[expandcomplex] eased e-value for the 2nd alignment

steineggerlab · Jan 20, 2024 · bb09017 · bb09017
1 parent e9f76df
commit bb09017
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Showing 3 changed files with 11 additions and 2 deletions.
diff --git a/src/commons/LocalParameters.cpp b/src/commons/LocalParameters.cpp
@@ -26,7 +26,8 @@ LocalParameters::LocalParameters() :
         PARAM_FILE_INCLUDE(PARAM_FILE_INCLUDE_ID, "--file-include", "File Inclusion Regex", "Include file names based on this regex", typeid(std::string), (void *) &fileInclude, "^.*$"),
         PARAM_FILE_EXCLUDE(PARAM_FILE_EXCLUDE_ID, "--file-exclude", "File Exclusion Regex", "Exclude file names based on this regex", typeid(std::string), (void *) &fileExclude, "^.*$"),
         PARAM_INDEX_EXCLUDE(PARAM_INDEX_EXCLUDE_ID, "--index-exclude", "Index Exclusion", "Exclude parts of the index:\n0: Full index\n1: Exclude k-mer index (for use with --prefilter-mode 1)\n2: Exclude C-alpha coordinates (for use with --sort-by-structure-bits 0)\nFlags can be combined bit wise", typeid(int), (void *) &indexExclude, "^[0-3]{1}$", MMseqsParameter::COMMAND_EXPERT),
-        PARAM_COMPLEX_REPORT_MODE(PARAM_COMPLEX_REPORT_MODE_ID, "--complex-report-mode", "Complex report mode", "Complex report mode:\n0: No report\n1: Write complex report", typeid(int), (void *) &complexReportMode, "^[0-1]{1}$", MMseqsParameter::COMMAND_EXPERT)
+        PARAM_COMPLEX_REPORT_MODE(PARAM_COMPLEX_REPORT_MODE_ID, "--complex-report-mode", "Complex report mode", "Complex report mode:\n0: No report\n1: Write complex report", typeid(int), (void *) &complexReportMode, "^[0-1]{1}$", MMseqsParameter::COMMAND_EXPERT),
+        PARAM_EXPAND_COMPLEX_EVALUE(PARAM_EXPAND_COMPLEX_EVALUE_ID, "--expand-complex-evalue", "E-value threshold for expandcomplex", "E-value threshold for expandcomplex (range 0.0-inf)", typeid(double), (void *) &eValueThrExpandComplex, "^([-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)|[0-9]*(\\.[0-9]+)?$", MMseqsParameter::COMMAND_ALIGN)
 {
     PARAM_ALIGNMENT_MODE.description = "How to compute the alignment:\n0: automatic\n1: only score and end_pos\n2: also start_pos and cov\n3: also seq.id";
     PARAM_ALIGNMENT_MODE.regex = "^[0-3]{1}$";
@@ -178,6 +179,7 @@ LocalParameters::LocalParameters() :
 
     // complexsearchworkflow
     complexsearchworkflow = combineList(structuresearchworkflow, scorecomplex);
+    complexsearchworkflow.push_back(&PARAM_EXPAND_COMPLEX_EVALUE);
 
     // easycomplexsearchworkflow
     easyscomplexsearchworkflow = combineList(structurecreatedb, complexsearchworkflow);
@@ -212,6 +214,7 @@ LocalParameters::LocalParameters() :
     dbSuffixList = "_h,_ss,_ca";
     indexExclude = 0;
     complexReportMode = 1;
+    eValueThrExpandComplex = 10000.0;
     citations.emplace(CITATION_FOLDSEEK, "van Kempen, M., Kim, S.S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C.L.M., Söding, J., and Steinegger, M. Fast and accurate protein structure search with Foldseek. Nature Biotechnology, doi:10.1038/s41587-023-01773-0 (2023)");
 
     //rewrite param vals.

diff --git a/src/commons/LocalParameters.h b/src/commons/LocalParameters.h
@@ -112,6 +112,7 @@ class LocalParameters : public Parameters {
     PARAMETER(PARAM_FILE_EXCLUDE)
     PARAMETER(PARAM_INDEX_EXCLUDE)
     PARAMETER(PARAM_COMPLEX_REPORT_MODE)
+    PARAMETER(PARAM_EXPAND_COMPLEX_EVALUE)
 
     int prefMode;
     float tmScoreThr;
@@ -131,6 +132,7 @@ class LocalParameters : public Parameters {
     std::string fileExclude;
     int indexExclude;
     int complexReportMode;
+    double eValueThrExpandComplex;
 
     static std::vector<int> getOutputFormat(int formatMode, const std::string &outformat, bool &needSequences, bool &needBacktrace, bool &needFullHeaders,
                                             bool &needLookup, bool &needSource, bool &needTaxonomyMapping, bool &needTaxonomy, bool &needQCa, bool &needTCa, bool &needTMaligner,

diff --git a/src/workflow/ComplexSearch.cpp b/src/workflow/ComplexSearch.cpp
@@ -8,6 +8,7 @@
 
 #include "complexsearch.sh.h"
 
+
 int complexsearch(int argc, const char **argv, const Command &command) {
     LocalParameters &par = LocalParameters::getLocalInstance();
     par.PARAM_ADD_BACKTRACE.addCategory(MMseqsParameter::COMMAND_EXPERT);
@@ -70,14 +71,17 @@ int complexsearch(int argc, const char **argv, const Command &command) {
     tmpDir = FileUtil::createTemporaryDirectory(tmpDir, hash);
     par.filenames.pop_back();
     CommandCaller cmd;
+    double eval =  par.evalThr;
     if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_TMALIGN){
+        par.evalThr = par.eValueThrExpandComplex;
         cmd.addVariable("COMPLEX_ALIGNMENT_ALGO", "tmalign");
         cmd.addVariable("COMPLEX_ALIGN_PAR", par.createParameterString(par.tmalign).c_str());
     }else if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI_AA || par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI){
+        par.evalThr = par.eValueThrExpandComplex;
         cmd.addVariable("COMPLEX_ALIGNMENT_ALGO", "structurealign");
         cmd.addVariable("COMPLEX_ALIGN_PAR", par.createParameterString(par.structurealign).c_str());
     }
-
+    par.evalThr = eval;
     switch(par.prefMode){
         case LocalParameters::PREF_MODE_KMER:
             cmd.addVariable("PREFMODE", "KMER");