom_idx2oatom[ i1]
oa2 = patom_idx2oatom[ i2]
omol.add_edge( oa1, oa2, ob)
return omol, patom_idx2oatom
def _read_body( self, file):
atoms = read_molfile_value( file, 3, conversion=int)
bonds = read_molfile_value( file, 3, conversion=int)
# nothing more interesting
file.readline()
# read the structure
self.structure = molecule()
for i in range( atoms):
a = self._read_atom( file)
self.structure.add_vertex( v=a)
for k in range( bonds):
b, i, j = self._read_bond( file)
self.structure.add_edge( i, j, e=b)
for line in file:
if line.strip() == "M END":
break
if line.strip().startswith( "M "):
self._read_property( line.strip())
def _read_body(self, file):
atoms = read_molfile_value(file, 3, conversion=int)
bonds = read_molfile_value(file, 3, conversion=int)
# nothing more interesting
file.readline()
# read the structure
self.structure = molecule()
for i in range(atoms):
a = self._read_atom(file)
self.structure.add_vertex(v=a)
for k in range(bonds):
b, i, j = self._read_bond(file)
self.structure.add_edge(i, j, e=b)
for line in file:
if line.strip() == "M END":
break
if line.strip().startswith("M "):
self._read_property(line.strip())
def all_file_to_molecules(self,
file_name,
class_label="",
pos_class="active",
neg_class="inactive"):
compounds = []
f = open(file_name, "r")
while 1:
txt = rf.creat_local_txt(f)
if txt == -1: return compounds
else:
mol_loc = self.mol_to_nodes_and_edges(txt, class_label,
pos_class)
#print mol_loc
if mol_loc["nodes"] != [] and mol_loc["edges"] != []:
compounds.append([
molecule.molecule(mol_loc["nodes"], mol_loc["edges"],
mol_loc["covalences"], self.p_q),
mol_loc["class"]
])
return compounds
def add_template_from_CDML( self, file):
if not os.path.isfile( file):
file = os_support.get_path( file, "template")
if not file:
warn( "template file %s does not exist - ignoring" % file)
return
try:
doc = dom.parse( file).getElementsByTagName( 'cdml')[0]
except xml.sax.SAXException:
warn( "template file %s cannot be parsed - ignoring" % file)
return
# when loading old versions of CDML try to convert them, but do nothing when they cannot be converted
import CDML_versions
CDML_versions.transform_dom_to_version( doc, config.current_CDML_version)
Store.app.paper.onread_id_sandbox_activate()
added = []
for tmp in doc.getElementsByTagName('molecule'):
self.templates.append( tmp)
m = molecule( Store.app.paper, package=tmp)
self._prepared_templates.append( m)
added.append( m)
Store.app.paper.onread_id_sandbox_finish( apply_to=[]) # just switch the id_managers, no id mangling
def show_dump():
from molecule import molecule
from graph.graph import graph
imp = molecule()
imp.read_simple_text_file(file("aaa9.txt", "r"))
removed = True
while removed:
removed = False
for e in list(imp.edges):
a1, a2 = e.vertices
for e2 in list(imp.edges):
if (e is not e2) and set(e.vertices) == set(e2.vertices):
imp.disconnect_edge(e2)
removed = True
break
if removed:
break
import coords_generator
for part in imp.get_disconnected_subgraphs():
if len(part.vertices) > 1:
coords_generator.calculate_coords(part, force=1)
coords_generator.show_mol(part)
def show_dump():
from molecule import molecule
from graph.graph import graph
imp = molecule()
imp.read_simple_text_file( file("aaa9.txt","r"))
removed = True
while removed:
removed = False
for e in list(imp.edges):
a1,a2 = e.vertices
for e2 in list(imp.edges):
if (e is not e2) and set(e.vertices) == set(e2.vertices):
imp.disconnect_edge( e2)
removed = True
break
if removed:
break
import coords_generator
for part in imp.get_disconnected_subgraphs():
if len( part.vertices) > 1:
coords_generator.calculate_coords( part, force=1)
coords_generator.show_mol( part)
def add_template_from_CDML(self, file):
if not os.path.isfile(file):
file = os_support.get_path(file, "template")
if not file:
warn("template file %s does not exist - ignoring" % file)
return
try:
doc = dom.parse(file).getElementsByTagName('cdml')[0]
except xml.sax.SAXException:
warn("template file %s cannot be parsed - ignoring" % file)
return
# when loading old versions of CDML try to convert them, but do nothing when they cannot be converted
import CDML_versions
CDML_versions.transform_dom_to_version(doc,
config.current_CDML_version)
Store.app.paper.onread_id_sandbox_activate()
added = []
for tmp in doc.getElementsByTagName('molecule'):
self.templates.append(tmp)
m = molecule(Store.app.paper, package=tmp)
self._prepared_templates.append(m)
added.append(m)
Store.app.paper.onread_id_sandbox_finish(
apply_to=[]) # just switch the id_managers, no id mangling
def write_restraints(start, end, start_xvg, end_xvg, top, includes, n, ndx, Nchains):
start_xvg=open(start_xvg,'r').readlines()
end_xvg=open(end_xvg,'r').readlines()
selection=res_selection.res_select(start,ndx)
n=int(n)
# create the path
startpts={}
endpts={}
for r in selection:
startpts[r]=[]
chain=0
for line in start_xvg:
if re.search(r'\-%s$'%r,line):
startpts[r].append([float(line.split()[0]),float(line.split()[1])])
chain+=1
for r in selection:
endpts[r]=[]
chain=0
for line in end_xvg:
if re.search(r'\-%s$'%r,line):
endpts[r].append([float(line.split()[0]),float(line.split()[1])])
chain+=1
sys.stderr.write('%s'%includes)
for k in range(1,n-1):
in_top=open(top).read()
for mol in range(Nchains):
if len(includes)>0:
includename=includes[mol].split('/')[-1]
in_top=re.sub(includename,'dihre_%d_chain_%d.itp'%(k,mol),in_top)
out_top=open('topol_%d.top'%k,'w')
# sys.stderr.write('%s'%in_top)
out_top.write(in_top)
for k in range(1,n-1):
# make the directory for the restraints
for mol in range(Nchains):
restraint_itp=open('dihre_%d_chain_%d.itp'%(k,mol),'w')
if Nchains>1:
moltop=open(includes[mol]).read()
restraint_itp.write(moltop)
# write the initial part of the topology file
restraint_itp.write("[ dihedral_restraints ]\n")
restraint_itp.write("; ai aj ak al phi dphi kfac\n")
if len(includes)>0:
protein=molecule(includes[mol])
# replace the chain names with the chain names
else:
out_top=open('topol_%d.top'%k,'w')
protein=molecule(top)
in_itp=open(top,'r').read().split('; Include Position restraint file')
out_top.write(in_itp[0])
out_top.write('#include "dihre_%d_chain_%d.itp"\n'%(k,mol))
#out_top.write('#include "dihre_%d_chain_%d.itp"\n'%(k,mol))
out_top.write(in_itp[1])
out_top.close()
for r in selection:
phi = [a for a in protein if (a.resnr == int(r) and
(a.atomname == 'CA' or a.atomname == 'N' or a.atomname == 'C')) or
(a.resnr == int(r)-1 and a.atomname == 'C')]
psi = [a for a in protein if (a.resnr == int(r) and
(a.atomname == 'N' or a.atomname == 'CA' or a.atomname == 'C')) or
(a.resnr == int(r)+1 and a.atomname == 'N')]
# write phi, psi angles
phi_val=startpts[r][mol][0]+(endpts[r][mol][0]-startpts[r][mol][0])/n*k
psi_val=startpts[r][mol][1]+(endpts[r][mol][1]-startpts[r][mol][1])/n*k
restraint_itp.write("%5d%5d%5d%5d %8.4f%5d%5d\n"
%(phi[0].atomnr,phi[1].atomnr,phi[2].atomnr, phi[3].atomnr, phi_val, 0, 1))
restraint_itp.write("%5d%5d%5d%5d %8.4f%5d%5d\n"
%(psi[0].atomnr,psi[1].atomnr,psi[2].atomnr, psi[3].atomnr, psi_val, 0, 1))
restraint_itp.close()
def get_molecules( self, file_name):
doc = dom.parse( file_name)
molecules = []
# read colors
colors=[]
for elem7 in doc.getElementsByTagName("color"):
red=(float(elem7.getAttribute("r"))*255)
green=(float(elem7.getAttribute("g"))*255)
blue=(float(elem7.getAttribute("b"))*255)
colors.append("#%02x%02x%02x" % (red,green,blue))
# read fonts
fonts={}
for elem8 in doc.getElementsByTagName("font"):
family=str(elem8.getAttribute("name"))
fonts[int(elem8.getAttribute("id"))]=family
# read molecules
for elem1 in doc.getElementsByTagName("fragment"):
if elem1.parentNode.nodeName=="page":
mol = molecule( paper=self.paper)
atom_id_to_atom = {}
atom_id_to_text = {}
for elem2 in elem1.childNodes:
# atom
if elem2.nodeName=="n":
font = ""
Size = 12
text = "C"
color1="#000000"
for elem3 in elem2.childNodes:
if elem3.nodeName=="t":
if elem3.hasAttribute("color"):
color1=colors[int(elem3.getAttribute("color"))-2]
text = ""
for elem4 in elem3.childNodes:
if elem4.nodeName=="s":
if elem3.hasAttribute("color"):
color1=colors[int(elem3.getAttribute("color"))-2]
for Id, Font in fonts.items():
if Id==int(elem4.getAttribute("font")):
font=Font
Size= int(elem4.getAttribute("size"))
text += dom_ext.getAllTextFromElement( elem4).strip()
position = elem2.getAttribute("p").split()
assert len( position) == 2
# we must postpone symbol assignment until we know the valency of the atoms
atom_id_to_text[ elem2.getAttribute('id')] = text
atom = mol.create_vertex()
atom.line_color = color1
atom.font_family = font
atom.font_size = Size
atom.x = float( position[0])
atom.y = float( position[1])
mol.add_vertex( atom)
atom_id_to_atom[ elem2.getAttribute('id')] = atom
# bond
#{"v BKChemu bond.type":"v ChemDraw hodnota atributu Display elementu b"}
bondType2={"WedgeBegin":"w",
"WedgedHashBegin":"h",
"Wavy":"a",
"Bold":"b",
"Dash":"d"
}
if elem2.nodeName=="b":
if elem2.hasAttribute("color"):
color2 = colors[(int(elem2.getAttribute("color"))-2)]
else:
color2="#000000"
order = 1
if elem2.hasAttribute("Order"):
order = int( elem2.getAttribute("Order"))
bond = mol.create_edge()
if elem2.hasAttribute("Display"):
display = elem2.getAttribute("Display").strip()
for bondC, bondB in bondType2.items():
if bondC ==display:
bond.type = bondB
bond.line_color = color2
bond.order = order
atom1 = atom_id_to_atom[ elem2.getAttribute("B")]
atom2 = atom_id_to_atom[ elem2.getAttribute("E")]
mol.add_edge( atom1, atom2, bond)
# here we reassign the symbols
for id, atom in atom_id_to_atom.items():
text = atom_id_to_text[ id]
v = mol.create_vertex_according_to_text( atom, text)
atom.copy_settings( v)
mol.replace_vertices( atom, v)
atom.delete()
# finally we add the molecule to the list of molecules for output
molecules.append( mol)
# read texts
textik={2:"i",
1:"b",
32:"sub",
64:"sup"}
for elem5 in doc.getElementsByTagName("t"):
if elem5.parentNode.nodeName=="page":
position = map( float, elem5.getAttribute("p").split())
assert len( position) == 2
celyText=""
for elem51 in elem5.childNodes:
if elem51.nodeName=="s":
for elem52 in elem51.childNodes:
if isinstance( elem52, dom.Text):
rodice=[]
text100=elem52.data
if elem51.hasAttribute("face"):
Face01=int(elem51.getAttribute("face"))
for face, parent in textik.items():
for i in range(9):
if not Face01&2**i==0:
if face==Face01&2**i:
rodice.append(parent)
for rodic in rodice:
text100 = "<%s>%s</%s>" % (rodic,text100,rodic)
celyText += text100
if elem5.hasAttribute("color"):
color3=colors[(int(elem5.getAttribute("color"))-2)]
else:
color3="#000000"
font_id = elem51.getAttribute("font")
if font_id != "":
font=fonts[int(font_id)]
#text = dom_ext.getAllTextFromElement(elem51)
#print celyText
text = celyText
t = text_class( self.paper, position, text=text)
t.line_color = color3
#print elem51
if elem51.hasAttribute("size"):
t.font_size = int( elem51.getAttribute("size"))
if font:
t.font_family = font
molecules.append(t)
# read graphics - plus
for elem6 in doc.getElementsByTagName("graphic"):
if elem6.getAttribute("GraphicType")=="Symbol" and elem6.getAttribute("SymbolType")=="Plus":
position = map( float, elem6.getAttribute("BoundingBox").split())
position2=[position[0],position[1]]
assert len(position2) == 2
if elem6.hasAttribute("color"):
color4=colors[(int(elem6.getAttribute("color"))-2)]
else:
color4="#000000"
pl = plus(self.paper, position2)
pl.line_color = color4
molecules.append(pl)
sipka=[]
#for elem71 in doc.getElementsByTagName("graphic"):
#if elem71.getAttribute("GraphicType")=="Line":
for elem7 in doc.getElementsByTagName("arrow"):
sipka.insert(0,elem7.getAttribute('Head3D') )
sipka.insert(1,elem7.getAttribute('Tail3D') )
if elem7.hasAttribute("color"):
sipka.insert(0,colors[(int(elem7.getAttribute("color"))-2)])
point1 = map( float, sipka[1].split())
point2 = map( float, sipka[2].split())
arr = arrow( self.paper, points=[point2[0:2],point1[0:2]], fill=sipka[0])
arr.line_color=sipka[0]
molecules.append( arr)
sipka=[]
return molecules
def write_restraints(inp, initial_confs, start, end, start_xvg, end_xvg, tpr, top, includes, n, ndx_file, Nchains):
# Get the atoms involved with the residues to use for dihedrals (might be more than one atom in the index
# per residue, since it's probably generated by make_ndx)
ndx_atoms = res_selection.read_ndx(ndx_file)
# Map them to each affected residue so we just get the residue numbers back
selection = res_selection.res_select(start, ndx_atoms)
n = int(n) # number of points in the string, including start and end point
use_interpolation = False
if initial_confs is None or len(initial_confs) == 0:
use_interpolation = True
# Read the starting and ending dihedrals for later interpolation
startpts = readxvg.readxvg(start_xvg, selection)
endpts = readxvg.readxvg(end_xvg, selection)
else:
# Have to generate the dihedrals ourselves from the given initial structures
# Note: when we get an initial_confs[] array, we use it for all points and
# the start/end input parameters are completely ignored
# TODO: assert that len(initial_confs) == n otherwise?
ramaprocs = {}
# Run g_rama (in parallel) on each structure and output to a temporary .xvg
FNULL = open(os.devnull, 'w') # dont generate spam from g_rama
for i in range(n):
# TODO: check for and use g_rama_mpi.. like everywhere else
ramaprocs[i] = Popen(['g_rama', '-f', initial_confs[i], '-s', tpr, '-o', '0%3d.xvg' % i],
stdout=FNULL, stderr=FNULL)
# Go through the output from the rama sub-processes and read the xvg outputs
stringpts = {} # Will have 4 levels: stringpoint, residue, chain, phi/psi value
for i in range(n):
# Start array indexed by residue
xvg_i = os.path.join(inp.getOutputDir(), '0%3d.xvg' % i)
# Make sure the corresponding g_rama task has ended
ramaprocs[i].communicate()
# Read back and parse like for the start/end_xvg above
stringpts[i] = readxvg.readxvg(xvg_i, selection)
# Rewrite the topology to include the res itp files instead of the original per-chain itps (if any)
# There will be one topol_x.top per string point
sys.stderr.write('%s' % includes)
for k in range(n):
with open(top) as in_topf:
in_top = in_topf.read()
for mol in range(Nchains):
if len(includes) > 0:
includename = includes[mol].split('/')[-1]
in_top = re.sub(includename, 'res_%d_chain_%d.itp' % (k, mol), in_top)
with open('topol_%d.top' % k,'w') as out_top:
# sys.stderr.write('%s'%in_top)
out_top.write(in_top)
# Generate/copy and write-out the dihedrals for each point
for k in range(n):
for mol in range(Nchains):
# TODO: use with statement for restraint_itp as well
restraint_itp = open('res_%d_chain_%d.itp' % (k, mol), 'w')
if Nchains > 1:
with open(includes[mol]) as moltop_f:
moltop = moltop_f.read()
restraint_itp.write(moltop)
# write the initial part of the topology file
# Note: gromacs 4.6+ required
restraint_itp.write("[ dihedral_restraints ]\n")
restraint_itp.write("; ai aj ak al type phi dphi kfac\n")
if len(includes) > 0:
protein = molecule(includes[mol])
# replace the chain names with the chain names
else:
with open('topol_%d.top' % k, 'w') as out_top:
protein = molecule(top)
with open(top,'r') as in_itp_f:
in_itp = in_itp_f.read().split('; Include Position restraint file')
out_top.write(in_itp[0])
out_top.write('#include "res_%d_chain_%d.itp"\n' % (k, mol))
out_top.write(in_itp[1])
# Create a lookup-table for the protein topology that maps residue to dihedrally relevant
# backbone atom indices for N, CA and C.
dih_atoms = {}
for a in protein:
if (a.atomname == 'CA' or a.atomname == 'N' or a.atomname == 'C'):
try:
dih_atoms[a.resnr][a.atomname] = a.atomnr;
except KeyError:
dih_atoms[a.resnr] = { a.atomname: a.atomnr }
# Use the lookup-table built above and get the dihedral specification atoms needed for each
# residue in the selection. This is O(n) in residues, thanks to the dih_atoms table.
for r in selection:
# Get the atom numbers to use for the phi and psi dihedrals (4 atoms each)
# phi is C on the previous residue, and N, CA, C on this
phi = [ dih_atoms[r - 1]['C'], dih_atoms[r]['N'], dih_atoms[r]['CA'], dih_atoms[r]['C'] ]
# psi is N, CA and C on this residue and N on the next
psi = [ dih_atoms[r]['N'], dih_atoms[r]['CA'], dih_atoms[r]['C'], dih_atoms[r + 1]['N'] ]
# Write phi, psi angles and the associated k factor into a row in the restraint file
# Note: in the Gromacs 4.6+ format, the k-factor is here. Before, it was in the .mdp as
# dihre_fc.
# Also see reparametrize.py
if use_interpolation:
# k is from 0 to n-1, so map it so we get a factor from 0 to 1
phi_val = startpts[r][mol][0] + k * (endpts[r][mol][0] - startpts[r][mol][0]) / (n - 1)
psi_val = startpts[r][mol][1] + k * (endpts[r][mol][1] - startpts[r][mol][1]) / (n - 1)
else:
# Use the values extracted from the initial_confs[] structures above
phi_val = stringpts[k][r][mol][0]
psi_val = stringpts[k][r][mol][1]
# Since we need different force constants in different stages, we need to put
# a searchable placeholder in the file here and replace it later. KFAC is normally
# a %8.4f number.
restraint_itp.write("%5d%5d%5d%5d%5d %8.4f%5d KFAC\n"
%(phi[0], phi[1], phi[2], phi[3], 1, phi_val, 0))
restraint_itp.write("%5d%5d%5d%5d%5d %8.4f%5d KFAC\n"
%(psi[0], psi[1], psi[2], psi[3], 1, psi_val, 0))
restraint_itp.close()
def _read_inchi( self, text):
if not text:
raise oasa_inchi_error( "No inchi was given")
self.structure = molecule()
self.layers = self.split_layers( text)
# version support (very crude)
self.version = self._check_version( self.layers[0])
if not self.version:
raise oasa_unsupported_inchi_version_error( self.layers[0])
elif str( self.version[0]) != '1' or str( self.version[1]) != '0':
raise oasa_unsupported_inchi_version_error( self.layers[0])
self.hs_in_hydrogen_layer = self.get_number_of_hydrogens_in_hydrogen_layer()
self.read_sum_layer()
self.read_connectivity_layer()
self._charge_mover = self._move_charge_somewhere_else()
repeat = True
run = 0
# we have to repeat this step in order to find the right positioning of movable hydrogens
while repeat and not self._no_possibility_to_improve:
# cleanup
for h in self._added_hs:
self.structure.remove_vertex( h)
for b in self.structure.edges:
b.order = 1
for v in self.structure.vertices:
v.symbol = v.symbol
v.charge = 0
self.cleanup()
# the code itself
run += 1
assert run < 50
self._deal_with_notorious_groups()
self.process_forced_charges()
self.read_hydrogen_layer( run=run)
self.read_charge_layer()
self.read_p_layer()
self.deal_with_da_bonds()
#self._deal_with_valencies()
self.compensate_for_forced_charges()
self.structure.add_missing_bond_orders()
#self.read_double_bond_stereo_layer()
# here we check out if the molecule seems ok
fvs = [v for v in self.structure.vertices if v.free_valency]
if not fvs and not filter( None, [not v.order for v in self.structure.edges]):
repeat = False
else:
if len( fvs) == 1:
a = fvs[0]
a.symbol = a.symbol # this resets the valency
a.raise_valency_to_senseful_value()
if not a.free_valency:
repeat = False
if repeat and self._no_possibility_to_improve and self.charge:
try:
self._charge_mover.next()
except StopIteration:
pass
else:
self._no_possibility_to_improve = False
run = 0
if repeat and self._no_possibility_to_improve:
## if len( filter( None, [v.free_valency for v in self.structure.vertices])) == 1:
## print
## print [(v.symbol, v.valency, v.free_valency) for v in self.structure.vertices if v.free_valency], filter( None, [not v.order for v in self.structure.edges]), text
## if sum( [v.charge for v in self.structure.vertices]) != self.charge:
## print "Charge problem", sum( [v.charge for v in self.structure.vertices]), self.charge
#pass
raise oasa_inchi_error( "Localization of bonds, charges or movable hydrogens failed")
ValveDefaultActualFlow = 800 / 3600.0 #//From average HX flow in unit CW circuit.
ValveDefaultDP = 1.2 * Ps
ValveDefaultOpening = 0.5 #//Default valve opening.
ValveEqualPercR = 40.0 #//Dimensionless constant for valve equalpercentage.
ValveDefaultCv = ValveDefaultActualFlow / \
(math.pow(ValveEqualPercR, ValveDefaultOpening - 1) * math.sqrt(ValveDefaultDP)) # //m^3/s/(Pa^0.5)
ValveHydraulicTau = 10.0 #//seconds. Time constant of valve hydraulics.
ValveLength = 0.5 #//m
ValveWidth = 0.4 #//m
#fluidpackage constants -------------------------------------------------------------------------------------------------
fluidpackage = list() #list of component object
fluidpackage.append(component.component(molecule.molecule("Naphtha", "GTL Naphtha", 0.157, 0.00164, 661.4959, 273 + 495, 1.2411 * 10**7, \
-1 - np.log10(110000 /1.2411 * (10**7)) , 150.5, 0.6, 0, 0), 0))
fluidpackage.append(component.component(molecule.molecule("Air", "Air", 0.02897, 1.983 * math.pow(10, -5), 1.225, 132.41, \
3.72 * math.pow(10, 6), \
0.0335,
0.8*31.15 + 0.2*28.11, 0.8*(-0.01357) + 0.2*(-3.7) * math.pow(10, -6), 0.8*2.68*math.pow(10,-5) + 0.2*1.746 * math.pow(10, -5),
0.8 * (-1.168) * math.pow(10, -8) + 0.2 * (-1.065) * math.pow(10, -8)), 0))
#//Density: 1.977 kg/m3 (gas at 1 atm and 0 °C)
fluidpackage.append( component.component( molecule.molecule("CO2", "Carbon Dioxide", 0.018, 0.07 * 0.001, 1.977, 304.25, 7.39 * math.pow(10, 6), 0.228,
19.8, 0.07344, -5.602E-05, 1.715E-08), 0))
#//Density: 1.977 kg/m3 (gas at 1 atm and 0 °C)
fluidpackage.append( component.component( molecule.molecule("CO", "Carbon Monoxide", 0.02801, 0.0001662 * 0.001, 1.145), 0))
#//Density: 1.145 kg/m3 at 25 °C, 1 atm
fluidpackage.append( component.component( molecule.molecule("H2", "Hydrogen", 0.0020158, 8.76 * math.pow(10, -6), 0.08988), 0))
#//Density: 0.08988 g/L = 0.08988 kg/m3 (0 °C, 101.325 kPa)
fluidpackage.append( component.component( molecule.molecule("He", "Helium", HeMolarMass, 0, 0.1786, 5.1953, 5.1953E6, -0.390,
20.8, 0, 0, 0), 0))
def get_transformed_template(self, n, coords, type='empty', paper=None):
"""type is type of connection - 'bond', 'atom1'(for single atom), 'atom2'(for atom with more than 1 bond), 'empty'"""
pap = paper or Store.app.paper
pap.onread_id_sandbox_activate() # must be here to mangle the ids
current = molecule(pap, package=self.templates[n])
pap.onread_id_sandbox_finish(apply_to=[current]) # id mangling
current.name = ''
self._scale_ratio = 1
trans = transform()
# type empty - just draws the template - no conection
if type == 'empty':
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1 = coords
bond_length = Screen.any_to_px(
Store.app.paper.standard.bond_length)
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
trans.set_move(-xt2, -yt2)
trans.set_scaling(bond_length / math.sqrt((xt1 - xt2)**2 +
(yt1 - yt2)**2))
trans.set_move(x1, y1)
#type atom
elif type == 'atom1' or type == 'atom2':
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1, x2, y2 = coords
trans.set_move(-xt2, -yt2)
trans.set_scaling(
math.sqrt((x1 - x2)**2 + (y1 - y2)**2) /
math.sqrt((xt1 - xt2)**2 + (yt1 - yt2)**2))
trans.set_rotation(
math.atan2(xt1 - xt2, yt1 - yt2) -
math.atan2(x1 - x2, y1 - y2))
trans.set_move(x2, y2)
#type bond
elif type == 'bond':
if not (current.t_bond_first and current.t_bond_second):
warn(
"this template is not capable to be added to bond - sorry."
)
return None
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
xt1, yt1 = current.t_bond_first.get_xy()
xt2, yt2 = current.t_bond_second.get_xy()
x1, y1, x2, y2 = coords
self._scale_ratio = math.sqrt(
(x1 - x2)**2 + (y1 - y2)**2) / math.sqrt(
(xt1 - xt2)**2 + (yt1 - yt2)**
2) # further needed for bond.bond_width transformation
trans.set_move(-xt1, -yt1)
trans.set_rotation(
math.atan2(xt1 - xt2, yt1 - yt2) -
math.atan2(x1 - x2, y1 - y2))
trans.set_scaling(self._scale_ratio)
trans.set_move(x1, y1)
self.transform_template(current, trans)
#remove obsolete info from template
if type == 'atom1':
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
elif type == 'atom2':
current.t_atom.x = x1
current.t_atom.y = y1
current.t_atom = None
current.t_bond_first = None
current.t_bond_second = None
#return ready template
return current
def __init__(self, source, outfile, molfile, goalsnr, nphot, kappa=None,
tnorm=2.735, velocity_function=None, seed=1971, minpop=1e-4,
fixset=1.e-6, blending=False, nchan=50, rt_lines=[0,1,2], velres=0.1):
"""
Initlize a simulation.
Args:
source (str): Model file.
outfile (str): File to write population levels to.
molfile (str): Molecular data file in the LAMDA format.
goalsnr (float): Goal signal-to-noise ratio of the run.
nphot (float): Number of photons to use in the radiative transfer.
kappa (optional[str]): A string decribing the dust parameters. For
the use of Ossenkopf & Henning (1994) opacities it must take
the form:
kappa_params = 'jena, TYPE, COAG'
where TYPE must be 'bare', 'thin' or 'thick' and COAG must be
'no', 'e5', 'e6', 'e7' or 'e8'. Otherwise a power law profile
can be included. Alternatively, a simple power law can be used
where the parameters are given by:
kappa_params = 'powerlaw, freq0, kappa0, beta'
where freq0 is in [Hz], kappa0 in [cm^2/g], and beta is the
frequency index. If nothing is given, we assume no opacity.
tnorm (optional[float]): Background temperature in [K]. Default is
the CMB at 2.735K.
velo (optional[str]): Type of velocity structure to use.
seed (optional[int]): Seed for the random number generators.
minpop (optional[float]): Minimum population for each energy level.
fixset (optional [float]): The smallest number to be counted.
blending (optional [bool]): Whether to include line blending or not.
nchan (optional [int]): Number of channels per trans for raytracing.
rt_lines (optional [int list]): List of transitions to raytrace.
velres (optional [float]): Channel res for raytracing (km/s).
"""
self.source = source
self.outfile = outfile
self.molfile = molfile
self.goalsnr = goalsnr
# not setting nphot yet, setting later as array w/ size ncell
self.kappa_params = kappa
self.tnorm = tnorm
# self.velocity = velocity
self.seed = seed
self.minpop = minpop
self.fixset = fixset
self.blending = blending
self.nchan = nchan
self.rt_lines = rt_lines
self.velres = velres*1000. # convert to m/s
t0 = time()
# Read in the source model (default is RATRAN).
self.model = model(self.source, 'ratran')
self.ncell = self.model.ncell
# Have user input velocity function.
if velocity_function is not None:
self.model.velo = simulation.import_velocity(velocity_function)
# Read in the molfile
try:
self.mol = molecule(self, self.molfile)
except:
raise Exception("Couldn't parse molecular data.")
self.nlev = self.mol.nlev
self.nline = self.mol.nline
self.ntrans = self.mol.ntrans
self.ntrans2 = self.mol.ntrans2
self.ntemp = self.mol.ntemp
self.ntemp2 = self.mol.ntemp2
# Include thermal broadening the to widths.
v_turb2 = self.model.doppb**2.0
v_therm2 = 2 * sc.k * self.model.tkin / sc.m_p / self.mol.molweight
self.model.doppb = np.sqrt(v_turb2 + v_therm2)
# Calculate the collisional rates.
self.mol.set_rates(self.model.tkin)
if self.mol.up is None or self.mol.down is None:
raise ValueError("Need to calculate rates.")
# Initialize dust emissivity, convertiong from [m^2/kg] to [m^-1/n(H2)]
# such that tau_dust = knu.
self.norm = simulation.planck(self.mol.freq[0], self.tnorm)
self.norm = self.norm * np.ones(self.nline)
self.cmb = simulation.planck(self.mol.freq, self.model.tcmb)
self.cmb /= self.norm
# Parse kappa parameters and generate the kappa function
self.kappa = simulation.generate_kappa(self.kappa_params)
# Do not normalize dust; will be done in photon.
# Funky looping as functions fail to broadcast.
self.knu = np.zeros((self.nline, self.ncell))
self.dust = np.zeros((self.nline, self.ncell))
for l in range(self.nline):
for i in range(self.ncell):
self.knu[l, i] = self.kappa(i, self.mol.freq[l]) * 2.4 * sc.m_p
self.knu[l, i] *= self.model.nh2[i] / self.model.g2d
self.dust[l, i] = simulation.planck(self.mol.freq[l],
self.model.tdust[i])
# Set up the Monte Carlo simulation
self.nphot = np.full(self.ncell, nphot) # Set nphot to initial number.
self.niter = self.ncell # Estimated crossing time.
self.fixseed = self.seed
t1 = time()
print("Set up took %.1f ms." % ((t1 - t0) * 1e3))
def write_restraints(inp, initial_confs, start, end, start_xvg, end_xvg, tpr, top, includes, n, ndx_file, Nchains):
cmdnames = cmds.GromacsCommands()
# Get the atoms involved with the residues to use for dihedrals (might be more than one atom in the index
# per residue, since it's probably generated by make_ndx)
ndx_atoms = res_selection.read_ndx(ndx_file)
# Map them to each affected residue so we just get the residue numbers back
selection = res_selection.res_select(start, ndx_atoms)
n = int(n) # number of points in the string, including start and end point
use_interpolation = False
if initial_confs is None or len(initial_confs) == 0:
use_interpolation = True
# Read the starting and ending dihedrals for later interpolation
startpts = readxvg.readxvg(start_xvg, selection)
endpts = readxvg.readxvg(end_xvg, selection)
else:
# Have to generate the dihedrals ourselves from the given initial structures
# Note: when we get an initial_confs[] array, we use it for all points and
# the start/end input parameters are completely ignored
# TODO: assert that len(initial_confs) == n otherwise?
ramaprocs = {}
# Run g_rama (in parallel) on each structure and output to a temporary .xvg
FNULL = open(os.devnull, 'w') # dont generate spam from g_rama
for i in range(n):
# TODO: check for and use g_rama_mpi.. like everywhere else
cmd = cmdnames.rama.split() + ['-f', initial_confs[i], '-s', tpr,
'-o', '0%3d.xvg' % i]
ramaprocs[i] = Popen(cmd, stdout=FNULL, stderr=FNULL)
# Go through the output from the rama sub-processes and read the xvg outputs
stringpts = {} # Will have 4 levels: stringpoint, residue, chain, phi/psi value
for i in range(n):
# Start array indexed by residue
xvg_i = os.path.join(inp.getOutputDir(), '0%3d.xvg' % i)
# Make sure the corresponding g_rama task has ended
ramaprocs[i].communicate()
# Read back and parse like for the start/end_xvg above
stringpts[i] = readxvg.readxvg(xvg_i, selection)
# Rewrite the topology to include the res itp files instead of the original per-chain itps (if any)
# There will be one topol_x.top per string point
sys.stderr.write('%s' % includes)
for k in range(n):
with open(top) as in_topf:
in_top = in_topf.read()
for mol in range(Nchains):
if len(includes) > 0:
includename = includes[mol].split('/')[-1]
in_top = re.sub(includename, 'res_%d_chain_%d.itp' % (k, mol), in_top)
with open('topol_%d.top' % k,'w') as out_top:
# sys.stderr.write('%s'%in_top)
out_top.write(in_top)
# Generate/copy and write-out the dihedrals for each point
for k in range(n):
for mol in range(Nchains):
# TODO: use with statement for restraint_itp as well
restraint_itp = open('res_%d_chain_%d.itp' % (k, mol), 'w')
if Nchains > 1:
with open(includes[mol]) as moltop_f:
moltop = moltop_f.read()
restraint_itp.write(moltop)
# write the initial part of the topology file
# Note: gromacs 4.6+ required
restraint_itp.write("[ dihedral_restraints ]\n")
restraint_itp.write("; ai aj ak al type phi dphi kfac\n")
if len(includes) > 0:
protein = molecule(includes[mol])
# replace the chain names with the chain names
else:
with open('topol_%d.top' % k, 'w') as out_top:
protein = molecule(top)
with open(top,'r') as in_itp_f:
in_itp = in_itp_f.read().split('; Include Position restraint file')
out_top.write(in_itp[0])
out_top.write('#include "res_%d_chain_%d.itp"\n' % (k, mol))
out_top.write(in_itp[1])
# Create a lookup-table for the protein topology that maps residue to dihedrally relevant
# backbone atom indices for N, CA and C.
dih_atoms = {}
for a in protein:
if (a.atomname == 'CA' or a.atomname == 'N' or a.atomname == 'C'):
try:
dih_atoms[a.resnr][a.atomname] = a.atomnr;
except KeyError:
dih_atoms[a.resnr] = { a.atomname: a.atomnr }
# Use the lookup-table built above and get the dihedral specification atoms needed for each
# residue in the selection. This is O(n) in residues, thanks to the dih_atoms table.
for r in selection:
# Get the atom numbers to use for the phi and psi dihedrals (4 atoms each)
# phi is C on the previous residue, and N, CA, C on this
phi = [ dih_atoms[r - 1]['C'], dih_atoms[r]['N'], dih_atoms[r]['CA'], dih_atoms[r]['C'] ]
# psi is N, CA and C on this residue and N on the next
psi = [ dih_atoms[r]['N'], dih_atoms[r]['CA'], dih_atoms[r]['C'], dih_atoms[r + 1]['N'] ]
# Write phi, psi angles and the associated k factor into a row in the restraint file
# Note: in the Gromacs 4.6+ format, the k-factor is here. Before, it was in the .mdp as
# dihre_fc.
# Also see reparametrize.py
if use_interpolation:
# k is from 0 to n-1, so map it so we get a factor from 0 to 1
phi_val = startpts[r][mol][0] + k * (endpts[r][mol][0] - startpts[r][mol][0]) / (n - 1)
psi_val = startpts[r][mol][1] + k * (endpts[r][mol][1] - startpts[r][mol][1]) / (n - 1)
else:
# Use the values extracted from the initial_confs[] structures above
phi_val = stringpts[k][r][mol][0]
psi_val = stringpts[k][r][mol][1]
# Since we need different force constants in different stages, we need to put
# a searchable placeholder in the file here and replace it later. KFAC is normally
# a %8.4f number.
restraint_itp.write("%5d%5d%5d%5d%5d %8.4f%5d KFAC\n"
%(phi[0], phi[1], phi[2], phi[3], 1, phi_val, 0))
restraint_itp.write("%5d%5d%5d%5d%5d %8.4f%5d KFAC\n"
%(psi[0], psi[1], psi[2], psi[3], 1, psi_val, 0))
restraint_itp.close()
def get_molecules(self, file_name):
doc = dom.parse(file_name)
molecules = []
# read colors
colors = []
for elem7 in doc.getElementsByTagName("color"):
red = (float(elem7.getAttribute("r")) * 255)
green = (float(elem7.getAttribute("g")) * 255)
blue = (float(elem7.getAttribute("b")) * 255)
colors.append("#%02x%02x%02x" % (red, green, blue))
# read fonts
fonts = {}
for elem8 in doc.getElementsByTagName("font"):
family = str(elem8.getAttribute("name"))
fonts[int(elem8.getAttribute("id"))] = family
# read molecules
for elem1 in doc.getElementsByTagName("fragment"):
if elem1.parentNode.nodeName == "page":
mol = molecule(paper=self.paper)
atom_id_to_atom = {}
atom_id_to_text = {}
for elem2 in elem1.childNodes:
# atom
if elem2.nodeName == "n":
font = ""
Size = 12
text = "C"
color1 = "#000000"
for elem3 in elem2.childNodes:
if elem3.nodeName == "t":
if elem3.hasAttribute("color"):
color1 = colors[
int(elem3.getAttribute("color")) - 2]
text = ""
for elem4 in elem3.childNodes:
if elem4.nodeName == "s":
if elem3.hasAttribute("color"):
color1 = colors[int(
elem3.getAttribute("color")) -
2]
for Id, Font in fonts.items():
if Id == int(
elem4.getAttribute(
"font")):
font = Font
Size = int(elem4.getAttribute("size"))
text += dom_ext.getAllTextFromElement(
elem4).strip()
position = elem2.getAttribute("p").split()
assert len(position) == 2
# we must postpone symbol assignment until we know the valency of the atoms
atom_id_to_text[elem2.getAttribute('id')] = text
atom = mol.create_vertex()
atom.line_color = color1
atom.font_family = font
atom.font_size = Size
atom.x = float(position[0])
atom.y = float(position[1])
mol.add_vertex(atom)
atom_id_to_atom[elem2.getAttribute('id')] = atom
# bond
#{"v BKChemu bond.type":"v ChemDraw hodnota atributu Display elementu b"}
bondType2 = {
"WedgeBegin": "w",
"WedgedHashBegin": "h",
"Wavy": "a",
"Bold": "b",
"Dash": "d"
}
if elem2.nodeName == "b":
if elem2.hasAttribute("color"):
color2 = colors[(int(elem2.getAttribute("color")) -
2)]
else:
color2 = "#000000"
order = 1
if elem2.hasAttribute("Order"):
order = int(elem2.getAttribute("Order"))
bond = mol.create_edge()
if elem2.hasAttribute("Display"):
display = elem2.getAttribute("Display").strip()
for bondC, bondB in bondType2.items():
if bondC == display:
bond.type = bondB
bond.line_color = color2
bond.order = order
atom1 = atom_id_to_atom[elem2.getAttribute("B")]
atom2 = atom_id_to_atom[elem2.getAttribute("E")]
mol.add_edge(atom1, atom2, bond)
# here we reassign the symbols
for id, atom in atom_id_to_atom.items():
text = atom_id_to_text[id]
v = mol.create_vertex_according_to_text(atom, text)
atom.copy_settings(v)
mol.replace_vertices(atom, v)
atom.delete()
# finally we add the molecule to the list of molecules for output
molecules.append(mol)
# read texts
textik = {2: "i", 1: "b", 32: "sub", 64: "sup"}
for elem5 in doc.getElementsByTagName("t"):
if elem5.parentNode.nodeName == "page":
position = map(float, elem5.getAttribute("p").split())
assert len(position) == 2
celyText = ""
for elem51 in elem5.childNodes:
if elem51.nodeName == "s":
for elem52 in elem51.childNodes:
if isinstance(elem52, dom.Text):
rodice = []
text100 = elem52.data
if elem51.hasAttribute("face"):
Face01 = int(elem51.getAttribute("face"))
for face, parent in textik.items():
for i in range(9):
if not Face01 & 2**i == 0:
if face == Face01 & 2**i:
rodice.append(parent)
for rodic in rodice:
text100 = "<%s>%s</%s>" % (rodic, text100,
rodic)
celyText += text100
if elem5.hasAttribute("color"):
color3 = colors[(int(elem5.getAttribute("color")) -
2)]
else:
color3 = "#000000"
font_id = elem51.getAttribute("font")
if font_id != "":
font = fonts[int(font_id)]
#text = dom_ext.getAllTextFromElement(elem51)
#print celyText
text = celyText
t = text_class(self.paper, position, text=text)
t.line_color = color3
#print elem51
if elem51.hasAttribute("size"):
t.font_size = int(elem51.getAttribute("size"))
if font:
t.font_family = font
molecules.append(t)
# read graphics - plus
for elem6 in doc.getElementsByTagName("graphic"):
if elem6.getAttribute(
"GraphicType") == "Symbol" and elem6.getAttribute(
"SymbolType") == "Plus":
position = map(float,
elem6.getAttribute("BoundingBox").split())
position2 = [position[0], position[1]]
assert len(position2) == 2
if elem6.hasAttribute("color"):
color4 = colors[(int(elem6.getAttribute("color")) - 2)]
else:
color4 = "#000000"
pl = plus(self.paper, position2)
pl.line_color = color4
molecules.append(pl)
sipka = []
#for elem71 in doc.getElementsByTagName("graphic"):
#if elem71.getAttribute("GraphicType")=="Line":
for elem7 in doc.getElementsByTagName("arrow"):
sipka.insert(0, elem7.getAttribute('Head3D'))
sipka.insert(1, elem7.getAttribute('Tail3D'))
if elem7.hasAttribute("color"):
sipka.insert(0, colors[(int(elem7.getAttribute("color")) - 2)])
point1 = map(float, sipka[1].split())
point2 = map(float, sipka[2].split())
arr = arrow(self.paper,
points=[point2[0:2], point1[0:2]],
fill=sipka[0])
arr.line_color = sipka[0]
molecules.append(arr)
sipka = []
return molecules
###GENERATE 3D MOL FILE WITH OBGEN###
os.chdir('../public/uploads/structures')
#3D conformer search with obgen
subprocess.call([os.path.join(config.babeldir,'obgen'),'{}.mol'.format(molid)],stdout=open('{}-3dt.mol'.format(molid),'w'),stderr=open(os.devnull,'w'))
#Remove warning flags
subprocess.call(['/bin/grep','-v','WARNING','{}-3dt.mol'.format(molid)],stdout=open('{}-3d.mol'.format(molid),'w'),stderr=open(os.devnull,'w'))
os.remove('{}-3dt.mol'.format(molid))
#Convert to PDB without hydrogens
subprocess.call([os.path.join(config.babeldir,'babel'),'-imol','{}-3d.mol'.format(molid),'-d','-opdb','{}-3d.pdb'.format(molid)],stdout=open(os.devnull,'w'),stderr=open(os.devnull,'w'))
#Neutralize atoms
subprocess.call(['/bin/sed','-i',r"s/1[\+-]$//g",'{}-3d.pdb'.format(molid)],stdout=open(os.devnull,'w'),stderr=open(os.devnull,'w'))
#Finally convert to 3D SDF with hydrogens in neutral state
subprocess.call([config.babeldir+'babel','-ipdb','{}-3d.pdb'.format(molid),'-h','--title',molname,'-osdf','{}-3d.mol'.format(molid)],stdout=open(os.devnull,'w'),stderr=open(os.devnull,'w'))
os.remove('{}-3d.pdb'.format(molid))
molobj = molecule('{}-3d.mol'.format(molid))
os.chdir(cgidir)
####UPATE MOLECULE DATA IN DATABASE############
dbconn = psycopg2.connect(config.dsn)
q = dbconn.cursor()
query = 'UPDATE molecules SET molweight=%s,molformula=%s WHERE molid=%s'
options = [str(molobj.molweight),molobj.formula(),str(molid)]
q.execute(query,options)
dbconn.commit()
q.close()
dbconn.close()
######EXTENSIONS###############
os.chdir('../extensions')
##### RUN QIKPROP##############
def write_restraints(inp, initial_confs, start, end, tpr, top, includes, n,
ndxfn, Nchains):
n = int(n) # number of points in the string, including start and end point
ndx_atoms = res_selection.read_ndx(ndxfn)
use_interpolation = False
if initial_confs is None or len(initial_confs) == 0:
use_interpolation = True
# Read the starting and ending atom configurations for later interpolation TODO
#startpts = readxvg.readxvg(start_xvg, selection)
#endpts = readxvg.readxvg(end_xvg, selection)
# Rewrite the topology to include the res itp files instead of the original per-chain itps (if any)
# There will be one topol_x.top per intermediate string point
sys.stderr.write('%s' % includes)
for k in range(n):
with open(top) as in_topf:
in_top = in_topf.read()
for mol in range(Nchains):
if len(includes) > 0:
includename = includes[mol].split('/')[-1]
in_top = re.sub(includename,
'res_%d_chain_%d.itp' % (k, mol), in_top)
with open('topol_%d.top' % k, 'w') as out_top:
# sys.stderr.write('%s'%in_top)
out_top.write(in_top)
# Generate/copy and write-out the restraint atom and force spec for each intermediate point
# This is really unnecessary here since the restraint positions are not in these files so they are the same
# for all points and chains. TODO
for k in range(n):
for mol in range(Nchains):
with open('res_%d_chain_%d.itp' % (k, mol), 'w') as restraint_itp:
if Nchains > 1:
with open(includes[mol]) as moltop_f:
moltop = moltop_f.read()
restraint_itp.write(moltop)
if len(includes) > 0:
protein = molecule(includes[mol])
# replace the chain names with the chain names
else:
with open('topol_%d.top' % k, 'w') as out_top:
protein = molecule(top)
with open(top, 'r') as in_itp_f:
in_itp = in_itp_f.read().split(
'; Include Position restraint file')
out_top.write(in_itp[0])
out_top.write('#include "res_%d_chain_%d.itp"\n' %
(k, mol))
out_top.write(in_itp[1])
# Go through the atoms in the selection index and write one row for each one with the KFAC
# force constant placeholder
restraint_itp.write("\n[ position_restraints ]\n")
restraint_itp.write("; atom type fx fy fz\n")
for a in ndx_atoms:
if a < 5566: # GLIC HACK: only write one chain, and do it relative atom 1 since the .itp maps to the topology molecule.
restraint_itp.write("%6d 1 KFAC KFAC KFAC\n" %
int(a))
def _read_inchi(self, text):
if not text:
raise oasa_inchi_error("No inchi was given")
self.structure = molecule()
self.layers = self.split_layers(text)
# version support (very crude)
self.version = self._check_version(self.layers[0])
if not self.version:
raise oasa_unsupported_inchi_version_error(self.layers[0])
elif str(self.version[0]) != '1' or str(self.version[1]) != '0':
raise oasa_unsupported_inchi_version_error(self.layers[0])
self.hs_in_hydrogen_layer = self.get_number_of_hydrogens_in_hydrogen_layer(
)
self.read_sum_layer()
self.read_connectivity_layer()
self._charge_mover = self._move_charge_somewhere_else()
repeat = True
run = 0
# we have to repeat this step in order to find the right positioning of movable hydrogens
while repeat and not self._no_possibility_to_improve:
# cleanup
for h in self._added_hs:
self.structure.remove_vertex(h)
for b in self.structure.edges:
b.order = 1
for v in self.structure.vertices:
v.symbol = v.symbol
v.charge = 0
self.cleanup()
# the code itself
run += 1
assert run < 50
self._deal_with_notorious_groups()
self.process_forced_charges()
self.read_hydrogen_layer(run=run)
self.read_charge_layer()
self.read_p_layer()
self.deal_with_da_bonds()
#self._deal_with_valencies()
self.compensate_for_forced_charges()
self.structure.add_missing_bond_orders()
#self.read_double_bond_stereo_layer()
# here we check out if the molecule seems ok
fvs = [v for v in self.structure.vertices if v.free_valency]
if not fvs and not filter(
None, [not v.order for v in self.structure.edges]):
repeat = False
else:
if len(fvs) == 1:
a = fvs[0]
a.symbol = a.symbol # this resets the valency
a.raise_valency_to_senseful_value()
if not a.free_valency:
repeat = False
if repeat and self._no_possibility_to_improve and self.charge:
try:
self._charge_mover.next()
except StopIteration:
pass
else:
self._no_possibility_to_improve = False
run = 0
if repeat and self._no_possibility_to_improve:
## if len( filter( None, [v.free_valency for v in self.structure.vertices])) == 1:
## print
## print [(v.symbol, v.valency, v.free_valency) for v in self.structure.vertices if v.free_valency], filter( None, [not v.order for v in self.structure.edges]), text
## if sum( [v.charge for v in self.structure.vertices]) != self.charge:
## print "Charge problem", sum( [v.charge for v in self.structure.vertices]), self.charge
#pass
raise oasa_inchi_error(
"Localization of bonds, charges or movable hydrogens failed")
def write_restraints(start, end, start_xvg, end_xvg, top, includes, n, ndx,
Nchains):
start_xvg = open(start_xvg, 'r').readlines()
end_xvg = open(end_xvg, 'r').readlines()
selection = res_selection.res_select(start, ndx)
n = int(n)
# create the path
startpts = {}
endpts = {}
for r in selection:
startpts[r] = []
chain = 0
for line in start_xvg:
if re.search(r'\-%s$' % r, line):
startpts[r].append(
[float(line.split()[0]),
float(line.split()[1])])
chain += 1
for r in selection:
endpts[r] = []
chain = 0
for line in end_xvg:
if re.search(r'\-%s$' % r, line):
endpts[r].append(
[float(line.split()[0]),
float(line.split()[1])])
chain += 1
sys.stderr.write('%s' % includes)
for k in range(1, n - 1):
in_top = open(top).read()
for mol in range(Nchains):
if len(includes) > 0:
includename = includes[mol].split('/')[-1]
in_top = re.sub(includename,
'dihre_%d_chain_%d.itp' % (k, mol), in_top)
out_top = open('topol_%d.top' % k, 'w')
# sys.stderr.write('%s'%in_top)
out_top.write(in_top)
for k in range(1, n - 1):
# make the directory for the restraints
for mol in range(Nchains):
restraint_itp = open('dihre_%d_chain_%d.itp' % (k, mol), 'w')
if Nchains > 1:
moltop = open(includes[mol]).read()
restraint_itp.write(moltop)
# write the initial part of the topology file
restraint_itp.write("[ dihedral_restraints ]\n")
restraint_itp.write("; ai aj ak al phi dphi kfac\n")
if len(includes) > 0:
protein = molecule(includes[mol])
# replace the chain names with the chain names
else:
out_top = open('topol_%d.top' % k, 'w')
protein = molecule(top)
in_itp = open(
top, 'r').read().split('; Include Position restraint file')
out_top.write(in_itp[0])
out_top.write('#include "dihre_%d_chain_%d.itp"\n' % (k, mol))
#out_top.write('#include "dihre_%d_chain_%d.itp"\n'%(k,mol))
out_top.write(in_itp[1])
out_top.close()
for r in selection:
phi = [
a for a in protein
if (a.resnr == int(r) and (a.atomname == 'CA' or a.atomname
== 'N' or a.atomname == 'C')) or
(a.resnr == int(r) - 1 and a.atomname == 'C')
]
psi = [
a for a in protein
if (a.resnr == int(r) and (a.atomname == 'N' or a.atomname
== 'CA' or a.atomname == 'C'))
or (a.resnr == int(r) + 1 and a.atomname == 'N')
]
# write phi, psi angles
phi_val = startpts[r][mol][0] + (endpts[r][mol][0] -
startpts[r][mol][0]) / n * k
psi_val = startpts[r][mol][1] + (endpts[r][mol][1] -
startpts[r][mol][1]) / n * k
restraint_itp.write(
"%5d%5d%5d%5d %8.4f%5d%5d\n" %
(phi[0].atomnr, phi[1].atomnr, phi[2].atomnr,
phi[3].atomnr, phi_val, 0, 1))
restraint_itp.write(
"%5d%5d%5d%5d %8.4f%5d%5d\n" %
(psi[0].atomnr, psi[1].atomnr, psi[2].atomnr,
psi[3].atomnr, psi_val, 0, 1))
restraint_itp.close()
def write_restraints(inp, initial_confs, start, end, tpr, top, includes, n, ndxfn, Nchains):
n = int(n) # number of points in the string, including start and end point
ndx_atoms = res_selection.read_ndx(ndxfn)
use_interpolation = False
if initial_confs is None or len(initial_confs) == 0:
use_interpolation = True
# Read the starting and ending atom configurations for later interpolation TODO
#startpts = readxvg.readxvg(start_xvg, selection)
#endpts = readxvg.readxvg(end_xvg, selection)
# Rewrite the topology to include the res itp files instead of the original per-chain itps (if any)
# There will be one topol_x.top per intermediate string point
sys.stderr.write('%s' % includes)
for k in range(n):
with open(top) as in_topf:
in_top = in_topf.read()
for mol in range(Nchains):
if len(includes) > 0:
includename = includes[mol].split('/')[-1]
in_top = re.sub(includename, 'res_%d_chain_%d.itp' % (k, mol), in_top)
with open('topol_%d.top' % k, 'w') as out_top:
# sys.stderr.write('%s'%in_top)
out_top.write(in_top)
# Generate/copy and write-out the restraint atom and force spec for each intermediate point
# This is really unnecessary here since the restraint positions are not in these files so they are the same
# for all points and chains. TODO
for k in range(n):
for mol in range(Nchains):
with open('res_%d_chain_%d.itp' % (k, mol), 'w') as restraint_itp:
if Nchains > 1:
with open(includes[mol]) as moltop_f:
moltop = moltop_f.read()
restraint_itp.write(moltop)
if len(includes) > 0:
protein = molecule(includes[mol])
# replace the chain names with the chain names
else:
with open('topol_%d.top' % k, 'w') as out_top:
protein = molecule(top)
with open(top, 'r') as in_itp_f:
in_itp = in_itp_f.read().split('; Include Position restraint file')
out_top.write(in_itp[0])
out_top.write('#include "res_%d_chain_%d.itp"\n' % (k, mol))
out_top.write(in_itp[1])
# Go through the atoms in the selection index and write one row for each one with the KFAC
# force constant placeholder
restraint_itp.write("\n[ position_restraints ]\n")
restraint_itp.write("; atom type fx fy fz\n")
for a in ndx_atoms:
if a < 5566: # GLIC HACK: only write one chain, and do it relative atom 1 since the .itp maps to the topology molecule.
restraint_itp.write("%6d 1 KFAC KFAC KFAC\n" % int(a))
def reparametrize(use_posres, fix_endpoints, cvs, ndx_file, Nchains,
start_conf, start_xvg, end_conf, end_xvg, last_resconfs, top,
includes):
Nswarms = len(cvs[0])
ndx_atoms = res_selection.read_ndx(ndx_file)
# For dihedrals, we map the atoms to residues for a single chain, and the readxvg etc. will read the entire file and
# select the same residues in each chain. But for the position restraints which use the atom indices directly, we have
# to first expand the index so it covers all chains.
# TODO: have to figure out or input atoms per chain in the .gro's so we can repeat the atom-selection Nchains times
# for the posres case. The ndx file is for atoms inside the chain, but the .gro will contain global numbering.
# We can detect the chain-repeat in rwgro, by looking for repeating first residue name.
# Hardcode a repeat for testing for now.
if use_posres == 0:
# Map atoms to residues for the dihedral selection
rsel = res_selection.res_select('%s' % start_conf, ndx_atoms)
#sys.stderr.write('Residue selection: %s' %rsel)
# else:
# selected_atoms = []
# for ch in range(5):
# for i in range(len(ndx_atoms)):
# selected_atoms += [ ndx_atoms[i] + ch * 5566 ]
# Calculate the average drift in CV space
# newpts is a per-swarm-point list of CV points (each a list of the CV dimension length)
newpts = []
# Note: the cvs[][] array is indexed after the number of stringpoints that actually were swarm-processed,
# so depending on the fix_endpoints option it may or may not exactly match the path[] which always include
# all points. If we only read in N-2 points here, the start/end will be added to newpts in the code further below.
for pathpt in range(len(cvs)):
swarmpts = []
for i in range(len(cvs[pathpt])):
if use_posres == 1:
zpt = rwgro.readgro_flat(cvs[pathpt][i], ndx_atoms)
#sys.stderr.write('Read pathpt %d swarm %d (%s), got %d CVs\n' % (pathpt, i, cvs[pathpt][i], len(zpt)))
else:
zpt = readxvg.readxvg_flat(cvs[pathpt][i], rsel)
swarmpts.append(zpt)
zptsum = reduce(mapadd, swarmpts)
avgdrift = scale((1 / float(Nswarms)), zptsum)
newpts.append(avgdrift)
# Read in the fixed start and end CV values, for the fix_endpoints case (otherwise the start/end will
# be allowed to drift just like the other points, and they will already then be a part of the newpts array)
if fix_endpoints == 1:
if use_posres == 1:
# TODO: the start/end_conf are full Systems so the atom numbering aliases for the ndx_atoms array :/
# Currently fixed in readgro_flat temporary, hardcoded for the GLIC Protein number.
initpt = rwgro.readgro_flat(start_conf, ndx_atoms)
targetpt = rwgro.readgro_flat(end_conf, ndx_atoms)
else:
initpt = readxvg.readxvg_flat(start_xvg, rsel)
targetpt = readxvg.readxvg_flat(end_xvg, rsel)
sys.stderr.write('Length of initpt %d, targetpt %d\n' %
(len(initpt), len(targetpt)))
# Insert the start/end in the beginning and last of newpts
newpts.insert(0, initpt)
newpts.append(targetpt)
# something with 1 indexing makes this padding necessary. TODO: check if this is needed anymore
paddingpt = [0] * len(newpts[0])
newpts.append(paddingpt)
# Do the actual reparameterization
# newpts is a 2D list, first level is one per stringpoint, second is the linear list of CVs
# rep_pts returns the maximum spread of the CV distances between points in [0] and the adjusted
# points in [1]
# Initial iteration
rep_it1 = ext_rep_pts(newpts)
adjusted = rep_it1[1] # get the points only, ignore the spread result
# Keep iterating, feeding the result of the previous result into rep_pts again
# Note that with long CV vectors (> 4000 dimensions) iterations takes a long time
# (at least 45 min for 25 iterations on a single-core 3.5 GHz) when using the python rep_pts.
# We can abort early when the maximum spread between points in the updated string goes
# below a threshold
iters = [adjusted]
i = 0
maxspread = 100.0
# Do max 150 iterations even if we don't reach our goal
while i < 150 and maxspread > 0.012:
sys.stderr.write('Rep iter %d: \n' % i)
sys.stderr.flush()
rep_it = ext_rep_pts(iters[i])
maxspread = rep_it[0]
sys.stderr.write(' maxspread was %f\n' % maxspread)
# Remember the adjusted points
iters.append(rep_it[1])
i = i + 1
sys.stderr.write('Final maximum spread %f after %d iterations.\n' %
(maxspread, i))
# Get the final iteration's result
adjusted = iters[-1]
# delete the padding point
adjusted = adjusted[:-1]
newpts = newpts[:-1]
#sys.stderr.write('Pts before repa:\n %s\n' % newpts)
#sys.stderr.write('The adjusted pts:\n %s\n' % adjusted)
# Possibility to test skipping reparametrize by uncommenting the next row.
# The stringpoints will drift along the string and probably end up in the
# endpoints or a minima along the string.
#adjusted = newpts
# calculate reparam distance
sys.stderr.write('Length of the adjusted vector: %d\n' % len(adjusted))
# TODO Nchains should depend on the specific residue (?)
# Given as function argument now.
#Nchains = len(initpt) / (2 * len(rsel))
# write the CV control data for the next iteration
# The output file expected for the posres case is rep_resconf_%d.gro for each stringpoint.
# For dihedrals its res_%d_chain_%d.itp for each stringpoint and chain.
#
for k in range(len(adjusted)):
# Not necessary to do this output for the start/end-points in the fix_endpoints case, the data is
# just bypassed in the caller script
if fix_endpoints == 1 and (k == 0 or k == (len(adjusted) - 1)):
continue
if use_posres == 1:
# Open the output resconf which will go into the next iteration as minimization target
with open('rep_resconf_%d.gro' % k, 'w') as rep_resconf:
# Open and read the previous (input) resconf, which has basically tagged along since the last
# reparametrization step (or was set initially at swarm-start)
with open(last_resconfs[k], 'r') as in_resconf_f:
in_resconf = in_resconf_f.readlines()
# TODO: maybe this chunk of code could be done by the rwgro module for us.
# Copy the first 2 rows (title and number of atoms) straight over
rep_resconf.write(in_resconf[0])
rep_resconf.write(in_resconf[1])
# Go through the atoms row-by-row and update the xyz coordinates for the atoms the reparametrize
# step moved
# Note: we are only copying over positions here. The velocities are not needed as the use for these files
# will only be as a base for the next iterations position restraint coordinates.
pathpoint = adjusted[
k] # the 1-D list of CVs (positions): x,y,z * nbr atoms in index
if len(pathpoint) != (1555 *
3): # assert on GLIC length (TODO)
sys.stderr.write('adjusted[] entry of wrong length %d\n' %
len(pathpoint))
cvpos = 0
for line in in_resconf[2:][:-1]:
resname = line[
0:
8] # python-ranges are inclusive the first index and exclusive the second...
atname = line[8:15]
atomnr = int(line[15:20])
x = float(line[20:28])
y = float(line[28:36])
z = float(line[36:44])
if atomnr in ndx_atoms:
# Update to new coords
x = pathpoint[cvpos]
y = pathpoint[cvpos + 1]
z = pathpoint[cvpos + 2]
cvpos += 3
# Write out the row, updated or not
rep_resconf.write('%s%s%5d%8.3f%8.3f%8.3f\n' %
(resname, atname, atomnr, x, y, z))
# Copy the last row which was the cell dimensions
rep_resconf.write(in_resconf[len(in_resconf) - 1])
else:
for chain in range(Nchains):
with open('res_%d_chain_%d.itp' % (k, chain),
'w') as restraint_itp:
with open(includes[k][chain], 'r') as in_itpf:
in_itp = in_itpf.read()
moltop = in_itp.split('[ dihedral_restraints ]')[0]
restraint_itp.write('%s' % moltop)
sys.stderr.write(
"Writing restraints for stringpoint %d chain %d\n" %
(k, chain))
# Note: this format is for Gromacs 4.6+
restraint_itp.write("[ dihedral_restraints ]\n")
restraint_itp.write(
"; ai aj ak al type phi dphi kfac phiB dphiB kfacB\n"
)
pathpoint = adjusted[k] # just a list of phi/psi angles
if Nchains == 1:
protein = molecule(top)
else:
protein = molecule('%s' % includes[k][chain])
# Create a lookup-table for the protein topology that maps residue to dihedrally relevant
# backbone atom indices for N, CA and C.
dih_atoms = {}
for a in protein:
if (a.atomname == 'CA' or a.atomname == 'N'
or a.atomname == 'C'):
try:
dih_atoms[a.resnr][a.atomname] = a.atomnr
except KeyError:
dih_atoms[a.resnr] = {a.atomname: a.atomnr}
# Use the lookup-table built above and get the dihedral specification atoms needed for each
# residue in the selection. This is O(n) in residues, thanks to the dih_atoms table.
pos = 0
for r in rsel:
# Get the atom numbers to use for the phi and psi dihedrals (4 atoms each)
# phi is C on the previous residue, and N, CA, C on this
phi = [
dih_atoms[r - 1]['C'], dih_atoms[r]['N'],
dih_atoms[r]['CA'], dih_atoms[r]['C']
]
# psi is N, CA and C on this residue and N on the next
psi = [
dih_atoms[r]['N'], dih_atoms[r]['CA'],
dih_atoms[r]['C'], dih_atoms[r + 1]['N']
]
# get phi and psi values from the reparametrization vector
phi_val = pathpoint[pos + chain]
psi_val = pathpoint[pos + chain + 1]
# Go to the next residue (phi,phi vals * number of chains apart)
pos += 2 * Nchains
# write phi, psi angles and k-factor
# Note: in the Gromacs 4.6+ format, the k-factor is here. Before, it was in the .mdp as
# dihre_fc.
# Since we need different force constants in different stages, we need to put
# a searchable placeholder in the file here and replace it later
restraint_itp.write(
"%5d%5d%5d%5d%5d %8.4f%5d KFAC\n" %
(phi[0], phi[1], phi[2], phi[3], 1, phi_val, 0))
restraint_itp.write(
"%5d%5d%5d%5d%5d %8.4f%5d KFAC\n" %
(psi[0], psi[1], psi[2], psi[3], 1, psi_val, 0))
pass
if(cstart>0):
for i in range(cstart,len(l)):
if l[i].find('$$$$')>=0:
break
try:
cc50s.append(float(l[i]))
except Exception:
pass
except Exception:
print 'Problem reading experimental data.'
sys.exit()
try:
#Load molecule
molobj=molecule(molfilename)
molweight=molobj.molweight
molformula=molobj.formula()
except Exception:
print 'Problem loading mol file.'
sys.exit()
try:
query = 'INSERT INTO molecules (molname, authorid, dateadded, molweight, molformula) VALUES (%s,%s,localtimestamp,%s,%s) RETURNING molid'
options = [molfilename[:-4],1,molweight,molformula]
q.execute(query,options)
molid=q.fetchone()[0]
except Exception:
print 'Problem inserting molecule into database.'
sys.exit()
def reparametrize(
use_posres,
fix_endpoints,
cvs,
ndx_file,
Nchains,
start_conf,
start_xvg,
end_conf,
end_xvg,
last_resconfs,
top,
includes,
):
Nswarms = len(cvs[0])
ndx_atoms = res_selection.read_ndx(ndx_file)
# For dihedrals, we map the atoms to residues for a single chain, and the readxvg etc. will read the entire file and
# select the same residues in each chain. But for the position restraints which use the atom indices directly, we have
# to first expand the index so it covers all chains.
# TODO: have to figure out or input atoms per chain in the .gro's so we can repeat the atom-selection Nchains times
# for the posres case. The ndx file is for atoms inside the chain, but the .gro will contain global numbering.
# We can detect the chain-repeat in rwgro, by looking for repeating first residue name.
# Hardcode a repeat for testing for now.
if use_posres == 0:
# Map atoms to residues for the dihedral selection
rsel = res_selection.res_select("%s" % start_conf, ndx_atoms)
# sys.stderr.write('Residue selection: %s' %rsel)
# else:
# selected_atoms = []
# for ch in range(5):
# for i in range(len(ndx_atoms)):
# selected_atoms += [ ndx_atoms[i] + ch * 5566 ]
# Calculate the average drift in CV space
# newpts is a per-swarm-point list of CV points (each a list of the CV dimension length)
newpts = []
# Note: the cvs[][] array is indexed after the number of stringpoints that actually were swarm-processed,
# so depending on the fix_endpoints option it may or may not exactly match the path[] which always include
# all points. If we only read in N-2 points here, the start/end will be added to newpts in the code further below.
for pathpt in range(len(cvs)):
swarmpts = []
for i in range(len(cvs[pathpt])):
if use_posres == 1:
zpt = rwgro.readgro_flat(cvs[pathpt][i], ndx_atoms)
# sys.stderr.write('Read pathpt %d swarm %d (%s), got %d CVs\n' % (pathpt, i, cvs[pathpt][i], len(zpt)))
else:
zpt = readxvg.readxvg_flat(cvs[pathpt][i], rsel)
swarmpts.append(zpt)
zptsum = reduce(mapadd, swarmpts)
avgdrift = scale((1 / float(Nswarms)), zptsum)
newpts.append(avgdrift)
# Read in the fixed start and end CV values, for the fix_endpoints case (otherwise the start/end will
# be allowed to drift just like the other points, and they will already then be a part of the newpts array)
if fix_endpoints == 1:
if use_posres == 1:
# TODO: the start/end_conf are full Systems so the atom numbering aliases for the ndx_atoms array :/
# Currently fixed in readgro_flat temporary, hardcoded for the GLIC Protein number.
initpt = rwgro.readgro_flat(start_conf, ndx_atoms)
targetpt = rwgro.readgro_flat(end_conf, ndx_atoms)
else:
initpt = readxvg.readxvg_flat(start_xvg, rsel)
targetpt = readxvg.readxvg_flat(end_xvg, rsel)
sys.stderr.write("Length of initpt %d, targetpt %d\n" % (len(initpt), len(targetpt)))
# Insert the start/end in the beginning and last of newpts
newpts.insert(0, initpt)
newpts.append(targetpt)
# something with 1 indexing makes this padding necessary. TODO: check if this is needed anymore
paddingpt = [0] * len(newpts[0])
newpts.append(paddingpt)
# Do the actual reparameterization
# newpts is a 2D list, first level is one per stringpoint, second is the linear list of CVs
# rep_pts returns the maximum spread of the CV distances between points in [0] and the adjusted
# points in [1]
# Initial iteration
rep_it1 = ext_rep_pts(newpts)
adjusted = rep_it1[1] # get the points only, ignore the spread result
# Keep iterating, feeding the result of the previous result into rep_pts again
# Note that with long CV vectors (> 4000 dimensions) iterations takes a long time
# (at least 45 min for 25 iterations on a single-core 3.5 GHz) when using the python rep_pts.
# We can abort early when the maximum spread between points in the updated string goes
# below a threshold
iters = [adjusted]
i = 0
maxspread = 100.0
# Do max 150 iterations even if we don't reach our goal
while i < 150 and maxspread > 0.012:
sys.stderr.write("Rep iter %d: \n" % i)
sys.stderr.flush()
rep_it = ext_rep_pts(iters[i])
maxspread = rep_it[0]
sys.stderr.write(" maxspread was %f\n" % maxspread)
# Remember the adjusted points
iters.append(rep_it[1])
i = i + 1
sys.stderr.write("Final maximum spread %f after %d iterations.\n" % (maxspread, i))
# Get the final iteration's result
adjusted = iters[-1]
# delete the padding point
adjusted = adjusted[:-1]
newpts = newpts[:-1]
# sys.stderr.write('Pts before repa:\n %s\n' % newpts)
# sys.stderr.write('The adjusted pts:\n %s\n' % adjusted)
# Possibility to test skipping reparametrize by uncommenting the next row.
# The stringpoints will drift along the string and probably end up in the
# endpoints or a minima along the string.
# adjusted = newpts
# calculate reparam distance
sys.stderr.write("Length of the adjusted vector: %d\n" % len(adjusted))
# TODO Nchains should depend on the specific residue (?)
# Given as function argument now.
# Nchains = len(initpt) / (2 * len(rsel))
# write the CV control data for the next iteration
# The output file expected for the posres case is rep_resconf_%d.gro for each stringpoint.
# For dihedrals its res_%d_chain_%d.itp for each stringpoint and chain.
#
for k in range(len(adjusted)):
# Not necessary to do this output for the start/end-points in the fix_endpoints case, the data is
# just bypassed in the caller script
if fix_endpoints == 1 and (k == 0 or k == (len(adjusted) - 1)):
continue
if use_posres == 1:
# Open the output resconf which will go into the next iteration as minimization target
with open("rep_resconf_%d.gro" % k, "w") as rep_resconf:
# Open and read the previous (input) resconf, which has basically tagged along since the last
# reparametrization step (or was set initially at swarm-start)
with open(last_resconfs[k], "r") as in_resconf_f:
in_resconf = in_resconf_f.readlines()
# TODO: maybe this chunk of code could be done by the rwgro module for us.
# Copy the first 2 rows (title and number of atoms) straight over
rep_resconf.write(in_resconf[0])
rep_resconf.write(in_resconf[1])
# Go through the atoms row-by-row and update the xyz coordinates for the atoms the reparametrize
# step moved
# Note: we are only copying over positions here. The velocities are not needed as the use for these files
# will only be as a base for the next iterations position restraint coordinates.
pathpoint = adjusted[k] # the 1-D list of CVs (positions): x,y,z * nbr atoms in index
if len(pathpoint) != (1555 * 3): # assert on GLIC length (TODO)
sys.stderr.write("adjusted[] entry of wrong length %d\n" % len(pathpoint))
cvpos = 0
for line in in_resconf[2:][:-1]:
resname = line[0:8] # python-ranges are inclusive the first index and exclusive the second...
atname = line[8:15]
atomnr = int(line[15:20])
x = float(line[20:28])
y = float(line[28:36])
z = float(line[36:44])
if atomnr in ndx_atoms:
# Update to new coords
x = pathpoint[cvpos]
y = pathpoint[cvpos + 1]
z = pathpoint[cvpos + 2]
cvpos += 3
# Write out the row, updated or not
rep_resconf.write("%s%s%5d%8.3f%8.3f%8.3f\n" % (resname, atname, atomnr, x, y, z))
# Copy the last row which was the cell dimensions
rep_resconf.write(in_resconf[len(in_resconf) - 1])
else:
for chain in range(Nchains):
with open("res_%d_chain_%d.itp" % (k, chain), "w") as restraint_itp:
with open(includes[k][chain], "r") as in_itpf:
in_itp = in_itpf.read()
moltop = in_itp.split("[ dihedral_restraints ]")[0]
restraint_itp.write("%s" % moltop)
sys.stderr.write("Writing restraints for stringpoint %d chain %d\n" % (k, chain))
# Note: this format is for Gromacs 4.6+
restraint_itp.write("[ dihedral_restraints ]\n")
restraint_itp.write("; ai aj ak al type phi dphi kfac phiB dphiB kfacB\n")
pathpoint = adjusted[k] # just a list of phi/psi angles
if Nchains == 1:
protein = molecule(top)
else:
protein = molecule("%s" % includes[k][chain])
# Create a lookup-table for the protein topology that maps residue to dihedrally relevant
# backbone atom indices for N, CA and C.
dih_atoms = {}
for a in protein:
if a.atomname == "CA" or a.atomname == "N" or a.atomname == "C":
try:
dih_atoms[a.resnr][a.atomname] = a.atomnr
except KeyError:
dih_atoms[a.resnr] = {a.atomname: a.atomnr}
# Use the lookup-table built above and get the dihedral specification atoms needed for each
# residue in the selection. This is O(n) in residues, thanks to the dih_atoms table.
pos = 0
for r in rsel:
# Get the atom numbers to use for the phi and psi dihedrals (4 atoms each)
# phi is C on the previous residue, and N, CA, C on this
phi = [dih_atoms[r - 1]["C"], dih_atoms[r]["N"], dih_atoms[r]["CA"], dih_atoms[r]["C"]]
# psi is N, CA and C on this residue and N on the next
psi = [dih_atoms[r]["N"], dih_atoms[r]["CA"], dih_atoms[r]["C"], dih_atoms[r + 1]["N"]]
# get phi and psi values from the reparametrization vector
phi_val = pathpoint[pos + chain]
psi_val = pathpoint[pos + chain + 1]
# Go to the next residue (phi,phi vals * number of chains apart)
pos += 2 * Nchains
# write phi, psi angles and k-factor
# Note: in the Gromacs 4.6+ format, the k-factor is here. Before, it was in the .mdp as
# dihre_fc.
# Since we need different force constants in different stages, we need to put
# a searchable placeholder in the file here and replace it later
restraint_itp.write(
"%5d%5d%5d%5d%5d %8.4f%5d KFAC\n" % (phi[0], phi[1], phi[2], phi[3], 1, phi_val, 0)
)
restraint_itp.write(
"%5d%5d%5d%5d%5d %8.4f%5d KFAC\n" % (psi[0], psi[1], psi[2], psi[3], 1, psi_val, 0)
)
