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Change default PDB chain ID from blank to 'Z' (#747)
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* DRR - Cpptraj: Make a blank chain ID null, and make the default chain ID when null 'Z'.

* DRR - Cpptraj: Ensure a blank character can be used as a chain ID if necessary

* DRR - Cpptraj: Set blank chain IDs for backwards compat. Add default chain ID test.

* DRR - Cpptraj: Changes related to default chainID now being Z

* DRR - Cpptraj: Set blank chain ID

* DRR - Cpptraj: Set blank chain IDs

* DRR - Cpptraj: Add 'trajargs' keyword to 'mask' command for passing in additional output trajectory options.

* DRR - Cpptraj: Set chainID to ' '

* DRR - Cpptraj: Update 'mask' command doc and PDB trajectory out doc.

* DRR - Cpptraj: Use blank chain id

* DRR - Cpptraj: Blank chain ID

* DRR - Cpptraj: Fix documentation for residue selection by chain ID.

* DRR - Cpptraj: Ensure blank chain ID

* DRR - Cpptraj: Make the internal default chain id still a space; only use the default chain id when writing. This makes it so that e.g. selection by chainid wont return a false positive when specifying the default chain id, printing the topology wont make it seem like the default chain ID is actually part of the topology, etc.

* DRR - Cpptraj: Since the PQR format breaks the PDB standard anyway, do not bother with a default chain ID

* DRR - Cpptraj: Minor version bump; default PDB chain ID set to 'Z'

* DRR - Cpptraj: Fix text going off the page in output pdf

* DRR - Cpptraj: Update manual

* DRR - Cpptraj: Slight rework of default and blank chain IDs.

* DRR - Cpptraj: Set CPPTRAJ_ERROR to an actual file on windows since windows doesnt know about /dev/stderr

* DRR - Do not replace valgrind.out on windows

* DRR - Cpptraj: No /dev/stdout on windows

* DRR - Cpptraj: Do not explicitly redirect test header to stdout

* DRR - Cpptraj: Remove reference to /dev/stdout in ParseValgrindOut

* DRR - Cpptraj: All error messages wrapped in ErrMsg
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@drroe
drroe authored Aug 22, 2019
1 parent 76a0e34 commit de38e93
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189 changes: 134 additions & 55 deletions doc/cpptraj.lyx
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Original file line number Diff line number Diff line change
Expand Up @@ -1456,12 +1456,12 @@ namelist} e.g.
\end_layout

\begin_layout Description
:/{chain
::{chain
\begin_inset space ~
\end_inset

id} e.g.
':/B', ':/A,D'.
'::B', '::A,D'.
Requires chain ID information be present in the topology.
\end_layout

Expand Down Expand Up @@ -1601,7 +1601,7 @@ More examples:
\end_layout

\begin_layout Description
:/A,D@CA All atoms named 'CA' in chains A and D.
::A,D@CA All atoms named 'CA' in chains A and D.
\end_layout

\begin_layout Subsubsection*
Expand Down Expand Up @@ -2592,11 +2592,11 @@ status open
\begin_inset Tabular
<lyxtabular version="3" rows="15" columns="5">
<features tabularvalignment="middle">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top" width="20text%">
<column alignment="center" valignment="top" width="20text%">
<column alignment="center" valignment="top" width="20text%">
<column alignment="center" valignment="top" width="20text%">
<column alignment="center" valignment="top" width="20text%">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
Expand Down Expand Up @@ -4035,10 +4035,10 @@ would take the square root of each member of D0, add it to the corresponding
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="4">
<features tabularvalignment="middle">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="25text%">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
Expand Down Expand Up @@ -5487,8 +5487,8 @@ The following COORDS data set commands are available:
\begin_inset Tabular
<lyxtabular version="3" rows="12" columns="2">
<features tabularvalignment="middle">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="75text%">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
Expand Down Expand Up @@ -5989,8 +5989,11 @@ permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}]
\end_layout

\begin_layout LyX-Code
[outtraj <filename> [<outfmt>]] [crdout <output COORDS>] [<dihedra
l types>]
[outtraj <filename> [<outfmt>]] [crdout <output COORDS>]
\end_layout

\begin_layout LyX-Code
[<dihedral types>]
\end_layout

\begin_layout LyX-Code
Expand Down Expand Up @@ -6020,7 +6023,11 @@ l types>]

\begin_layout LyX-Code
<dihedral types> = alpha beta gamma delta epsilon zeta nu1 nu2 h1p c2p
chin phi psi chip omega
chin
\end_layout

\begin_layout LyX-Code
phi psi chip omega
\begin_inset Separator latexpar
\end_inset

Expand Down Expand Up @@ -6307,8 +6314,11 @@ rotatedihedral crdset <COORDS set> [frame <#>] [name <output set name>]
\end_layout

\begin_layout LyX-Code
<dih type> = alpha beta gamma delta epsilon zeta nu1 nu2 h1p c2p chin phi
psi chip omega
<dih type> = alpha beta gamma delta epsilon zeta nu1 nu2 h1p c2p chin
\end_layout

\begin_layout LyX-Code
phi psi chip omega
\end_layout

\begin_deeper
Expand Down Expand Up @@ -7582,7 +7592,10 @@ e'

\begin_layout LyX-Code
[bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium]
[noe_weak]
\end_layout

\begin_layout LyX-Code
[noe_weak]
\begin_inset Separator latexpar
\end_inset

Expand Down Expand Up @@ -7797,8 +7810,11 @@ selection>] Remove data sets from <set selection> according to specified
\end_layout

\begin_layout LyX-Code
<select> : 'equal' '==' 'notequal' '!=' 'lessthan' '<' 'greaterthan'
'>' 'between' 'outside'
<select> : 'equal' '==' 'notequal' '!=' 'lessthan' '<'
\end_layout

\begin_layout LyX-Code
'greaterthan' '>' 'between' 'outside'
\end_layout

\begin_layout Description
Expand Down Expand Up @@ -11999,10 +12015,10 @@ Cpptraj currently understands the following trajectory file formats:
\begin_inset Tabular
<lyxtabular version="3" rows="20" columns="4">
<features tabularvalignment="middle">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="25text%">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
Expand Down Expand Up @@ -14097,6 +14113,12 @@ occmax
\end_layout

\end_deeper
\begin_layout Standard
Note that if the input topology does not contain chain IDs, a default chain
ID of 'Z' will be used if no other chain ID option is specified in order
to remain consistent with the PDB standard.
\end_layout

\begin_layout Subsubsection

\shape italic
Expand Down Expand Up @@ -14621,9 +14643,9 @@ Mod
\begin_inset Tabular
<lyxtabular version="3" rows="86" columns="3">
<features islongtable="true" longtabularalignment="center">
<column alignment="center" valignment="top" width="1.3in">
<column alignment="center" valignment="top" width="4.5in">
<column alignment="center" valignment="top" width="0pt">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="65text%">
<column alignment="center" valignment="top" width="10text%">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
Expand Down Expand Up @@ -17422,7 +17444,10 @@ areapermol

\begin_layout LyX-Code
areapermol [<name>] {[<mask1>] [nlayers <#>] | nmols <#>} [out <filename>]
[{xy | xz | yz}]
\end_layout

\begin_layout LyX-Code
[{xy | xz | yz}]
\begin_inset Separator latexpar
\end_inset

Expand Down Expand Up @@ -20251,8 +20276,11 @@ dipole
\end_layout

\begin_layout LyX-Code
dipole <filename> {data <dsname> | <nx> <dx> <ny> <dy> <nz> <dz> [gridcenter
<cx> <cy> <cz>]}
dipole <filename> {data <dsname> | <nx> <dx> <ny> <dy> <nz> <dz>
\end_layout

\begin_layout LyX-Code
[gridcenter <cx> <cy> <cz>]}
\end_layout

\begin_layout LyX-Code
Expand Down Expand Up @@ -25827,11 +25855,15 @@ mask

\end_inset

<mask> [maskout <filename>] [maskpdb <pdbname>] [maskmol2 <mol2name>]
\begin_inset Separator latexpar
\end_inset
<mask> [maskout <filename>]
\end_layout

\begin_layout LyX-Code
[ {maskpdb <filename> | maskmol2 <filename>}
\end_layout

\begin_layout LyX-Code
[trajargs <comma-separated args>] ]
\end_layout

\begin_deeper
Expand All @@ -25840,27 +25872,40 @@ mask
\end_layout

\begin_layout Description
[maskout
maskout
\begin_inset space ~
\end_inset

<filename> Write information on atoms in <mask> to <filename>.
\end_layout

\begin_layout Description
maskpdb
\begin_inset space ~
\end_inset

<filename>] Write information on atoms in <mask> to <filename>.
<filename> Write PDB of atoms in <mask> to <name>.X.
\end_layout

\begin_layout Description
[maskpdb
maskmol2
\begin_inset space ~
\end_inset

<name>] Write PDB of atoms in <mask> to <name>.X.
<filename> Write Mol2 of atoms in <mask> to <name>.X.
\end_layout

\begin_layout Description
[maskmol2
trajargs
\begin_inset space ~
\end_inset

<comma-separated
\begin_inset space ~
\end_inset

<name>] Write Mol2 of atoms in <mask> to <name>.X.
args> When writing output PDB/Mol2, additional trajectory arguments to pass
to the output trajectory.
\end_layout

\end_deeper
Expand Down Expand Up @@ -25938,8 +25983,8 @@ maskmol2
\end_layout

\begin_layout Standard
For example, to write out all atoms within 3.0 Angstroms of residue 195 that
are part of residues named WAT to
For example, to write out all residues within 3.0 Angstroms of residue 195
that are named WAT to
\begin_inset Quotes eld
\end_inset

Expand All @@ -25962,6 +26007,23 @@ mask
maskout Res195WAT.dat maskpdb Res195WAT.pdb
\end_layout

\begin_layout Standard
To write all out atoms outside of 5.0 Angstroms of residues named ARG to
PDB files with a chain ID of 'B':
\end_layout

\begin_layout LyX-Code
mask :ARG>@5.0 maskpdb Outside5Arg.pdb trajargs
\begin_inset Quotes eld
\end_inset

chainid 'B'
\begin_inset Quotes erd
\end_inset


\end_layout

\begin_layout Subsection
matrix
\end_layout
Expand Down Expand Up @@ -27522,8 +27584,11 @@ nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>]
\end_layout

\begin_layout LyX-Code
[name <dsname>] [byresidue] [map [mapout <mapfile>]] [series
[seriesout <file>]]
[name <dsname>] [byresidue] [map [mapout <mapfile>]]
\end_layout

\begin_layout LyX-Code
[series [seriesout <file>]]
\begin_inset Separator latexpar
\end_inset

Expand Down Expand Up @@ -33477,9 +33542,9 @@ trajin
\begin_inset Tabular
<lyxtabular version="3" rows="46" columns="3">
<features islongtable="true" longtabularalignment="center">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top" width="0pt">
<column alignment="center" valignment="top" width="25text%">
<column alignment="center" valignment="top" width="50text%">
<column alignment="center" valignment="top" width="25text%">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
Expand Down Expand Up @@ -37063,8 +37128,8 @@ Solvent pH is <pH>
\end_layout

\begin_layout LyX-Code
<residue name> <residue number> : Offset <offset from predicted> Pred <predicted
pH> Frac Prot <fraction> Transitions <number of transitions>
<res name> <res num> : Offset <off> Pred <pred> Frac Prot <frac> Transitions
<#trans>
\end_layout

\begin_layout LyX-Code
Expand All @@ -37080,7 +37145,16 @@ Average total molecular protonation: <avg>
\end_layout

\begin_layout Standard
A line is printed for each residue.
Where
\series bold
<off>
\series default
is offset from predicted,
\series bold
<pred>
\series default
is predicted pH, and <#trans> is the number of transitions.
A line is printed for each residue.
This functionality is similar to the
\series bold
cphstats
Expand Down Expand Up @@ -37453,8 +37527,8 @@ curvefit <dset> { <equation> |
\end_layout

\begin_layout LyX-Code
name <dsname> { gauss | nexp <m> [form {mexp|mexpk|mexpk_penal
ty} } }
name <dsname> {gauss | nexp <m> [form {mexp|mexpk|mexpk_penalt
y}} }
\end_layout

\begin_layout LyX-Code
Expand Down Expand Up @@ -39107,8 +39181,13 @@ diagmatrix matired vecs 6 out ired.vec name ired.vec
\end_layout

\begin_layout LyX-Code
ired relax NHdist 1.02 freq 500.0 tstep 1.0 tcorr 100.0 out v0.out noefile noe
order 2
ired relax NHdist 1.02 freq 500.0 tstep 1.0 tcorr 100.0 out v0.out
\backslash

\end_layout

\begin_layout LyX-Code
noefile noe order 2
\end_layout

\begin_layout Subsection
Expand Down
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