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ReliaSolve / Molprobity2

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Consider including CH..O bond-scale factor #130

Open russell-taylor opened 3 years ago

russell-taylor commented 3 years ago

Probe has a CHOHBfactor that is used to scale the visible spike length for CH..O bonds. This scaling is on top of the spikelen scaling. It happens when there is a CH_DONOR_PROP flag set on at least one side of an interaction for particular hydrogen bonds. The default for this factor is 0.5 but it can be set on the command line.

CH_DONOR_PROP is set on HD2, HE1, DD2, DE1 on HIS; on H2 and H8 of ": A:ADE:ATP:ADP:AMP:1MA:RIA:T6A: I: DA: DI: AR:" and on H8 of ": G:GUA:GTP:GDP:GMP:GSP:OMG:1MG:2MG:M2G:7MG: YG: DG: GR:".

However, this kind of Hydrogen is only treated as a hydrogen bond if there is a special argument set on the command line; otherwise, we never get to this case. By default, these hydrogens are not donors. The PermitCHXHB flag must be set using the -DOCHO option to have these considered at all. Only when they are considered do we have the possibility of handling them, and then they are scaled down by the specified factor.

Decide whether to keep this factor. If we do, we'll add another flag to ExtraAtomInfo flag telling that a hydrogen is a CH..O atom and then pass a factor into the Scoring class. This flag will be added to the That factor will be applied on top of the current factors when a hydrogen bond involving this type of atom is found.

russell-taylor commented 3 years ago

There is a setProperties() method in select.c that can set the CH_DONOR_PROP differently based on an argument.

russell-taylor commented 3 years ago

We'll add this if there is time.