| import sys | |
| filename = sys.argv[1] | |
| hchain = sys.argv[2] | |
| lchain = sys.argv[3] | |
| achain = sys.argv[4] | |
| with open(filename,'r') as f: | |
| for l in f.readlines(): | |
| l = l.strip().rstrip() |
| #!/bin/bash | |
| # recently ran `sed -i 's/\t/@/g'` | |
| cat 20231018_0264070_summary.ATsv | awk -F'@' ' | |
| BEGIN{ | |
| COUNT=1; pdb=COUNT; COUNT=COUNT+1; Hchain=COUNT; COUNT=COUNT+1; Lchain=COUNT; COUNT=COUNT+1; model=COUNT; COUNT=COUNT+1; antigen_chain=COUNT; COUNT=COUNT+1; antigen_type=COUNT; COUNT=COUNT+1; antigen_het_name=COUNT; COUNT=COUNT+1; antigen_name=COUNT; COUNT=COUNT+1; short_header=COUNT; COUNT=COUNT+1; date=COUNT; COUNT=COUNT+1; compound=COUNT; COUNT=COUNT+1; organism=COUNT; COUNT=COUNT+1; heavy_species=COUNT; COUNT=COUNT+1; light_species=COUNT; COUNT=COUNT+1; antigen_species=COUNT; COUNT=COUNT+1; authors=COUNT; COUNT=COUNT+1; resolution=COUNT; COUNT=COUNT+1; method=COUNT; COUNT=COUNT+1; r_free=COUNT; COUNT=COUNT+1; r_factor=COUNT; COUNT=COUNT+1; scfv=COUNT; COUNT=COUNT+1; engineered=COUNT; COUNT=COUNT+1; heavy_subclass=COUNT; COUNT=COUNT+1; light_subclass=COUNT; COUNT=COUNT+1; light_ctype=COUNT; COUNT=COUNT+1; affinity=COUNT; COUNT=COUNT+1; delta_g=COUNT; COUNT=COUNT+1; affinity_method=COUNT; COUNT=COUNT+1; |
| #include <vector> | |
| #include <array> | |
| #include <algorithm> | |
| #include <iostream> | |
| using Size = unsigned char; | |
| using Graph = std::array< Size, 6 >; | |
| std::vector< Graph > | |
| remix_all( Graph const & input ){ |
| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <style> | |
| #game-container { | |
| position: relative; | |
| width: 1000px; | |
| height: 700px; | |
| border: 1px solid #000; | |
| } |
Sure, here is an example of JavaScript code for a simple paint function that allows the user to draw on an HTML canvas element:
// Create a canvas element and set its dimensions
var canvas = document.createElement('canvas');
canvas.width = 800;
canvas.height = 600;
| import sys | |
| import pyrosetta | |
| from pyrosetta import * | |
| from pyrosetta.rosetta import core, protocols | |
| def relax( pose ): | |
| xml = '''<ROSETTASCRIPTS> | |
| <SCOREFXNS> | |
| <ScoreFunction name="sfxn" weights="ref2015_cst"/> |
| <ROSETTASCRIPTS> | |
| <SIMPLE_METRICS> | |
| <TimingProfileMetric name="t0" custom_type="t0" /> | |
| <TimingProfileMetric name="t1" custom_type="t1" /> | |
| <TimingProfileMetric name="t2" custom_type="t2" /> | |
| <TimingProfileMetric name="t3" custom_type="t3" /> | |
| </SIMPLE_METRICS> | |
| <PROTOCOLS> |
| std::string get_line_for_resid( char chain, core::Size resnum, char aa = 'x' ){ | |
| std::stringstream ss; | |
| ss << resnum << " " << chain; | |
| if( aa == 'x' ) ss << " NATAA"; | |
| else ss << " PIKAA " << aa; | |
| ss << " USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1"; | |
| return ss.str(); | |
| } | |
| void make_resfile( std::string const & filename, core::Size resid, char aa, core::pose::Pose & pose, utility::graph::GraphOP packer_neighbor_graph ){ |
Rosetta uses 1-indexing for its vector class
(utility::vectorL< 1 >, aliased as utility::vector1).
We are told in bootcamp that this is only a compile-time slowdown and not a runtime slowdown.
I took that with a grain of salt, because surely there must be some slowdown with this implementation:
T &
operator []( index_type const i )
| template< typename... Args > | |
| _Edge * add_edge( uint32_t node1, uint32_t node2 , Args&&... args ) { | |
| debug_assert( ! get_edge_exists( node1, node2 ) ); | |
| platform::Size temp = node1 < node2 ? node1 : node2; | |
| node2 = node1 < node2 ? node2 : node1; | |
| node1 = temp; | |
| platform::Size edge_offset = internal_create_new_edge( node1, node2, std::forward<Args>(args)... ); | |
| nodes_[ node1 ].internal_add_edge( edge_offset ); | |
| nodes_[ node2 ].internal_add_edge( edge_offset ); | |
| return internal_get_edge( edge_offset ); |