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Reduce2 input file telling what flips to make and which way to make them #174

Closed russell-taylor closed 1 year ago

russell-taylor commented 2 years ago

MolProbity has a "Review flips" page that tells which flips to apply and which not.

It then re-runs Reduce, locking down those flips and otherwise optimizing. It currently only does the renaming flip, but it should do the full fixup.

@chrissciwilliams Add notes here if there are other constraints that we need to be able to control (rotations of Movers, Histidine protenation states).

This will be done in concert with the Mover output formatting, so that MolProbity can both know and request flips using meaningful names.

russell-taylor commented 2 years ago

I propose that the format of the file telling how to lock down individual Movers in Reduce be a subset of the format that the report is generated in, with the option to use the entire format so that someone can copy/paste it and then delete the lines for the Movers that they don't want to lock down, having Reduce adjust the rest. I put an output for 1xso at the end and then discuss the subset of the format that is required. this would be used for flipkin construction and could also be used to optimize only parts of a file.

The section for each Model/Alt conformation will begin with a line that contains the work 'Model' followed by an integer then 'Alt' followed by a quoted string.

Each Mover description line will include the name of the Mover (for example, SingleHydrogenRotator or AmideFlip) followed by "at chain" followed by a chain ID, residue name, residue number, atom name followed by some number of words and then the word 'pose' followed by the appropriate pose description for that type:

SingleHydrogenRotator, NH3Rotator,MoverAromaticMethylRotator:   Angle -179.9 deg
AmideFlip:              Flipped
HisFlip:                Unflipped HD1Placed HE2Placed

A minimalist file would be something like:

Model 0 Alt 'B'
HisFlip at chain A HIS 41 NE2 pose Unflipped HD1Placed HE2Placed

The whole file (which could be used) would look like:

 BEGIN REPORT: Model 0 Alt 'B':
  Set of 3 Movers:  Totals: initial score -1.01, final score 2.97
   SingleHydrogenRotator at chain A THR 52 HG1 Initial score: 0.40 final score: 0.41 pose Angle -179.0 deg .
   AmideFlip at chain A ASN 53 ND2 Initial score: 0.08 final score: 1.40 pose Flipped . . .
   SingleHydrogenRotator at chain A SER 57 HG Initial score: -1.49 final score: 1.17 pose Angle 69.0 deg .
  Set of 3 Movers:  Totals: initial score 0.80, final score 3.92
   SingleHydrogenRotator at chain B THR 52 HG1 Initial score: 0.58 final score: 0.73 pose Angle -177.0 deg .
   AmideFlip at chain B ASN 53 ND2 Initial score: 1.67 final score: 1.67 pose Unflipped . . .
   SingleHydrogenRotator at chain B SER 57 HG Initial score: -1.45 final score: 1.52 pose Angle 29.0 deg .
  Set of 2 Movers:  Totals: initial score 8.62, final score 8.82
   AmideFlip at chain A GLN 22 NE2 Initial score: 7.05 final score: 7.05 pose Unflipped . . .
   SingleHydrogenRotator at chain A SER 103 HG Initial score: 1.57 final score: 1.77 pose Angle -151.0 deg .
  Set of 2 Movers:  Totals: initial score 5.66, final score 7.36
   SingleHydrogenRotator at chain A THR 37 HG1 Initial score: 0.64 final score: 2.18 pose Angle -77.0 deg .
   HisFlip at chain A HIS 41 NE2 Initial score: 5.02 final score: 5.19 pose Unflipped HD1Placed HE2Placed .
  Set of 2 Movers:  Totals: initial score 8.77, final score 8.18
   AmideFlip at chain A ASN 129 ND2 Initial score: 3.76 final score: 3.17 pose Unflipped . . .
   AmideFlip at chain A ASN 137 ND2 Initial score: 5.01 final score: 5.01 pose Unflipped . . Uncertain
  Set of 2 Movers:  Totals: initial score 5.94, final score 7.96
   SingleHydrogenRotator at chain B THR 37 HG1 Initial score: 0.35 final score: 1.98 pose Angle -67.0 deg .
   HisFlip at chain B HIS 41 NE2 Initial score: 5.59 final score: 5.98 pose Unflipped HD1Placed HE2Placed .
  Set of 2 Movers:  Totals: initial score 3.76, final score 4.26
   SingleHydrogenRotator at chain B SER 103 HG Initial score: 1.37 final score: 1.87 pose Angle 159.0 deg .
   AmideFlip at chain B ASN 108 ND2 Initial score: 2.39 final score: 2.39 pose Unflipped . . .
  Set of 2 Movers:  Totals: initial score 8.11, final score 10.30
   AmideFlip at chain B ASN 129 ND2 Initial score: 3.05 final score: 3.79 pose Unflipped . . .
   AmideFlip at chain B ASN 137 ND2 Initial score: 5.06 final score: 6.51 pose Flipped . . .
  Singleton Movers:
   NH3Rotator at chain A LYS 3 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   SingleHydrogenRotator at chain A CYS 6 HG Initial score: -0.32 final score: 1.22 pose Angle 129.0 deg .
   SingleHydrogenRotator at chain A SER 11 HG Initial score: 0.20 final score: 1.06 pose Angle -81.0 deg .
   NH3Rotator at chain A LYS 15 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   HisFlip at chain A HIS 19 NE2 Initial score: 2.93 final score: 2.98 pose Unflipped HD1Placed HE2NotPlaced .
   AmideFlip at chain A GLN 23 NE2 Initial score: 0.37 final score: 0.37 pose Unflipped . . Uncertain
   SingleHydrogenRotator at chain A SER 28 HG Initial score: 0.20 final score: 0.50 pose Angle 49.0 deg .
   NH3Rotator at chain A LYS 32 NZ Initial score: 0.21 final score: 0.35 pose Angle 44.0 deg .
   AmideFlip at chain A ASN 51 ND2 Initial score: 2.43 final score: 2.43 pose Unflipped . . .
   SingleHydrogenRotator at chain A SER 60 HG Initial score: 0.20 final score: 1.42 pose Angle -63.9 deg .
   AmideFlip at chain A ASN 63 ND2 Initial score: 5.76 final score: 5.76 pose Unflipped . . .
   AmideFlip at chain A ASN 66 ND2 Initial score: 2.36 final score: 2.36 pose Unflipped . . Uncertain
   NH3Rotator at chain A LYS 67 NZ Initial score: 0.29 final score: 0.42 pose Angle 167.0 deg .
   AmideFlip at chain A ASN 68 ND2 Initial score: 2.76 final score: 3.37 pose Flipped . . .
   SingleHydrogenRotator at chain A THR 75 HG1 Initial score: 0.29 final score: 0.68 pose Angle -61.0 deg .
   AmideFlip at chain A ASN 84 ND2 Initial score: 4.27 final score: 4.27 pose Unflipped . . .
   SingleHydrogenRotator at chain A THR 86 HG1 Initial score: 0.36 final score: 1.69 pose Angle 9.0 deg .
   AmideFlip at chain A GLN 94 NE2 Initial score: 1.44 final score: 1.44 pose Unflipped . . .
   NH3Rotator at chain A LYS 96 NZ Initial score: 0.60 final score: 0.79 pose Angle -31.0 deg .
   SingleHydrogenRotator at chain A THR 98 HG1 Initial score: 0.33 final score: 0.76 pose Angle 39.0 deg .
   SingleHydrogenRotator at chain A SER 100 HG Initial score: 0.20 final score: 1.10 pose Angle 9.0 deg .
   NH3Rotator at chain A LYS 105 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   AmideFlip at chain A ASN 108 ND2 Initial score: 4.26 final score: 4.26 pose Unflipped . . .
   SingleHydrogenRotator at chain A SER 109 HG Initial score: 1.39 final score: 1.68 pose Angle -121.0 deg .
   SingleHydrogenRotator at chain A THR 114 HG1 Initial score: 0.65 final score: 1.74 pose Angle 102.5 deg .
   NH3Rotator at chain A LYS 120 NZ Initial score: 0.57 final score: 1.07 pose Angle -91.0 deg .
   NH3Rotator at chain A LYS 126 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   SingleHydrogenRotator at chain A SER 132 HG Initial score: -3.73 final score: 1.65 pose Angle 19.0 deg .
   NH3Rotator at chain A LYS 134 NZ Initial score: 1.50 final score: 2.10 pose Angle -43.0 deg .
   SingleHydrogenRotator at chain A THR 135 HG1 Initial score: 1.77 final score: 2.13 pose Angle -61.0 deg .
   SingleHydrogenRotator at chain A TYR 149 HH Initial score: 1.05 final score: 1.18 pose Angle 7.2 deg .
   SingleHydrogenRotator at chain A SER 150 HG Initial score: 1.06 final score: 1.08 pose Angle -171.0 deg .
   NH3Rotator at chain B LYS 3 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   SingleHydrogenRotator at chain B CYS 6 HG Initial score: -0.27 final score: 0.87 pose Angle 69.0 deg .
   SingleHydrogenRotator at chain B SER 11 HG Initial score: 0.20 final score: 0.86 pose Angle -71.0 deg .
   NH3Rotator at chain B LYS 15 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   HisFlip at chain B HIS 19 NE2 Initial score: 2.18 final score: 2.73 pose Flipped HD1Placed HE2NotPlaced .
   AmideFlip at chain B GLN 22 NE2 Initial score: 4.84 final score: 4.84 pose Unflipped . . .
   AmideFlip at chain B GLN 23 NE2 Initial score: 0.00 final score: 0.00 pose Unflipped . . Uncertain
   SingleHydrogenRotator at chain B SER 28 HG Initial score: 0.20 final score: 0.70 pose Angle 9.0 deg .
   NH3Rotator at chain B LYS 32 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   AmideFlip at chain B ASN 51 ND2 Initial score: 2.08 final score: 2.08 pose Unflipped . . Uncertain
   SingleHydrogenRotator at chain B SER 60 HG Initial score: 0.20 final score: 1.38 pose Angle -81.0 deg .
   AmideFlip at chain B ASN 63 ND2 Initial score: 6.32 final score: 6.32 pose Unflipped . . .
   AmideFlip at chain B ASN 66 ND2 Initial score: 0.60 final score: 0.60 pose Unflipped . . Uncertain
   NH3Rotator at chain B LYS 67 NZ Initial score: 0.26 final score: 0.52 pose Angle -1.0 deg .
   AmideFlip at chain B ASN 68 ND2 Initial score: 2.51 final score: 3.41 pose Flipped . . .
   SingleHydrogenRotator at chain B THR 75 HG1 Initial score: 0.31 final score: 0.95 pose Angle -71.0 deg .
   AmideFlip at chain B ASN 84 ND2 Initial score: 4.97 final score: 4.97 pose Unflipped . . .
   SingleHydrogenRotator at chain B THR 86 HG1 Initial score: 0.30 final score: 1.61 pose Angle -1.0 deg .
   AmideFlip at chain B GLN 94 NE2 Initial score: 1.46 final score: 1.46 pose Unflipped . . .
   NH3Rotator at chain B LYS 96 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   SingleHydrogenRotator at chain B THR 98 HG1 Initial score: 0.29 final score: 0.99 pose Angle -1.0 deg .
   SingleHydrogenRotator at chain B SER 100 HG Initial score: 0.20 final score: 0.62 pose Angle -51.0 deg .
   NH3Rotator at chain B LYS 105 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   SingleHydrogenRotator at chain B SER 109 HG Initial score: 0.99 final score: 1.25 pose Angle -131.0 deg .
   SingleHydrogenRotator at chain B THR 114 HG1 Initial score: 0.54 final score: 1.55 pose Angle 109.0 deg .
   NH3Rotator at chain B LYS 120 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   NH3Rotator at chain B LYS 126 NZ Initial score: 0.20 final score: 0.20 pose Angle 179.0 deg .
   SingleHydrogenRotator at chain B SER 132 HG Initial score: -2.99 final score: 1.72 pose Angle 49.0 deg .
   NH3Rotator at chain B LYS 134 NZ Initial score: 0.24 final score: 0.45 pose Angle 149.0 deg .
   SingleHydrogenRotator at chain B THR 135 HG1 Initial score: 1.54 final score: 2.41 pose Angle -61.0 deg .
   SingleHydrogenRotator at chain B TYR 149 HH Initial score: 0.77 final score: 1.03 pose Angle -151.0 deg .
   SingleHydrogenRotator at chain B SER 150 HG Initial score: 0.20 final score: 1.53 pose Angle -79.1 deg .
 END REPORT
russell-taylor commented 2 years ago

@todo: The above format overspecifies the HIS state; it should only state whether or not to flip the Histidine and let Reduce2 decide whether to add each hydrogen (ensure that Reduce was doing this).

@todo: We do not need to be able to specify anything about the state of rotators.

Make a new plan that just tells whether to keep or to flip each flip that is in the model and does not allow specifying other details.

russell-taylor commented 1 year ago

Added command-line option.