Revised interface
-----------------

delete                      # deletes this nlenergy instance (to free memory)

# coordinate wrapping for periodic boundaries is performed
# internally for correct energy computation,
# but coordinate input and output is unwrapped

get coord                   # return list of all atom coords {{x0 y0 z0} ...}
get coord <atom>            # return list of one atom coordinate {x y z}

set coord {{x0 y0 z0} ...}  # set all atom coords, list must be length N
set coord <atom> {x y z}    # set one atom coordinate

get atom                    # {{index m q name type residue resname} ... }
get atom <index>
get atom <index> index
get atom <index> mass
get atom <index> charge
get atom <index> name
get atom <index> type
get atom <index> residue
get atom <index> resname

set atom <index> {<m> <q> <name> <type> <residue> <resname>}
set atom <index> mass <m>
set atom <index> charge <q>
set atom <index> name <name>
set atom <index> type <type>
set atom <index> residue <residue>
set atom <index> resname <resname>

get bond                    # list all bond pairs
get bond <atom>             # list bonds involving atom
get bond <atom1> <atom2>    # list this bond if defined
get bond residue <resid>   [-self|-all|-join]
     # return list of bonds having atoms of specified residue number
get bond resname <resname> [-self|-all|-join]
     # return list of bonds having atoms of specified resname
get bond type <type1> <type2>   # return list of bonds of specified type

get angle
get angle <atom>
get angle <atom1> <atom2> <atom3>  # return angle if defined
get angle residue <resid>   [-self|-all|-join]
     # return list of angles having atoms of specified residue number
get angle resname <resname> [-self|-all|-join]
     # return list of angles having atoms of specified resname
get angle type <type1> <type2> <type3>

get dihed
get dihed <atom>
get dihed <atom1> <atom2>       # return list of diheds centered at pair
get dihed <atom1> <atom2> <atom3> <atom4>  # return dihed if defined
get dihed residue <resid>   [-self|-all|-join]
     # return list of diheds having atoms of specified residue number
get dihed resname <resname> [-self|-all|-join]
     # return list of diheds having atoms of specified resname
get dihed type <type1> <type2> <type3> <type4>

get impr
get impr <atom>
get impr <atom1> <atom2> <atom3> <atom4>   # return impr if defined
get impr residue <resid>   [-self|-all|-join]
     # return list of imprs having atoms of specified residue number
get impr resname <resname> [-self|-all|-join]
     # return list of imprs having atoms of specified resname
get impr type <type1> <type2> <type3> <type4>

add bond <atom1> <atom2>
add angle <atom1> <atom2> <atom3>
add dihed <atom1> <atom2> <atom3> <atom4>
add impr <atom1> <atom2> <atom3> <atom4>

remove bond <atom1> <atom2>
remove angle <atom1> <atom2> <atom3>
remove dihed <atom1> <atom2> <atom3> <atom4>
remove impr <atom1> <atom2> <atom3> <atom4>

read xplor <file>
read charmm <file>
read psf <file>
read pdb <file>        # for coordinates
read namdbin <file>    # read NAMD binary file for coordinates

write xplor <file>     # writing is lower priority
write charmm <file>
write topology <file>  # is this CHARMM topology file?
write pdb <file>       # save coordinates using ATOM records
write namdbin <file>   # write NAMD binary file of coordinates

# list all:  {t emin rmin emin14 rmin14} ...
# list for one type:  t emin rmin emin14 rmin14
get atomprm
get atomprm <type>
get atomrpm <type> emin
get atomprm <type> rmin
get atomrpm <type> emin14
get atomprm <type> rmin14

set atomprm <type> {<emin> <rmin> <emin14> <rmin14>}
set atomprm <type> emin <emin>
set atomprm <type> rmin <rmin>
set atomprm <type> emin14 <emin14>
set atomprm <type> rmin14 <rmin14>

# list all:  {t t k r0} ...
# list for one type:  t t k r0
get bondprm
get bondprm <type1> <type2>
get bondprm <type1> <type2> k
get bondprm <type1> <type2> r0

set bondprm <type1> <type2> {<k> <r0>}
set bondprm <type1> <type2> k <k>
set bondprm <type1> <type2> r0 <r0>

# list all:  {t t t ktheta theta0 kub rub} ...
# list for one type:  t t t ktheta theta0 kub rub
get angleprm
get angleprm <type1> <type2> <type3>
get angleprm <type1> <type2> <type3> ktheta
get angleprm <type1> <type2> <type3> theta0
get angleprm <type1> <type2> <type3> kub
get angleprm <type1> <type2> <type3> rub

set angleprm <type1> <type2> <type3> {<k> <thets0> <kub> <rub>}
set angleprm <type1> <type2> <type3> ktheta <ktheta>
set angleprm <type1> <type2> <type3> theta0 <theta0>
set angleprm <type1> <type2> <type3> kub <kub>
set angleprm <type1> <type2> <type3> rub <rub>

# list all:  {t t t t nterms {kdihed phi0 n} ...} ...
# list for one type:  t t t t nterms {kdihed phi0 n} ...
# list for one term:  kdihed phi0 n
get dihedprm
get dihedprm <type1> <type2> <type3> <type4>
get dihedprm <type1> <type2> <type3> <type4> term  # returns number of terms
get dihedprm <type1> <type2> <type3> <type4> term <index>
get dihedprm <type1> <type2> <type3> <type4> term <index> kdihed
get dihedprm <type1> <type2> <type3> <type4> term <index> phi0
get dihedprm <type1> <type2> <type3> <type4> term <index> n

# when setting all terms, the list length must match the number of terms
set dihedprm <type1> <type2> <type3> <type4> {{<k> <phi0> <n>} ...}
set dihedprm <type1> <type2> <type3> <type4> term <index> {<k> <phi0> <n>}
set dihedprm <type1> <type2> <type3> <type4> term <index> kdihed <kdihed>
set dihedprm <type1> <type2> <type3> <type4> term <index> phi0 <phi0>
set dihedprm <type1> <type2> <type3> <type4> term <index> n <n>

# list all:  {t t t t kimpr psi0} ...
# list for one type:  t t t t kimpr psi0
get imprprm
get imprprm <type1> <type2> <type3> <type4>
get imprprm <type1> <type2> <type3> <type4> kimpr
get imprprm <type1> <type2> <type3> <type4> psi0

set imprprm <type1> <type2> <type3> <type4> {<k> <psi0>}
set imprprm <type1> <type2> <type3> <type4> kimpr <kimpr>
set imprprm <type1> <type2> <type3> <type4> psi0 <psi0>

# list all:  {t t emin rmin emin14 rmin14} ...
# list for one type:  t t emin rmin emin14 rmin14
get vdwpairprm
get vdwpairprm <type1> <type2>
get vdwpairprm <type1> <type2> emin
get vdwpairprm <type1> <type2> rmin
get vdwpairprm <type1> <type2> emin14
get vdwpairprm <type1> <type2> rmin14

set vdwpairprm <type1> <type2> {<emin> <rmin> <emin14> <rmin14>}
set vdwpairprm <type1> <type2> emin <emin>
set vdwpairprm <type1> <type2> rmin <rmin>
set vdwpairprm <type1> <type2> emin14 <emin14>
set vdwpairprm <type1> <type2> rmin14 <rmin14>

missing atomprm
missing bondprm
missing angleprm
missing dihedprm
missing imprprm

add atomprm <type> { <emin> <rmin> <emin14> <rmin12> }
add bondprm <t1> <t2> { <k>, <r0> }
add angleprm <t1> <t2> <t3> { <ktheta> <theta0> <kub> <rub> }
add dihedprm <t1> <t2> <t3> <t4> { <nterms> { <kdihed> <phi0> <n> } ... }
add imprprm <t1> <t2> <t3> <t4> { <kimpr> <psi0> }
add vdwpairprm <t1> <t2> { <emin> <rmin> <emin14> <rmin12> }

remove atomprm <type>
remove bondprm <type1> <type2>
remove angleprm <type1> <type2> <type3>
remove dihedprm <type1> <type2> <type3> <type4>
remove imprprm <type1> <type2> <type3> <type4>
remove vdwpairprm <type1> <type2>

get nonbprm cutoff
get nonbprm switching
get nonbprm switchdist
get nonbprm exclude
get nonbprm dielectric
get nonbprm 1-4scaling
get nonbprm fulldirect
get nonbprm fulldirectvdw

set nonbprm cutoff <r0>             # defaults to 12 A
set nonbprm switching <boolean>     # "on" (default) or "off"
set nonbprm switchdist <r1>         # defaults to 10 A
set nonbprm exclude <exclpolicy>    # "none" "1-2" "1-3" "1-4" "scaled1-4"
set nonbprm dielectric <epsilon>    # defaults to 1
set nonbprm 1-4scaling <s>          # defaults to 1
set nonbprm fulldirect <boolean>    # (for elec) "off" (default) or "on"
set nonbprm fulldirectvdw <boolean> # (for vdw)  "off" (default) or "on"

get cellbasis                 # returns {{x0 y0 z0} {x1 y1 z1} {x2 y2 z2}}
set cellbasis {x0 y0 z0} {x1 y1 z1} {x2 y2 z2}  # initialized from vmd

energy  # total potential energy, units kcal/mol

energy [+|-]bond <bondlist> [+|-]angle <anglelist> \
       [+|-]dihed <dihedlist> [+|-]impr <imprlist> \
       [+|-]elec <atomlist> [<atomlist2>]          \
       [+|-]vdw <atomlist> [<atomlist2>]
  # '+' is the default
  # '-' means to include those bonds/angles/etc. not listed
  #   (this means that multiple use of 'bond'/etc. are additive)
  # 'nonb' can be used to mean both elec & vdw
  # the two atomlists for elec/vdw/nonb must be disjoint and gives
  #   interaction energies between the two sets (so '-' here is an error)
  # multiple instances of elec/vdw/nonb treats the single atomlist case
  #   as belonging to the first atomlist, in the even that there is a
  #   case with two atomlists specified.  An error occurs in the event
  #   that the two sets are not disjoint resulting from the union over
  #   all <atomlist> and from the union over all <atomlist2>.

force  # has same selection syntax as 'energy', units kcal/mol/A
  # returns a list of atom indices (including only those atoms that
  #   requested via the evaluation function) followed by a list of
  #   the corresponding x y z forces