Monte Carlo Drug Design, base code. #282
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This is code from the long-running drug design branch (PR 1036 in the old repo), and consists of everything which hasn't already been merged and is probably worth still merging. This is being merged at this time primarily as Tracy Tang based her work on this branch, and is getting ready to merge & publish her stuff.
roccomoretti
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YidanTang
reviewed
Jan 29, 2025
source/src/numeric/Calculator.cc
Outdated
| runtime_assert( max_trans >= 0 ); | ||
| if ( x >= min && x <= max ) { return 1.0; } | ||
| if ( x <= min - min_trans || x >= max + max_trans ) { return 0.0; } | ||
| if ( x < min && x >= min - min_trans ) { |
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this should run ok and return 0 for values at the edge of the transition region, but the x == min - min_trans case is included in both this if statement and the above one. Same with max.
YidanTang
reviewed
Feb 6, 2025
| "Filter is false if the metric is greater than this value" ); | ||
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| protocols::filters::xsd_type_definition_w_attributes( xsd, class_name(), | ||
| "Test the number of heteroatom-heteroatom (non C/H) bonds in a residue.", |
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This is probably a copy-paste from another filter and forgot to update the definition for this filter.
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This is code from the long-running drug design branch (PR 1036 in the old repo), and consists of everything which hasn't already been merged and is probably worth still merging.
This is being merged at this time primarily as Tracy Tang (@YidanTang) has based her work on this branch, and is getting ready to merge & publish her stuff.
The changes are primarily Movers, Filters and and Chemistries added to
src/protocols/drug_design/Other changes of notes are additions of the
src/protocols/rotamer_gen/directory, which contains two Chemistry objects, one which adds RDKit rotamers, and one which adds BCL rotamers (and requires the extras=bcl build).