Merge pull request #37 from choderalab/am16

AmberTools v16 upgrade with tests

Resolves #36

.travis.yml

@@ -8,6 +8,7 @@ addons:
       - g++
       - gfortran
       - bison
+      - csh
 
 install:
   - ./configure --prefix=$HOME/appveyor
@@ -17,4 +18,10 @@ script:
   - $HOME/appveyor/bin/sqm -h
   - $HOME/appveyor/bin/antechamber -h
   - $HOME/appveyor/bin/tleap -h
+  # Run tests
+  - cd $HOME/appveyor/test && make test.antechamber
+  - cd $HOME/appveyor/test && make test.sqm
+  - cd $HOME/appveyor/test && make test.leap
+  - cd $HOME/appveyor/test && make test.paramfit
+  - cd $HOME/appveyor/test && make clean
 

Makefile

@@ -8,19 +8,24 @@ endif
 
 PROGS=antechamber$(WRAPPER_SFX) acdoctor$(SFX) am1bcc$(SFX) antechamber_pvt$(SFX) \
 		atomtype$(SFX) bondtype$(SFX) charmmgen$(SFX) database$(SFX) espgen$(SFX) \
-		parmcal$(SFX) parmchk$(WRAPPER_SFX) parmchk2$(WRAPPER_SFX) prepgen$(SFX) \
-		residuegen$(SFX) sqm$(SFX) teLeap$(SFX) tleap$(WRAPPER_SFX) translate$(SFX) \
+		match$(SFX) match_atomname$(SFX) parmcal$(SFX) parmchk$(WRAPPER_SFX) \
+		paramfit$(WRAPPER_SFX) parmchk2$(WRAPPER_SFX) prepgen$(SFX) residuegen$(SFX) respgen$(SFX) sqm$(SFX) \
+		teLeap$(SFX) tleap$(WRAPPER_SFX) translate$(SFX)  \
+		paramfit_pvt$(SFX) \
 		parmchk_pvt$(SFX) parmchk2_pvt$(SFX)
 
 all: prep libs
 	$(MAKE) antechamber
 	$(MAKE) leap
+	$(MAKE) paramfit
 	$(MAKE) sqm
 
 install: all
 	$(MKDIR) -p $(PREFIX)/bin $(PREFIX)/share
 	cd bin && mv $(PROGS) $(PREFIX)/bin
 	cp -r share/amber/dat $(PREFIX)
+	cp -r test $(PREFIX)
+	cp config.h $(PREFIX)/test
 
 prep:
 	$(MKDIR) -p bin
@@ -31,6 +36,9 @@ antechamber::
 leap::
 	cd leap && $(MAKE) install
 
+paramfit::
+	cd paramfit && $(MAKE) install
+
 sqm::
 	cd sqm && $(MAKE) install
 

README.md

@@ -1,10 +1,18 @@
-`ambermini` is an internal dependency for [omnia](http://omnia.md), and contains a stripped-down set of just antechamber, sqm, and tleap.
+[![Travis Build Status](https://travis-ci.org/choderalab/ambermini.png)](https://travis-ci.org/choderalab/ambermini)
+
+`ambermini` is an internal dependency for [omnia](http://omnia.md), and 
+contains a stripped-down set of just antechamber, sqm, paramfit, and tleap.
 
 **NOTE: This is not an officially-supported AmberTools distribution.**
 
 To obtain AmberTools, go to [the Amber webpage](http://ambermd.org).
 
-This version has been updated to match AmberTools 15 as of 23 Jun 2015.
+This version has been updated to match AmberTools 16, patch 16 as of 19 Oct 2016.
+
+Release versions are denoted by the following X.Y.Z Syntax:
+* X = AmberTools version
+* Y = AMBER patch number
+* Z = AmberMini bug fix number
 
 ### To install
 ```

antechamber/Makefile

@@ -12,6 +12,8 @@ PROGS = \
 	$(BINDIR)/charmmgen$(SFX) \
 	$(BINDIR)/database$(SFX) \
 	$(BINDIR)/espgen$(SFX) \
+	$(BINDIR)/match$(SFX) \
+	$(BINDIR)/match_atomname$(SFX) \
 	$(BINDIR)/parmcal$(SFX) \
 	$(BINDIR)/parmchk$(SFX) \
 	$(BINDIR)/parmchk_pvt$(SFX) \
@@ -163,6 +165,27 @@ ncsu-penalties.o: ncsu-penalties.h
 parmcal.o: common.h
 parmcal.o: define.h
 parmcal.o: utility.c
+match.o: common.h
+match.o: define.h
+match.o: atom.h
+match.o: utility.c
+match.o: common.c
+match.o: ring.c
+match.o: ac.c
+match.o: pdb.c
+match.o: mol2.c
+match.o: mdl.c
+match.o: rst.c
+match_atomname.o: common.h
+match_atomname.o: define.h
+match_atomname.o: atom.h
+match_atomname.o: utility.c
+match_atomname.o: common.c
+match_atomname.o: equatom2.c
+match_atomname.o: ac.c
+match_atomname.o: pdb.c
+match_atomname.o: mol2.c
+match_atomname.o: prep.c
 parmchk.o: common.h
 parmchk.o: define.h
 parmchk.o: atom.h
@@ -274,6 +297,12 @@ $(BINDIR)/delphigen$(SFX): delphigen.o
 $(BINDIR)/espgen$(SFX): espgen.o
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) espgen.o $(LM) -o $(BINDIR)/espgen$(SFX)
 
+$(BINDIR)/match$(SFX): match.o
+	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) match.o $(LM) -o $(BINDIR)/match$(SFX)
+
+$(BINDIR)/match_atomname$(SFX): match_atomname.o
+	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) match_atomname.o $(LM) -o $(BINDIR)/match_atomname$(SFX)
+
 $(BINDIR)/parmcal$(SFX): parmcal.o
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) parmcal.o $(LM) -o $(BINDIR)/parmcal$(SFX)
 

antechamber/antechamber.c

@@ -54,11 +54,11 @@ int default_flag  = 0;				/*assign default information? */
 int atomname_flag = 0;				/*assign atom name? */
 int atomicnum_flag = 0;				/*judge atomic number according to atom name ? */
 int adjustatomname_flag = 0;			/*adjust atom name? */
-int usr_aan_flag = -99;			/*the user's input for adjusting atom names */
+int usr_aan_flag = -99;				/*the user's input for adjusting atom names */
 int duplicatedname_flag = 0;			/*check atom name duplication? */
 int cartcoord_flag = 0;				/*generate coordinate from internal coordinate ? */
 int connect_flag = 0;				/*judge atom connectivity and generate bond ? */
-int chargemethod_flag = 0;     /* is there a "-c" flag on the input line? */
+int chargemethod_flag = 0;   	  		/* is there a "-c" flag on the input line? */
 int divcon_flag = 2;  
 int ek_flag = 0; 				/* read empircal calculation keyword or not */
 int max_path_length = -1;
@@ -113,12 +113,12 @@ void usage()
 			   "                   -a   additional file name\n"
 			   "                   -fa  additional file format\n"
 			   "                   -ao  additional file operation\n"
-			   "[35m                        crd   [0m: only read in coordinate\n"
-			   "[35m                        crg   [0m: only read in charge\n"
-			   "[35m                        radius[0m: only read in radius\n"
-			   "[35m                        name  [0m: only read in atom name\n"
-			   "[35m                        type  [0m: only read in atom type\n"
-			   "[35m                        bond  [0m: only read in bond type \n"
+			   "[34m                        crd   [0m: only read in coordinate\n"
+			   "[34m                        crg   [0m: only read in charge\n"
+			   "[34m                        radius[0m: only read in radius\n"
+			   "[34m                        name  [0m: only read in atom name\n"
+			   "[34m                        type  [0m: only read in atom type\n"
+			   "[34m                        bond  [0m: only read in bond type \n"
 			   "                   -m   multiplicity (2S+1), default is 1\n"
 			   "                   -rn  residue name, overrides input file, default is MOL\n"
 			   "                   -rf  residue toplogy file name in prep input file,\n"
@@ -129,27 +129,32 @@ void usage()
 			   "                   -gm  gaussian memory keyword, inside a pair of quotes, such as\"%%mem=1000MB\"\n"
 			   "                   -gn  gaussian number of processors keyword, inside a pair of quotes, such as \"%%nproc=8\"\n"
 			   "                   -gv  add keyword to generate gesp file (for Gaussian 09 only)\n"
-			   "[35m                        1    [0m: yes\n"
-			   "[35m                        0    [0m: no, the default\n"
+			   "[34m                        1    [0m: yes\n"
+			   "[34m                        0    [0m: no, the default\n"
 			   "                   -ge  gaussian esp file generated by iop(6/50=1), default is g09.gesp\n"
 			   "                   -df  am1-bcc precharge flag, 2 - use sqm(default); 0 - use mopac\n"
-			   "                   -at  atom type, can be gaff (the default), amber (for PARM94/99/99SB), bcc and sybyl\n"
+			   "                   -at  atom type\n"
+			   "                        gaff : the default\n"
+			   "                        gaff2: for gaff2 (beta-version)\n"
+			   "                        amber: for PARM94/99/99SB\n"
+			   "                        bcc  : bcc \n"
+			   "                        sybyl: sybyl \n"
 			   "                   -du  fix duplicate atom names: yes(y)[default] or no(n)\n"
 			   "                   -bk  4-character component Id, for ccif\n"
 			   "                   -an  adjust atom names: yes(y) or no(n)\n"
 			   "                        the default is 'y' for 'mol2' and 'ac' and 'n' for the other formats \n"
 			   "                   -j   atom type and bond type prediction index, default is 4 \n"
-			   "[35m                        0    [0m: no assignment\n"
-			   "[35m                        1    [0m: atom type \n"
-			   "[35m                        2    [0m: full  bond types \n"
-			   "[35m                        3    [0m: part  bond types \n"
-			   "[35m                        4    [0m: atom and full bond type \n"
-			   "[35m                        5    [0m: atom and part bond type \n"
+			   "[34m                        0    [0m: no assignment\n"
+			   "[34m                        1    [0m: atom type \n"
+			   "[34m                        2    [0m: full  bond types \n"
+			   "[34m                        3    [0m: part  bond types \n"
+			   "[34m                        4    [0m: atom and full bond type \n"
+			   "[34m                        5    [0m: atom and part bond type \n"
 			   "                   -s   status information: 0(brief), 1(default) or 2(verbose)\n"
 			   "                   -eq  equalizing atomic charge, default is 1 for '-c resp' and '-c bcc' and 0 for the other charge methods \n"
-			   "[35m                        0    [0m: no use\n"
-			   "[35m                        1    [0m: by atomic paths \n"
-			   "[35m                        2    [0m: by atomic paths and structural information, i.e. E/Z configurations \n"
+			   "[34m                        0    [0m: no use\n"
+			   "[34m                        1    [0m: by atomic paths \n"
+			   "[34m                        2    [0m: by atomic paths and structural information, i.e. E/Z configurations \n"
 			   "                   -pf  remove intermediate files: yes(y) or no(n)[default]\n"
 			   "                   -pl  maximum path length to determin equivalence of atomic charges for resp and bcc,\n"
 			   "                        the smaller the value, the faster the algorithm, default is -1 (use full length),\n"
@@ -1173,7 +1178,7 @@ int main(int argc, char *argv[])
 	} else
 
 	if (strcmp("prepc", cinfo.intype) == 0
-		|| strcmp("5", cinfo.intype) == 0) {
+		|| strcmp("6", cinfo.intype) == 0) {
 		overflow_flag = rprepc(ifilename, &atomnum, atom, &cinfo, &minfo);
 		if (overflow_flag) {
 			cinfo.maxatom = atomnum + 10;
@@ -1891,6 +1896,28 @@ int main(int argc, char *argv[])
 		(strcmp("mpdb", cinfo.outtype) == 0 || strcmp("4", cinfo.outtype) == 0))
 		read_radius(minfo.radius_file, atomnum, atom);
 
+/*	This part may not necessary
+	if(atomtype_flag == 0 && (strcmp("charmm", cinfo.outtype) == 0|| strcmp("23", cinfo.outtype) == 0  ||
+	                         strcmp("ac", cinfo.outtype) == 0 || strcmp("1", cinfo.outtype) == 0 ||
+	                         strcmp("mol2", cinfo.outtype) == 0 || strcmp("2", cinfo.outtype) == 0 ||
+	                         strcmp("csd", cinfo.outtype) == 0 || strcmp("14", cinfo.outtype) == 0 ||
+	                         strcmp("mdl", cinfo.outtype) == 0 || strcmp("15", cinfo.outtype) == 0 ||
+	                         strcmp("sdf", cinfo.outtype) == 0 || strcmp("sd", cinfo.outtype) == 0 ||
+	                         strcmp("alc", cinfo.outtype) == 0 || strcmp("13", cinfo.outtype) == 0 ||
+	                         strcmp("hin", cinfo.outtype) == 0 || strcmp("16", cinfo.outtype) == 0)) {
+        	memory(8, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
+        	overflow_flag =
+			ringdetect(atomnum, atom, bondnum, bond, &ringnum, ring, arom,
+			  	 cinfo.maxatom, cinfo.maxring, minfo.inf_filename, 0);
+        	if (overflow_flag) {
+			cinfo.maxring = ringnum + 10;
+                	memory(8, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
+        		overflow_flag =
+				ringdetect(atomnum, atom, bondnum, bond, &ringnum, ring, arom,
+			   		cinfo.maxatom, cinfo.maxring, minfo.inf_filename, 0);
+		}
+	}
+*/
 	if(ra_flag==1)	
 		read_at(at_filename);
 	if(rb_flag==1)	
@@ -1901,7 +1928,7 @@ int main(int argc, char *argv[])
 		|| strcmp("1", cinfo.outtype) == 0){
 		wac(ofilename, atomnum, atom, bondnum, bond, cinfo, minfo);
 	} else if (strcmp("charmm", cinfo.outtype) == 0
-		|| strcmp("23", cinfo.outtype) == 0){
+		|| strcmp("25", cinfo.outtype) == 0){
                 wcharmm(ofilename, ifilename, atomnum, atom, bondnum, bond, cinfo, minfo);
 	} else if (strcmp("mol2", cinfo.outtype) == 0
 		|| strcmp("2", cinfo.outtype) == 0)  {
@@ -1974,7 +2001,7 @@ int main(int argc, char *argv[])
 		|| strcmp("22", cinfo.outtype) == 0){
 		wdivout(ofilename, atomnum, atom, cinfo, minfo);
 	} else if (strcmp("gesp", cinfo.outtype) == 0
-		|| strcmp("25", cinfo.outtype) == 0){
+		|| strcmp("26", cinfo.outtype) == 0){
 		wgesp();
 	} else if (strcmp("sqmcrt", cinfo.outtype) == 0
 		|| strcmp("23", cinfo.outtype) == 0){

antechamber/atom.h

@@ -21,6 +21,7 @@ typedef struct {
 	int id;
         int ter;
 	int resno;
+	int resseqno;
 	int hdonor;
 	int haccept;
 	int atomtype;
@@ -225,3 +226,25 @@ typedef struct {
 typedef struct {
         int aps[10];
 } AV;
+
+/*parameters for calculationg bond stretching force constant*/
+typedef struct {
+	double bfkai;
+	double refbondlength;	
+	int    id1;
+	int    id2;
+	char   elem1[10];
+	char   elem2[10];
+} BLF_PARM;
+
+/*parameters for calculationg bond bending force constant*/
+typedef struct {
+	double anglec;
+	double anglez;	
+	int    id;
+	char   elem[10];
+} BAF_PARM;
+BLF_PARM blf_parm[MAXBLFPARM];
+BAF_PARM baf_parm[120];
+double blf_exp_const = 4.5; /*exponential parameter for calculating blf*/
+