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CanonicalizeConformer(...)
CanonicalizeConformer( (Conformer)conf [, (Point3D)center=None [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]]) -> None :
Canonicalize the orientation of a conformer so that its principal axes
around the specified center point coincide with the x, y, z axes |
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CanonicalizeMol(...)
CanonicalizeMol( (Mol)mol [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]) -> None :
Loop over the conformers in a molecule and canonicalize their orientation |
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ComputeCanonicalTransform(...)
ComputeCanonicalTransform( (Conformer)conf [, (Point3D)center=None [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]]) -> object :
Compute the transformation required aligna conformer so that
the the principal axes align up with the x,y, z axes
The conformer itself is left unchanged
ARGUMENTS:
- conf : the conformer of interest
- center : optional center point to compute the principal axes around (defaults to the centroid)
- normalizeCovar : optionally normalize the covariance matrix by the number of atoms |
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ComputeCentroid(...)
ComputeCentroid( (Conformer)conf [, (bool)ignoreHs=True]) -> Point3D :
Compute the centroid of the conformation - hydrogens are ignored and no attention
if paid to the difference in sizes of the heavy atoms |
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GetAngleDeg(...)
GetAngleDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId) -> float :
Returns the angle in degrees between atoms i, j, k |
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GetAngleRad(...)
GetAngleRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId) -> float :
Returns the angle in radians between atoms i, j, k |
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GetBondLength(...)
GetBondLength( (Conformer)conf, (int)iAtomId, (int)jAtomId) -> float :
Returns the bond length in angstrom between atoms i, j |
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GetDihedralDeg(...)
GetDihedralDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId) -> float :
Returns the dihedral angle in degrees between atoms i, j, k, l |
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GetDihedralRad(...)
GetDihedralRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId) -> float :
Returns the dihedral angle in radians between atoms i, j, k, l |
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SetAngleDeg(...)
SetAngleDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (float)value) -> None :
Sets the angle in degrees between atoms i, j, k; all atoms bonded to atom k are moved |
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SetAngleRad(...)
SetAngleRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (float)value) -> None :
Sets the angle in radians between atoms i, j, k; all atoms bonded to atom k are moved |
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SetBondLength(...)
SetBondLength( (Conformer)conf, (int)iAtomId, (int)jAtomId, (float)value) -> None :
Sets the bond length in angstrom between atoms i, j; all atoms bonded to atom j are moved |
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SetDihedralDeg(...)
SetDihedralDeg( (Conformer)arg1, (int)arg2, (int)arg3, (int)arg4, (int)arg5, (float)arg6) -> None :
Sets the dihedral angle in degrees between atoms i, j, k, l; all atoms bonded to atom l are moved |
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SetDihedralRad(...)
SetDihedralRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId, (float)value) -> None :
Sets the dihedral angle in radians between atoms i, j, k, l; all atoms bonded to atom l are moved |
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TransformConformer(...)
TransformConformer( (Conformer)arg1, (AtomPairsParameters)arg2) -> None :
Transform the coordinates of a conformer |
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