def testFit(self):
cmd.fragment("gly", "m1")
cmd.create("m2", "m1")
rms = cmd.fit("m1", "m2")
self.assertEqual(rms, 0.0)
rms = cmd.rms("m1", "m2")
self.assertEqual(rms, 0.0)
rms = cmd.rms_cur("m1", "m2")
self.assertEqual(rms, 0.0)
def testFit(self):
cmd.fragment("gly", "m1")
cmd.create("m2", "m1")
rms = cmd.fit("m1", "m2")
self.assertEqual(rms, 0.0)
rms = cmd.rms("m1", "m2")
self.assertEqual(rms, 0.0)
rms = cmd.rms_cur("m1", "m2")
self.assertEqual(rms, 0.0)
def conf_search(selection='all', forcefield='MMFF94s', method='Weighted', nsteps=500, conformers=25, lowest_conf=5):
pdb_string = cmd.get_pdbstr(selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('pdb', 'pdb')
mol = ob.OBMol()
obconversion.ReadString(mol, pdb_string)
mol.AddHydrogens()
ff = ob.OBForceField.FindForceField(forcefield) # GAFF, MMFF94s, MMFF94, UFF, Ghemical
ff.Setup(mol)
if method == 'Weighted':
ff.WeightedRotorSearch(conformers, nsteps)
elif method == 'Random':
ff.RandomRotorSearch(conformers, nsteps)
else:
ff.SystematicRotorSearch(nsteps)
if name == 'all':
name = 'all_'
if method in ['Weighted', 'Random']:
ff.GetConformers(mol)
print '##############################################'
print ' Conformer | Energy | RMSD'
nrg_unit = ff.GetUnit()
rmsd = 0
ff.GetCoordinates(mol)
nrg = ff.Energy()
conf_list = []
for i in range(conformers):
mol.SetConformer(i)
ff.Setup(mol)
nrg = ff.Energy()
conf_list.append((nrg, i))
conf_list.sort()
lenght_conf_list = len(conf_list)
if lowest_conf > lenght_conf_list:
lowest_conf = lenght_conf_list
for i in range(lowest_conf):
nrg, orden = conf_list[i]
name_n = '%s%02d' % (name, i)
cmd.delete(name_n)
mol.SetConformer(orden)
pdb_string = obconversion.WriteString(mol)
cmd.read_pdbstr(pdb_string, name_n)
if i != 0:
rmsd = cmd.fit(name_n, '%s00' % name, quiet=1)
print '%15s | %10.2f%9s |%6.1f' % (name_n, nrg, nrg_unit, rmsd)
print '##############################################'
else:
ff.GetCoordinates(mol)
nrg = ff.Energy()
pdb_string = obconversion.WriteString(mol)
cmd.delete(name)
cmd.read_pdbstr(pdb_string, name)
print '#########################################'
print 'The Energy of %s is %8.2f %s ' % (name, nrg, ff.GetUnit())
print '#########################################'
def conf_search(selection="all", forcefield="MMFF94s", method="Weighted", nsteps=500, conformers=25, lowest_conf=5):
pdb_string = cmd.get_pdbstr(selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats("pdb", "pdb")
mol = ob.OBMol()
obconversion.ReadString(mol, pdb_string)
mol.AddHydrogens()
ff = ob.OBForceField.FindForceField(forcefield) ## GAFF, MMFF94s, MMFF94, UFF, Ghemical
ff.Setup(mol)
if method == "Weighted":
ff.WeightedRotorSearch(conformers, nsteps)
elif method == "Random":
ff.RandomRotorSearch(conformers, nsteps)
else:
ff.SystematicRotorSearch(nsteps)
if name == "all":
name = "all_"
if method in ["Weighted", "Random"]:
ff.GetConformers(mol)
print "##############################################"
print " Conformer | Energy | RMSD"
nrg_unit = ff.GetUnit()
rmsd = 0
ff.GetCoordinates(mol)
nrg = ff.Energy()
conf_list = []
for i in range(conformers):
mol.SetConformer(i)
ff.Setup(mol)
nrg = ff.Energy()
conf_list.append((nrg, i))
conf_list.sort()
lenght_conf_list = len(conf_list)
if lowest_conf > lenght_conf_list:
lowest_conf = lenght_conf_list
for i in range(lowest_conf):
nrg, orden = conf_list[i]
name_n = "%s%02d" % (name, i)
cmd.delete(name_n)
mol.SetConformer(orden)
pdb_string = obconversion.WriteString(mol)
cmd.read_pdbstr(pdb_string, name_n)
if i != 0:
rmsd = cmd.fit(name_n, "%s00" % name, quiet=1)
print "%15s | %10.2f%9s |%6.1f" % (name_n, nrg, nrg_unit, rmsd)
print "##############################################"
else:
ff.GetCoordinates(mol)
nrg = ff.Energy()
pdb_string = obconversion.WriteString(mol)
cmd.delete(name)
cmd.read_pdbstr(pdb_string, name)
print "#########################################"
print "The Energy of %s is %8.2f %s " % (name, nrg, ff.GetUnit())
print "#########################################"
def RenderImage(files, index, reference, OutDir):
"""This function issues commands to pymol. Alter these commands to change
what the final output looks like. Note that 'reference' is a reference structure
that allows you to align everything to that structure"""
cmd.do('reinitialize')
cmd.do('set_color lblue= [0.86 , 1.00 , 1.00]')
for i,f in enumerate(files):
cmd.load(f, 'Structure%d'%i)
cmd.load(f, 'Overlay')
cmd.load(reference, 'Reference')
cmd.hide('all')
cmd.do('dss')
cmd.do('bg white')
cmd.do('show cartoon, Overlay')
cmd.fit('Overlay', 'Reference')
cmd.fit('Structure0', 'Reference')
for i in range(len(files)):
cmd.do('show cartoon, Structure%d'%i)
cmd.fit('Structure%d'%i, 'Structure0')
cmd.do('color lblue, Structure%d'%i)
cmd.do('set cartoon_transparency, 0.5, Structure%d'%i)
cmd.do('spectrum count, rainbow, Overlay')
cmd.do('translate [0,0,10], Overlay')
cmd.do('ray')
cmd.do('png %s/State%d'% (OutDir, index))
return
def testCreate(self):
cmd.fragment("ala")
cmd.create("foo", "ala", 1, 1)
names = cmd.get_names()
names.sort()
self.assertEquals(names, ["ala", "foo"])
# TODO: Create a function to compare to chempy models
# m1 = cmd.get_model("foo")
# m2 = cmd.get_model("ala")
# self.assertChempyModelEquals(m1, m2)
self.assertEquals(cmd.fit("ala", "foo"), 0.0)
self.assertEquals(cmd.count_states(), 1)
def testCreate(self):
cmd.fragment("ala")
cmd.create("foo", "ala", 1, 1)
names = cmd.get_names()
names.sort()
self.assertEquals(names, ["ala", "foo"])
# TODO: Create a function to compare to chempy models
# m1 = cmd.get_model("foo")
# m2 = cmd.get_model("ala")
# self.assertChempyModelEquals(m1, m2)
self.assertEquals(cmd.fit("ala", "foo"), 0.0)
self.assertEquals(cmd.count_states(), 1)
def fitting(obj1, select1, obj2, select2):
"""
DESCRIPTION
"fitting" allows the superpositioning of object1 onto object2 using
the atoms in selection1 and selection2 (side chains are ignored). The
residue names, residue numbers chain identifiers, segment identifiers,
and alt ids of selection1 are changed to match those in selection2,
temporarily. This allows the normal "fit" command to work. They are
reset after "fit" is run and two new selections are created showing
the selected atoms.
Be careful when creating your selection strings. Within the
selections, do not include the object name because the chain, residue
name, residue number etc. of selection1 of object1 are converted to
match those in selection2. If the object names are included in the
selections, no atoms will be selected since an atom cannot exist in
both object1 and object2 at the same time.
It is important that the beginning residue numbers specify the
aligned residues, but the ending numbers are not critical. The
shorter of the two selections is used in the fit calculation.
USAGE
fitting object1, selection1, object2, selection2
DO NOT include object names in selections!
EXAMPLES
fitting 1xuu, c. a & (i. 296-309 or i. 335-340), 1ame, i. 8-21 or i. 47-52
"""
list_m = []
list_n = []
backbone = "n. n+ca+c+o &! r. hoh+wat"
select1 = "(%s) & %s" % (select1, backbone)
select2 = "(%s) & %s" % (select2, backbone)
m = cmd.get_model("%s & %s" % (obj1, select1))
n = cmd.get_model("%s & %s" % (obj2, select2))
# for the atoms to be used in fit:
# store id, chain, resn, resi, name, segi, alt
for at in m.atom:
list_m.append((at.id, at.chain, at.resn, at.resi, at.name, at.segi, at.alt))
for at in n.atom:
list_n.append((at.id, at.chain, at.resn, at.resi, at.name, at.segi, at.alt))
if len(m.atom) <= len(n.atom):
total = len(m.atom)
else:
total = len(n.atom)
# set a new segi for the atoms to be used in fit command and to allow resetting later
seg_fit = "1fit"
# change the chain,resn,resi,segi and alt of select1 to match select2
for i in range(total):
cmd.do("alter %s & id %s, chain='%s'" % (obj1, list_m[i][0], list_n[i][1]))
cmd.do("alter %s & id %s, resn='%s'" % (obj1, list_m[i][0], list_n[i][2]))
cmd.do("alter %s & id %s, resi=%s" % (obj1, list_m[i][0], list_n[i][3]))
cmd.do("alter %s & id %s, segi='%s'" % (obj1, list_m[i][0], seg_fit))
cmd.do("alter %s & id %s, alt='%s'" % (obj1, list_m[i][0], list_n[i][6]))
# change the segid for obj2 and select2
cmd.do("alter %s & id %s, segi='%s'" % (obj2, list_n[i][0], seg_fit))
print "Fitting %s and %s\n to %s and %s" % (obj1, select1, obj2, select2)
print "Altered to:"
print "%s & %s & segi %s\n" % (obj1, select2, seg_fit),
print "%s & %s & segi %s\n" % (obj2, select2, seg_fit),
print "--------------------------------------------\n"
rms = cmd.fit(
"%s & %s & segi %s" % (obj1, select2, seg_fit), "%s & %s & segi %s" % (obj2, select2, seg_fit), quiet=0
)
cmd.delete("%s_fitting" % obj1)
cmd.delete("%s_fitting" % obj2)
# create new objects to show the fit atoms
cmd.create("%s_fitting" % obj1, "%s & %s & segi %s" % (obj1, select2, seg_fit))
cmd.create("%s_fitting" % obj2, "%s & %s & segi %s" % (obj2, select2, seg_fit))
# reset chain,resn,resi,segi & alt of obj1 & select1 from stored list
for atoms_m in list_m:
cmd.do("alter %s & id %s, chain='%s'" % (obj1, atoms_m[0], atoms_m[1]))
cmd.do("alter %s & id %s, resn='%s'" % (obj1, atoms_m[0], atoms_m[2]))
cmd.do("alter %s & id %s, resi=%s" % (obj1, atoms_m[0], atoms_m[3]))
cmd.do("alter %s & id %s, segi='%s'" % (obj1, atoms_m[0], atoms_m[5]))
cmd.do("alter %s & id %s, alt='%s'" % (obj1, atoms_m[0], atoms_m[6]))
# reset segi of obj2 & select2 from stored list
for atoms_n in list_n:
cmd.do("alter %s & id %s, segi='%s'" % (obj2, atoms_n[0], atoms_n[5]))
print "RMSD for fitting selection %s of %s onto \n selection %s of %s = %6.3f" % (
select1,
obj1,
select2,
obj2,
rms,
)
def fitting(obj1, select1, obj2, select2):
"""
DESCRIPTION
"fitting" allows the superpositioning of object1 onto object2 using
the atoms in selection1 and selection2 (side chains are ignored). The
residue names, residue numbers chain identifiers, segment identifiers,
and alt ids of selection1 are changed to match those in selection2,
temporarily. This allows the normal "fit" command to work. They are
reset after "fit" is run and two new selections are created showing
the selected atoms.
Be careful when creating your selection strings. Within the
selections, do not include the object name because the chain, residue
name, residue number etc. of selection1 of object1 are converted to
match those in selection2. If the object names are included in the
selections, no atoms will be selected since an atom cannot exist in
both object1 and object2 at the same time.
It is important that the beginning residue numbers specify the
aligned residues, but the ending numbers are not critical. The
shorter of the two selections is used in the fit calculation.
USAGE
fitting object1, selection1, object2, selection2
DO NOT include object names in selections!
EXAMPLES
fitting 1xuu, c. a & (i. 296-309 or i. 335-340), 1ame, i. 8-21 or i. 47-52
"""
list_m = []
list_n = []
backbone = 'n. n+ca+c+o &! r. hoh+wat'
select1 = '(%s) & %s' % (select1, backbone)
select2 = '(%s) & %s' % (select2, backbone)
m = cmd.get_model("%s & %s" % (obj1, select1))
n = cmd.get_model("%s & %s" % (obj2, select2))
# for the atoms to be used in fit:
# store id, chain, resn, resi, name, segi, alt
for at in m.atom:
list_m.append(
(at.id, at.chain, at.resn, at.resi, at.name, at.segi, at.alt))
for at in n.atom:
list_n.append(
(at.id, at.chain, at.resn, at.resi, at.name, at.segi, at.alt))
if len(m.atom) <= len(n.atom):
total = len(m.atom)
else:
total = len(n.atom)
# set a new segi for the atoms to be used in fit command and to allow resetting later
seg_fit = "1fit"
# change the chain,resn,resi,segi and alt of select1 to match select2
for i in range(total):
cmd.do("alter %s & id %s, chain='%s'" %
(obj1, list_m[i][0], list_n[i][1]))
cmd.do("alter %s & id %s, resn='%s'" %
(obj1, list_m[i][0], list_n[i][2]))
cmd.do("alter %s & id %s, resi=%s" %
(obj1, list_m[i][0], list_n[i][3]))
cmd.do("alter %s & id %s, segi='%s'" % (obj1, list_m[i][0], seg_fit))
cmd.do("alter %s & id %s, alt='%s'" %
(obj1, list_m[i][0], list_n[i][6]))
# change the segid for obj2 and select2
cmd.do("alter %s & id %s, segi='%s'" % (obj2, list_n[i][0], seg_fit))
print "Fitting %s and %s\n to %s and %s" % (obj1, select1, obj2,
select2)
print "Altered to:"
print "%s & %s & segi %s\n" % (obj1, select2, seg_fit),
print "%s & %s & segi %s\n" % (obj2, select2, seg_fit),
print "--------------------------------------------\n"
rms = cmd.fit("%s & %s & segi %s" % (obj1, select2, seg_fit),
"%s & %s & segi %s" % (obj2, select2, seg_fit),
quiet=0)
cmd.delete("%s_fitting" % obj1)
cmd.delete("%s_fitting" % obj2)
# create new objects to show the fit atoms
cmd.create("%s_fitting" % obj1,
"%s & %s & segi %s" % (obj1, select2, seg_fit))
cmd.create("%s_fitting" % obj2,
"%s & %s & segi %s" % (obj2, select2, seg_fit))
# reset chain,resn,resi,segi & alt of obj1 & select1 from stored list
for atoms_m in list_m:
cmd.do("alter %s & id %s, chain='%s'" % (obj1, atoms_m[0], atoms_m[1]))
cmd.do("alter %s & id %s, resn='%s'" % (obj1, atoms_m[0], atoms_m[2]))
cmd.do("alter %s & id %s, resi=%s" % (obj1, atoms_m[0], atoms_m[3]))
cmd.do("alter %s & id %s, segi='%s'" % (obj1, atoms_m[0], atoms_m[5]))
cmd.do("alter %s & id %s, alt='%s'" % (obj1, atoms_m[0], atoms_m[6]))
# reset segi of obj2 & select2 from stored list
for atoms_n in list_n:
cmd.do("alter %s & id %s, segi='%s'" % (obj2, atoms_n[0], atoms_n[5]))
print "RMSD for fitting selection %s of %s onto \n selection %s of %s = %6.3f" % (
select1, obj1, select2, obj2, rms)
print "the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n" % pymol.random()
pymol.random = random
cmd.load("dat/pept.pdb", "ref")
for a in xrange(1, 11):
cmd.create("trg", "ref", 1, a, quiet=0)
cmd.alter_state(a, "trg", "x=x+random()/2")
cmd.alter_state(a, "trg", "y=y+random()/2")
cmd.alter_state(a, "trg", "z=z+random()/2", quiet=0)
cmd.frame(1)
print "%8.3f" % cmd.fit("ref", "trg")
# asdf
for a in xrange(1, 14):
print a,
print "%8.3f" % cmd.fit("ref and resi %d" % a, "trg"),
print "%8.3f" % cmd.rms("ref", "trg"),
print "%8.3f" % cmd.rms_cur("ref", "trg")
cmd.frame(10)
print "%8.3f" % cmd.fit("ref", "trg")
for a in xrange(1, 14):
print a,
print "the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n" % pymol.random(
)
pymol.random = random
cmd.load("dat/pept.pdb", "ref")
for a in xrange(1, 11):
cmd.create("trg", "ref", 1, a, quiet=0)
cmd.alter_state(a, "trg", "x=x+random()/2")
cmd.alter_state(a, "trg", "y=y+random()/2")
cmd.alter_state(a, "trg", "z=z+random()/2", quiet=0)
cmd.frame(1)
print "%8.3f" % cmd.fit("ref", "trg")
# asdf
for a in xrange(1, 14):
print a,
print "%8.3f" % cmd.fit("ref and resi %d" % a, "trg"),
print "%8.3f" % cmd.rms("ref", "trg"),
print "%8.3f" % cmd.rms_cur("ref", "trg")
cmd.frame(10)
print "%8.3f" % cmd.fit("ref", "trg")
for a in xrange(1, 14):
print a,
print "%8.3f" % cmd.fit("ref and resi %d" % a, "trg"),
