def test_good_coordinates(self):
"""Correct coordinates are well read. Must be floats"""
for test_input in self.good_inputs:
atom = atoms.Atom(test_input[0], test_input[1])
self.assertEqual(atom.x(), float(test_input[1][0]))
self.assertEqual(atom.y(), float(test_input[1][1]))
self.assertEqual(atom.z(), float(test_input[1][2]))
def graphene(na, nb, nc, includePeriodic=True):
lattice = 1.42
planar = 3.35
a = numpy.array([lattice * math.sqrt(3), 0., 0.])
b = numpy.array([0., 3. * lattice, 0.])
c = numpy.array([0., 0., planar])
boxSize = numpy.vstack([a, b, c, numpy.array([0., 0., 0.])])
# make two basic atoms
a = atoms.Atom()
a.aName = 'C'
a.rName = 'GRA'
a.rNo = 1
a.chain = 'G'
a.ffType = 'ca'
b = copy.deepcopy(a)
b.xyz = numpy.array([0., lattice, 0.])
a.makeBond(b)
al = [a, b]
cal = copy.deepcopy(al)
geometry.moveAtoms(
cal, numpy.array([lattice * math.sqrt(3) / 2.0, lattice * 1.5, 0.]))
al.extend(cal)
boxSize = replicate(al,
boxSize,
na,
nb,
nc,
cutoff=lattice * 1.05,
maxBonds=3,
includePeriodic=includePeriodic)
return (al, boxSize)
def proc_atom(atName):
'''This checks the atomDict for the atom, creates it if necessary,
and returns it.'''
if atName not in atomDict.keys():
atomDict[atName] = atom_lib.Atom(atName, eqivDict, xyzDict, gij,
UijDict, sUijDict)
return atomDict[atName]
def alignAtoms(al1,al2,sel1=None,sel2=None):
""" another interface to the align function
will align atoms in al2 to atoms in al1
optional: sel1: list of indices af atoms in al1 (does not have to be numpy.array)
optional: sel2: list of indices af atoms in al2 (does not have to be numpy.array)
lengths of these two selections have to be the same
"""
if sel1 == None:
sel1 = range(len(al1))
if sel2 == None:
sel2 = range(len(al2))
assert len(sel1) == len(sel2), 'Error: lenghts of the two selections in geometry.alignAtomsAngle is not the same: %d and %d' % (len(sel1), len(sel2))
# create a list of dumme atoms with the target orientations that we are aligning to
bl2 = []
for i in range(len(al2)):
b = atoms.Atom()
bl2.append(b)
for i in range(len(sel1)):
b = bl2[sel2[i]]
b.xyz = al1[sel1[i]].xyz.copy()
set1_orig = atoms.getXyzFromList(bl2)
set2_orig = atoms.getXyzFromList(al2)
set2, RMSD, RMSDnonsel, RMSDall = align( set1_orig, set2_orig, selection = numpy.array(sel2))
atoms.putXyzIntoList(al2,set2)
return RMSD
def convert_args(self, args):
if len(args) != len(self.types):
raise ValueError('%s must have the same length as %s' %
(args, self.types))
new_args = []
for ty, arg in zip(self.types, args):
if isinstance(ty, EasyType) and not isinstance(arg, Object):
new_args.append(ty.get_const(arg))
else:
new_args.append(arg)
return atoms.Atom(self, new_args)
def sphFileToAtoms(sphereFilename):
lines = open(sphereFilename).readlines()
al = []
for line in lines[1:]:
if line.strip() != '':
a = atoms.Atom()
a.aName = 'Sc'
a.rNo = 1
a.rName = 'SPH'
a.chain = 'S'
a.xyz = getXyzFromSphLine(line)
al.append(a)
return al
def readAtomList(filename):
""" read single frame from xyz file """
al = []
with open(filename) as f:
natoms = int(f.readline())
f.readline() # comment line
for i in range(natoms):
atom = atoms.Atom()
s = f.readline().split()
atom.aName = s[0]
atom.xyz[0] = float(s[1])
atom.xyz[1] = float(s[2])
atom.xyz[2] = float(s[3])
al.append(atom)
return al
def readLine(line):
"""store bgf line info into atom and return the atom"""
a = atoms.Atom()
a.rNo = int(line[0:5])
a.rName = line[5:10].strip()
a.aName = line[10:15].strip()
a.aNo = int(line[15:20])
a.xyz = 10.0 * numpy.array(
[float(line[20:28]),
float(line[28:36]),
float(line[36:44])])
a.velocities = numpy.array(
[float(line[44:52]),
float(line[52:60]),
float(line[60:68])])
return a
def readFile(fileName):
with open(fileName, 'r') as f:
line = f.readline()
while not (line.startswith('@<TRIPOS>MOLECULE') or line == ''):
line = f.readline()
line = f.readline()
line = f.readline()
s = line.split()
numAtoms = int(s[0])
numBonds = int(s[1])
numRes = int(s[2])
AL = [atoms.Atom() for i in range(numAtoms)]
while not (line.startswith('@<TRIPOS>ATOM') or line == ''):
line = f.readline()
for i in range(numAtoms):
line = f.readline()
readAtomLine(line, AL[i])
while not (line.startswith('@<TRIPOS>BOND') or line == ''):
line = f.readline()
for i in range(numBonds):
line = f.readline()
readBondLine(line, AL)
while not (line.startswith('@<TRIPOS>SUBSTRUCTURE') or line == ''):
line = f.readline()
resRoot = []
resChain = []
for i in range(numRes):
line = f.readline()
s = line.split()
root = int(s[2])
chain = s[5]
resRoot.append(root)
resChain.append(chain)
chainIndex = 0
if len(resChain) > 0:
for a in AL:
if len(resRoot) > chainIndex + 1:
if a.aNo > resRoot[chainIndex + 1]:
chainIndex = chainIndex + 1
chain = resChain[chainIndex]
a.chain = chain
return AL
def readLine(line):
"""store bgf line info into atom and return the atom"""
a = atoms.Atom()
if line[0:6] != 'ATOM ' and line[0:6] != 'HETATM':
print >> sys.stderr, 'This line is not ATOM/HETATM line: %s' % line
sys.exit(1)
a.aTag = line[0:6]
a.aNo = int(line[6:12])
a.aName = line[13:18].strip()
a.rName = line[19:23].strip()
a.chain = line[23:24]
try:
a.rNo = int(
line[24:30]) # vmd saves the residue number until characted 30
except ValueError:
if line[24:29].strip() == '':
a.rNo = 0
else:
a.rNo = int(
line[24:29]) # but normally character 29 can be a letter
a.xyz = numpy.array(
[float(line[30:40]),
float(line[40:50]),
float(line[50:60])])
a.ffType = line[61:66]
a.lpair = int(line[69:71])
a.charge = float(line[72:80])
try:
fixed = int(line[80:82])
except ValueError:
fixed = 0
if fixed == 1: a.fixed = True
elif fixed == 0: a.fixed = False
else:
print >> sys.stderr, 'Value of fixed is invalid %d, should be 0 or 1. ' % fixed
sys.exit(1)
return a
def readLine(line):
"""store bgf line info into atom and return the atom"""
a = atoms.Atom()
if line[0:6] != 'ATOM ' and line[0:6] != 'HETATM':
print >> sys.stderr, 'This line is not ATOM/HETATM line: %s' % line
sys.exit(1)
a.aTag = line[0:6]
a.aNo = int(line[6:11])
a.aName = line[12:16].strip()
a.rName = line[17:20].strip()
a.chain = line[21]
a.rNo = int(line[22:26])
a.xyz = numpy.array(
[float(line[30:38]),
float(line[38:46]),
float(line[46:54])])
try:
a.occupancy = float(line[54:60])
except ValueError:
a.occupancy = 1.0
try:
a.beta = float(line[60:66])
except ValueError:
a.beta = 0.0
a.lpair = 0
a.charge = 0.0
a.fixed = False
try:
a.ffType = line[76:78]
except ValueError:
a.ffType = ''
return a
def readOutCoordinates(fileName):
'''reads the coordinates sets from the out file, as the structure is minimized, returns xyzlist and al (only with atom names)'''
lines = open(fileName).readlines()
lineIndex = 0
for i in range(len(lines)):
if lines[i].startswith(' Input geometry:'):
lineIndex = i
xyz = [[]]
lineIndex = lineIndex + 3
s = lines[lineIndex].split()
al = []
while len(s) > 0:
al.append(atoms.Atom())
al[-1].aName = s[0]
x = float(s[1])
y = float(s[2])
z = float(s[3])
xyz[0].append([x, y, z])
lineIndex += 1
s = lines[lineIndex].split()
while lineIndex < len(lines):
if lines[lineIndex].startswith(' new geometry:') or lines[
lineIndex].startswith(' final geometry:'):
xyzitem = []
lineIndex += 3
for i in range(lineIndex, lineIndex + len(al)):
s = lines[i].split()
x = float(s[1])
y = float(s[2])
z = float(s[3])
xyzitem.append([x, y, z])
xyz.append(xyzitem)
lineIndex += 1
return numpy.array(xyz), al
def test_distance(self):
"""Distances between atoms are well calculated"""
for pair in self.distance_pairs:
atom_A = atoms.Atom(pair[0][0], pair[0][1])
atom_B = atoms.Atom(pair[1][0], pair[1][1])
self.assertAlmostEqual(atom_A.GetDistance(atom_B), pair[2])
def test_set_coordinates_good(self):
"""Correct atom coordinates are well read into Atom"""
for test_input in self.good_inputs:
atom = atoms.Atom(test_input[0], test_input[1])
self.assertEqual((atom.x(), atom.y(), atom.z()), test_input[1])
def test_set_element_good(self):
"""Correct atom types are well read into Atom"""
for test_input in self.good_inputs:
atom = atoms.Atom(test_input[0], test_input[1])
self.assertEqual(atom.GetType(), test_input[0])
def readTopology(fileName, debug=False):
"""reading topology only from amber prmtop file
bonds between H1 and H2 in WAT are removed """
if debug: print 'Reading amber topology file %s...' % fileName
with open(fileName, 'r') as f:
# parsing the file line by line
# POINTERS
line = f.readline()
while not line.startswith('%FLAG POINTERS'):
line = f.readline()
if len(line) == 0: sys.exit(1)
line = f.readline()
NATOM = int(f.read(8)) # total number of atoms
NTYPES = int(f.read(8)) # total number of distinct atom types
NBONH = int(f.read(8)) # number of bonds containing hydrogen
MBONA = int(f.read(8)) # number of bonds not containing hydrogen
NTHETH = int(f.read(8)) # number of angles containing hydrogen
MTHETA = int(f.read(8)) # number of angles not containing hydrogen
NPHIH = int(f.read(8)) # number of dihedrals containing hydrogen
MPHIA = int(f.read(8)) # number of dihedrals not containing hydrogen
NHPARM = int(f.read(8)) # currently not used
NPARM = int(f.read(8)) # used to determine if addles created prmtop
f.readline()
NNB = int(f.read(8)) # number of excluded atoms
NRES = int(f.read(8)) # number of residues
NBONA = int(f.read(8)) # MBONA + number of constraint bonds
NTHETA = int(f.read(8)) # MTHETA + number of constraint angles
NPHIA = int(f.read(8)) # MPHIA + number of constraint dihedrals
NUMBND = int(f.read(8)) # number of unique bond types
NUMANG = int(f.read(8)) # number of unique angle types
NPTRA = int(f.read(8)) # number of unique dihedral types
NATYP = int(f.read(
8)) # number of atom types in parameter file, see SOLTY below
NPHB = int(
f.read(8)) # number of distinct 10-12 hydrogen bond pair types
f.readline()
IFPERT = int(
f.read(8)) # set to 1 if perturbation info is to be read in
NBPER = int(f.read(8)) # number of bonds to be perturbed
NGPER = int(f.read(8)) # number of angles to be perturbed
NDPER = int(f.read(8)) # number of dihedrals to be perturbed
MBPER = int(f.read(
8)) # number of bonds with atoms completely in perturbed group
MGPER = int(f.read(
8)) # number of angles with atoms completely in perturbed group
MDPER = int(
f.read(8)
) # number of dihedrals with atoms completely in perturbed groups
IFBOX = int(
f.read(8)
) # set to 1 if standard periodic box, 2 when truncated octahedral
NMXRS = int(f.read(8)) # number of atoms in the largest residue
IFCAP = int(
f.read(8)) # set to 1 if the CAP option from edit was specified
f.readline()
NUMEXTRA = int(f.read(8)) # number of extra points found in topology
# NCOPY = int(f.read(8)) # number of PIMD slices / number of beads
# ATOM_NAME
AL = [atoms.Atom() for i in range(NATOM)]
for i in range(len(AL)):
AL[i].aNo = i + 1
f.readline()
f.readline()
f.readline()
for i in range(NATOM):
AL[i].aName = f.read(4).strip()
if (i + 1) % 20 == 0: f.readline()
# CHARGE
line = f.readline()
while not line.startswith('%FLAG CHARGE'):
line = f.readline()
if len(line) == 0: sys.exit(1)
line = f.readline()
for i in range(NATOM):
AL[i].charge = float(f.read(16)) / 18.2223
if (i + 1) % 5 == 0: f.readline()
# MASS
# ATOM_TYPE_INDEX
# NUMBER_EXCLUDED_ATOMS
# NONBONDED_PARM_INDEX
# RESIDUE_LABEL
while not line.startswith('%FLAG RESIDUE_LABEL'):
line = f.readline()
if len(line) == 0: sys.exit(1)
line = f.readline()
resLabel = ['' for i in range(NRES)]
for i in range(NRES):
resLabel[i] = f.read(4)
if (i + 1) % 20 == 0: f.readline()
# RESIDUE_POINTER
while not line.startswith('%FLAG RESIDUE_POINTER'):
line = f.readline()
if len(line) == 0: sys.exit(1)
line = f.readline()
resPointer = [0 for i in range(NRES)]
for i in range(NRES):
resPointer[i] = int(f.read(8))
if (i + 1) % 10 == 0: f.readline()
resPointer.append(1 + NATOM)
# now fill the residue info
for i in range(NRES):
for j in range(resPointer[i], resPointer[i + 1]):
AL[j - 1].rName = resLabel[i].strip()
AL[j - 1].rNo = i + 1
# BOND_FORCE_CONSTANT
# BOND_EQUIL_VALUE
# ANGLE_FORCE_CONSTANT
# ANGLE_EQUIL_VALUE
# DIHEDRAL_FORCE_CONSTANT
# DIHEDRAL_PERIODICITY
# DIHEDRAL_PHASE
# SCEE_SCALE_FACTOR -- not even present in prmtop
# SCNB_SCALE_FACTOR -- not even present in prmtop
# SOLTY -- currently unused (reserved for future use)
# LENNARD_JONES_ACOEF
# LENNARD_JONES_BCOEF
# BONDS_INC_HYDROGEN
while not line.startswith('%FLAG BONDS_INC_HYDROGEN'):
line = f.readline()
if len(line) == 0: sys.exit(1)
line = f.readline()
for i in range(NBONH):
atom1 = int(f.read(8)) / 3
if (3 * i + 1) % 10 == 0: f.readline()
atom2 = int(f.read(8)) / 3
if (3 * i + 2) % 10 == 0: f.readline()
f.read(8)
if (3 * i + 3) % 10 == 0: f.readline()
AL[atom1].makeBond(AL[atom2])
# BONDS_WITHOUT_HYDROGEN
while not line.startswith('%FLAG BONDS_WITHOUT_HYDROGEN'):
line = f.readline()
if len(line) == 0: sys.exit(1)
line = f.readline()
for i in range(NBONA):
atom1 = int(f.read(8)) / 3
if (3 * i + 1) % 10 == 0: f.readline()
atom2 = int(f.read(8)) / 3
if (3 * i + 2) % 10 == 0: f.readline()
f.read(8)
if (3 * i + 3) % 10 == 0: f.readline()
AL[atom1].makeBond(AL[atom2])
# ANGLES_INC_HYDROGEN
# ANGLES_WITHOUT_HYDROGEN
# DIHEDRALS_INC_HYDROGEN
# DIHEDRALS_WITHOUT_HYDROGEN
# EXCLUDED_ATOMS_LIST
# HBOND_ACOEF
# HBOND_BCOEF
# HBCUT
# AMBER_ATOM_TYPE
while not line.startswith('%FLAG AMBER_ATOM_TYPE'):
line = f.readline()
if len(line) == 0: sys.exit(1)
line = f.readline()
for i in range(NATOM):
AL[i].ffType = f.read(4)[0:2]
if (i + 1) % 20 == 0: f.readline()
# TREE_CHAIN_CLASSIFICATION
# JOIN_ARRAY
# IROTAT
# SOLVENT_POINTERS
# ATOMS_PER_MOLECULE
# BOX_DIMENSIONS
# FLAG RADIUS_SET
# RADII
# SCREEN
if IFCAP > 0:
print >> sys.stderr, 'IFCAP > 0 is not implemented (IFCAP is %d here )' % IFCAP
sys.exit(1)
if IFPERT > 0:
print >> sys.stderr, 'IFPERT > 0 is not implemented (IFPERT is %d here )' % IFPERT
sys.exit(1)
if debug: print '%d atoms read from %s.' % (len(AL), fileName)
# removing bonds between H1 and H2 in WAT
for a in AL:
if a.rName == 'WAT' and a.aName == 'O':
if len(a.bonds) != 2:
print 'WARNING: atom %s is WATER oxygen, but is not bonded to two atoms' % a
else:
h1 = a.bonds[0]
h2 = a.bonds[1]
if (h1.aName not in ['H1', 'H2']) or (h2.aName
not in ['H1', 'H2']):
print 'WARNING: atom %s is WATER oxygen, the two atoms it is bonded to are not H1, H2' % a
else:
h1.deleteBond(h2)
return AL