[med-svn] [king-probe] 02/02: Add manpage
Malihe Asemani
mali-guest at moszumanska.debian.org
Tue Sep 1 19:01:30 UTC 2015
This is an automated email from the git hooks/post-receive script.
mali-guest pushed a commit to branch master
in repository king-probe.
commit c18ae0fc93fd0ed6840b1ca8462863fe55703853
Author: Malihe Asemani <ml.asemani at gmail.com>
Date: Tue Sep 1 18:15:13 2015 +0000
Add manpage
---
debian/king-probe.1 | 387 ++++++++++++++++++++++++++++++++++++++++++++++++++++
debian/links | 4 +
2 files changed, 391 insertions(+)
diff --git a/debian/king-probe.1 b/debian/king-probe.1
new file mode 100644
index 0000000..7bc799b
--- /dev/null
+++ b/debian/king-probe.1
@@ -0,0 +1,387 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH KING-PROBE "1" "September 2015" "king-probe 2.13.110909-1" "User Commands"
+.SH NAME
+king-probe \- Evaluate and visualize protein interatomic packing
+.SH DESCRIPTION
+Syntax: probe input.pdb >> out.kin
+.IP
+or: probe [flags] "src pattern" ["target pattern"] pdbfiles... >> out.kin
+.SS "Flags:"
+.TP
+\fB\-SElf\fR
+self intersection: src \-> src (default)
+.TP
+\fB\-Both\fR
+intersect both ways: src <=> targ
+.TP
+\fB\-ONce\fR
+single intersection: src \-> targ
+.TP
+\fB\-OUt\fR
+external van der Waals surface of src (solvent contact surface)
+.TP
+\fB\-AUTObondrot\fR filename
+read and process an autobondrot file
+.IP
+shortcuts:
+.IP
+<<NO FLAGS>>same as: \fB\-4H\fR \fB\-mc\fR \fB\-het\fR \fB\-self\fR "altA ogt33"
+.TP
+\fB\-DEFAULTs\fR
+same as: <<NO FLAGS>>, but allows some other flags
+.HP
+\fB\-SCSurface\fR same as: \fB\-drop\fR \fB\-rad1\fR.4 \fB\-out\fR "not water"
+.TP
+\fB\-EXPOsed\fR
+same as: \fB\-drop\fR \fB\-rad1\fR.4 \fB\-out\fR (note: user supplies pattern)
+.TP
+\fB\-ASurface\fR
+same as: \fB\-drop\fR \fB\-rad0\fR.0 \fB\-add1\fR.4 \fB\-out\fR "not water"
+.TP
+\fB\-ACCESS\fR
+same as: \fB\-drop\fR \fB\-rad0\fR.0 \fB\-add1\fR.4 \fB\-out\fR (note: user supplies pattern)
+.HP
+\fB\-SCAN0\fR same as: \fB\-4H\fR \fB\-mc\fR \fB\-self\fR "alta blt40 ogt33"
+.HP
+\fB\-SCAN1\fR same as: \fB\-4H\fR \fB\-once\fR "sc alta blt40 ogt33" "alta blt40 ogt65,(not water ogt33)"
+.TP
+\fB\-DUMPAtominfo\fR
+count the atoms in the selection: src
+.IP
+(note that BOTH and ONCE require two patterns while
+.IP
+OUT, SELF and DUMPATOMINFO require just one pattern)
+.TP
+\fB\-Implicit\fR
+implicit hydrogens
+.TP
+\fB\-Explicit\fR
+explicit hydrogens (default)
+.TP
+\fB\-DEnsity\fR#
+set dot density (default 16 dots/sq A)
+.TP
+\fB\-Radius\fR#.#
+set probe radius (default 0.25 A)
+.TP
+\fB\-ADDvdw\fR#.#
+offset added to Van der Waals radii (default 0.0)
+.HP
+\fB\-SCALEvdw\fR#.# scale factor for Van der Waals radii (default 1.0)
+.TP
+\fB\-COSCale\fR#.#
+scale C=O carbon Van der Waals radii (default 0.94)
+.TP
+\fB\-SPike\fR
+draw spike instead of dots (default)
+.TP
+\fB\-SPike\fR#.#
+set spike scale (default=0.5)
+.TP
+\fB\-NOSpike\fR
+draw only dots
+.HP
+\fB\-HBRegular\fR#.# max overlap for regular Hbonds(default=0.6)
+.HP
+\fB\-HBCharged\fR#.# max overlap for charged Hbonds(default=0.8)
+.TP
+\fB\-Keep\fR
+keep nonselected atoms (default)
+.TP
+\fB\-DRop\fR
+drop nonselected atoms
+.TP
+\fB\-LIMit\fR
+limit bump dots to max dist when kissing (default)
+.TP
+\fB\-NOLIMit\fR
+do not limit bump dots
+.TP
+\fB\-LENs\fR
+add lens keyword to kin file
+.TP
+\fB\-NOLENs\fR
+do not add lens keyword to kin file (default)
+.TP
+\fB\-MC\fR
+include mainchain\->mainchain interactions
+.TP
+\fB\-HETs\fR
+include dots to non\-water HET groups (default)
+.TP
+\fB\-NOHETs\fR
+exclude dots to non\-water HET groups
+.TP
+\fB\-WATers\fR
+include dots to water (default)
+.TP
+\fB\-NOWATers\fR
+exclude dots to water
+.TP
+\fB\-WAT2wat\fR
+show dots between waters
+.TP
+\fB\-DUMPH2O\fR
+include water H? vectorlist in output
+.TP
+\fB\-4H\fR
+extend bond chain dot removal to 4 for H (default)
+.TP
+\fB\-3\fR
+limit bond chain dot removal to 3
+.TP
+\fB\-2\fR
+limit bond chain dot removal to 2
+.TP
+\fB\-1\fR
+limit bond chain dot removal to 1
+.HP
+\fB\-IGNORE\fR "pattern" explicit drop: ignore atoms selected by pattern
+.TP
+\fB\-DOCHO\fR
+recognize CH..O Hbonds
+.TP
+\fB\-CHO\fR#.#
+scale factor for CH..O Hbond score (default=0.5)
+.TP
+\fB\-PolarH\fR
+use short radii of polar hydrogens (default)
+.TP
+\fB\-NOPolarH\fR
+do not shorten radii of polar hydrogens
+.HP
+\fB\-NOFACEhbond\fR do not identify HBonds to aromatic faces
+.HP
+\fB\-Name\fR "name" specify the group name (default "dots")
+.TP
+\fB\-DOTMASTER\fR
+group name used as extra master={name} on lists
+.TP
+\fB\-NOGroup\fR
+do not generate @group statement in .kin format output
+.TP
+\fB\-KINemage\fR
+add @kinemage 1 statement to top of .kin format output
+.TP
+\fB\-Countdots\fR
+produce a count of dots\-not a dotlist
+.TP
+\fB\-Unformated\fR
+output raw dot info
+.IP
+name:pat:type:srcAtom:targAtom:mingap:gap:spX:
+spY:spZ:spikeLen:score:stype:ttype:x:y:z:sBval:tBval:
+.TP
+\fB\-OFORMAT\fR
+output dot info formatted for display in O
+.TP
+\fB\-XVFORMAT\fR
+output dot info formatted for display in XtalView
+.TP
+\fB\-ONELINE\fR
+output one line :contacts:by:severity:type:
+.TP
+\fB\-GAPcolor\fR
+color dots by gap amount (default)
+.TP
+\fB\-ATOMcolor\fR
+color dots by atom type
+.TP
+\fB\-BASEcolor\fR
+color dots by nucleic acid base type
+.TP
+\fB\-COLORBase\fR
+color dots by gap and nucleic acid base type
+.HP
+\fB\-OUTCOLor\fR "name" specify the point color for \fB\-OUT\fR (default "gray")
+.TP
+\fB\-GAPWeight\fR#
+set weight for scoring gaps (default 0.25)
+.HP
+\fB\-BUMPWeight\fR# set relative scale for scoring bumps (default 10.0)
+.TP
+\fB\-HBWeight\fR#
+set relative scale for scoring Hbonds (default 4.0)
+.TP
+\fB\-DIVLow\fR#.#
+Division for Bump categories (default \fB\-0\fR.4)
+.TP
+\fB\-DIVHigh\fR#.#
+Division for Contact categories (default 0.25)
+.TP
+\fB\-MINOCCupancy\fR#.#
+Occupancy below this is same as zero (default 0.02)
+.TP
+\fB\-ELEMent\fR
+add master buttons for different elements in kin output
+.TP
+\fB\-NOHBOUT\fR
+do not output contacts for HBonds
+.TP
+\fB\-NOCLASHOUT\fR
+do not output contacts for clashes
+.TP
+\fB\-NOVDWOUT\fR
+do not output contacts for van der Waals interactions
+.TP
+\fB\-ONLYBADOUT\fR
+onlybadout output bad clashes (severe overlap contacts)
+.TP
+\fB\-SUMMARY\fR
+output summary list of contacts and clashes
+.TP
+\fB\-ONELINE\fR
+output summary list on oneline
+.TP
+\fB\-NOTICKs\fR
+do not display the residue name ticker during processing
+.TP
+\fB\-STDBONDs\fR
+assume only standard bonding patterns in standard residues
+.TP
+\fB\-NOPARENT\fR
+do not bond hydrogens based on table of parent heavy atoms
+.TP
+\fB\-SEGID\fR
+use the PDB SegID field to descriminate between residues
+.TP
+\fB\-OLDU\fR
+generate old style \fB\-u\fR output: kissEdge2BullsEye, etc
+.TP
+\fB\-VErbose\fR
+verbose mode (default)
+.TP
+\fB\-REFerence\fR
+display reference string
+.TP
+\fB\-CHANGEs\fR
+display a list of program changes
+.TP
+\fB\-Quiet\fR
+quiet mode
+.TP
+\fB\-Help\fR
+show expanded help notice (includes other flags)
+.TP
+\fB\-VERSION\fR
+one line version to stdout
+.PP
+Pattern elements: (should be put in quotes on the command line)
+.TP
+FILE#
+within file #
+.TP
+MODEL#
+within model #
+.TP
+CHAINaa
+within chain a
+.TP
+SEGaaaa
+segment identifier aaaa (where _ represents blank)
+.TP
+ALTa
+alternate conformation a
+.TP
+ATOMaaaa
+atom name aaaa (where _ represents blank)
+(all 4 characters are used so H would be ATOM_H__)
+.TP
+RESaaa
+residue aaa
+.TP
+#
+residue #
+.TP
+#a
+residue #, insert a
+.TP
+#\-#
+residue range # (insert codes ignored)
+.TP
+a
+residue type by one letter codes (eg. y)
+.TP
+aaa
+residue type by three letter codes (eg. tyr)
+.IP
+ALL,PROTEIN,MC,SC,BASE,ALPHA,BETA,NITROGEN,CARBON,
+OXYGEN,SULFUR,PHOSPHORUS,HYDROGEN,METAL,POLAR,
+NONPOLAR,CHARGED,DONOR,ACCEPTOR,AROMATIC,METHYL,
+HET,WATER,DNA,RNA
+.IP
+all or a subset of the atoms
+.TP
+OLT#
+Occupancy less than # (integer percent)
+.TP
+OGT#
+Occupancy greater than # (integer percent)
+.TP
+BLT#
+B\-value less than # (integer)
+.TP
+BGT#
+B\-value greater than # (integer)
+.TP
+INSa
+Insert code a (where _ represents blank)
+.TP
+WITHIN #.# OF #.#, #.#, #.#
+atoms within distance from point
+.IP
+Patterns can be combined into comma separated lists
+such as "trp,phe,tyr" meaning TRP or PHE or TYR.
+.IP
+Patterns that are sepatated by blanks must all be true
+such as "chainb 1\-5" meaning residues 1 to 5 in chain B.
+.IP
+You can also group patterns with parenthesis, separate
+multiple patterns with | meaning 'or' and choose the
+complement with NOT as in "not file1" meaning not in file 1.
+.IP
+An autobondrot file is similar to other PDB input files
+but it includes information identifying atoms subject to rotations
+and other transformations.
+.IP
+Example autobondrot file fragment showing Calpha\-Cbeta bond rotation
+and a periodic torsion penalty function for this rotation
+.TP
+ATOM
+1 CB TYR 61 34.219 17.937 4.659 1.00 0.00
+.TP
+bondrot:chi1:78.7:
+0:359:5:33.138:18.517: 5.531:34.219:17.937: 4.659
+.IP
+cos:\-3:60:3:
+ATOM 1 1HB TYR 61 34.766 18.777 4.206 1.00 0.00
+ATOM 1 2HB TYR 61 34.927 17.409 5.315 1.00 0.00
+ATOM 1 CG TYR 61 33.836 16.989 3.546 1.00 0.00
+\&...
+.IP
+Autobondrot commands use colons to separate values
+Transformations: BONDROT:id:currAng:start:end:stepSz:x1:y1:z1:x2:y2:z2
+.TP
+TRANS:
+id:currpos:start:end:stepSz:x1:y1:z1:x2:y2:z2
+.TP
+NULL
+# dummy
+.TP
+Bias functions:
+COS:scale:phaseOffset:frequency
+POLY:scale:offset:polynomialDegree
+CONST:value
+.TP
+Branching:
+SAVE and RESTORE or "(" and ")"
+.IP
+(e.g. to rotate each Chi and the methyls for isoleucine the
+.IP
+sequence is: rotChi1/SAVE/rotChi2/rotCD1/RESTORE/rotCG2)
+.IP
+Set orientation: GO:angle1:angle2:...
+Include files: @filename
+Comments: # comment text
+.PP
+probe: version 2.13.110909, Copyright 1996\-2011, J. Michael Word
diff --git a/debian/links b/debian/links
index 4395a29..bec626d 100644
--- a/debian/links
+++ b/debian/links
@@ -1,2 +1,6 @@
# For compatibility reasons (i.e. scripts written using probe package <= 2.13.110909)
usr/lib/debian-med/bin/probe usr/bin/king-probe
+
+# Also link the manpage to the Debian Med name space
+usr/share/man/man1/king-probe.1.gz usr/lib/debian-med/share/man/man1/probe.1.gz
+
--
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