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99 lines
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99 lines
4.2 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> - <A HREF = "Manual.html">Pizza.py Documentation</A> - <A HREF = "Section_tools.html">Pizza.py Tools</A>
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<HR>
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<H3>pdbfile tool
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</H3>
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<P><B>Purpose:</B>
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</P>
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<P>Read, write PDB files in combo with LAMMPS snapshots.
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</P>
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<P><B>Description:</B>
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</P>
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<P>The pdbfile tool reads in PDB (Protein Data Bank) files of protein
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coordinates and uses them in conjunction with LAMMPS snapshots in
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various ways. The PDB format is commonly used by various
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vizualization and analysis programs.
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</P>
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<P>The pdbfile constructor takes a string argument listing one or more
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PDB filenames and a data argument with LAMMPS atom information
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(<A HREF = "data.html">data</A> or <A HREF = "dump.html">dump</A> object). The atom snapshots
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must have "id", "type", "x", "y", and "z" defined; see the map()
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methods of those tools.
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</P>
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<P>Both arguments to the constructor are optional, as described below.
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If a single PDB file is given as a constructor argument, and it is 4
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letters long, and it does not exist on your system, then it is treated
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as a PDB identifier and the matching PDB file is downloaded from a PDB
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repository on the WWW to your machine.
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</P>
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<P>The one(), many(), and single() methods write out PDB files in various
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manners, depending on the 1 or 2 arguments used in the constructor.
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If only a string was specified (no data object), the specified PDB
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files are written out as-is. Thus the one() method concatenates the
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files together. If only a data object was specified (no string of PDB
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files), then PDB files in a generic format (Lennard-Jones atoms) are
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created. If both arguments are specified, then only a single PDB file
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can be listed. It is treated as a template file, and the atom
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coordinates in the data object replace the atom coordinates in the
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template PDB file to create a series of new PDB files. This
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replacement is only done for selected atoms (in the dump object) and
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for atom IDs that appear in the PDB file.
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</P>
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<P>The iterator() method is called by the <A HREF = "rasmol.html">rasmol</A> tool to
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create a series of PDB files for visualization purposes.
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</P>
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<P><B>Usage:</B>
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</P>
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<PRE>p = pdbfile("3CRO") create pdb object from PDB file or WWW
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p = pdbfile("pep1 pep2") read in multiple PDB files
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p = pdbfile("pep*") can use wildcards
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p = pdbfile(d) read in snapshot data with no PDB file
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p = pdbfile("3CRO",d) read in single PDB file with snapshot data
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</PRE>
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<PRE> string arg contains one or more PDB files
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don't need .pdb suffix except wildcard must expand to file.pdb
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if only one 4-char file specified and it is not found,
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it will be downloaded from http://www.rcsb.org as 3CRO.pdb
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d arg is object with atom coordinates (dump, data)
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</PRE>
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<PRE>p.one() write all output as one big PDB file to tmp.pdb
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p.one("mine") write to mine.pdb
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p.many() write one PDB file per snapshot: tmp0000.pdb, ...
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p.many("mine") write as mine0000.pdb, mine0001.pdb, ...
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p.single(N) write timestamp N as tmp.pdb
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p.single(N,"new") write as new.pdb
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</PRE>
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<PRE> how new PDB files are created depends on constructor inputs:
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if no d: one new PDB file for each file in string arg (just a copy)
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if only d specified: one new PDB file per snapshot in generic format
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if one file in str arg and d: one new PDB file per snapshot
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using input PDB file as template
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multiple input PDB files with a d is not allowed
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</PRE>
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<PRE>index,time,flag = p.iterator(0)
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index,time,flag = p.iterator(1)
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</PRE>
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<PRE> iterator = loop over number of PDB files
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call first time with arg = 0, thereafter with arg = 1
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N = length = # of snapshots or # of input PDB files
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index = index of snapshot or input PDB file (0 to N-1)
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time = timestep value (time stamp for snapshot, index for multiple PDB)
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flag = -1 when iteration is done, 1 otherwise
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typically call p.single(time) in iterated loop to write out one PDB file
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</PRE>
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<P><B>Related tools:</B>
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</P>
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<P><A HREF = "data.html">data</A>, <A HREF = "dump.html">dump</A>, <A HREF = "rasmol.html">rasmol</A>
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</P>
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<P><B>Prerequisites:</B> none
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</P>
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</HTML>
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