schrodinger.structutils.interactions.steric_clash module¶
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schrodinger.structutils.interactions.steric_clash.
clash_iterator
(struc1, atoms1=None, struc2=None, atoms2=None, allowable_overlap=0.4)¶ Iterate through all steric clashes between two groups of atoms
Parameters: - struc1 (
schrodinger.structure.Structure
) – The first structure to examine - atoms1 (list(int)) – A list of atom numbers for
struc1
. If given, only the specified atoms will be examined. If not given, all atoms ofstruc1
will be used. - struc1 – The second structure to examine. If not given
struc1
will be used - atoms2 (list(int)) – A list of atom numbers for
struc2
. If given, only the specified atoms will be examined. If not given, all atoms ofstruc2
will be used. - allowable_overlap (float) – Steric clashes smaller than this will be ignored. The default (0.4 A) is a reasonable value when examining protein- protein interactions.
Returns: A generator that iterates through steric clashes. Each iteration will yield a tuple of (atom from
struc1
, atom fromstruc2
, distance). The distance between the two specified atoms in Angstroms (float). Note that this is the distance between the nuclear centers, not the size of the overlap.Return type: generator
- struc1 (
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schrodinger.structutils.interactions.steric_clash.
sphere_overlap_volume
(radius1, radius2, dist)¶ Calculate the volume of the overlap between two spheres
Parameters: - radius1 (float) – The radius of the first sphere
- radius2 (float) – The radius of the second sphere
- dist (float) – The distance between the centers of the two spheres
Returns: The overlap volume
Return type: float
Note: The equation implemented here is taken from http://mathworld.wolfram.com/Sphere-SphereIntersection.html, equation 16
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schrodinger.structutils.interactions.steric_clash.
clash_volume
(struc1, atoms1=None, struc2=None, atoms2=None)¶ Calculate the volume of the steric overlap between two structures
Parameters: - struc1 (
schrodinger.structure.Structure
) – The first structure to examine - atoms1 (list) – A list of atom numbers for
struc1
. If given, only the specified atoms will be examined. If not given, all atoms ofstruc1
will be used. - struc1 – The second structure to examine. If not given
struc1
will be used - atoms2 (list) – A list of atom numbers for
struc2
. If given, only the specified atoms will be examined. If not given, all atoms ofstruc2
will be used.
Returns: The steric overlap volume in cubic Angstroms
Return type: float
Note: The overlap volume is calculated as a sum of pair-wise steric clashes. This may double count overlaps for very severe steric clashes where there are really three spheres overlapping.
- struc1 (