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Change bond length/angle parameters for sidechain and backbone construction
Sidechains and BackboneLists now use bond length and angle parameters that are extracted from a non-redundant set of high resolution X-ray structures. IC data from CHARMM36 was used before. The new parameters slightly improve sidechain modelling accuracy.
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- CHANGELOG 8 additions, 0 deletionsCHANGELOG
- CMakeLists.txt 1 addition, 1 deletionCMakeLists.txt
- extras/code_generation/cullpdb_pc30.0_res0.0-2.0_len40-10000_R0.25_Xray_d2023_08_01_chains11548 11549 additions, 0 deletions...res0.0-2.0_len40-10000_R0.25_Xray_d2023_08_01_chains11548
- extras/code_generation/ideal_bb_param.py 0 additions, 220 deletionsextras/code_generation/ideal_bb_param.py
- extras/code_generation/parameter_extraction.py 443 additions, 0 deletionsextras/code_generation/parameter_extraction.py
- extras/code_generation/sidechain_atom_rule_lookup.py 0 additions, 431 deletionsextras/code_generation/sidechain_atom_rule_lookup.py
- extras/code_generation/top_all36_prot.rtf 0 additions, 1777 deletionsextras/code_generation/top_all36_prot.rtf
- loop/pymod/export_backbone.cc 11 additions, 0 deletionsloop/pymod/export_backbone.cc
- loop/src/bb_trace_param.cc 120 additions, 120 deletionsloop/src/bb_trace_param.cc
- loop/src/bb_trace_param.hh 2 additions, 2 deletionsloop/src/bb_trace_param.hh
- loop/src/sidechain_atom_rule_lookup.cc 108 additions, 72 deletionsloop/src/sidechain_atom_rule_lookup.cc
- loop/tests/data/all_aa.pdb 68 additions, 68 deletionsloop/tests/data/all_aa.pdb
- loop/tests/data/all_aa_prot_polar_hisd.pdb 85 additions, 85 deletionsloop/tests/data/all_aa_prot_polar_hisd.pdb
- loop/tests/data/all_aa_prot_polar_hise.pdb 85 additions, 85 deletionsloop/tests/data/all_aa_prot_polar_hise.pdb
- loop/tests/data/all_aa_prot_polar_hish.pdb 86 additions, 86 deletionsloop/tests/data/all_aa_prot_polar_hish.pdb
- loop/tests/data/all_aa_prot_ref.pdb 181 additions, 181 deletionsloop/tests/data/all_aa_prot_ref.pdb
- loop/tests/test_backbone.cc 39 additions, 8 deletionsloop/tests/test_backbone.cc
- modelling/tests/test_loop_closing.cc 39 additions, 8 deletionsmodelling/tests/test_loop_closing.cc
- scoring/tests/test_backbone_scorer.cc 68 additions, 67 deletionsscoring/tests/test_backbone_scorer.cc
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