- sire.restraints.bond(*args, **kwargs)#
Synonym for distance(), as a bond restraint is treated the same as a distance restraint
- sire.restraints.boresch(mols, receptor, ligand, kr=None, ktheta=None, kphi=None, name: str = None, map=None)#
Create a set of Boresch restraints that will hold the passed ligand in a its relative binding mode relative to the passed receptor. All of the atoms in both ‘ligand’ and ‘receptor’ must be contained in ‘mols’.
The BoreschRestraint will be a set of six restraints between three identified ligand atoms, and three identified receptor atoms.
A single distance restraint, with specified kr and r0 parameters
Two angle restraints, with the specified two ktheta and theta0 parameters
Three torsion restraints, with the specified three kphi and phi0 parameters
This will create a single BoreschRestraint, which will be passed back in a BoreschRestraints object.
If the force constants (kr, ktheta and kphi) are None, then they will have default values of 150 kcal mol-1 A-2 and 150 kcal mol-1 rad-2
The equilibium distances and angles are based on the current coordinates of that atoms
- sire.restraints.distance(mols, atoms0, atoms1, r0=None, k=None, name: str = None, map=None)#
Create a set of distance restraints from all of the atoms in ‘atoms0’ to all of the atoms in ‘atoms1’ where all atoms are contained in the container ‘mols’, using the passed values of the force constant ‘k’ and equilibrium bond length r0.
These restraints will be per atom-atom distance. If a list of k and/or r0 values are passed, then different values could be used for different atom-atom distances (assuming the same number as the number of atom-atom distances). Otherwise, all atom-atom distances will use the same parameters.
If r0 is None, then the current atom-atom distance for each atom-atom pair will be used as the equilibium value.
If k is None, then a default value of 150 kcal mol-1 A-2 will be used
- sire.restraints.positional(mols, atoms, k=None, r0=None, position=None, name: str = None, map=None)#
Create a set of position restraints for the atoms specified in ‘atoms’ that are contained in the container ‘mols’, using the passed values of the force constant ‘k’ and flat-bottom potential well-width ‘r0’ for the restraints.
These restraints will be per atom. If a list of k and/or r0 values are passed, then different values could be used for different atoms (assuming the same number as the number of atoms). Otherwise, all atoms will use the same parameters.
If ‘r0’ is not specified, then a simple harmonic restraint is used.
If ‘k’ is not specified, then a default of 150 kcal mol-1 A-2 will be used.