#!/usr/bin/env python
#
from openeye.oechem import *
import os,sys
import math

def DoubleArrayFromList(alist):
    array = DoubleArray(len(alist))
    for i in xrange(len(alist)):
        array[i] = alist[i]
    return array


# open our trusty example file
ifs=oemolistream("drugs.sdf")
mol=OECreateOEGraphMol()

# get acetsali
OEReadMolecule(ifs, mol)
OETriposAtomNames(mol)

# open an output file for the modified geometries
ofs=oemolostream("newgeom.sdf")

# write out the original molecule for reference
OEWriteMolecule(ofs, mol)

# get some atom references
c1 = mol.GetAtom(OEHasAtomName("C1"))
c2 = mol.GetAtom(OEHasAtomName("C2"))
o1 = mol.GetAtom(OEHasAtomName("O1"))
c8 = mol.GetAtom(OEHasAtomName("C8"))

print "c1->c2 distance = %6.3f A" % OEGetDistance(mol, c1, c2)
print "c1->c2 dist. squared = %6.3f A" % OEGetDistance2(mol, c1, c2)
print "c1-c2-o1 angle = %6.3f" % OEGetAngle(mol, c1, c2, o1)

tor = OEGetTorsion(mol, c1, c2, o1, c8) * cvar.Rad2Deg
print "c1-c2-o1-c8 torsion = %6.3f deg." % tor

print "Setting torsion to 90 deg."
OESetTorsion(mol, c1, c2, o1, c8, 90.0 * cvar.Deg2Rad)

tor = OEGetTorsion(mol, c1, c2, o1, c8) * cvar.Rad2Deg
print "c1-c2-o1-c8 torsion now = %6.3f deg." % tor
 
OEWriteMolecule(ofs, mol)

trans = DoubleArray(3)
OECenter(mol, trans)
print trans[0], trans[1], trans[2]

OEWriteMolecule(ofs, mol)

trans = DoubleArrayFromList((-3.0, -3.0, -3.0))
OETranslate(mol, trans)

OEWriteMolecule(ofs, mol)

trans = DoubleArrayFromList((3.0, 3.0, 3.0))
OETranslate(mol,trans)

OEWriteMolecule(ofs, mol)

rmat = DoubleArrayFromList((0.0, 1.0, 0.0,
                            1.0, 0.0, 0.0,
                            0.0, 0.0, 1.0 ))

OERotate(mol, rmat)

OEWriteMolecule(ofs, mol)