def ExtrudeNA(chain):
"""Computes ribbons for DNA/RNA"""
coord = []
coord.append(chain.residues[0].atoms[0].coords)
NA_type = chain.residues[0].type.strip()
atoms = chain.residues[0].atoms
if NA_type in ["A", "G"]:
N9 = Numeric.array(atoms.objectsFromString("N9")[0].coords)
C8 = Numeric.array(atoms.objectsFromString("C8")[0].coords)
C4 = Numeric.array(atoms.objectsFromString("C4")[0].coords)
N9_C8 = C8 - N9
N9_C4 = C4 - N9
normal = Numeric.array(crossProduct(N9_C8, N9_C4, normal=True))
else:
N1 = Numeric.array(atoms.objectsFromString("N1")[0].coords)
C2 = Numeric.array(atoms.objectsFromString("C2")[0].coords)
C6 = Numeric.array(atoms.objectsFromString("C6")[0].coords)
N1_C2 = C2 - N1
N1_C6 = C6 - N1
normal = Numeric.array(crossProduct(N1_C2, N1_C6, normal=True))
base_normal = Numeric.array(chain.residues[0].atoms[0].coords)
coord.append((base_normal + normal).tolist())
for res in chain.residues[1:]:
if res.atoms.objectsFromString("P"):
P_coord = res.atoms.objectsFromString("P")[0].coords
coord.append(P_coord)
else: # this in case last residue does not have P
P_coord = res.atoms.objectsFromString("C5\*")[0].coords
NA_type = res.type.strip()
atoms = res.atoms
if NA_type in ["A", "G"]:
N9 = Numeric.array(atoms.objectsFromString("N9")[0].coords)
C8 = Numeric.array(atoms.objectsFromString("C8")[0].coords)
C4 = Numeric.array(atoms.objectsFromString("C4")[0].coords)
N9_C8 = C8 - N9
N9_C4 = C4 - N9
normal = Numeric.array(crossProduct(N9_C8, N9_C4, normal=True))
else:
N1 = Numeric.array(atoms.objectsFromString("N1")[0].coords)
C2 = Numeric.array(atoms.objectsFromString("C2")[0].coords)
C6 = Numeric.array(atoms.objectsFromString("C6")[0].coords)
N1_C2 = C2 - N1
N1_C6 = C6 - N1
normal = Numeric.array(crossProduct(N1_C2, N1_C6, normal=True))
base_normal = Numeric.array(P_coord)
coord.append((base_normal + normal).tolist())
chain.sheet2D["ssSheet2D"] = Sheet2D()
chain.sheet2D["ssSheet2D"].compute(
coord, len(chain.residues) * (False,), width=2.0, off_c=0.9, offset=0.0, nbchords=4
)
chain.sheet2D["ssSheet2D"].resInSheet = chain.residues
def make_purine(residue, height = 0.4, scale = 1.2):
"""Creates vertices and normals for purines: Adenine Guanine"""
atoms = residue.atoms
names = [name.split("@")[0] for name in atoms.name]
idx=names.index('N9'); N9 = Numeric.array(atoms[idx].coords)
idx=names.index('C8'); C8 = Numeric.array(atoms[idx].coords)
idx=names.index('N7'); N7 = Numeric.array(atoms[idx].coords)
idx=names.index('C5'); C5 = Numeric.array(atoms[idx].coords)
idx=names.index('C4'); C4 = Numeric.array(atoms[idx].coords)
idx=names.index('C6'); C6 = Numeric.array(atoms[idx].coords)
idx=names.index('N1'); N1 = Numeric.array(atoms[idx].coords)
idx=names.index('C2'); C2 = Numeric.array(atoms[idx].coords)
idx=names.index('N3'); N3 = Numeric.array(atoms[idx].coords)
N9_C8 = C8-N9
N9_C4 = C4-N9
C8_C4 = height*norm(C4-C8)
normal = height*Numeric.array(crossProduct(N9_C8, N9_C4, normal=True))
#center1 = (N9+C8+N7+C4+C5)/5.0
#center2 = (C4+C5+C6+N1+C2+N3)/6.0
center2 = (C4+C5+C6+N1+C2+N3+N9+C8+N7)/9.0
center1 = center2
vertices = Numeric.zeros((20,3),Numeric.Float)
vertices[0] = scale*(C8 - normal - center1) + center1
vertices[1] = scale*(N7 - normal - center1) + center1
vertices[2] = scale*(C5 - normal - center2) + center2
vertices[3] = scale*(C4 - normal - center2) + center2
vertices[4] = scale*(C6 - normal - center2) + center2
vertices[5] = scale*(N1 - normal - center2) + center2
vertices[6] = scale*(C2 - normal - center2) + center2
vertices[7] = scale*(N3 - normal - center2) + center2
vertices[8] = scale*(C8 + normal - center1) + center1
vertices[9] = scale*(N7 + normal - center1) + center1
vertices[10] = scale*(C5 + normal - center2) + center2
vertices[11] = scale*(C4 + normal - center2) + center2
vertices[12] = scale*(C6 + normal - center2) + center2
vertices[13] = scale*(N1 + normal - center2) + center2
vertices[14] = scale*(C2 + normal - center2) + center2
vertices[15] = scale*(N3 + normal - center2) + center2
vertices[16] = scale*(N9 - C8_C4 - normal - center1) + center1
vertices[17] = scale*(N9 - C8_C4 + normal - center1) + center1
vertices[18] = scale*(N9 + C8_C4 + normal - center1) + center1
vertices[19] = scale*(N9 + C8_C4 - normal - center1) + center1
faces = Numeric.array([[19,3,2,1,0,16,16],
[17,8,9,10,11,18,18],
[3,7,6,5,4,2,2],
[10,12,13,14,15,11,11],
[16,0,8,17,17,17,17], [0,1,9,8,8,8,8], [1,2,10,9,9,9,9],
[2,4,12,10,10,10,10],
[4,5,13,12,12,12,12], [5,6,14,13,13,13,13],
[6,7,15,14,14,14,14],
[7,3,11,15,15,15,15],
[3,19,18,11,11,11,11] ])
return vertices,faces
def make_pyrimidine(residue, height=0.4, scale=1.2):
"""Creates vertices and normals for pyrimidines:Thymine Uracil Cytosine"""
atoms = residue.atoms
names = [name.split("@")[0] for name in atoms.name]
idx = names.index('N1')
N1 = Numeric.array(atoms[idx].coords)
idx = names.index('C2')
C2 = Numeric.array(atoms[idx].coords)
idx = names.index('N3')
N3 = Numeric.array(atoms[idx].coords)
idx = names.index('C4')
C4 = Numeric.array(atoms[idx].coords)
idx = names.index('C5')
C5 = Numeric.array(atoms[idx].coords)
idx = names.index('C6')
C6 = Numeric.array(atoms[idx].coords)
N1_C2 = C2 - N1
N1_C6 = C6 - N1
C2_C6 = height * norm(C6 - C2)
normal = height * Numeric.array(crossProduct(N1_C2, N1_C6, normal=True))
center = (N1 + C2 + N3 + C4 + C5 + C6) / 6.0
vertices = Numeric.zeros((14, 3), Numeric.Float)
vertices[0] = scale * (C2 - normal - center) + center
vertices[1] = scale * (N3 - normal - center) + center
vertices[2] = scale * (C4 - normal - center) + center
vertices[3] = scale * (C5 - normal - center) + center
vertices[4] = scale * (C6 - normal - center) + center
vertices[5] = scale * (C2 + normal - center) + center
vertices[6] = scale * (N3 + normal - center) + center
vertices[7] = scale * (C4 + normal - center) + center
vertices[8] = scale * (C5 + normal - center) + center
vertices[9] = scale * (C6 + normal - center) + center
vertices[10] = scale * (N1 - C2_C6 - normal - center) + center
vertices[11] = scale * (N1 - C2_C6 + normal - center) + center
vertices[12] = scale * (N1 + C2_C6 + normal - center) + center
vertices[13] = scale * (N1 + C2_C6 - normal - center) + center
faces = Numeric.array([[13, 4, 3, 2, 1, 0, 10], [11, 5, 6, 7, 8, 9, 12],
[0, 5, 11, 10, 10, 10, 10], [
1,
6,
5,
0,
0,
0,
0,
], [2, 7, 6, 1, 1, 1, 1], [3, 8, 7, 2, 2, 2, 2],
[4, 9, 8, 3, 3, 3, 3], [13, 12, 9, 4, 4, 4, 4]])
return vertices, faces
def make_pyrimidine(residue, height = 0.4, scale = 1.2):
"""Creates vertices and normals for pyrimidines:Thymine Uracil Cytosine"""
atoms = residue.atoms
names = [name.split("@")[0] for name in atoms.name]
idx=names.index('N1'); N1 = Numeric.array(atoms[idx].coords)
idx=names.index('C2'); C2 = Numeric.array(atoms[idx].coords)
idx=names.index('N3'); N3 = Numeric.array(atoms[idx].coords)
idx=names.index('C4'); C4 = Numeric.array(atoms[idx].coords)
idx=names.index('C5'); C5 = Numeric.array(atoms[idx].coords)
idx=names.index('C6'); C6 = Numeric.array(atoms[idx].coords)
N1_C2 = C2-N1
N1_C6 = C6-N1
C2_C6 = height*norm(C6-C2)
normal = height*Numeric.array(crossProduct(N1_C2, N1_C6, normal=True))
center = (N1+C2+N3+C4+C5+C6)/6.0
vertices = Numeric.zeros((14,3),Numeric.Float)
vertices[0] = scale*(C2 - normal - center) + center
vertices[1] = scale*(N3 - normal - center) + center
vertices[2] = scale*(C4 - normal - center) + center
vertices[3] = scale*(C5 - normal - center) + center
vertices[4] = scale*(C6 - normal - center) + center
vertices[5] = scale*(C2 + normal - center) + center
vertices[6] = scale*(N3 + normal - center) + center
vertices[7] = scale*(C4 + normal - center) + center
vertices[8] = scale*(C5 + normal - center) + center
vertices[9] = scale*(C6 + normal - center) + center
vertices[10] = scale*(N1 - C2_C6 - normal - center) + center
vertices[11] = scale*(N1 - C2_C6 + normal - center) + center
vertices[12] = scale*(N1 + C2_C6 + normal - center) + center
vertices[13] = scale*(N1 + C2_C6 - normal - center) + center
faces = Numeric.array([[13,4,3,2,1,0,10],
[11,5,6,7,8,9,12],
[0,5,11,10,10,10,10], [1,6,5,0,0,0,0,], [2,7,6,1,1,1,1],
[3,8,7,2,2,2,2], [4,9,8,3,3,3,3], [13,12,9,4,4,4,4]])
return vertices, faces
def detectPiInteractions(self, tolerance=0.95, debug=False, use_all_cycles=False):
if debug: print("in detectPiInteractions")
self.results['pi_pi'] = [] #stacked rings...?
self.results['t_shaped'] = [] #one ring perpendicular to the other
self.results['cation_pi'] = [] #
self.results['pi_cation'] = [] #
self.results['macro_cations'] = []#
self.results['lig_cations'] = [] #
#at this point have self.results
if not len(self.results['lig_close_atoms']):
return
lig_atoms = self.results['lig_close_atoms'].parent.uniq().atoms
macro_res = self.results['macro_close_atoms'].parent.uniq()
if not len(macro_res):
return
macro_atoms = macro_res.atoms
l_rf = RingFinder()
#Ligand
l_rf.findRings2(lig_atoms, lig_atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print("LIG: len(l_rf.rings)=", len(l_rf.rings))
if not len(l_rf.rings):
if debug: print("no lig rings found by l_rf!")
return
acbs = self.aromatic_cycle_bond_selector
#acbs = AromaticCycleBondSelector()
lig_rings = []
for r in l_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
lig_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
lig_rings.append(arom_bnds)
if debug: print("LIG: len(lig_arom_rings)=", len(lig_rings))
self.results['lig_rings'] = lig_rings
self.results['lig_ring_atoms'] = AtomSet()
#only check for pi-cation if lig_rings exist
if len(lig_rings):
macro_cations = self.results['macro_cations'] = self.getCations(macro_atoms)
macro_cations = macro_cations.get(lambda x: x.element!='H')
lig_ring_atoms = AtomSet()
u = {}
for r in lig_rings:
for a in BondSet(r).getAtoms():
u[a] = 1
if len(u):
lig_ring_atoms = AtomSet(list(u.keys()))
lig_ring_atoms.sort()
self.results['lig_ring_atoms'] = lig_ring_atoms
if len(macro_cations):
if debug: print("check distances from lig_rings to macro_cations here")
#macro cations->lig rings
pairDict2 = self.distanceSelector.select(lig_ring_atoms,macro_cations)
z = {}
for key,v in list(pairDict2.items()):
val = v.tolist()[0]
if val in macro_cations:
z[val] = [key]
if len(z):
self.results['pi_cation'] = (list(z.items()))
else:
self.results['pi_cation'] = []
#check the distance between the rings and the macro_cations
self.results['lig_cations'] = self.getCations(lig_atoms)
lig_cations = self.results['lig_cations']
#remove hydrogens
lig_cations = lig_cations.get(lambda x: x.element!='H')
#Macromolecule
m_rf = RingFinder()
m_rf.findRings2(macro_res.atoms, macro_res.atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print("MACRO: len(m_rf.rings)=", len(m_rf.rings))
if not len(m_rf.rings):
if debug: print("no macro rings found by m_rf!")
return
macro_rings = []
for r in m_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
macro_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
macro_rings.append(arom_bnds)
if debug: print("len(macro_arom_rings)=", len(macro_rings))
self.results['macro_rings'] = macro_rings
self.results['macro_ring_atoms'] = AtomSet()
#only check for pi-cation if macro_rings exist
if len(macro_rings):
macro_ring_atoms = AtomSet()
u = {}
for r in macro_rings:
for a in BondSet(r).getAtoms(): #new method of bondSets
u[a] = 1
if len(u):
macro_ring_atoms = AtomSet(list(u.keys()))
macro_ring_atoms.sort()
self.results['macro_ring_atoms'] = macro_ring_atoms
if len(lig_cations):
if debug: print("check distances from macro_rings to lig_cations here")
pairDict3 = self.distanceSelector.select(macro_ring_atoms,lig_cations)
z = {}
for x in list(pairDict3.items()):
#lig cations->macro rings
z.setdefault(x[1].tolist()[0], []).append(x[0])
if len(z):
self.results['cation_pi'] = (list(z.items()))
else:
self.results['cation_pi'] = []
#macro_pi_atoms = AtomSet(pairDict3.keys())
#l_cations = AtomSet()
#for v in pairDict3.values():
# for x in v:
# l_cations.append(x)
#self.results['cation_pi'] = pairDict3.items()
#self.results['cation_pi'] = (l_cations, macro_pi_atoms)
#check for intermol distance <6 Angstrom (J.ComputChem 29:275-279, 2009)
#compare each lig_ring vs each macro_ring
for lig_ring_bnds in lig_rings:
lig_atoms = acbs.getAtoms(lig_ring_bnds)
lig_atoms.sort()
if debug: print("len(lig_atoms)=", len(lig_atoms))
#---------------------------------
# compute the normal to lig ring
#---------------------------------
a1 = numpy.array(lig_atoms[0].coords)
a2 = numpy.array(lig_atoms[2].coords)
a3 = numpy.array(lig_atoms[4].coords)
if debug: print("a1,a2, a3=", a1.tolist(), a2.tolist(), a3.tolist())
for macro_ring_bnds in macro_rings:
macro_atoms = acbs.getAtoms(macro_ring_bnds)
macro_atoms.sort()
if debug: print("len(macro_atoms)=", len(macro_atoms))
pD_dist = self.distanceSelectorWithCutoff.select(macro_ring_atoms, lig_atoms, cutoff=self.dist_cutoff)
if not len(pD_dist[0]):
if debug:
print("skipping ligand ring ", lig_rings.index(lig_ring_bnds), " vs ", end=' ')
print("macro ring", macro_rings.index(macro_ring_bnds))
continue
#---------------------------------
# compute the normal to macro ring
#---------------------------------
b1 = numpy.array(macro_atoms[0].coords)
b2 = numpy.array(macro_atoms[2].coords)
b3 = numpy.array(macro_atoms[4].coords)
if debug: print("b1,b2, b3=", b1.tolist(), b2.tolist(), b3.tolist())
# check for stacking
a2_1 = a2-a1
a3_1 = a3-a1
b2_1 = b2-b1
b3_1 = b3-b1
if debug: print("a2_1 = ", a2-a1)
if debug: print("a3_1 = ", a3-a1)
if debug: print("b2_1 = ", b2-b1)
if debug: print("b3_1 = ", b3-b1)
n1 = crossProduct(a3_1,a2_1) #to get the normal for the first ring
n2 = crossProduct(b3_1,b2_1) #to get the normal for the second ring
if debug: print("n1=", n1)
if debug: print("n2=", n2)
n1 = numpy.array(n1)
n2 = numpy.array(n2)
n1_dot_n2 = numpy.dot(n1,n2)
if debug: print("n1_dot_n2", numpy.dot(n1,n2))
if abs(n1_dot_n2) >= 1*tolerance:
if debug: print("The rings are stacked vertically")
new_result = (acbs.getAtoms(lig_ring_bnds), acbs.getAtoms(macro_ring_bnds))
self.results['pi_pi'].append(new_result)
if abs(n1_dot_n2) <= 0.01*tolerance:
if debug: print("The rings are stacked perpendicularly")
new_result = (acbs.getAtoms(lig_ring_bnds), acbs.getAtoms(macro_ring_bnds))
self.results['t_shaped'].append(new_result)
def ExtrudeNA(chain):
"""Computes ribbons for DNA/RNA"""
coord = []
coord.append(chain.DNARes[0].atoms[0].coords)
NA_type = chain.DNARes[0].type.strip()
atoms = chain.DNARes[0].atoms
missingAts = False
normal = Numeric.array([0.,1.,0.])
if NA_type in ['A', 'G']:
listesel = ['N9.*','C8.*','C4.*']
listeCoord,missingAts = getAtsRes(atoms,listesel)
if not missingAts :
N9 = listeCoord[0]#Numeric.array(atoms.objectsFromString('N9.*')[0].coords)
C8 = listeCoord[1]#Numeric.array(atoms.objectsFromString('C8.*')[0].coords)
C4 = listeCoord[2]#Numeric.array(atoms.objectsFromString('C4.*')[0].coords)
N9_C8 = C8-N9
N9_C4 = C4-N9
normal = Numeric.array(crossProduct(N9_C8, N9_C4, normal=True))
else:
listesel = ['N1.*','C2.*','C6.*']
listeCoord = []
listeCoord,missingAts = getAtsRes(atoms,listesel)
if not missingAts :
N1 = listeCoord[0]#Numeric.array(atoms.objectsFromString('N1.*')[0].coords)
C2 = listeCoord[1]#Numeric.array(atoms.objectsFromString('C2.*')[0].coords)
C6 = listeCoord[2]#Numeric.array(atoms.objectsFromString('C6.*')[0].coords)
N1_C2 = C2-N1
N1_C6 = C6-N1
normal = Numeric.array(crossProduct(N1_C2, N1_C6, normal=True))
base_normal = Numeric.array(chain.DNARes[0].atoms[0].coords)
coord.append((base_normal + normal).tolist())
for res in chain.DNARes[1:]:
normal = Numeric.array([0.,1.,0.])
if res.atoms.objectsFromString('P.*'):
P_coord = res.atoms.objectsFromString('P.*')[0].coords
coord.append(P_coord)
else: # this in case last residue does not have P
P_coord = res.atoms[0].coords
NA_type = res.type.strip()
atoms = res.atoms
if NA_type in ['A', 'G']:
listesel = ['N9.*','C8.*','C4.*']
listeCoord,missingAts = getAtsRes(atoms,listesel)
if not missingAts :
N9 = listeCoord[0]#Numeric.array(atoms.objectsFromString('N9.*')[0].coords)
C8 = listeCoord[1]#Numeric.array(atoms.objectsFromString('C8.*')[0].coords)
C4 = listeCoord[2]#Numeric.array(atoms.objectsFromString('C4.*')[0].coords)
N9_C8 = C8-N9
N9_C4 = C4-N9
normal = Numeric.array(crossProduct(N9_C8, N9_C4, normal=True))
else:
listesel = ['N1.*','C2.*','C6.*']
listeCoord = []
listeCoord,missingAts = getAtsRes(atoms,listesel)
if not missingAts :
N1 = listeCoord[0]#Numeric.array(atoms.objectsFromString('N1.*')[0].coords)
C2 = listeCoord[1]#Numeric.array(atoms.objectsFromString('C2.*')[0].coords)
C6 = listeCoord[2]#Numeric.array(atoms.objectsFromString('C6.*')[0].coords)
N1_C2 = C2-N1
N1_C6 = C6-N1
normal = Numeric.array(crossProduct(N1_C2, N1_C6, normal=True))
base_normal = Numeric.array(P_coord)
coord.append((base_normal + normal).tolist())
chain.sheet2D['ssSheet2D'] = Sheet2D()
chain.sheet2D['ssSheet2D'].compute(coord, len(chain.DNARes)*(False,),
width = 2.0,off_c = 0.9,offset=0.0, nbchords=4)
chain.sheet2D['ssSheet2D'].resInSheet = chain.DNARes
def detectPiInteractions(self, tolerance=0.95, debug=False, use_all_cycles=False):
if debug: print "in detectPiInteractions"
self.results['pi_pi'] = [] #stacked rings...?
self.results['t_shaped'] = [] #one ring perpendicular to the other
self.results['cation_pi'] = [] #
self.results['pi_cation'] = [] #
self.results['macro_cations'] = []#
self.results['lig_cations'] = [] #
#at this point have self.results
lig_res = self.results['lig_close_res']
if not len(lig_res):
return
lig_atoms = lig_res.atoms
macro_res = self.results['macro_close_res']
if not len(macro_res):
return
macro_atoms = macro_res.atoms
l_rf = RingFinder()
#Ligand
l_rf.findRings2(lig_res.atoms, lig_res.atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print "LIG: len(l_rf.rings)=", len(l_rf.rings)
if not len(l_rf.rings):
if debug: print "no lig rings found by l_rf!"
return
acbs = AromaticCycleBondSelector()
lig_rings = []
for r in l_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
lig_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
lig_rings.append(arom_bnds)
if debug: print "LIG: len(lig_arom_rings)=", len(lig_rings)
self.results['lig_rings'] = lig_rings
self.results['lig_ring_atoms'] = AtomSet()
#only check for pi-cation if lig_rings exist
if len(lig_rings):
macro_cations = self.results['macro_cations'] = self.getCations(macro_atoms)
lig_ring_atoms = AtomSet()
u = {}
for r in lig_rings:
for a in BondSet(r).getAtoms():
u[a] = 1
if len(u):
lig_ring_atoms = AtomSet(u.keys())
lig_ring_atoms.sort()
self.results['lig_ring_atoms'] = lig_ring_atoms
if len(macro_cations):
if debug: print "check distances from lig_rings to macro_cations here"
#macro cations->lig rings
pairDict2 = self.distanceSelector.select(lig_ring_atoms,macro_cations)
z = {}
for key,v in pairDict2.items():
val = v.tolist()[0]
if val in macro_cations:
z[val] = [key]
if len(z):
self.results['pi_cation'] = (z.items())
else:
self.results['pi_cation'] = []
#check the distance between the rings and the macro_cations
self.results['lig_cations'] = self.getCations(lig_atoms)
#Macromolecule
m_rf = RingFinder()
m_rf.findRings2(macro_res.atoms, macro_res.atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print "MACRO: len(m_rf.rings)=", len(m_rf.rings)
if not len(m_rf.rings):
if debug: print "no macro rings found by m_rf!"
return
macro_rings = []
for r in m_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
macro_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
macro_rings.append(arom_bnds)
if debug: print "len(macro_arom_rings)=", len(macro_rings)
self.results['macro_rings'] = macro_rings
self.results['macro_ring_atoms'] = AtomSet()
#only check for pi-cation if macro_rings exist
if len(macro_rings):
lig_cations = self.results['lig_cations'] = self.getCations(lig_atoms)
macro_ring_atoms = AtomSet()
u = {}
for r in macro_rings:
for a in BondSet(r).getAtoms(): #new method of bondSets
u[a] = 1
if len(u):
macro_ring_atoms = AtomSet(u.keys())
macro_ring_atoms.sort()
self.results['macro_ring_atoms'] = macro_ring_atoms
if len(lig_cations):
if debug: print "check distances from macro_rings to lig_cations here"
pairDict3 = self.distanceSelector.select(macro_ring_atoms,lig_cations)
z = {}
for x in pairDict3.items():
#lig cations->macro rings
z.setdefault(x[1].tolist()[0], []).append(x[0])
if len(z):
self.results['cation_pi'] = (z.items())
else:
self.results['cation_pi'] = []
#macro_pi_atoms = AtomSet(pairDict3.keys())
#l_cations = AtomSet()
#for v in pairDict3.values():
# for x in v:
# l_cations.append(x)
#self.results['cation_pi'] = pairDict3.items()
#self.results['cation_pi'] = (l_cations, macro_pi_atoms)
#check for intermol distance <6 Angstrom (J.ComputChem 29:275-279, 2009)
#compare each lig_ring vs each macro_ring
for lig_ring_bnds in lig_rings:
lig_atoms = acbs.getAtoms(lig_ring_bnds)
lig_atoms.sort()
if debug: print "len(lig_atoms)=", len(lig_atoms)
#---------------------------------
# compute the normal to lig ring
#---------------------------------
a1 = Numeric.array(lig_atoms[0].coords)
a2 = Numeric.array(lig_atoms[2].coords)
a3 = Numeric.array(lig_atoms[4].coords)
if debug: print "a1,a2, a3=", a1.tolist(), a2.tolist(), a3.tolist()
for macro_ring_bnds in macro_rings:
macro_atoms = acbs.getAtoms(macro_ring_bnds)
macro_atoms.sort()
if debug: print "len(macro_atoms)=", len(macro_atoms)
pD_dist = self.distanceSelectorWithCutoff.select(macro_ring_atoms, lig_atoms, cutoff=self.dist_cutoff)
if not len(pD_dist[0]):
if debug:
print "skipping ligand ring ", lig_rings.index(lig_ring_bnds), " vs ",
print "macro ring", macro_rings.index(macro_ring_bnds)
continue
#---------------------------------
# compute the normal to macro ring
#---------------------------------
b1 = Numeric.array(macro_atoms[0].coords)
b2 = Numeric.array(macro_atoms[2].coords)
b3 = Numeric.array(macro_atoms[4].coords)
if debug: print "b1,b2, b3=", b1.tolist(), b2.tolist(), b3.tolist()
# check for stacking
a2_1 = a2-a1
a3_1 = a3-a1
b2_1 = b2-b1
b3_1 = b3-b1
if debug: print "a2_1 = ", a2-a1
if debug: print "a3_1 = ", a3-a1
if debug: print "b2_1 = ", b2-b1
if debug: print "b3_1 = ", b3-b1
n1 = crossProduct(a3_1,a2_1) #to get the normal for the first ring
n2 = crossProduct(b3_1,b2_1) #to get the normal for the second ring
if debug: print "n1=", n1
if debug: print "n2=", n2
n1 = Numeric.array(n1)
n2 = Numeric.array(n2)
n1_dot_n2 = Numeric.dot(n1,n2)
if debug: print "n1_dot_n2", Numeric.dot(n1,n2)
if abs(n1_dot_n2) >= 1*tolerance:
if debug: print "The rings are stacked vertically"
new_result = (acbs.getAtoms(lig_ring_bnds), acbs.getAtoms(macro_ring_bnds))
self.results['pi_pi'].append(new_result)
if abs(n1_dot_n2) <= 0.01*tolerance:
if debug: print "The rings are stacked perpendicularly"
new_result = (acbs.getAtoms(lig_ring_bnds), acbs.getAtoms(macro_ring_bnds))
self.results['t_shaped'].append(new_result)
def make_purine(residue, height=0.4, scale=1.2):
"""Creates vertices and normals for purines: Adenine Guanine"""
atoms = residue.atoms
names = [name.split("@")[0] for name in atoms.name]
idx = names.index('N9')
N9 = Numeric.array(atoms[idx].coords)
idx = names.index('C8')
C8 = Numeric.array(atoms[idx].coords)
idx = names.index('N7')
N7 = Numeric.array(atoms[idx].coords)
idx = names.index('C5')
C5 = Numeric.array(atoms[idx].coords)
idx = names.index('C4')
C4 = Numeric.array(atoms[idx].coords)
idx = names.index('C6')
C6 = Numeric.array(atoms[idx].coords)
idx = names.index('N1')
N1 = Numeric.array(atoms[idx].coords)
idx = names.index('C2')
C2 = Numeric.array(atoms[idx].coords)
idx = names.index('N3')
N3 = Numeric.array(atoms[idx].coords)
N9_C8 = C8 - N9
N9_C4 = C4 - N9
C8_C4 = height * norm(C4 - C8)
normal = height * Numeric.array(crossProduct(N9_C8, N9_C4, normal=True))
#center1 = (N9+C8+N7+C4+C5)/5.0
#center2 = (C4+C5+C6+N1+C2+N3)/6.0
center2 = (C4 + C5 + C6 + N1 + C2 + N3 + N9 + C8 + N7) / 9.0
center1 = center2
vertices = Numeric.zeros((20, 3), Numeric.Float)
vertices[0] = scale * (C8 - normal - center1) + center1
vertices[1] = scale * (N7 - normal - center1) + center1
vertices[2] = scale * (C5 - normal - center2) + center2
vertices[3] = scale * (C4 - normal - center2) + center2
vertices[4] = scale * (C6 - normal - center2) + center2
vertices[5] = scale * (N1 - normal - center2) + center2
vertices[6] = scale * (C2 - normal - center2) + center2
vertices[7] = scale * (N3 - normal - center2) + center2
vertices[8] = scale * (C8 + normal - center1) + center1
vertices[9] = scale * (N7 + normal - center1) + center1
vertices[10] = scale * (C5 + normal - center2) + center2
vertices[11] = scale * (C4 + normal - center2) + center2
vertices[12] = scale * (C6 + normal - center2) + center2
vertices[13] = scale * (N1 + normal - center2) + center2
vertices[14] = scale * (C2 + normal - center2) + center2
vertices[15] = scale * (N3 + normal - center2) + center2
vertices[16] = scale * (N9 - C8_C4 - normal - center1) + center1
vertices[17] = scale * (N9 - C8_C4 + normal - center1) + center1
vertices[18] = scale * (N9 + C8_C4 + normal - center1) + center1
vertices[19] = scale * (N9 + C8_C4 - normal - center1) + center1
faces = Numeric.array([[19, 3, 2, 1, 0, 16, 16],
[17, 8, 9, 10, 11, 18, 18], [3, 7, 6, 5, 4, 2, 2],
[10, 12, 13, 14, 15, 11, 11],
[16, 0, 8, 17, 17, 17, 17], [0, 1, 9, 8, 8, 8, 8],
[1, 2, 10, 9, 9, 9, 9], [2, 4, 12, 10, 10, 10, 10],
[4, 5, 13, 12, 12, 12, 12],
[5, 6, 14, 13, 13, 13, 13],
[6, 7, 15, 14, 14, 14, 14],
[7, 3, 11, 15, 15, 15, 15],
[3, 19, 18, 11, 11, 11, 11]])
return vertices, faces
def ExtrudeNA(chain):
"""Computes ribbons for DNA/RNA"""
coord = []
coord.append(chain.DNARes[0].atoms[0].coords)
NA_type = chain.DNARes[0].type.strip()
atoms = chain.DNARes[0].atoms
missingAts = False
normal = Numeric.array([0., 1., 0.])
if NA_type in ['A', 'G']:
listesel = ['N9.*', 'C8.*', 'C4.*']
listeCoord, missingAts = getAtsRes(atoms, listesel)
if not missingAts:
N9 = listeCoord[
0] #Numeric.array(atoms.objectsFromString('N9.*')[0].coords)
C8 = listeCoord[
1] #Numeric.array(atoms.objectsFromString('C8.*')[0].coords)
C4 = listeCoord[
2] #Numeric.array(atoms.objectsFromString('C4.*')[0].coords)
N9_C8 = C8 - N9
N9_C4 = C4 - N9
normal = Numeric.array(crossProduct(N9_C8, N9_C4, normal=True))
else:
listesel = ['N1.*', 'C2.*', 'C6.*']
listeCoord = []
listeCoord, missingAts = getAtsRes(atoms, listesel)
if not missingAts:
N1 = listeCoord[
0] #Numeric.array(atoms.objectsFromString('N1.*')[0].coords)
C2 = listeCoord[
1] #Numeric.array(atoms.objectsFromString('C2.*')[0].coords)
C6 = listeCoord[
2] #Numeric.array(atoms.objectsFromString('C6.*')[0].coords)
N1_C2 = C2 - N1
N1_C6 = C6 - N1
normal = Numeric.array(crossProduct(N1_C2, N1_C6, normal=True))
base_normal = Numeric.array(chain.DNARes[0].atoms[0].coords)
coord.append((base_normal + normal).tolist())
for res in chain.DNARes[1:]:
normal = Numeric.array([0., 1., 0.])
if res.atoms.objectsFromString('P.*'):
P_coord = res.atoms.objectsFromString('P.*')[0].coords
coord.append(P_coord)
else: # this in case last residue does not have P
P_coord = res.atoms[0].coords
NA_type = res.type.strip()
atoms = res.atoms
if NA_type in ['A', 'G']:
listesel = ['N9.*', 'C8.*', 'C4.*']
listeCoord, missingAts = getAtsRes(atoms, listesel)
if not missingAts:
N9 = listeCoord[
0] #Numeric.array(atoms.objectsFromString('N9.*')[0].coords)
C8 = listeCoord[
1] #Numeric.array(atoms.objectsFromString('C8.*')[0].coords)
C4 = listeCoord[
2] #Numeric.array(atoms.objectsFromString('C4.*')[0].coords)
N9_C8 = C8 - N9
N9_C4 = C4 - N9
normal = Numeric.array(crossProduct(N9_C8, N9_C4, normal=True))
else:
listesel = ['N1.*', 'C2.*', 'C6.*']
listeCoord = []
listeCoord, missingAts = getAtsRes(atoms, listesel)
if not missingAts:
N1 = listeCoord[
0] #Numeric.array(atoms.objectsFromString('N1.*')[0].coords)
C2 = listeCoord[
1] #Numeric.array(atoms.objectsFromString('C2.*')[0].coords)
C6 = listeCoord[
2] #Numeric.array(atoms.objectsFromString('C6.*')[0].coords)
N1_C2 = C2 - N1
N1_C6 = C6 - N1
normal = Numeric.array(crossProduct(N1_C2, N1_C6, normal=True))
base_normal = Numeric.array(P_coord)
coord.append((base_normal + normal).tolist())
chain.sheet2D['ssSheet2D'] = Sheet2D()
chain.sheet2D['ssSheet2D'].compute(coord,
len(chain.DNARes) * (False, ),
width=2.0,
off_c=0.9,
offset=0.0,
nbchords=4)
chain.sheet2D['ssSheet2D'].resInSheet = chain.DNARes