Other Scoring Functions¶

Scoring Functions from SCWRL3¶

promod3.scoring.SCWRL3PairwiseScore(d, Rij)¶

Pairwise score from the SCWRL3 sidechain construction algorithm [canutescu2003b].

Parameters:

• d (float) – Distance between the two interacting particles

• Rij (float) –

  Summed hard-sphere radii of the interacting particles. Suggestions from the paper:

  • carbon: 1.6

  • oxygen: 1.3

  • nitrogen: 1.3

  • sulfur: 1.7

Returns:

The score

Return type:

float

promod3.scoring.SCWRL3DisulfidScore(ca_pos_one, cb_pos_one, sg_pos_one                              ca_pos_two, cb_pos_two, sg_pos_two)¶

Implements the empirically derived disulfid score from the SCWRL3 sidechain construction algorithm [canutescu2003b].

Parameters:

• ca_pos_one (ost.geoom.Vec3) – CA carbon position of first amino acid

• cb_pos_one (ost.geoom.Vec3) – CB carbon position of first amino acid

• sg_pos_one (ost.geoom.Vec3) – SG sulfur position of first amino acid

• ca_pos_two (ost.geoom.Vec3) – CA carbon position of second amino acid

• cb_pos_two (ost.geoom.Vec3) – CB carbon position of second amino acid

• sg_pos_two (ost.geoom.Vec3) – SG sulfur position of second amino acid

Returns:

The score

Return type:

float