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# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
files_in.py -- reading AMBER .in file fragments
@author: EricM
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
# Various standard residues appear in AMBER data files with .in
# extensions. These describe the residue with internal coordinates,
# each atom placed with respect to other previously placed atoms.
# Actual .in files in the AMBER source tree contain multiple residues,
# each of which has data specified beyond just the z-matrix of
# internal coordinates. This routine is designed to read a single
# fragment from one of those files, where the fragment consists of
# just the lines defining the z-matrix for a single residue.
# Here is a sample of such a fragment, Glycene:
# i igraph isymbl itree na nb nc r theta phi chrg
#
# 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
# 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
# 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
# 4 N N M 3 2 1 1.335 116.600 180.000 -0.374282
# 5 H H E 4 3 2 1.010 119.800 0.000 0.253981
# 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.128844
# 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 0.088859
# 8 HA3 H0 E 6 4 3 1.090 109.500 60.000 0.088859
# 9 C C M 6 4 3 1.522 110.400 180.000 0.580584
# 10 O O E 9 6 4 1.229 120.500 0.000 -0.509157
# The format is columns of data separated by whitespace. Different
# AMBER .in files use different widths for the various columns. The
# first column is the atom index number (i). The first three atoms
# are dummy atoms, used to establish the coordinate system.
# The second column is a unique atom name for each of the non-dummy
# atoms (igraph).
# The third column is the AMBER atom type (isymbl).
# Column 4 is the topology for the atom (itree). It determines the
# number of non-loop bonds. We're going to ignore this, and just
# create a bond for each radius specification.
# Columns 5, 6, and 7 are indices for three previous atoms (na, nb,
# nc)
# Columns 8, 9, and 10 are the radius (r), angle (theta), and torsion
# angle (phi) parameters.
# The last column is the fractional charge on the atom (chrg). We are
# ignoring the charge here.
# The radius parameter is in Angstroms, the angle and torsion
# parameters are in degrees.
# Taking line ten an an example, the Oxygen atom it represents is
# 1.229 Angstroms away from Carbon atom number 9. The O-C-C angle
# between atoms 10, 9, and 6 is 120.5 degrees. The O-C-C-N torsion
# angle between atoms 10, 9, 6, and 4 is 0 degrees, indicating that
# the O and N are on the same side of the C-C bond.
# See: http://amber.scripps.edu/doc/prep.html
import os
from geometry.InternalCoordinatesToCartesian import InternalCoordinatesToCartesian
from geometry.VQT import A
from model.chunk import Chunk
from model.chem import Atom
from model.bonds import bond_atoms
from model.elements import PeriodicTable
AMBER_AtomTypes = {}
_is_initialized = False
def _init():
global _is_initialized
if (_is_initialized):
return
AMBER_AtomTypes["C"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CA"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CB"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CC"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CD"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CK"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CM"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CN"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CQ"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CR"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CT"] = PeriodicTable.getElement("C").find_atomtype("sp3")
AMBER_AtomTypes["CV"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CW"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["C*"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CY"] = PeriodicTable.getElement("C").find_atomtype("sp")
AMBER_AtomTypes["CZ"] = PeriodicTable.getElement("C").find_atomtype("sp")
AMBER_AtomTypes["C0"] = PeriodicTable.getElement("Ca").find_atomtype("?")
AMBER_AtomTypes["H"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H0"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HC"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H1"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H2"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H3"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HA"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H4"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H5"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HO"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HS"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HW"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HP"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HZ"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["F"] = PeriodicTable.getElement("F").find_atomtype("?")
AMBER_AtomTypes["Cl"] = PeriodicTable.getElement("Cl").find_atomtype("?")
AMBER_AtomTypes["Br"] = PeriodicTable.getElement("Br").find_atomtype("?")
AMBER_AtomTypes["I"] = PeriodicTable.getElement("I").find_atomtype("?")
AMBER_AtomTypes["IM"] = PeriodicTable.getElement("Cl").find_atomtype("?")
AMBER_AtomTypes["IB"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["MG"] = PeriodicTable.getElement("Mg").find_atomtype("?")
AMBER_AtomTypes["N"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NA"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NB"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NC"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["N2"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["N3"] = PeriodicTable.getElement("N").find_atomtype("sp3")
AMBER_AtomTypes["NT"] = PeriodicTable.getElement("N").find_atomtype("sp3")
AMBER_AtomTypes["N*"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NY"] = PeriodicTable.getElement("N").find_atomtype("sp")
AMBER_AtomTypes["O"] = PeriodicTable.getElement("O").find_atomtype("sp2")
AMBER_AtomTypes["O2"] = PeriodicTable.getElement("O").find_atomtype("sp2")
AMBER_AtomTypes["OW"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["OH"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["OS"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["P"] = PeriodicTable.getElement("P").find_atomtype("sp3(p)") #sp3(p) is 'sp3(phosphate)
AMBER_AtomTypes["S"] = PeriodicTable.getElement("S").find_atomtype("sp3") # ?
AMBER_AtomTypes["SH"] = PeriodicTable.getElement("S").find_atomtype("sp3") # ?
AMBER_AtomTypes["CU"] = PeriodicTable.getElement("Cu").find_atomtype("?")
AMBER_AtomTypes["FE"] = PeriodicTable.getElement("Fe").find_atomtype("?")
AMBER_AtomTypes["Li"] = PeriodicTable.getElement("Li").find_atomtype("?")
AMBER_AtomTypes["IP"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["Na"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["K"] = PeriodicTable.getElement("K").find_atomtype("?")
#AMBER_AtomTypes["Rb"] = PeriodicTable.getElement("Rb").find_atomtype("?")
#AMBER_AtomTypes["Cs"] = PeriodicTable.getElement("Cs").find_atomtype("?")
AMBER_AtomTypes["Zn"] = PeriodicTable.getElement("Zn").find_atomtype("?")
_is_initialized = True
def insertin(assy, filename):
_init()
dir, nodename = os.path.split(filename)
mol = Chunk(assy, nodename)
mol.showOverlayText = True
file = open(filename)
lines = file.readlines()
atoms = {}
transform = InternalCoordinatesToCartesian(len(lines), None)
for line in lines:
columns = line.strip().split()
index = int(columns[0])
name = columns[1]
type = columns[2]
na = int(columns[4])
nb = int(columns[5])
nc = int(columns[6])
r = float(columns[7])
theta = float(columns[8])
phi = float(columns[9])
transform.addInternal(index, na, nb, nc, r, theta, phi)
xyz = transform.getCartesian(index)
if (index > 3):
if (AMBER_AtomTypes.has_key(type)):
sym = AMBER_AtomTypes[type]
else:
print "unknown AMBER atom type, substituting Carbon: %s" % type
sym = "C"
a = Atom(sym, A(xyz), mol)
atoms[index] = a
a.setOverlayText(type)
if (na > 3):
a2 = atoms[na]
bond_atoms(a, a2)
assy.addmol(mol)
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