COORDINATE_IO contains procedures for reading and writing coordinate files in DYNAMO format.
This module is discussed in chapter 2 of the book A Practical Introduction to the Simulation of Molecular Systems.
Module | Variables |
---|---|
CONSTANTS | UNDEFINED |
DEFINITIONS | DP |
ELEMENTS | MASS |
FILES | NEXT_UNIT |
IO_UNITS | INPUT, OUTPUT |
PARSING | Most public items in the module. |
STATUS | ERROR |
STRING | DECODE_INTEGER, TO_UPPER_CASE |
ATOMS | Most public items in the module. |
SEQUENCE | Most public items in the module. |
SYMMETRY | Most public items in the module. |
None.
There are three public subroutines in this module.
Subroutine | Purpose |
---|---|
COORDINATES_DEFINE | Read a DYNAMO coordinate file and redefine the system. |
COORDINATES_READ | Read a DYNAMO coordinate file using an existing system definition. |
COORDINATES_WRITE | Write a DYNAMO coordinate file for the current system. |
Argument | Type | Intent | Optional | Purpose |
---|---|---|---|---|
FILE | Character ( Len = * ) | In | Yes | The coordinate file name. |
Error | Meaning |
---|---|
I/O Error. | There is a problem with the coordinate file. |
Invalid atoms, residue or subsystem counter. | The number of atoms, residues or subsystems is zero or negative. |
SUBSYSTEM label invalid. | There is no "Subsystem" tag. |
SUBSYSTEM name length invalid. | The subsystem name is either too short or too long. |
Two SUBSYSTEM names are the same. | Two subsystems have the same name. |
Invalid number of residues in a subsystem. | The number of residues in the subsystem is either zero or negative or so large that the number of residues specified at the top of the file is exceeded. |
RESIDUE label invalid. | There is no "Residue" tag. |
RESIDUE number invalid. | The residue number does not correspond to that expected in the sequence. |
RESIDUE name length invalid. | The residue name is either too short or too long. |
Invalid number of atoms in a residue. | The number of atoms in the residue is either zero or negative or so large that the number of atoms specified at the top of the file is exceeded. |
ATOM name length invalid. | The atom name is either too short or too long. |
Two ATOM names are the same. | Two atoms in a residue have the same name. |
ATOM or RESIDUE number mismatch. | The numbers of atoms or residues obtained after reading the file do not correspond to the numbers given at the top of the file. |
Argument | Type | Intent | Optional | Purpose |
---|---|---|---|---|
FILE | Character ( Len = * ) | In | Yes | The coordinate file name. |
DATA | Real(1:3,1:NATOMS) | Out | Yes | The data read from the file is to be put here. |
SELECTION | Logical(1:NATOMS) | In | Yes | An atom selection array. |
Error | Meaning |
---|---|
I/O Error. | There is a problem with the coordinate file. |
Invalid atoms, residue or subsystem counter. | The number of atoms, residues or subsystems does not correspond to that of the system already defined. |
SUBSYSTEM label invalid. | There is no "Subsystem" tag. |
SUBSYSTEM name length invalid. | The subsystem name is either too short or too long. |
SUBSYSTEM name mismatch. | The subsystem in the file does not correspond to that expected from the sequence. |
Invalid number of residues in a subsystem. | The number of residues in the subsystem does not correspond to that expected from the sequence. |
RESIDUE label invalid. | There is no "Residue" tag. |
RESIDUE number invalid. | The residue number does not correspond to that expected in the sequence. |
RESIDUE name length invalid. | The residue name is either too short or too long. |
RESIDUE name mismatch. | The residue name does not correspond to that expected from the sequence. |
Too many atoms in a residue. | There are too many atoms for a residue. |
ATOM name length invalid. | The atom name is either too short or too long. |
ATOM number mismatch. | There is a mismatch in the atomic numbers of equivalent atoms. |
Unknown ATOM name in residue. | A atom in the file does not correspond to one in the sequence. |
Argument | Type | Intent | Optional | Purpose |
---|---|---|---|---|
FILE | Character ( Len = * ) | In | Yes | The coordinate file name. |
DATA | Real(1:3,1:NATOMS) | In | Yes | The data to be written. |
SELECTION | Logical(1:NATOMS) | In | Yes | An atom selection array. |
Error | Meaning |
---|---|
I/O Error. | There is a problem with the coordinate file. |
COORDINATES_READ is in need of overhaul. Otherwise, stable.