corrections in POPSC and added options to popscomp.R script

Author: jkleinj

Docker/README.md

@@ -1,13 +1,17 @@
 # POPScomp Docker container
-Since end of 2025, the 'Dockerfile' performs all the necessary
-installation steps and can be invoked using the scripts:
-```
-make_Docker_[Mac|Linux].bash
-```
 
 Installation instructions are given in the Wiki of the
-POPScomp GitHub repository.
+POPScomp GitHub repository:
+https://github.com/Fraternalilab/POPScomp/wiki/Docker-Image
+
+The simplest installation route is downloading the POPScomp
+image from the Docker repository.
 
+Alternatively the 'Dockerfile' can be run locally to compile
+that image.
+```
+make_Docker_[Mac|Linux].bash
+```
 
 The legacy installations scripts 'onContainer_\*.bash'
 are kept here as a fall-back solution. 

Docker/make_Docker_Linux.bash Docker/build_DockerImage_onLinux.bashDocker/make_Docker_Linux.bash renamed to Docker/build_DockerImage_onLinux.bash

@@ -191,19 +191,24 @@ int parse_args(int argc, char **argv, Arg *arg, Argpdb *argpdb)
 	int c;
 	const char usage[] = "\npops [--pdb ... | --pdbml ...] [OPTIONS ...]\n\
 	 INPUT OPTIONS\n\
-	   Input syntax is either '--pdb <name>.pdb[.gz]' or '--pdbml <name>.xml[.gz]'.\n\
-	   --mmcif <PDB input>\t\t(type: char  , default: void)\n\
+	   Specify one format option: '--pdb', '--pdbml', '--mmcif'.\n\
+       Input structures can be read compressed ('.gz');\n\
+         specify '--pdb --zipped', the other formats detect compression.\n\
+       \n\
+	   --mmcif <MMCIF input>\t\t(type: char  , default: void)\n\
 	   --pdb <PDB input>\t\t(type: char  , default: void)\n\
 	   --pdbml <PDBML input>\t(type: char  , default: void)\n\
 	   --traj <trajectory input>\t(type: char  , default: void)\n\
 	   --zipped\t\t\t(type: no_arg, default: off)\n\
+       \n\
 	 MODE OPTIONS\n\
 	   --coarse\t\t\t(type: no_arg, default: off)\n\
 	   --hydrogens\t\t\t(type: no_arg, default: off)\n\
 	   --multiModel\t\t\t(type: no_arg, default: off)\n\
 	   --partOcc\t\t\t(type: no_arg, default: off)\n\
 	   --rProbe <probe radius [A]>\t(type: float , default: 1.4)\n\
 	   --silent\t\t\t(type: no_arg, default: off)\n\
+       \n\
 	 OUTPUT OPTIONS\n\
 	   --outDirName <output dir>\t(type: char  , default: NULL)\n\
 	   --popsOut <POPS output>\t(type: char  , default: pops.out)\n\
@@ -227,6 +232,7 @@ int parse_args(int argc, char **argv, Arg *arg, Argpdb *argpdb)
 	   --rout\t\t\t(type: no_arg, default: off)\n\
 	   --routPrefix <prefix>\t(type: char   , default: NULL)\n\
 	   --jsonOut\t\t\t(type: no_arg, default: off)\n\
+       \n\
 	 INFO OPTIONS\n\
 	   --cite\t\t\t(type: no_arg, default: off)\n\
 	   --version\t\t\t(type: no_arg, default: off)\n\
@@ -288,6 +294,7 @@ int parse_args(int argc, char **argv, Arg *arg, Argpdb *argpdb)
             case 1:
                 arg->pdbInFileName = optarg;
 				arg->pdbIn = basename(optarg);
+				arg->pdb = 1;
                 break;
             case 2:
                 arg->trajInFileName = optarg;

Docker/make_Docker_Mac.bash Docker/build_DockerImage_onMac.bashDocker/make_Docker_Mac.bash renamed to Docker/build_DockerImage_onMac.bash

@@ -96,16 +96,21 @@ int main(int argc, char *argv[])
     /** read input structure: mmcif, xml or pdb format */
 	if (! arg.silent) fprintf(stdout, "Input structure\n");
 	strcpy(pdb.pdbID, "");
+
 	if (arg.mmcif) {
+		printf("Reading MMCIF file\n");
 		/* 'gemmi' library function to read PDB entries */
 		s = read_cif(arg.mmcifInFileName);
 		/* map function to copy PDB entries to C structure */
 		map_structure_mmcif(&arg, &argpdb, &pdb, s);
 	} else if (arg.pdbml) {
+		printf("Reading PDBML file\n");
 		read_structure_xml(&arg, &argpdb, &pdb);
 	} else if (arg.pdb) {
+		printf("Reading PDB file\n");
 		read_structure(&arg, &argpdb, &pdb);
 	} else {
+		printf("Failed to read an input structure!\n");
 		exit(EXIT_FAILURE);
 	}
 

POPSC/src/arg.c

@@ -306,7 +306,7 @@ void print_neighbour_parameter(FILE *parameterOutFile, Str *pdb, Type *type, \
 }
 
 /*____________________________________________________________________________*/
-/** print interface residue pairs */
+/** print interface (residue pairs) */
 /* nearest neighbour atom pairs on different chains */
 void print_interface(FILE *interfaceOutFile, Arg *arg, Str *pdb, Type *type, Topol *topol)
 {
@@ -442,13 +442,25 @@ void print_sasa(Arg *arg, Argpdb *argpdb, Str *pdb, Type *type, Topol *topol, \
 
 	/* neighbour list */
 	if (arg->neighbourOut) {
-		if (frame < 0)
-			arg->neighbourOutFile = safe_open(arg->neighbourOutFileName, "w");
-		else
-			arg->neighbourOutFile = safe_open(arg->neighbourOutFileName, "a");
-
-		print_neighbour_list(arg->neighbourOutFile, arg, pdb, topol);
-		fclose(arg->neighbourOutFile);
+		if (arg->rout) {
+			sprintf(rpopsOutFileName, "%s/%s.%s",
+				arg->outDirName, arg->routPrefix, "neighbours.out");
+			if (frame < 0) {
+				rpopsOutFile = safe_open(rpopsOutFileName, "w");
+			} else {
+				rpopsOutFile = safe_open(rpopsOutFileName, "a");
+			}		
+			print_neighbour_list(arg->neighbourOutFile, arg, pdb, topol);
+			fclose(rpopsOutFile);
+		} else {
+			if (frame < 0) {
+				arg->neighbourOutFile = safe_open(arg->neighbourOutFileName, "w");
+			} else {
+				arg->neighbourOutFile = safe_open(arg->neighbourOutFileName, "a");
+			}
+			print_neighbour_list(arg->neighbourOutFile, arg, pdb, topol);
+			fclose(arg->neighbourOutFile);
+		}
 	}
 
 	/* neighbour parameters (for benchmarking) */
@@ -464,13 +476,25 @@ void print_sasa(Arg *arg, Argpdb *argpdb, Str *pdb, Type *type, Topol *topol, \
 
 	/* interface residue pairs */
 	if (arg->interfaceOut) {
-		if (frame < 0)
-			arg->interfaceOutFile = safe_open(arg->interfaceOutFileName, "w");
-		else
-			arg->interfaceOutFile = safe_open(arg->interfaceOutFileName, "a");
-
-		print_interface(arg->interfaceOutFile, arg, pdb, type, topol);
-		fclose(arg->interfaceOutFile);
+		if (arg->rout) {
+			sprintf(rpopsOutFileName, "%s/%s.%s",
+				arg->outDirName, arg->routPrefix, "interface.out");
+			if (frame < 0) {
+				rpopsOutFile = safe_open(rpopsOutFileName, "w");
+			} else {
+				rpopsOutFile = safe_open(rpopsOutFileName, "a");
+			}		
+			print_interface(arg->interfaceOutFile, arg, pdb, type, topol);
+			fclose(rpopsOutFile);
+		} else {
+			if (frame < 0) {
+				arg->interfaceOutFile = safe_open(arg->interfaceOutFileName, "w");
+			} else {
+				arg->interfaceOutFile = safe_open(arg->interfaceOutFileName, "a");
+			}
+			print_interface(arg->interfaceOutFile, arg, pdb, type, topol);
+			fclose(arg->interfaceOutFile);
+		}
 	}
 }
 

POPSC/src/pops

@@ -4,5 +4,5 @@ echo "--------------------------------------------------------------"
 echo " test4a.sh                                                    "
 echo "--------------------------------------------------------------"
 
-../src/pops --mmcif 1F3R.cif --compositionOut --typeOut --topologyOut --atomOut --residueOut --chainOut --neighboutOut --interfaceOut || exit 1
+../src/pops --mmcif 1F3R.cif --compositionOut --typeOut --topologyOut --atomOut --residueOut --chainOut --neighbourOut --interfaceOut || exit 1
 

POPSC/src/pops.c

@@ -0,0 +1 @@
+../../POPSC/tests/1F3R.cif