Merge pull request #330 from stromjm/interface_v2.0

Addition of createdb "--db-extraction-mode" (chain or interface)

lib/mmseqs/src/commons/MathUtil.h

@@ -256,6 +256,13 @@ class MathUtil {
         return sum;
     }
 
+    static float squareDist(const float xx, const float xy, const float xz,
+               const float yx, const float yy, const float yz){
+        float d1 = xx - yx;
+        float d2 = xy - yy;
+        float d3 = xz - yz;
+        return (d1 * d1 + d2 * d2 + d3 * d3);
+    }
 
 };
 

src/commons/LocalParameters.cpp

@@ -36,6 +36,8 @@ LocalParameters::LocalParameters() :
         PARAM_PDB_OUTPUT_MODE(PARAM_PDB_OUTPUT_MODE_ID, "--pdb-output-mode", "PDB output mode", "PDB output mode:\n0: Single multi-model PDB file\n1: One PDB file per chain\n2: One PDB file per complex", typeid(int), (void *) &pdbOutputMode, "^[0-2]{1}$", MMseqsParameter::COMMAND_MISC),
         PARAM_PROSTT5_MODEL(PARAM_PROSTT5_MODEL_ID, "--prostt5-model", "Path to ProstT5", "Path to ProstT5 model", typeid(std::string), (void *) &prostt5Model, "^.*$", MMseqsParameter::COMMAND_COMMON),
         PARAM_GPU(PARAM_GPU_ID, "--gpu", "Use GPU", "Use GPU (CUDA) if possible", typeid(int), (void *) &gpu, "^[0-1]{1}$", MMseqsParameter::COMMAND_COMMON),
+        PARAM_DB_EXTRACTION_MODE(PARAM_DB_EXTRACTION_MODE_ID, "--db-extraction-mode", "Createdb extraction mode", "createdb extraction mode: 0: chain 1: interface", typeid(int), (void *) &dbExtractionMode, "^[0-1]{1}$"),
+        PARAM_DISTANCE_THRESHOLD(PARAM_DISTANCE_THRESHOLD_ID, "--distance-threshold", "Interface distance threshold", "Residues with C-beta below this threshold will be part of interface", typeid(float), (void *) &distanceThreshold, "^[0-9]*(\\.[0-9]+)?$"),
         PARAM_MULTIMER_TM_THRESHOLD(PARAM_MULTIMER_TM_THRESHOLD_ID,"--multimer-tm-threshold", "TMscore threshold for filtermultimer", "accept alignments with a tmsore > thr [0.0,1.0]",typeid(float), (void *) &filtMultimerTmThr, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
         PARAM_CHAIN_TM_THRESHOLD(PARAM_CHAIN_TM_THRESHOLD_ID,"--chain-tm-threshold", "chain TMscore threshold for filtermultimer", "accept alignments with a tmsore > thr [0.0,1.0]",typeid(float), (void *) &filtChainTmThr, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
         PARAM_INTERFACE_LDDT_THRESHOLD(PARAM_INTERFACE_LDDT_THRESHOLD_ID,"--interface-lddt-threshold", "Interface LDDT threshold", "accept alignments with a lddt > thr [0.0,1.0]",typeid(float), (void *) &filtInterfaceLddtThr, "^0(\\.[0-9]+)?|1(\\.0+)?$")
@@ -88,6 +90,8 @@ LocalParameters::LocalParameters() :
 #endif
     structurecreatedb.push_back(&PARAM_PROSTT5_MODEL);
     structurecreatedb.push_back(&PARAM_CHAIN_NAME_MODE);
+    structurecreatedb.push_back(&PARAM_DB_EXTRACTION_MODE);
+    structurecreatedb.push_back(&PARAM_DISTANCE_THRESHOLD);
     structurecreatedb.push_back(&PARAM_WRITE_MAPPING);
     structurecreatedb.push_back(&PARAM_MASK_BFACTOR_THRESHOLD);
     structurecreatedb.push_back(&PARAM_COORD_STORE_MODE);
@@ -272,6 +276,8 @@ LocalParameters::LocalParameters() :
     eValueThrExpandMultimer = 10000.0;
     prostt5Model = "";
     gpu = 0;
+    dbExtractionMode = DB_EXTRACT_MODE_CHAIN;
+    distanceThreshold = 8.0;
     filtMultimerTmThr = 0.0;
     filtChainTmThr = 0.0;
     filtInterfaceLddtThr = 0.0;

src/commons/LocalParameters.h

@@ -70,6 +70,9 @@ class LocalParameters : public Parameters {
     static const int OUTFMT_COMPLEX_U = 56;
     static const int OUTFMT_COMPLEX_T = 57;
 
+    static const int DB_EXTRACT_MODE_CHAIN = 0;
+    static const int DB_EXTRACT_MODE_INTERFACE = 1;
+
     static const int COORD_STORE_MODE_CA_FLOAT = 1;
     static const int COORD_STORE_MODE_CA_DIFF  = 2;
     static const int COORD_STORE_MODE_CA_PLAIN_TEXT  = 3;
@@ -143,6 +146,8 @@ class LocalParameters : public Parameters {
     PARAMETER(PARAM_PDB_OUTPUT_MODE)
     PARAMETER(PARAM_PROSTT5_MODEL)
     PARAMETER(PARAM_GPU)
+    PARAMETER(PARAM_DB_EXTRACTION_MODE)
+    PARAMETER(PARAM_DISTANCE_THRESHOLD)
     PARAMETER(PARAM_MULTIMER_TM_THRESHOLD)
     PARAMETER(PARAM_CHAIN_TM_THRESHOLD)
     PARAMETER(PARAM_INTERFACE_LDDT_THRESHOLD)
@@ -176,6 +181,8 @@ class LocalParameters : public Parameters {
     float filtInterfaceLddtThr;
     std::string prostt5Model;
     int gpu;
+    int dbExtractionMode;
+    float distanceThreshold;
 
     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,

src/strucclustutils/GemmiWrapper.cpp

@@ -263,7 +263,8 @@ bool GemmiWrapper::loadFoldcompStructure(std::istream& stream, const std::string
     if (coordinates.size() == 0) {
         return false;
     }
-
+    seq3di.clear();
+    taxIds.clear();
     title.clear();
     chain.clear();
     names.clear();

src/strucclustutils/GemmiWrapper.h

@@ -40,6 +40,7 @@ class GemmiWrapper {
     std::vector<Vec3> c;
     std::vector<Vec3> cb;
     std::vector<char> ami;
+    std::vector<char> seq3di;
     std::vector<std::string> names;
     std::vector<std::string> chainNames;
     std::vector<unsigned int> modelIndices;