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jkleinjjkleinj
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CA distance matrix works
1 parent 53c3795 commit 3203ea5

14 files changed

Lines changed: 234 additions & 177 deletions

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‎POPSC/autom4te.cache/requests‎

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‎POPSC/config.log‎

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Original file line numberDiff line numberDiff line change
@@ -751,3 +751,47 @@ config.status:1185: cd src && sed -e '/# am--include-marker/d' Makefile
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make[1]: Entering directory '/home/jkleinj/develop/POPScomp/POPSC/src'
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make[1]: Leaving directory '/home/jkleinj/develop/POPScomp/POPSC/src'
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config.status:1190: $? = 0
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## ---------------------- ##
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## Running config.status. ##
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## ---------------------- ##
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This file was extended by pops config.status 3.4, which was
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generated by GNU Autoconf 2.71. Invocation command line was
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CONFIG_FILES =
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CONFIG_HEADERS =
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CONFIG_LINKS =
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CONFIG_COMMANDS =
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$ ./config.status src/Makefile depfiles
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on ac
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config.status:879: creating src/Makefile
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config.status:1108: executing depfiles commands
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config.status:1185: cd src && sed -e '/# am--include-marker/d' Makefile | make -f - am--depfiles
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make[1]: Entering directory '/home/jkleinj/develop/POPScomp/POPSC/src'
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make[1]: Leaving directory '/home/jkleinj/develop/POPScomp/POPSC/src'
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config.status:1190: $? = 0
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## ---------------------- ##
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## Running config.status. ##
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## ---------------------- ##
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This file was extended by pops config.status 3.4, which was
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generated by GNU Autoconf 2.71. Invocation command line was
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CONFIG_FILES =
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CONFIG_HEADERS =
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CONFIG_LINKS =
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CONFIG_COMMANDS =
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$ ./config.status src/Makefile depfiles
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on ac
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config.status:879: creating src/Makefile
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config.status:1108: executing depfiles commands
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config.status:1185: cd src && sed -e '/# am--include-marker/d' Makefile | make -f - am--depfiles
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make[1]: Entering directory '/home/jkleinj/develop/POPScomp/POPSC/src'
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make[1]: Leaving directory '/home/jkleinj/develop/POPScomp/POPSC/src'
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config.status:1190: $? = 0

‎POPSC/src/Makefile‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -113,7 +113,7 @@ am_pops_OBJECTS = arg.$(OBJEXT) atomgroup.$(OBJEXT) cJSON.$(OBJEXT) \
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getpdb.$(OBJEXT) getpdbml.$(OBJEXT) gettraj.$(OBJEXT) \
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json.$(OBJEXT) matrix.$(OBJEXT) modstring.$(OBJEXT) \
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pattern.$(OBJEXT) pops.$(OBJEXT) putsasa.$(OBJEXT) \
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putbsasa.$(OBJEXT) putsigma.$(OBJEXT) putCAdistMat.$(OBJEXT) \
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putbsasa.$(OBJEXT) putsigma.$(OBJEXT) putDistMatCA.$(OBJEXT) \
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safe.$(OBJEXT) sasa.$(OBJEXT) sigma.$(OBJEXT) topol.$(OBJEXT) \
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type.$(OBJEXT) vector.$(OBJEXT) cif_reader.$(OBJEXT) \
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../gemmi/src/mmcif.$(OBJEXT) ../gemmi/src/symmetry.$(OBJEXT) \
@@ -147,7 +147,7 @@ am__depfiles_remade = ../gemmi/src/$(DEPDIR)/mmcif.Po \
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./$(DEPDIR)/gettraj.Po ./$(DEPDIR)/json.Po \
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./$(DEPDIR)/matrix.Po ./$(DEPDIR)/modstring.Po \
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./$(DEPDIR)/pattern.Po ./$(DEPDIR)/pops.Po \
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./$(DEPDIR)/putCAdistMat.Po ./$(DEPDIR)/putbsasa.Po \
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./$(DEPDIR)/putDistMatCA.Po ./$(DEPDIR)/putbsasa.Po \
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./$(DEPDIR)/putsasa.Po ./$(DEPDIR)/putsigma.Po \
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./$(DEPDIR)/safe.Po ./$(DEPDIR)/sasa.Po ./$(DEPDIR)/sigma.Po \
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./$(DEPDIR)/topol.Po ./$(DEPDIR)/type.Po ./$(DEPDIR)/vector.Po
@@ -325,7 +325,7 @@ pops_SOURCES = arg.c arg.h argpdb.h atomgroup.c atomgroup.h \
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getpdbml.h gettraj.c gettraj.h json.c json.h matrix.c matrix.h \
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modstring.c modstring.h pattern.c pattern.h pdb_structure.h \
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pops.c pops.h putsasa.c putsasa.h putbsasa.c putbsasa.h \
328-
putsigma.c putsigma.h putCAdistMat.c putCAdistMat.h safe.c \
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putsigma.c putsigma.h putDistMatCA.c putDistMatCA.h safe.c \
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safe.h sasa.c sasa.h sasa_const.h sasa_data.h seq.h sigma.c \
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sigma.h sigma_const.h sigma_data.h topol.c topol.h type.c \
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type.h vector.c vector.h cif_reader.cpp cif_reader.h \
@@ -474,7 +474,7 @@ include ./$(DEPDIR)/matrix.Po # am--include-marker
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include ./$(DEPDIR)/modstring.Po # am--include-marker
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include ./$(DEPDIR)/pattern.Po # am--include-marker
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include ./$(DEPDIR)/pops.Po # am--include-marker
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include ./$(DEPDIR)/putCAdistMat.Po # am--include-marker
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include ./$(DEPDIR)/putDistMatCA.Po # am--include-marker
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include ./$(DEPDIR)/putbsasa.Po # am--include-marker
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include ./$(DEPDIR)/putsasa.Po # am--include-marker
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include ./$(DEPDIR)/putsigma.Po # am--include-marker
@@ -672,7 +672,7 @@ distclean: distclean-am
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-rm -f ./$(DEPDIR)/modstring.Po
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-rm -f ./$(DEPDIR)/pattern.Po
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-rm -f ./$(DEPDIR)/pops.Po
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-rm -f ./$(DEPDIR)/putCAdistMat.Po
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-rm -f ./$(DEPDIR)/putDistMatCA.Po
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-rm -f ./$(DEPDIR)/putbsasa.Po
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-rm -f ./$(DEPDIR)/putsasa.Po
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-rm -f ./$(DEPDIR)/putsigma.Po
@@ -746,7 +746,7 @@ maintainer-clean: maintainer-clean-am
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-rm -f ./$(DEPDIR)/modstring.Po
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-rm -f ./$(DEPDIR)/pattern.Po
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-rm -f ./$(DEPDIR)/pops.Po
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-rm -f ./$(DEPDIR)/putCAdistMat.Po
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-rm -f ./$(DEPDIR)/putDistMatCA.Po
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-rm -f ./$(DEPDIR)/putbsasa.Po
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-rm -f ./$(DEPDIR)/putsasa.Po
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-rm -f ./$(DEPDIR)/putsigma.Po

‎POPSC/src/Makefile.am‎

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@@ -23,7 +23,7 @@ json.c json.h \
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matrix.c matrix.h modstring.c modstring.h \
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pattern.c pattern.h pdb_structure.h pops.c pops.h \
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putsasa.c putsasa.h putbsasa.c putbsasa.h putsigma.c putsigma.h \
26-
putCAdistMat.c putCAdistMat.h \
26+
putDistMatCA.c putDistMatCA.h \
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safe.c safe.h sasa.c sasa.h sasa_const.h sasa_data.h seq.h \
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sigma.c sigma.h sigma_const.h sigma_data.h \
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topol.c topol.h type.c type.h vector.c vector.h \

‎POPSC/src/Makefile.in‎

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@@ -113,7 +113,7 @@ am_pops_OBJECTS = arg.$(OBJEXT) atomgroup.$(OBJEXT) cJSON.$(OBJEXT) \
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getpdb.$(OBJEXT) getpdbml.$(OBJEXT) gettraj.$(OBJEXT) \
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json.$(OBJEXT) matrix.$(OBJEXT) modstring.$(OBJEXT) \
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pattern.$(OBJEXT) pops.$(OBJEXT) putsasa.$(OBJEXT) \
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putbsasa.$(OBJEXT) putsigma.$(OBJEXT) putCAdistMat.$(OBJEXT) \
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putbsasa.$(OBJEXT) putsigma.$(OBJEXT) putDistMatCA.$(OBJEXT) \
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safe.$(OBJEXT) sasa.$(OBJEXT) sigma.$(OBJEXT) topol.$(OBJEXT) \
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type.$(OBJEXT) vector.$(OBJEXT) cif_reader.$(OBJEXT) \
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../gemmi/src/mmcif.$(OBJEXT) ../gemmi/src/symmetry.$(OBJEXT) \
@@ -147,7 +147,7 @@ am__depfiles_remade = ../gemmi/src/$(DEPDIR)/mmcif.Po \
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./$(DEPDIR)/gettraj.Po ./$(DEPDIR)/json.Po \
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./$(DEPDIR)/matrix.Po ./$(DEPDIR)/modstring.Po \
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./$(DEPDIR)/pattern.Po ./$(DEPDIR)/pops.Po \
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./$(DEPDIR)/putCAdistMat.Po ./$(DEPDIR)/putbsasa.Po \
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./$(DEPDIR)/putDistMatCA.Po ./$(DEPDIR)/putbsasa.Po \
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./$(DEPDIR)/putsasa.Po ./$(DEPDIR)/putsigma.Po \
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./$(DEPDIR)/safe.Po ./$(DEPDIR)/sasa.Po ./$(DEPDIR)/sigma.Po \
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./$(DEPDIR)/topol.Po ./$(DEPDIR)/type.Po ./$(DEPDIR)/vector.Po
@@ -325,7 +325,7 @@ pops_SOURCES = arg.c arg.h argpdb.h atomgroup.c atomgroup.h \
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getpdbml.h gettraj.c gettraj.h json.c json.h matrix.c matrix.h \
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modstring.c modstring.h pattern.c pattern.h pdb_structure.h \
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pops.c pops.h putsasa.c putsasa.h putbsasa.c putbsasa.h \
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putsigma.c putsigma.h putCAdistMat.c putCAdistMat.h safe.c \
328+
putsigma.c putsigma.h putDistMatCA.c putDistMatCA.h safe.c \
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safe.h sasa.c sasa.h sasa_const.h sasa_data.h seq.h sigma.c \
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sigma.h sigma_const.h sigma_data.h topol.c topol.h type.c \
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type.h vector.c vector.h cif_reader.cpp cif_reader.h \
@@ -474,7 +474,7 @@ distclean-compile:
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/modstring.Po@am__quote@ # am--include-marker
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pattern.Po@am__quote@ # am--include-marker
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pops.Po@am__quote@ # am--include-marker
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/putCAdistMat.Po@am__quote@ # am--include-marker
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/putDistMatCA.Po@am__quote@ # am--include-marker
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/putbsasa.Po@am__quote@ # am--include-marker
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/putsasa.Po@am__quote@ # am--include-marker
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/putsigma.Po@am__quote@ # am--include-marker
@@ -672,7 +672,7 @@ distclean: distclean-am
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-rm -f ./$(DEPDIR)/modstring.Po
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-rm -f ./$(DEPDIR)/pattern.Po
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-rm -f ./$(DEPDIR)/pops.Po
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-rm -f ./$(DEPDIR)/putCAdistMat.Po
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-rm -f ./$(DEPDIR)/putDistMatCA.Po
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-rm -f ./$(DEPDIR)/putbsasa.Po
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-rm -f ./$(DEPDIR)/putsasa.Po
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-rm -f ./$(DEPDIR)/putsigma.Po
@@ -746,7 +746,7 @@ maintainer-clean: maintainer-clean-am
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-rm -f ./$(DEPDIR)/modstring.Po
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-rm -f ./$(DEPDIR)/pattern.Po
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-rm -f ./$(DEPDIR)/pops.Po
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-rm -f ./$(DEPDIR)/putCAdistMat.Po
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-rm -f ./$(DEPDIR)/putDistMatCA.Po
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-rm -f ./$(DEPDIR)/putbsasa.Po
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-rm -f ./$(DEPDIR)/putsasa.Po
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-rm -f ./$(DEPDIR)/putsigma.Po

‎POPSC/src/arg.c‎

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@@ -96,7 +96,7 @@ static void set_defaults(Arg *arg, Argpdb *argpdb)
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arg->sigmaOutFileName = "sigma.out";
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arg->sigmatrajOutFileName = "sigmatraj";
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arg->interfaceOutFileName = "interface.out";
99-
arg->CAdistMatOutFileName = "CAdistMat.dat";
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arg->distMatCAOutFileName = "distMatCA.dat";
100100
arg->interfaceOut = 0; /* output of interface residue pairs */
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arg->typeOut = 0; /* output of atom/residue types */
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arg->topologyOut = 0; /* output of molecule topology */

‎POPSC/src/arg.h‎

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@@ -52,8 +52,8 @@ typedef struct
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char *sigmatrajOutFileName;
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FILE *interfaceOutFile;
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char *interfaceOutFileName;
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FILE *CAdistMatOutFile;
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char *CAdistMatOutFileName;
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FILE *distMatCAOutFile;
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char *distMatCAOutFileName;
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int interfaceOut;
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int compositionOut;
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int topologyOut;

‎POPSC/src/pops‎

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‎POPSC/src/pops.c‎

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@@ -178,6 +178,11 @@ int main(int argc, char *argv[])
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if (! argpdb.coarse && ! arg.jsonOut && ! arg.rout)
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print_sfe(&arg, &argpdb, &pdb, &type, &topol, &molSFE, constant_sigma, -1);
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181+
/*____________________________________________________________________________*/
182+
/** print Calpha distance matrix */
183+
calpha_distances(&arg, &pdb, &topol);
184+
print_distMatCA(&arg, &topol);
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/*____________________________________________________________________________*/
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/** free memory */
183188
free_topology(&pdb, &topol);
@@ -223,6 +228,7 @@ int main(int argc, char *argv[])
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free(pdb.resAtom);
224229
free(pdb.atomMap);
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free(pdb.sequence.res);
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free(pdb.sequence.name);
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/* trajectory */
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if (arg.trajInFileName) {

‎POPSC/src/pops.h‎

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@@ -37,6 +37,7 @@ POPS : Parameter OPtimised Surfaces at atomic resolution.
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#include "putsasa.h"
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#include "putbsasa.h"
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#include "putsigma.h"
40+
#include "putDistMatCA.h"
4041
#include "safe.h"
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#include "sasa.h"
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#include "sasa_const.h"

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