Enhancements and improvements to the 'prepareforleap' command

configure

@@ -324,7 +324,7 @@ LIB_FLAG[$LXDRFILE]='-lxdrfile'
 LIB_STTC[$LXDRFILE]='libxdrfile.a'
 LIB_D_ON[$LXDRFILE]=''
 LIB_DOFF[$LXDRFILE]='-DNO_XDRFILE'
-LIB_TYPE[$LXDRFILE]='ld'
+LIB_TYPE[$LXDRFILE]='cpp'
 
 LIB_STAT[$LSANDER]='amberopt'
 LIB_CKEY[$LSANDER]='sanderlib'
@@ -367,7 +367,7 @@ LIB_FLAG[$LTNGFILE]='-ltng_io'
 LIB_STTC[$LTNGFILE]='libtng_io.a'
 LIB_D_ON[$LTNGFILE]='-DHAS_TNGFILE'
 LIB_DOFF[$LTNGFILE]=''
-LIB_TYPE[$LTNGFILE]='ld'
+LIB_TYPE[$LTNGFILE]='cpp'
 
 LIB_STAT[$LOPENMM]='off'
 LIB_CKEY[$LOPENMM]='openmm'
@@ -2532,6 +2532,17 @@ fi
 # Basic checks and directives
 BasicChecks
 
+# Create directories if necessary 
+if [ ! -e "$CPPTRAJBIN" ] ; then
+  mkdir "$CPPTRAJBIN"
+fi
+if [ ! -e "$CPPTRAJLIB" ] ; then
+  mkdir "$CPPTRAJLIB"
+fi
+if [ ! -e "$CPPTRAJDAT" ] ; then
+  mkdir "$CPPTRAJDAT"
+fi
+
 # Set up compilers and compiler options
 SetupCompilers
 
@@ -2787,17 +2798,6 @@ if [ "${LIB_STAT[$LZIP]}" != 'off' ] ; then
   echo "ZLIB_INCL=${LIB_INCL[$LZIP]}" >> $external_config
 fi
 
-# ----- Create directories if necessary ----------
-if [ ! -e "$CPPTRAJBIN" ] ; then
-  mkdir "$CPPTRAJBIN"
-fi
-if [ ! -e "$CPPTRAJLIB" ] ; then
-  mkdir "$CPPTRAJLIB"
-fi
-if [ ! -e "$CPPTRAJDAT" ] ; then
-  mkdir "$CPPTRAJDAT"
-fi
-
 # ----- Create a resource file. ------------------
 # If PERFORM_CHECKS is 'no' assume we are in AmberTools, no resource file needed.
 RFILE=''

dat/Carbohydrate_PDB_Glycam_Names.txt

@@ -0,0 +1,110 @@
+# This file contains the mapping from common PDB names to Glycam residue codes.
+# Information obtained from mining the PDB chemical database (components.cif).
+# Last updated 11/12/21 12:05:19
+#ResName GlycamCode Anomer Config RingType "Name"
+64K A A D P "alpha-D-arabinopyranose"
+AHR A A L F "alpha-L-arabinofuranose"
+ARA A A L P "alpha-L-arabinopyranose"
+ARB A B L P "beta-L-arabinopyranose"
+AXR A A D F "methyl alpha-D-arabinofuranoside"
+BXX A B D F "beta-D-arabinofuranose"
+BXY A A D F "alpha-D-arabinofuranose"
+FUB A B L F "beta-L-arabinofuranose"
+SEJ A B D P "beta-D-arabinopyranose"
+LDY D A D P "alpha-D-lyxopyranose"
+Z4W D B D P "beta-D-lyxopyranose"
+0MK R B L P "beta-L-ribopyranose"
+32O R B L F "beta-L-ribofuranose"
+BDR R B D F "beta-D-ribofuranose"
+RIB R A D F "alpha-D-ribofuranose"
+RIP R B D P "beta-D-ribopyranose"
+YYM R A D P "alpha-D-ribopyranose"
+Z6J R A L F "alpha-L-ribofuranose"
+HSY X A L P "alpha-L-xylopyranose"
+HSZ X B D P "beta-D-xylopyranose"
+LXC X B L P "beta-L-xylopyranose"
+XYP X B D P "beta-D-xylopyranose"
+XYS X A D P "alpha-D-xylopyranose"
+XYZ X B D F "beta-D-xylofuranose"
+AFD N A D P "alpha-D-allopyranose"
+ALL N B D P "beta-D-allopyranose"
+VDS N B D F "beta-D-allofuranose"
+VDV N A D F "alpha-D-allofuranose"
+WOO N B L P "beta-L-allopyranose"
+Z2D N A L P "alpha-L-allopyranose"
+3MK E B L P "beta-L-altropyranose"
+SHD E A D P "alpha-D-altropyranose"
+Z6H E A L P "alpha-L-altropyranose"
+GAL L B D P "beta-D-galactopyranose"
+GIV L B L P "beta-L-galactopyranose"
+GLA L A D P "alpha-D-galactopyranose"
+GXL L A L P "alpha-L-galactopyranose"
+GZL L B D F "beta-D-galactofuranose"
+BGC G B D P "beta-D-glucopyranose"
+GLC G A D P "alpha-D-glucopyranose"
+GU4 G A D P "2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose"
+MGL G B D P "methyl beta-D-glucopyranoside"
+Z8T G B L P "beta-L-glucopyranose"
+4GL K A D P "alpha-D-gulopyranose"
+GL0 K B D P "beta-D-gulopyranose"
+GUP K A L P "alpha-L-gulopyranose"
+Z8H K B L P "beta-L-gulopyranose"
+BMA M B D P "beta-D-mannopyranose"
+MAN M A D P "alpha-D-mannopyranose"
+A5C T A L F "alpha-L-talofuranose"
+SDY T B D P "beta-D-talopyranose"
+ZEE T B L P "beta-L-talopyranose"
+BDF C B D P "beta-D-fructopyranose"
+FRU C B D F "beta-D-fructofuranose"
+LFR C B L F "beta-L-fructofuranose"
+YYJ C B D F "1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose"
+Z9N C A D F "alpha-D-fructofuranose"
+PSV P A D F "alpha-D-psicofuranose"
+SF6 P A L F "alpha-L-psicofuranose"
+SF9 P B L F "beta-L-psicofuranose"
+TTV P B D F "beta-D-psicofuranose"
+SOE B A L P "alpha-L-sorbopyranose"
+UEA B B D F "beta-D-sorbofuranose"
+T6T J A D P "alpha-D-tagatopyranose"
+FCA F A D P "alpha-D-fucopyranose"
+FCB F B D P "beta-D-fucopyranose"
+FUC F A L P "alpha-L-fucopyranose"
+FUL F B L P "beta-L-fucopyranose"
+GYE F B D F "beta-D-fucofuranose"
+MXY F B L P "2-O-methyl-beta-L-fucopyranose"
+MXZ F A L P "2-O-methyl-alpha-L-fucopyranose"
+G6D Q A D P "alpha-D-quinovopyranose"
+YYK Q B D P "beta-D-quinovopyranose"
+RAM H A L P "alpha-L-rhamnopyranose"
+RM4 H B L P "beta-L-rhamnopyranose"
+XXR H A D P "alpha-D-rhamnopyranose"
+ADA O A D P "alpha-D-galactopyranuronic acid"
+GTR O B D P "beta-D-galactopyranuronic acid"
+BDP Z B D P "beta-D-glucopyranuronic acid"
+GCU Z A D P "alpha-D-glucopyranuronic acid"
+GCV Z A D P "4-O-methyl-alpha-D-glucopyranuronic acid"
+IDR U A L P "alpha-L-idopyranuronic acid"
+IDS U A L P "2-O-sulfo-alpha-L-idopyranuronic acid"
+A2G V A D P "2-acetamido-2-deoxy-alpha-D-galactopyranose"
+ASG V B D P "2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose"
+NG6 V B D P "2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose"
+NGA V B D P "2-acetamido-2-deoxy-beta-D-galactopyranose"
+YYQ V A L P "2-acetamido-2-deoxy-alpha-L-galactopyranose"
+NAG Y B D P "2-acetamido-2-deoxy-beta-D-glucopyranose"
+NDG Y A D P "2-acetamido-2-deoxy-alpha-D-glucopyranose"
+NGZ Y A L P "2-acetamido-2-deoxy-alpha-L-glucopyranose"
+BM3 W A D P "2-acetamido-2-deoxy-alpha-D-mannopyranose"
+BM7 W B D P "2-acetamido-2-deoxy-beta-D-mannopyranose"
+SIA S A D P "N-acetyl-alpha-neuraminic acid"
+SLB S B D P "N-acetyl-beta-neuraminic acid"
+
+# PDB to glycam atom name maps
+V,W,Y C7,C2N  O7,O2N  C8,CME
+S     C10,C5N O10,O5N C11,CME
+H     C6,C6M,B
+
+# PDB to glycam linkage residue name maps
+SER OLS
+THR OLT
+HYP OLP
+ASN NLN

dat/GlycamCodes.csv

@@ -0,0 +1,68 @@
+Abbreviation,Name,PDB,Glycam
+Ara,Arabinose,64K ARA SEJ ARB BXY AHR BXX FUB AXR,A
+Lyx,Lyxose,LDY Z4W,D
+Rib,Ribose,YYM RIP 0MK RIB Z6J BDR 32O,R
+Xyl,Xylose,XYS HSY HSZ XYP LXC XYZ,X
+All,Allose,AFD Z2D ALL WOO VDV VDS,N
+Alt,Altrose,SHD Z6H 3MK,E
+Gal,Galactose,GLA GXL GAL GIV GZL,L
+Glc,Glucose,GLC BGC Z8T GU4,G
+Gul,Gulose,4GL GUP GL0 Z8H,K
+Ido,Idose,ZCD Z0F 4N2,.
+Man,Mannose,MAN BMA,M
+Tal,Talose,SDY ZEE A5C,T
+Fru,Fructose,BDF Z9N FRU LFR YYJ,C
+Psi,Psicose,PSV SF6 TTV SF9,P
+Sor,Sorbose,SOE UEA,B
+Tag,Tagatose,T6T,J
+Fuc,Fucose,FCA FUC FCB FUL GYE MXY MXZ,F
+Qui,Quinovose,G6D YYK,Q
+Rha,Rhamnose,XXR RAM RM4,H
+GalA,Galacturonic Acid,ADA GTR,O
+GlcA,Glucuronic Acid,GCU BDP GCV,Z
+IdoA,Iduronic Acid,IDR IDS,U
+GalNAc,N-Acetyl Galactosamine,A2G YYQ NGA NG6 ASG,V
+GlcNAc,N-Acetyl Glucosamine,NDG NGZ NAG,Y
+ManNAc,N-Acetyl Mannosamine,BM3 BM7,W
+Neu5Ac,N-Acetyl Neuraminic Acid,SIA SLB,S
+GlcN,Glucosamine,GCS,.
+QuiNAc,N-Acetyl Quinovosamine,.,.
+Oli,Olivose,OLI,.
+ManN,Mannosamine,.,.
+ManA,Mannuronic Acid,MAV BEM,.
+RhaNAc,N-Acetyl Rhamnosamine,.,.
+Tyv,Tyvelose,TYV,.
+GalN,Galactosamine,.,.
+GulNAc,N-Acetyl Gulosamine,.,.
+GulN,Gulosamine,.,.
+GulA,Guluronic Acid,LGU,.
+AltNAc,N-Acetyl Altrosamine,.,.
+AltN,Altrosamine,.,.
+AltA,Altruronic Acid,.,.
+6dAlt,6-Deoxy Altrose,.,.
+AllNAc,N-Acetyl Allosamine,.,.
+AllN,Allosamine,.,.
+AllA,Alluronic Acid,.,.
+TalNAc,N-Acetyl Talosamine,.,.
+TalN,Talosamine,.,.
+TalA,Taluronic Acid,.,.
+6dTal,6-Deoxy Talose,.,.
+IdoNAc,N-Acetyl Idosamine,.,.
+IdoN,Idosamine,.,.
+FucNAc,N-Acetyl Fucosamine,.,.
+Abe,Abequose,ABE,.
+Par,Paratose,PAR,.
+Dig,Digitoxose,DIG,.
+Col,Colitose,COL,.
+Bac,Bacillosamine,BAC,.
+Api,Apicose,API,.
+Dha,3-Deoxy Lyxo-Heptulosaric Acid,DHA,.
+Kdn,Keto-Deoxy Nonulonic Acid,KDN,.
+Kdo,Keto-Deoxy Octulonic Acid,KDO,.
+Neu,Neuraminic Acid,NEU,.
+Neu5Gc,N-Glycolyl Neuraminic Acid,.,.
+Mur,Muramic Acid,MUR,.
+MurNAc,N-Acetyl Muramic Acid,.,.
+MurNGc,N-Glycolyl Muramic Acid,.,.
+LDManHep,L-Glycero-D-Manno Heptose,GMH,.
+DDManHep,D-Glycero-D-Manno-Heptose,.,.

dat/PDB_ResidueNames.txt

@@ -0,0 +1,42 @@
+# A list of PDB residue names that Amber FFs will recognize.
+# Protein
+ACE
+ALA
+ARG
+ASH
+ASN
+ASP
+CYM
+CYS
+CYX
+GLH
+GLN
+GLU
+GLY
+HIE
+HIP
+HIS
+HYP
+ILE
+LEU
+LYN
+LYS
+MET
+NME
+PHE
+PRO
+SER
+THR
+TRP
+TYR
+VAL
+# DNA
+DA
+DC
+DG
+DT
+# RNA
+A
+C
+G
+U

dat/ResNames.sugar.dat

@@ -0,0 +1,95 @@
+0MK R
+32O R
+3MK E
+4GL K
+64K A
+A2G V
+A5C T
+ADA O
+AFD N
+AHR A
+ALL N
+ARA A
+ARB A
+ASG V
+AXR A
+BDF C
+BDP Z
+BDR R
+BGC G
+BM3 W
+BM7 W
+BMA M
+BXX A
+BXY A
+FCA F
+FCB F
+FRU C
+FUB A
+FUC F
+FUL F
+G6D Q
+GAL L
+GCU Z
+GCV Z
+GIV L
+GL0 K
+GLA L
+GLC G
+GTR O
+GU4 G
+GUP K
+GXL L
+GYE F
+GZL L
+HSY X
+HSZ X
+IDR U
+IDS U
+LDY D
+LFR C
+LXC X
+MAN M
+MGL G
+MXY F
+MXZ F
+NAG Y
+NDG Y
+NG6 V
+NGA V
+NGZ Y
+PSV P
+RAM H
+RIB R
+RIP R
+RM4 H
+SDY T
+SEJ A
+SF6 P
+SF9 P
+SHD E
+SIA S
+SLB S
+SOE B
+T6T J
+TTV P
+UEA B
+VDS N
+VDV N
+WOO N
+XXR H
+XYP X
+XYS X
+XYZ X
+YYJ C
+YYK Q
+YYM R
+YYQ V
+Z2D N
+Z4W D
+Z6H E
+Z6J R
+Z8H K
+Z8T G
+Z9N C
+ZEE T

devtools/converters/glycam.csv.to.dat/GlycamNames.txt

@@ -0,0 +1,26 @@
+# This file contains sugar names mapped to glycam codes.
+"Arabinose"                      A
+"Lyxose"                         D
+"Ribose"                         R
+"Xylose"                         X
+"Allose"                         N
+"Altrose"                        E
+"Galactose"                      L
+"Glucose"                        G
+"Gulose"                         K
+"Mannose"                        M
+"Talose"                         T
+"Fructose"                       C
+"Psicose"                        P
+"Sorbose"                        B
+"Tagatose"                       J
+"Fucose"                         F
+"Quinovose"                      Q
+"Rhamnose"                       H
+"Galacturonic Acid"              O
+"Glucuronic Acid"                Z
+"Iduronic Acid"                  U
+"N-Acetyl Galactosamine"         V
+"N-Acetyl Glucosamine"           Y
+"N-Acetyl Mannosamine"           W
+"N-Acetyl Neuraminic Acid"       S