You are reading the documentation for version 3.1 of ProMod3. You may also want to read the documentation for: 3.0 1.3 2.0 3.2 2.1

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

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